@article{du_xiang_soltis_soltis_2024, title={Addition to “An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data”}, url={https://doi.org/10.11646/bpn.1.3.3}, DOI={10.11646/bpn.1.3.3}, abstractNote={Du et al. (2023) produced a phylogeny of Cornus L. using three sets of genomic data, proposed a classification within the clade, and phylogenetically defined 13 clade names following the International Code of Phylogenetic Nomenclature (PhyloCode). However, the clade names were not fully established because no registration numbers were cited in the protologues, as required by the PhyloCode. That omission is remedied here, and expanded protologues are provided for the 13 names defined by Du et al. (2023). Ten of the 13 names are the same as those proposed by Du et al., (2023), while three names proposed by Du et al. (2023) are changed here (viz., Involucry to Involucratae, Bractishowy to Bractipetaloides, and Eurasiancherry to Eurasiamacrocarpium).}, journal={Bulletin of Phylogenetic Nomenclature}, author={Du, Zhi-Yuan and Xiang, Qiu-Yun and Soltis, Pamela S. and Soltis, Douglas E.}, year={2024}, month={Aug} }
 @article{xiang_kivlin_soltis_yu_chu_soltis_zhao_2024, title={Editorial: Mapping microbial diversity onto the phylogeny of associated plant species}, volume={15}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2024.1421637}, abstractNote={Qiu-Yun (Jenny) Xiang1*Stephanie N. Kivlin2Douglas E. Soltis3,4Shixiao Yu5Haiyan Chu6Pamela S. Soltis4Yunpeng Zhao7}, journal={FRONTIERS IN PLANT SCIENCE}, author={Xiang, Qiu-Yun and Kivlin, Stephanie N. and Soltis, Douglas E. and Yu, Shixiao and Chu, Haiyan and Soltis, Pamela S. and Zhao, Yunpeng}, year={2024}, month={May} }
 @article{pais_ristaino_whetten_xiang_2024, title={Metagenomic study reveals hidden relationships among fungal diversity, variation of plant disease, and genetic distance in <i>Cornus florida</i> (Cornaceae)}, volume={14}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2023.1282188}, abstractNote={IntroductionUnderstanding patterns of plant-microbe interactions across plant species and populations is a critical yet poorly characterized aspect in the field of plant pathology. Microbial DNA sequences present as contaminants in omics data of plants obtained using next-generation sequencing methods provide a valuable source to explore the relationships among endophytic microbial diversity, disease and genetic differentiation of host plants, and environmental variation, but few such studies have been conducted.  The flowering dogwood tree (Cornus florida L.), an ecologically important species in North America, is threatened by powdery mildew and dogwood anthracnose diseases, and knowledge of the microbial diversity harbored within genetically and environmental distinct populations of this species remains largely unknown.MethodsWe conducted a metagenomics study utilizing the sequences of RAD-tag/genotype-by-sequence libraries from leaf tissues of C. florida to examine such host-fungus interactions across the dogwood's US range. We performed various combinations of alignments to both host and pathogen genomes to obtain filtered sets sequences for metagenomics analysis. Taxonomic assignments were determined on each filtered set of sequences, followed by estimation of microbial diversity and correlation to environment and host-genetic variation.ResultsOur data showed that microbial community composition significantly differed between visually healthy and diseased sites. Several microbial taxa known to interact with dogwood were identified from these sequences. We found no correlation between microbial diversity and relative abundances of sequences aligning to draft genomes of either pathogen causing powdery mildew or dogwood anthracnose. We found a significant relationship between differences of fungal communities and geographic distances of plant populations, suggesting roles of environments in shaping fungal communities in leaf tissues.  Significant correlations between the genetic differentiation of plant samples and fungal community dissimilarity (beta diversity) were also observed in certain sets of our analyses—suggesting the possibility of a relationship between microbial community composition and plant genetic distance. This relationship persisted in significance even after controlling for significant effects of geographic-bioclimatic variation of microbial diversity.DiscussionOur results suggest that both genetics and the environment play a significant role in shaping foliar fungal communities. Our findings underscore the power of leveraging hidden microbial sequences within datasets originally collected for plant genetic studies to understand plant-pathogen interactions.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Pais, Andrew and Ristaino, Jean and Whetten, Ross and Xiang, Qiu-Yun}, year={2024}, month={Jan} }
 @article{yow_laosuntisuk_young_doherty_gillitt_perkins-veazie_jenny xiang_iorizzo_2023, title={Comparative transcriptome analysis reveals candidate genes for cold stress response and early flowering in pineapple}, volume={13}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-023-45722-y}, abstractNote={AbstractPineapple originates from tropical regions in South America and is therefore significantly impacted by cold stress. Periodic cold events in the equatorial regions where pineapple is grown may induce early flowering, also known as precocious flowering, resulting in monetary losses due to small fruit size and the need to make multiple passes for harvesting a single field. Currently, pineapple is one of the most important tropical fruits in the world in terms of consumption, and production losses caused by weather can have major impacts on worldwide exportation potential and economics. To further our understanding of and identify mechanisms for low-temperature tolerance in pineapple, and to identify the relationship between low-temperature stress and flowering time, we report here a transcriptomic analysis of two pineapple genotypes in response to low-temperature stress. Using meristem tissue collected from precocious flowering-susceptible MD2 and precocious flowering-tolerant Dole-17, we performed pairwise comparisons and weighted gene co-expression network analysis (WGCNA) to identify cold stress, genotype, and floral organ development-specific modules. Dole-17 had a greater increase in expression of genes that confer cold tolerance. The results suggested that low temperature stress in Dole-17 plants induces transcriptional changes to adapt and maintain homeostasis. Comparative transcriptomic analysis revealed differences in cuticular wax biosynthesis, carbohydrate accumulation, and vernalization-related gene expression between genotypes. Cold stress induced changes in ethylene and abscisic acid-mediated pathways differentially between genotypes, suggesting that MD2 may be more susceptible to hormone-mediated early flowering. The differentially expressed genes and module hub genes identified in this study are potential candidates for engineering cold tolerance in pineapple to develop new varieties capable of maintaining normal reproduction cycles under cold stress. In addition, a total of 461 core genes involved in the development of reproductive tissues in pineapple were also identified in this study. This research provides an important genomic resource for understanding molecular networks underlying cold stress response and how cold stress affects flowering time in pineapple.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Yow, Ashley G. and Laosuntisuk, Kanjana and Young, Roberto A. and Doherty, Colleen J. and Gillitt, Nicholas and Perkins-Veazie, Penelope and Jenny Xiang, Qiu-Yun and Iorizzo, Massimo}, year={2023}, month={Nov} }
 @article{zhou_shi_soltis_soltis_xiang_2023, title={Foliar endophyte diversity in Eastern Asian-Eastern North American disjunct tree species - influences of host identity, environment, phylogeny, and geographic isolation}, volume={14}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2023.1274746}, abstractNote={IntroductionThe well-known eastern Asian (EA) and eastern North American (ENA) floristic disjunction provides a unique system for biogeographic and evolutionary studies. Despite considerable interest in the disjunction, few studies have investigated the patterns and their underlying drivers of allopatric divergence in sister species or lineages isolated in the two areas. Endophyte diversity and assembly in disjunct sister taxa, as an ecological trait, may have played an important role in the processes of allopatric evolution, but no studies have examined endophytes in these lineages. Here we compared foliar endophytic fungi and bacteria-archaea (FEF and FEB) in 17 EA-ENA disjunct species or clade pairs from genera representing conifers and 10 orders of five major groups of angiosperms and 23 species of Cornus from EA and North America. MethodsMetagenomic sequencing of fungal ITS and bacterial-archaeal 16S rDNA was used to capture the foliar endophytic communities. Alpha and beta diversity of fungi and bacteria were compared at multiple scales and dimensions to gain insights into the relative roles of historical geographic isolation, host identity, phylogeny, and environment from samples at different sites in shaping endophytic diversity patterns. ResultsWe found that beta diversity of endophytes varied greatly among plant individuals within species and between species among genera at the same sampling site, and among three sampling sites, but little variation between region-of-origin of all plant species (EA vs ENA) and between EA-ENA disjunct counterparts within genera. Various numbers of indicator fungal species differing in abundance were identified for each plant genus and Cornus species. An overall significant correlation between endophyte community dissimilarity and phylogenetic distance of plants was detected among the disjunct genera but not among species of Cornus. However, significant correlations between beta diversities at different taxonomic scales of endophytes and phylogenetic distances of Cornus species were observed. DiscussionOur results suggest important roles of host identity and environment (sampling sites), and a likely minor role of phylogenetic divergence and historical biogeographic isolation in shaping the pattern of foliar endophyte diversity and assembly in the EA-ENA disjunct genera and Cornus. The results lead to a hypothesis that the sister taxa in EA and ENA likely differ in FEF and FEB when growing in native habitats due to differences in local environments, which may potentially drive allopatric divergence of the functional features of species.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Zhou, Wenbin and Shi, Wei and Soltis, Pamela S. and Soltis, Douglas E. and Xiang, Qiu-Yun}, year={2023}, month={Dec} }
 @article{yow_bostan_young_valacchi_gillitt_perkins-veazie_xiang_iorizzo_2023, title={Identification of bromelain subfamily proteases encoded in the pineapple genome}, volume={13}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-023-38907-y}, abstractNote={AbstractPapain (aka C1A) family proteases, including bromelain enzymes, are widespread across the plant kingdom and play critical regulatory functions in protein turnover during development. The proteolytic activity exhibited by papain family proteases has led to their increased usage for a wide range of cosmetic, therapeutic, and medicinal purposes. Bromelain enzymes, or bromelains in short, are members of the papain family that are specific to the bromeliad plant family. The only major commercial extraction source of bromelain is pineapple. The importance of C1A family and bromelain subfamily proteases in pineapple development and their increasing economic importance led several researchers to utilize available genomic resources to identify protease-encoding genes in the pineapple genome. To date, studies are lacking in screening bromelain genes for targeted use in applied science studies. In addition, the bromelain genes coding for the enzymes present in commercially available bromelain products have not been identified and their evolutionary origin has remained unclear. Here, using the newly developed MD2 v2 pineapple genome, we aimed to identify bromelain-encoding genes and elucidate their evolutionary origin. Orthologous and phylogenetic analyses of all papain-family proteases encoded in the pineapple genome revealed a single orthogroup (189) and phylogenetic clade (XIII) containing the bromelain subfamily. Duplication mode and synteny analyses provided insight into the origin and expansion of the bromelain subfamily in pineapple. Proteomic analysis identified four bromelain enzymes present in two commercially available bromelain products derived from pineapple stem, corresponding to products of four putative bromelain genes. Gene expression analysis using publicly available transcriptome data showed that 31 papain-family genes identified in this study were up-regulated in specific tissues, including stem, fruit, and floral tissues. Some of these genes had higher expression in earlier developmental stages of different tissues. Similar expression patterns were identified by RT-qPCR analysis with leaf, stem, and fruit. Our results provide a strong foundation for future applicable studies on bromelain, such as transgenic approaches to increase bromelain content in pineapple, development of bromelain-producing bioreactors, and studies that aim to determine the medicinal and/or therapeutic viability of individual bromelain enzymes.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Yow, Ashley G. and Bostan, Hamed and Young, Roberto and Valacchi, Giuseppe and Gillitt, Nicholas and Perkins-Veazie, Penelope and Xiang, Qiu-Yun and Iorizzo, Massimo}, year={2023}, month={Jul} }
 @article{sun_zhang_zhang_landis_zhang_sun_xiang_wang_2023, title={Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly Asexual Kingdonia uniflora (Circaeasteraceae, Ranunculales)}, volume={24}, ISSN={["1422-0067"]}, url={https://doi.org/10.3390/ijms24021451}, DOI={10.3390/ijms24021451}, abstractNote={Asexual lineages are perceived to be short-lived on evolutionary timescales. Hence, reports for exceptional cases of putative ‘ancient asexuals’ usually raise questions about the persistence of such species. So far, there have been few studies to solve the mystery in plants. The monotypic Kingdonia dating to the early Eocene, contains only K. uniflora that has no known definitive evidence for sexual reproduction nor records for having congeneric sexual species, raising the possibility that the species has persisted under strict asexuality for a long period of time. Here, we analyze whole genome polymorphism and divergence in K. uniflora. Our results show that K. uniflora is characterized by high allelic heterozygosity and elevated πN/πS ratio, in line with theoretical expectations under asexual evolution. Allele frequency spectrum analysis reveals the origin of asexuality in K. uniflora occurred prior to lineage differentiation of the species. Although divergence within K. uniflora individuals exceeds that between populations, the topologies of the two haplotype trees, however, fail to match each other, indicating long-term asexuality is unlikely to account for the high allele divergence and K. uniflora may have a recent hybrid origin. Phi-test shows a statistical probability of recombination for the conflicting phylogenetic signals revealed by the split network, suggesting K. uniflora engages in undetected sexual reproduction. Detection of elevated genetic differentiation and premature stop codons (in some populations) in genes regulating seed development indicates mutational degradation of sexuality-specific genes in K. uniflora. This study unfolds the origin and persistence mechanism of a plant lineage that has been known to reproduce asexually and presents the genomic consequences of lack of sexuality.}, number={2}, journal={INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, author={Sun, Yanxia and Zhang, Xu and Zhang, Aidi and Landis, Jacob B. and Zhang, Huajie and Sun, Hang and Xiang, Qiu-Yun and Wang, Hengchang}, year={2023}, month={Jan} }
 @article{du_cheng_xiang_2023, title={RAD-seq data provide new insights into biogeography, diversity anomaly, and species delimitation in eastern Asian-North American disjunct clade <i>Benthamidia</i> of <i>Cornus</i> (Cornaceae)}, volume={12}, ISSN={["1759-6831"]}, url={https://doi.org/10.1111/jse.13037}, DOI={10.1111/jse.13037}, abstractNote={AbstractThe big‐bracted dogwood clade Benthamidia of Cornus is a typical example of the well‐known eastern Asia (EA) and North America (NA) floristic disjunction, with greater species diversity in EA than in NA. The lineage provides an opportunity to explore factors contributing to the plant diversity unevenness between EA and NA and test hypotheses on the origin of disjunct distribution from a phylogenetic perspective. We generated RAD‐seq data, conducted phylogenomic and biogeographic analyses for the clade with sampling of all species (9) and subspecies (10) currently recognized in floras. We also assessed species delineation and calculated phylogenetic diversity to evaluate the diversity unevenness between EA and NA. Finally, we examined variation of diversification rates and ecological niches on the phylogeny to explore potential causes underlying the observed diversity pattern. Our results revealed phylogenetic relationships congruent with previous studies and suggested a trans‐Beringian ancestral distribution of the clade Benthamidia in the mid‐Oligocene, dispersal from Mexico to eastern United States in the mid‐Miocene, and early diversification of the EA clade in SW China. Our results also confirmed greater phylogenetic diversity and diversification rate of the EA clade. Species delimitation analysis suggested 17 species in the clade Benthamidia, including all recognized subspecies. By integrating the results of molecular data with morphology, we proposed to retain the subspecies without changing their ranks. Our data suggested increased diversification rate in EA as an intrinsic factor explaining the greater species diversity in the region driven mainly by biogeographic isolation and partially by niche divergence.}, journal={JOURNAL OF SYSTEMATICS AND EVOLUTION}, author={Du, Zhi-Yuan and Cheng, Jin and Xiang, Qiu-Yun}, year={2023}, month={Dec} }
 @article{du_xiang_cheng_zhou_wang_soltis_soltis_2023, title={An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data}, volume={2}, ISSN={["1537-2197"]}, url={https://doi.org/10.1002/ajb2.16116}, DOI={10.1002/ajb2.16116}, abstractNote={AbstractPremiseA major goal of systematic biology is to uncover the evolutionary history of organisms and translate that knowledge into stable classification systems. Here, we integrate three sets of genome‐wide data to resolve phylogenetic relationships in Cornaceae (containing only Cornus s.l.), reconstruct the biogeographic history of the clade, and provide a revised classification using the PhyloCode to stabilize names for this taxonomically controversial group.MethodsWe conducted phylogenetic analyses using 312 single‐copy nuclear genes and 70 plastid genes from Angiosperms353 Hyb‐Seq, plus numerous loci from RAD‐Seq. We integrated fossils using morphological data and produced a dated phylogeny for biogeographical analysis.ResultsA well‐resolved, strongly supported, comprehensive phylogeny was obtained. Biogeographic analyses support an origin and rapid diversification of Cornus into four morphologically distinct major clades in the Northern Hemisphere (with an eastern Asian ancestor) during the late Cretaceous. Dispersal into Africa from eastern Asia likely occurred along the Tethys Seaway during the Paleogene, whereas dispersal into South America likely occurred during the Neogene. Diversification within the northern hemisphere likely involved repeated independent colonization of new areas during the Paleogene and Neogene along the Bering Land Bridge, the North Atlantic Land Bridge, and the Tethys Seaway. Thirteen strongly supported clades were named following rules of the PhyloCode.ConclusionsOur study provides an example of integrating genomic and morphological data to produce a robust, explicit species phylogeny that includes fossil taxa, which we translate into an updated classification scheme using the PhyloCode to stabilize names.}, journal={AMERICAN JOURNAL OF BOTANY}, author={Du, Zhi-Yuan and Xiang, Qiu-Yun and Cheng, Jin and Zhou, Wenbin and Wang, Qing-Feng and Soltis, Douglas E. E. and Soltis, Pamela S. S.}, year={2023}, month={Feb} }
 @article{zhou_xiang_2022, title={Phylogenomics AND biogeography of Castanea (chestnut) and Hamamelis (witch-hazel) - Choosing between RAD-seq and Hyb-Seq approaches}, volume={176}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2022.107592}, abstractNote={Hyb-Seq and RAD-seq are well-established high throughput sequencing technologies that have been increasingly used for plant phylogenomic studies. Each method has its own pros and cons. The choice between them is a practical issue for plant systematists studying the evolutionary histories of biodiversity of relatively recent origins. However, few studies have compared the congruence and conflict between results from the two methods within the same group of organisms in plants. In this study, we employed RAD-seq and Hyb-Seq of Angiosperms353 genes in phylogenomic and biogeographic studies of Hamamelis (the witch-hazels) and Castanea (chestnuts), two classic examples exhibiting the well-known eastern Asian (EA) -eastern North American (ENA) disjunct distribution, and compared them side by side. Our results showed congruences in phylogenetic inference and divergence time dating between the two data sets obtained through our customized procedures of library preparation and sequence trimming, although they differed in the number of loci and informative sites, the amount of missing data, and sampling within species. We provide recommendations regarding the selection of the two methods for phylogenomic study at generic level based on fund availability and sampling scale. If funds and time are not constrained, we recommend Hyb-Seq. If funds and time are somewhat limited and sampling is large, we recommend RAD-seq. However, we found greater conflict among gene trees from the RAD-seq data due to the short sequences per locus. Therefore, species tree building and network detecting with the RAD-seq data with short RAD-seq loci (e.g., <150 bp) should avoid using analytical methods relying on gene trees of individual locus, but using site-based methods such as SVDQuartets and D-statistic method. Our phylogenetic analyses of RAD-seq and Hyb-Seq data resulted in well-resolved species relationships. Analyses of the data using the D-statistic test and PhyloNet revealed ancient introgressions in both genera. Biogeographic analyses including fossil data using total evidence-based dated tree and DEC model applying specific inter-area dispersal probabilities revealed a complicated history for each genus, indicating multiple interareal dispersals and local extinctions within and outside areas of the taxa's modern ranges in both the Paleogene and Neogene. The study demonstrates the importance of including fossil taxa for a more accurate reconstruction of biogeographic histories of taxa to understand the EA and ENA floristic disjunction. Our results support a widespread ancestral range in EA-western North America (WNA) followed by early diversification in EA and expansion to North America (NA) and Europe for Castanea and a more widespread ancestral range in EA-ENA-WNA for Hamamelis. The origins of the modern EA-ENA disjunction in both genera were suggested to be the result of vicariance from widespread ancestors in Eurasia-ENA of the mid-Miocene and in EA-NA of the late Oligocene, respectively.}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Zhou, Wenbin and Xiang, Qiu-Yun}, year={2022}, month={Nov} }
 @article{zhou_harris_xiang_2022, title={Phylogenomics and biogeography of Torreya (Taxaceae)-Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD-seq}, volume={2}, ISSN={["1759-6831"]}, url={https://doi.org/10.1111/jse.12838}, DOI={10.1111/jse.12838}, abstractNote={AbstractRestriction site‐associated DNA sequencing (RAD‐seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD‐seq data are subject to allele dropout (ADO) due to polymorphisms at enzyme cutting sites. We developed a new pipeline, RAD‐seq Allele Dropout Remedy in our study of the gymnosperm genus, Torreya, to mitigate ADO in outgroups by recovering missing loci from previously published transcriptomes. By using RADADOR to supplement Rad‐seq data in combination with plastome and mitochondrial gene sequences, morphology, and fossil records, we reconstructed the phylogenetic and biogeographic histories of the genus and tested hypotheses on anomalies of biodiversity  of the eastern Asian‐North American floristic disjunction. Our results showed that our pipeline recovered many loci missing from the outgroup, and the improved data yielded a more robust phylogeny for Torreya. Using the fossilized birth–death model and divergence–extinction–cladogenesis method, we resolved a detailed biogeographic history of Torreya that suggested a Jurassic origin spanning Laurasia and differential speciation and extinction among continents accounting for modern diversity, which is biased toward eastern Asia (EA). The biogeographic results also supported a vicariance origin of modern Torreya from a widespread ancestor in EA and North America (NA) in the mid‐Eocene, and cross Beringian exchange in the early Paleogene before the vicariant isolation, in contrast to the “out of NA” pattern common to gymnosperms and to the “out of EA” hypothesis previously proposed for the genus. Furthermore, we observed phylogenetic discordance between the nuclear and plastid phylogenies for Torreya jackii, suggesting differential lineage sorting of plastid genomes among species of Torreya or plastid genome capture in T. jackii.}, journal={JOURNAL OF SYSTEMATICS AND EVOLUTION}, publisher={Wiley}, author={Zhou, Wenbin and Harris, A. J. and Xiang, Qiu-Yun}, year={2022}, month={May} }
 @article{zhou_soghigian_xiang_2022, title={A New Pipeline for Removing Paralogs in Target Enrichment Data}, volume={71}, ISSN={["1076-836X"]}, DOI={10.1093/sysbio/syab044}, abstractNote={AbstractTarget enrichment (such as Hyb-Seq) is a well-established high throughput sequencing method that has been increasingly used for phylogenomic studies. Unfortunately, current widely used pipelines for analysis of target enrichment data do not have a vigorous procedure to remove paralogs in target enrichment data. In this study, we develop a pipeline we call Putative Paralogs Detection (PPD) to better address putative paralogs from enrichment data. The new pipeline is an add-on to the existing HybPiper pipeline, and the entire pipeline applies criteria in both sequence similarity and heterozygous sites at each locus in the identification of paralogs. Users may adjust the thresholds of sequence identity and heterozygous sites to identify and remove paralogs according to the level of phylogenetic divergence of their group of interest. The new pipeline also removes highly polymorphic sites attributed to errors in sequence assembly and gappy regions in the alignment. We demonstrated the value of the new pipeline using empirical data generated from Hyb-Seq and the Angiosperms353 kit for two woody genera Castanea (Fagaceae, Fagales) and Hamamelis (Hamamelidaceae, Saxifragales). Comparisons of data sets showed that the PPD identified many more putative paralogs than the popular method HybPiper. Comparisons of tree topologies and divergence times showed evident differences between data from HybPiper and data from our new PPD pipeline. We further evaluated the accuracy and error rates of PPD by BLAST mapping of putative paralogous and orthologous sequences to a reference genome sequence of Castanea mollissima. Compared to HybPiper alone, PPD identified substantially more paralogous gene sequences that mapped to multiple regions of the reference genome (31 genes for PPD compared with 4 genes for HybPiper alone). In conjunction with HybPiper, paralogous genes identified by both pipelines can be removed resulting in the construction of more robust orthologous gene data sets for phylogenomic and divergence time analyses. Our study demonstrates the value of Hyb-Seq with data derived from the Angiosperms353 probe set for elucidating species relationships within a genus, and argues for the importance of additional steps to filter paralogous genes and poorly aligned regions (e.g., as occur through assembly errors), such as our new PPD pipeline described in this study. [Angiosperms353; Castanea; divergence time; Hamamelis; Hyb-Seq, paralogs, phylogenomics.]}, number={2}, journal={SYSTEMATIC BIOLOGY}, author={Zhou, Wenbin and Soghigian, John and Xiang, Qiu-Yun Jenny}, year={2022}, month={Feb}, pages={410–425} }
 @article{thomas_liu_du_dong_cummings_pokorny_xiang_leebens-mack_2021, title={Comprehending Cornales: phylogenetic reconstruction of the order using the Angiosperms353 probe set}, volume={7}, ISSN={["1537-2197"]}, url={https://doi.org/10.1002/ajb2.1696}, DOI={10.1002/ajb2.1696}, abstractNote={PremiseCornales is an order of flowering plants containing ecologically and horticulturally important families, including Cornaceae (dogwoods) and Hydrangeaceae (hydrangeas), among others. While many relationships in Cornales are strongly supported by previous studies, some uncertainty remains with regards to the placement of Hydrostachyaceae and to relationships among families in Cornales and within Cornaceae. Here we analyzed hundreds of nuclear loci to test published phylogenetic hypotheses and estimated a robust species tree for Cornales.MethodsUsing the Angiosperms353 probe set and existing data sets, we generated phylogenomic data for 158 samples, representing all families in the Cornales, with intensive sampling in the Cornaceae.ResultsWe curated an average of 312 genes per sample, constructed maximum likelihood gene trees, and inferred a species tree using the summary approach implemented in ASTRAL‐III, a method statistically consistent with the multispecies coalescent model.ConclusionsThe species tree we constructed generally shows high support values and a high degree of concordance among individual nuclear gene trees. Relationships among families are largely congruent with previous molecular studies, except for the placement of the nyssoids and the Grubbiaceae‐Curtisiaceae clades. Furthermore, we were able to place Hydrostachyaceae within Cornales, and within Cornaceae, the monophyly of known morphogroups was well supported. However, patterns of gene tree discordance suggest potential ancient reticulation, gene flow, and/or ILS in the Hydrostachyaceae lineage and the early diversification of Cornus. Our findings reveal new insights into the diversification process across Cornales and demonstrate the utility of the Angiosperms353 probe set.}, journal={AMERICAN JOURNAL OF BOTANY}, author={Thomas, Shawn K. and Liu, Xiang and Du, Zhi-Yuan and Dong, Yibo and Cummings, Amanda and Pokorny, Lisa and Xiang, Qui-Yun and Leebens-Mack, James H.}, year={2021}, month={Jul} }
 @article{cavigelli_leips_xiang_lemke_konow_2022, title={Next Steps in Integrative Biology: Mapping Interactive Processes Across Levels of Biological Organization}, volume={61}, ISSN={["1557-7023"]}, DOI={10.1093/icb/icab161}, abstractNote={Synopsis
               Emergent biological processes result from complex interactions within and across levels of biological organization, ranging from molecular to environmental dynamics. Powerful theories, database tools, and modeling methods have been designed to characterize network connections within levels, such as those among genes, proteins, biochemicals, cells, organisms, and species. Here, we propose that developing integrative models of organismal function in complex environments can be facilitated by taking advantage of these methods to identify key nodes of communication across levels of organization. Mapping key drivers or connections among levels of organization will provide data and leverage to model potential rule-sets by which organisms respond and adjust to perturbations at any level of biological organization.}, number={6}, journal={INTEGRATIVE AND COMPARATIVE BIOLOGY}, author={Cavigelli, Sonia and Leips, Jeff and Xiang, Qiu-Yun and Lemke, Dawn and Konow, Nicolai}, year={2022}, month={Feb}, pages={2066–2074} }
 @article{melton_chen_zhao_fu_xiang_cheng_wong_soltis_soltis_gitzendanner_2020, title={Genetic insights into the evolution of genera with the eastern Asia–eastern North America floristic disjunction: a transcriptomics analysis}, volume={107}, ISSN={["1537-2197"]}, DOI={10.1002/ajb2.1579}, abstractNote={PremiseLarge disjunctions in species distributions provide excellent opportunities to study processes that shape biogeographic patterns. One such disjunction is the eastern Asia–eastern North America (EA‐ENA) floristic disjunction. For many genera with this disjunction, species richness is greater in EA than in ENA; this pattern has been attributed, in part, to higher rates of molecular evolution and speciation in EA. Longer branch lengths have been found in some EA clades, relative to their ENA sister clades, suggesting that the EA lineages have evolved at a higher rate, possibly due to environmental heterogeneity, potentially contributing to the species richness anomaly.MethodsTo evaluate whether rates of molecular evolution are elevated in EA relative to ENA, we used transcriptomes from species in 11 genera displaying this disjunction. Rates of molecular evolution were estimated for up to 385 orthologous nuclear loci per genus.ResultsNo statistically significant differences were identified in pairwise comparisons between EA and ENA sister species, suggesting equal rates of molecular evolution for both species; the data also suggest similar selection pressures in both regions. For larger genera, evidence likewise argues against more species‐rich clades having higher molecular evolutionary rates, regardless of region. Our results suggest that genes across multiple gene ontology categories are evolving at similar rates under purifying selection in species in both regions.ConclusionsOur data support the hypothesis that greater species richness in EA than ENA is due to factors other than an overall increase in rates of molecular evolution in EA.}, number={12}, journal={American Journal of Botany}, author={Melton, A.E. and Chen, S.C. and Zhao, Y.P. and Fu, C.X. and Xiang, Q.-Y. and Cheng, S.F. and Wong, G.K.S. and Soltis, P.S. and Soltis, D.E. and Gitzendanner, M.A.}, year={2020}, pages={1736–1748} }
 @article{xiang_chen_song_boufford_2020, title={In memory of Professor Tang Yan-Cheng: New perspectives in systematic and evolutionary biology}, volume={58}, ISSN={["1759-6831"]}, DOI={10.1111/jse.12677}, abstractNote={In China, three institutes for botanical research were established in the 1920s, namely the Department of Botany, Biological Laboratory of the Science Society of China (1922, Nanjing), the Fan Memorial Institute of Biology (1928, Peiping), and the Institute of Botany, Peiping Academy of Sciences (1929, Peiping). Since then, plant taxonomy, plant systematics, and phytogeography have advanced and prospered as scientific disciplines in China. Among the great botanists who studied at those institutes, and at others that were established over the following 100 years, was Prof. Tang (surname) Yan‐Cheng (given name) (汤彦承, abbreviated Y. C. Tang) (7 July 1926–6 August 2016). Professor Tang was a well‐known and highly respected plant taxonomist and an influential professor at the Institute of Botany, Chinese Academy of Sciences, Beijing. Prof. Tang played a pivotal role in leading taxonomic/systematic research in China from the 1970s into the 1990s. He not only provided new insights into the Chinese flora, but also helped to develop Chinese botany according to what were then new cladistic methods and to train the following generations of Chinese botanists. During his career, Prof. Tang keenly promoted novel theories and taxonomic and systematic methods, and he encouraged the application of up‐to‐date experimental approaches and analytical methodologies to study Chinese plants. His research had global implications for large, widely distributed plant families and provided a better understanding of the origin and evolution of the East Asian flora (see Wang et al., 2020a and more details below). Therefore, in this special issue, we have compiled articles that reflect current advances in plant taxonomy, systematics, and phytogeography to honor the contributions of Prof. Tang. The articles herein, including reviews and original articles, represent new perspectives in systematics and evolution, and also present research that integrates multifaceted data and interdisciplinary approaches. Several articles concern plant taxa studied in depth by Prof. Tang or those that were a focus of his interest. Modern systematic biology originated in the 1960s with the cladistic methods developed and expounded by Hennig (Hennig, 1966; Funk, 2018). In the past 30 years, the discipline of systematic biology has been transformed by the use of molecular approaches and phylogenetics (Hillis et al., 1996; Soltis et al., 1998). Subsequent advancements in molecular technology, phylogenetic methodologies, and comparative methods have led to an explosion of molecular systematics and phylogeny‐based comparative studies. The results have led to a better understanding of relationships and evolution of the organisms with which we share our planet (Chase et al., 1993; San Mauro & Agorreta, 2010; Losos et al., 2013; Hinchliff et al., 2015; Soltis & Soltis, 2016; Soltis et al., 2018; Bakker et al., 2020). Moreover, recent efforts in reconstructing the tree of life, integrating methods and sharing data across disciplines, digitizing biological collections, harvesting big data from high‐throughput DNA sequencing, and development of analytical and genetic tools (Wen et al., 2015, 2017; Soltis & Soltis, 2016; Soltis et al., 2018; Leebens‐Mack et al., 2019; Bakker et al., 2020) have empowered systematic and evolutionary biology to undertake novel and integrative studies from perspectives that were previously impossible (e.g., Chanderbali et al., 2017; Ma et al., 2017a, 2017b; Ellwood et al., 2018; Hodel et al., 2018; Landis et al., 2018; Lewin et al., 2018; Lu et al., 2018; Dong et al., 2019). Plant systematics plays a pivotal role in elucidating the evolution and assembly of the Earth's flora. Among the central applications of systematics is the sustenance, use, and conservation of plant resources, especially under many threats of the Anthropocene, including the modern threat of climate change. How will species adapt to environmental changes and what are the evolutionary constraints and drivers for adaptation? These are central questions in evolutionary ecology and conservation biology. Changing climates and global warming require urgent studies to address these questions through characterizing various factors affecting the rate and capacity of plant adaptability to change. Genetic variability, population structure, and genes/traits selected for local adaptation to environmental biotic and abiotic changes/stresses in a species lay the foundation for its survival. Our knowledge of such traits in regard to forest trees and crop species is particularly important in predicting the sustainability of forests and crops under changing environments and in understanding the constraints and drivers of ecological adaptation. At present, studies that are simultaneously broad in scope and detailed at the levels of plant traits and genes are feasible. By integrating and interfacing cutting‐edge tools, we can gain a comprehensive understanding of a species and advance our knowledge regarding plant adaptation to a changing climate. In this special issue, Anderson & Song (2020) present an overview of the recent progress, gaps, and perspectives, as well as integrative approaches regarding the adaptation of plants to climate change. They evaluate the impact of climate change on selection, local adaptation, and species interactions. They also discuss the effects of gene flow and phenotypic plasticity on the way plants respond to climate change. They argue that a comprehensive understanding of eco‐evolutionary dynamics will facilitate an understanding of a plant's adaptive potential under a rapid and intense climate}, number={5}, journal={JOURNAL OF SYSTEMATICS AND EVOLUTION}, author={Xiang, Qiu-Yun and Chen, Zhi-Duan and Song, Bao-Hua and Boufford, David E.}, year={2020}, month={Sep}, pages={527–532} }
 @article{zhou_xiang_wen_2020, title={Phylogenomics, biogeography, and evolution of morphology and ecological niche of the eastern Asian-eastern North AmericanNyssa(Nyssaceae)}, volume={58}, ISSN={["1759-6831"]}, DOI={10.1111/jse.12599}, abstractNote={AbstractNyssa (Nyssaceae, Cornales) represents a classical example of the well‐known eastern Asian–eastern North American floristic disjunction. The genus consists of three species in eastern Asia, four species in eastern North America, and one species in Central America. Species of the genus are ecologically important trees in eastern North American and eastern Asian forests. The distribution of living species and a rich fossil record of the genus make it an excellent model for understanding the origin and evolution of the eastern Asian–eastern North American floristic disjunction. However, despite the small number of species, relationships within the genus have remained unclear and have not been elucidated using a molecular approach. Here, we integrate data from 48 nuclear genes, fossils, morphology, and ecological niche to resolve species relationships, elucidate its biogeographical history, and investigate the evolution of morphology and ecological niches, aiming at a better understanding of the well‐known EA–ENA floristic disjunction. Results showed that the Central American (CAM) Nyssa talamancana was sister to the remaining species, which were divided among three, rapidly diversified subclades. Estimated divergence times and biogeographical history suggested that Nyssa had an ancestral range in Eurasia and western North America in the late Paleocene. The rapid diversification occurred in the early Eocene, followed by multiple dispersals between and within the Erasian and North American continents. The genus experienced two major episodes of extinction in the early Oligocene and end of Neogene, respectively. The Central American N. talamancana represents a relic lineage of the boreotropical flora in the Paleocene/Eocene boundary that once diversified in western North America. The results supported the importance of both the North Atlantic land bridge and the Bering land bridge (BLB) for the Paleogene dispersals of Nyssa and the Neogene dispersals, respectively, as well as the role of Central America as refugia of the Paleogene flora. The total‐evidence‐based dated phylogeny suggested that the pattern of macroevolution of Nyssa coincided with paleoclimatic changes. We found a number of evolutionary changes in morphology (including wood anatomy and leaf traits) and ecological niches (precipitation and temperature) between the EA–ENA disjunct, supporting the ecological selection driving trait evolutions after geographic isolation. We also demonstrated challenges in phylogenomic studies of lineages with rapid diversification histories. The concatenation of gene data can lead to inference of strongly supported relationships incongruent with the species tree. However, conflicts in gene genealogies did not seem to impose a strong effect on divergence time dating in our case. Furthermore, we demonstrated that rapid diversification events may not be recovered in the divergence time dating analysis using BEAST if critical fossil constraints of the relevant nodes are not available. Our study provides an example of complex bidirectional exchanges of plants between Eurasia and North America in the Paleogene, but “out of Asia” migrations in the Neogene, to explain the present disjunct distribution of Nyssa in EA and ENA.}, number={5}, journal={JOURNAL OF SYSTEMATICS AND EVOLUTION}, author={Zhou, Wenbin and Xiang, Qiu-Yun and Wen, Jun}, year={2020}, month={Sep}, pages={571–603} }
 @article{lindelof_lindo_zhou_ji_xiang_2020, title={Phylogenomics, biogeography, and evolution of the blue‐ or white‐fruited dogwoods (Cornus)—Insights into morphological and ecological niche divergence following intercontinental geographic isolation}, url={https://doi.org/10.1111/jse.12676}, DOI={10.1111/jse.12676}, abstractNote={AbstractThe eastern Asian (EA)–eastern North American (ENA) floristic disjunction represents a major pattern of phytogeography of the Northern Hemisphere. Despite 20 years of studies dedicated to identification of taxa that display this disjunct pattern, its origin and evolution remain an open question, especially regarding post‐isolation evolution. The blue‐ or white‐fruited dogwoods (BW) are the most species‐rich among the four major clades of Cornus L., consisting of ~35 species divided into three subgenera (subg. Yinquania, subg. Mesomora, and subg. Kraniopsis). The BW group provides an excellent example of the EA–ENA floristic disjunction for biogeographic study due to its diversity distribution centered in eastern Asia and eastern North America, yet its species relationships and delineation have remained poorly understood. In this study, we combined genome‐wide markers from RAD‐seq, morphology, fossils, and climate data to understand species relationships, biogeographic history, and ecological niche and morphological evolution. Our phylogenomic analyses with RAxML and MrBayes recovered a strongly supported and well‐resolved phylogeny of the BW group with three intercontinental disjunct clades in EA and ENA or Eurasia and North America, of which two are newly identified within subg. Kraniopsis. These analyses also recovered a potential new species but failed to resolve relationships within the C. hemsleyi–C. schindleri complex. In an effort to develop an approach to reduce computation time, analysis of different nodal age settings in treePL suggests setting a node's minimum age constraint to the lower bound of a fossil's age range to obtain similar ages to that of BEAST. Divergence time analyses with BEAST and treePL dated the BW stem back to the very Late Cretaceous and the divergence of the three subgenera in the Paleogene. By integrating fossil ages and morphology, a total evidence‐based dating approach was used in conjunction with time‐slice probabilities of dispersal under a DEC model to resolve ancestral ranges of each disjunct in the Miocene: Eurasia and ENA (disjunct 1), EA and western North America (disjunct 2), and EA (disjunct 3). The dated biogeographic history supports dispersal via the North Atlantic Land Bridge in the late Paleogene in disjunct 1 and dispersal via the Bering Land Bridge in the Miocene for disjuncts 2 and 3. Character mapping with a stochastic model in phytools and comparison of ecological niche, morphospace, and rate of evolution indicated differential divergence patterns in morphology, ecological niche, and molecules between disjunct sisters. Although morphological stasis was observed in most of the characters, evolutionary changes in growth habit and some features of leaf, flower, and fruit morphology occurred in one or both sister clades. A significant differentiation of ecological habitats in temperature, precipitation, and elevation between disjunct sisters was observed, suggesting a role of niche divergence in morphological evolution post‐isolation. The patterns of evolutionary rate between morphology and molecules varied among disjunct clades and were not always congruent between morphology and molecules, suggesting cases of non‐neutral morphological evolution driven by ecological selection. Our phylogenetic evidence and comparisons of evolutionary rate among disjunct lineages lend new insights into the formation of the diversity anomaly between EA and ENA, with particular support of an early diversification in EA. These findings, in conjunction with previous studies, again suggest that the EA–ENA disjunct floras are an assembly of lineages descended from the Mesophytic Forests that evolved from the early Paleogene “boreotropical flora” through varied evolutionary pathways across lineages.}, journal={Journal of Systematics and Evolution}, author={Lindelof, Kira and Lindo, Julieta A. and Zhou, Wenbin and Ji, Xiang and Xiang, Qiu‐Yun}, year={2020}, month={Sep} }
 @article{du_harris_xiang_2020, title={Phylogenomics, co-evolution of ecological niche and morphology, and historical biogeography of buckeyes, horsechestnuts, and their relatives (Hippocastaneae, Sapindaceae) and the value of RAD-Seq for deep evolutionary inferences back to the Late Cretaceous (vol 145, 106726, 2020)}, volume={150}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2020.106889}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Du, Zhi-Yuan and Harris, A. J. and Xiang, Qiu-Yun}, year={2020}, month={Sep} }
 @article{pais_whetten_xiang_2020, title={Population structure, landscape genomics, and genetic signatures of adaptation to exotic disease pressure in Cornus florida L.—Insights from GWAS and GBS data}, url={https://doi.org/10.1111/jse.12592}, DOI={10.1111/jse.12592}, abstractNote={AbstractUnderstanding the consequences of exotic diseases on native forests is important to evolutionary ecology and conservation biology because exotic pathogens have drastically altered US eastern deciduous forests. Cornus florida L. (flowering dogwood tree) is one such species facing heavy mortality. Characterizing the genetic structure of C. florida populations and identifying the genetic signature of adaptation to dogwood anthracnose (an exotic pathogen responsible for high mortality) remain vital for conservation efforts. By integrating genetic data from genotype by sequencing (GBS) of 289 trees across the host species range and distribution of disease, we evaluated the spatial patterns of genetic variation and population genetic structure of C. florida and compared the pattern to the distribution of dogwood anthracnose. Using genome‐wide association study and gradient forest analysis, we identified genetic loci under selection and associated with ecological and diseased regions. The results revealed signals of weak genetic differentiation of three or more subgroups nested within two clusters—explaining up to 2%–6% of genetic variation. The groups largely corresponded to the regions within and outside the eastern Hot‐Continental ecoregion, which also overlapped with areas within and outside the main distribution of dogwood anthracnose. The fungal sequences contained in the GBS data of sampled trees bolstered visual records of disease at sampled locations and were congruent with the reported range of Discula destructiva, suggesting that fungal sequences within‐host genomic data were informative for detecting or predicting disease. The genetic diversity between populations at diseased vs. disease‐free sites across the range of C. florida showed no significant difference. We identified 72 single‐nucleotide polymorphisms (SNPs) from 68 loci putatively under selection, some of which exhibited abrupt turnover in allele frequencies along the borders of the Hot‐Continental ecoregion and the range of dogwood anthracnose. One such candidate SNP was independently identified in two prior studies as a possible L‐type lectin‐domain containing receptor kinase. Although diseased and disease‐free areas do not significantly differ in genetic diversity, overall there are slight trends to indicate marginally smaller amounts of genetic diversity in disease‐affected areas. Our results were congruent with previous studies that were based on a limited number of genetic markers in revealing high genetic variation and weak population structure in C. florida.}, journal={Journal of Systematics and Evolution}, author={Pais, Andrew L. and Whetten, Ross W. and Xiang, Qiu‐Yun}, year={2020}, month={Sep} }
 @article{wahlsteen_zhou_xiang_rushforth_2021, title={Rediscovery of the lost little dogwood Cornus wardiana (Cornaceae)-Its phylogenetic and morphological distinction and implication in the origin of the Arctic-Sino-Himalayan disjunction}, volume={59}, ISSN={["1759-6831"]}, DOI={10.1111/jse.12576}, abstractNote={AbstractThe dwarf dogwoods (subgenus Arctocrania) have been widely known to consist of three circumboreal species Cornus suecica, Cornus canadensis, and Cornus unalaschkensis. A fourth putative species was discovered from the northern Myanmar in 1937, but it had never been formally reported on. Here, we formally report the species on the basis of phylogenetic and morphological evidence and name it Cornus wardiana Rushforth & Wahlsteen (sp. nov.). We conducted phylogenetic and morphometric analyses to determine its evolutionary relationship and differentiation from the existing relatives. We dated the phylogeny using molecular data and conducted a biogeographic analysis to gain insights into the evolution and biogeography of the Arctic‐Sino‐Himalayan disjunction. The phylogenetic analysis used sequences of the nrITS and plastid matK and rbcL genes and included all four dwarf dogwoods and 20 other species representing the three other major lineages of Cornus and the outgroup. The morphometric analyses included 60 populations and 102 specimens of dwarf dogwood, representing the entire range of the subgenus. The results showed that C. wardiana diverged first within subgenus Arctocrania in the Miocene, from a wide‐spread ancestor. Results from principal component analysis and discriminant analysis also showed that the Myanmar samples are well separated from the others. Taken together, these results suggest that the dwarf dogwood lineage split from the big‐bracted dogwoods in Asia or Asia‐western North America during the late Paleocene and spread widely to form a Eurasia‐North America distribution; the Arctic‐Sino‐Himalayan disjunction was the result of southward migration in the Miocene followed by extinction in the intervening highland areas.}, number={2}, journal={JOURNAL OF SYSTEMATICS AND EVOLUTION}, author={Wahlsteen, Eric and Zhou, Wenbin and Xiang, Qiuyun and Rushforth, Keith}, year={2021}, month={Mar}, pages={405–416} }
 @article{liu_zhang_xie_franks_xiang_2019, title={Functional characterization of Terminal Flower1 homolog in Cornus canadensis by genetic transformation}, volume={38}, ISSN={0721-7714 1432-203X}, url={http://dx.doi.org/10.1007/S00299-019-02369-2}, DOI={10.1007/S00299-019-02369-2}, abstractNote={TFL1homologCorcanTFL1suppresses the initiation of inflorescence development and regulates the inflorescence morphology inCornus canadensis. In flowering plants, there is a wide range of variation of inflorescence morphology. Despite the ecological and evolutionary importance, efforts devoted to the evolutionary study of the genetic basis of inflorescence morphology are far fewer compared to those on flower development. Our previous study on gene expression patterns suggested a CorTFL1-CorAP1 based model for the evolution of determinate umbels, heads, and mini dichasia from elongated inflorescences in Cornus. Here, we tested the function of CorcanTFL1 in regulating inflorescence development in Cornus canadensis through Agrobacterium-mediated transformation. We showed that transgenic plants overexpressing CorcanTFL1 displayed delayed or suppressed inflorescence initiation and development and extended periods of vegetative growth. Transgenic plants within which CorcanTFL1 had been down-regulated displayed earlier emergence of inflorescence and a reduction of bract and inflorescence sizes, conversions of leaves to bracts and axillary leaf buds to small inflorescences at the uppermost node bearing the inflorescence, or phyllotaxy changes of inflorescence branches and leaves from decussate opposite to spirally alternate. These observations support an important role of CorcanTFL1 in determining flowering time and the morphological destinies of leaves and buds at the node bearing the inflorescence. The evidence is in agreement with the predicted function of CorTFL1 from the gene expression model, supporting a key role of CorTFL1 in the evolutionary divergence of inflorescence forms in Cornus.}, number={3}, journal={Plant Cell Reports}, publisher={Springer Science and Business Media LLC}, author={Liu, Xiang and Zhang, Jian and Xie, Deyu and Franks, Robert G. and Xiang, Qiu-Yun}, year={2019}, month={Jan}, pages={333–343} }
 @article{dong_chen_cheng_zhou_ma_chen_fu_liu_zhao_soltis_et al._2019, title={Natural selection and repeated patterns of molecular evolution following allopatric divergence}, volume={8}, ISSN={2050-084X}, url={http://dx.doi.org/10.7554/eLife.45199}, DOI={10.7554/eLife.45199}, abstractNote={Although geographic isolation is a leading driver of speciation, the tempo and pattern of divergence at the genomic level remain unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) in 20 allopatric species/variety pairs from diverse angiosperm clades, with 16 pairs reflecting the classic eastern Asia-eastern North America floristic disjunction. In each pair, >90% of POGs are under purifying selection, and <10% are under positive selection. A set of POGs are under strong positive selection, 14 of which are shared by 10–15 pairs, and one shared by all pairs; 15 POGs are annotated to biological processes responding to various stimuli. The relative abundance of POGs under different selective forces exhibits a repeated pattern among pairs despite an ~10 million-year difference in divergence time. Species divergence times are positively correlated with abundance of POGs under moderate purifying selection, but negatively correlated with abundance of POGs under strong purifying selection.}, journal={eLife}, publisher={eLife Sciences Publications, Ltd}, author={Dong, Yibo and Chen, Shichao and Cheng, Shifeng and Zhou, Wenbin and Ma, Qing and Chen, Zhiduan and Fu, Cheng-Xin and Liu, Xin and Zhao, Yun-peng and Soltis, Pamela S and et al.}, year={2019}, month={Aug} }
 @article{du_harris_(jenny) xiang_2019, title={Phylogenomics, co-evolution of ecological niche and morphology, and historical biogeography of buckeyes, horsechestnuts, and their relatives (Hippocastaneae, Sapindaceae) and the value of RAD-Seq for deep evolutionary inferences back to the Late Cretaceous}, ISSN={1055-7903}, url={http://dx.doi.org/10.1016/j.ympev.2019.106726}, DOI={10.1016/j.ympev.2019.106726}, abstractNote={In this study, we used RAD-seq data to resolve the phylogeny of the tribe Hippocastaneae (Sapindaceae) and conducted comparative analyses to gain insights into the evolution and biogeography of the group that had fossils dating back to the late Cretaceous. Hippocastaneae, including the horsechestnuts and buckeyes, is a well-supported clade in Sapindaceae that comprises 12–14 species in Aesculus, two in Billia, and one in Handeliodendron. Most species in the tribe are distributed in Eurasia and North America and exhibit a classic pattern of intercontinental disjunction in the Northern Hemisphere, while Billia occurs from southern Mexico to northern South America. The earliest fossils of Aesculus date back to at least the earliest Paleocene of eastern Asia and western North America, where there are also putative occurrences from the latest Cretaceous. The group provides an excellent system for understanding floristic disjunction in the Northern Hemisphere extending to the Neotropics. However, a strongly supported and well resolved phylogeny is presently lacking for the tribe. Previous phylogenetic studies using several gene regions revealed five well-supported clades in Aesculus, largely corresponding to five recognized taxonomic sections, but relationships among these clades and among Aesculus, Billia, and Handeliodendron were not well supported. In this study, we used RAD-seq data from 68 samples representing all clades and species of Hippocastaneae except Billia, for which we used one of two species, to further resolve relationships within the tribe. Our phylogenomic analyses showed strong support for a sister relationship between Aesculus and Handeliodendron, in contrast to previous findings which supported Billia as sister to Aesculus. Within Aesculus, relationships among sections were strongly supported as (sect. Calothyrsus, (sect. Aesculus, (sect. Macrothyrsus, (sect. Parryana, sect. Pavia)))). We found that the traditionally recognized section Calothyrsus was monophyletic, with all eastern Asian species sister to the western North American species, A. californica. Analyses of divergence times combined with biogeographic analyses suggested a Late Cretaceous origin of Hippocastaneae, in eastern Asia, western North America, and Central America (including southern Mexico), followed by isolation of Billia in Central America, extinction of the tribe ancestor in western North America, and divergence of Aesculus from Handeliodendron in eastern Asia. A Late Cretaceous origin of the common ancestor of Aesculus in eastern Asia was followed by dispersals into western North America, Europe, and eastern North America during the Late Cretaceous and the Paleogene. Our results support Aesculus as a relic of the boreotropical flora and subsequent intercontinental spread of the genus through the Bering and North Atlantic land bridges. We performed character mapping analyses, which revealed that biogeographic isolation and niche divergence may have played important roles in driving morphological evolution and lineage divergence in Aesculus. Our study demonstrates the value of RAD-seq data for reconstructing phylogeny back to the Late Cretaceous.}, journal={Molecular Phylogenetics and Evolution}, publisher={Elsevier BV}, author={Du, Zhi-Yuan and Harris, AJ and (Jenny) Xiang, Qiu-Yun}, year={2019}, month={Dec}, pages={106726} }
 @article{fu_mo_yang_ge_li_xiang_gao_2019, title={Plastid phylogenomics and biogeographic analysis support a trans-Tethyan origin and rapid early radiation of Cornales in the Mid-Cretaceous}, volume={140}, ISSN={1055-7903}, url={http://dx.doi.org/10.1016/j.ympev.2019.106601}, DOI={10.1016/j.ympev.2019.106601}, abstractNote={The Cornales is a relatively small but morphologically diverse order in the basal position of the Asterids clade. Previous study hypothesized that the order might have undergone ancient rapid radiation during the Cretaceous when major angiosperm lineages were established. We conducted the phylogenomic analysis of Cornales using 81 plastid genome sequences with 67 newly generated in this study to test the hypothesis. This sampling represents all the families and 31 out of 48 genera in the order. Phylogenetic analyses were conducted using different datasets to examine the effects of different coding positions and character coding methods. We further conducted divergence time, diversification rate, and biogeographic analyses to understand the early evolutionary history of Cornales in space and time. Our phylogenetic analyses of four datasets (the amino acid characters, the 1st and 2nd codon positions of protein coding genes, nucleotide characters with degenerated coding method, and noncoding regions) resulted in a robust phylogeny congruent with results of previous studies, showing (((Cornaceae-Alangiaceae)-(Curtisiaceae-Grubbiaceae))-(((Nyssaceae-Davidiaceae)-Mastixiaceae)-((Hydrostachyaceae-(Hydrangeaceae-Loasaceae)))). Phylogenetic relationships within families were also well resolved. Conflicts in the placement of Hydrostachyaceae were found from analyses of two datasets, the nucleotide characters of all codon position and the 3rd codon positions, where the family was united with Loasaceae, but not strongly supported. Results from divergence time analyses suggested a mid-Cretaceous origin of Cornales followed by rapid early diversification into major clades/families within 10 million years. The early diversification of Cornales may have been facilitated by divergence in habitat and morphology following geographic dispersals. The ancestral distribution of the order was inferred as a widespread range covering Asia, Europe, North America, and Africa when including fossils in the analyses, suggesting an origin of the order likely along the Tethys Seaway where the areas were connected in the mid-Cretaceous. Inferred geographic origins of each family differed to some extent between analyses including fossils vs excluding fossils. In the analysis with extant and fossil species, the origins of the African Hydrostachyaceae and Grubbiaceae-Curtisiaceae clade were inferred to have involved two independent events, an intercontinental dispersal from the northern hemisphere to Africa and an intercontinental vicariance between the northern hemisphere and Africa, respectively. Other families were inferred to have evolved in the northern hemisphere with subsequent intercontinental dispersal(s) to other areas including to Central and South America, during their subsequent diversification. Net diversification rate analysis based on treePL dated phylogeny using MEDUSA detected a nearly 5-fold decrease in the African endemic Curtisiaceae-Grubbiaceae (CuG) clade and an increase of rate in the Hydrangeaceae-Loasaceae (HL) clade. Within HL, a decrease in the Fendlera-Jamesia clade and an increase in the Philadelphus clade were also detected. The findings are also consistent with the level of present species diversity in these lineages. Our study demonstrated the value of plastid genome in phylogenomic study, but posed an old challenge of biogeographic study with fossil data and raised caution for the synonymous substitution sites of plastid genome in phylogenomics studies.}, journal={Molecular Phylogenetics and Evolution}, publisher={Elsevier BV}, author={Fu, Chao-Nan and Mo, Zhi-Qiong and Yang, Jun-Bo and Ge, Xue-Jun and Li, De-Zhu and Xiang, Qiu-Yun (Jenny) and Gao, Lian-Ming}, year={2019}, month={Nov}, pages={106601} }
 @article{pais_li_xiang_2018, title={Discovering variation of secondary metabolite diversity and its relationship with disease resistance in Cornus florida
 L.}, volume={8}, ISSN={2045-7758}, url={http://dx.doi.org/10.1002/ece3.4090}, DOI={10.1002/ece3.4090}, abstractNote={AbstractUnderstanding intraspecific relationships between genetic and functional diversity is a major goal in the field of evolutionary biology and is important for conserving biodiversity. Linking intraspecific molecular patterns of plants to ecological pressures and trait variation remains difficult due to environment‐driven plasticity. Next‐generation sequencing, untargeted liquid chromatography–mass spectrometry (LC‐MS) profiling, and interdisciplinary approaches integrating population genomics, metabolomics, and community ecology permit novel strategies to tackle this problem. We analyzed six natural populations of the disease‐threatened Cornus florida L. from distinct ecological regions using genotype‐by‐sequencing markers and LC‐MS‐based untargeted metabolite profiling. We tested the hypothesis that higher genetic diversity in C. florida yielded higher chemical diversity and less disease susceptibility (screening hypothesis), and we also determined whether genetically similar subpopulations were similar in chemical composition. Most importantly, we identified metabolites that were associated with candidate loci or were predictive biomarkers of healthy or diseased plants after controlling for environment. Subpopulation clustering patterns based on genetic or chemical distances were largely congruent. While differences in genetic diversity were small among subpopulations, we did observe notable similarities in patterns between subpopulation averages of rarefied‐allelic and chemical richness. More specifically, we found that the most abundant compound of a correlated group of putative terpenoid glycosides and derivatives was correlated with tree health when considering chemodiversity. Random forest biomarker and genomewide association tests suggested that this putative iridoid glucoside and other closely associated chemical features were correlated to SNPs under selection.}, number={11}, journal={Ecology and Evolution}, publisher={Wiley}, author={Pais, Andrew L. and Li, Xu and Xiang, Qiu-Yun (Jenny)}, year={2018}, month={May}, pages={5619–5636} }
 @article{nowicki_boggess_saxton_hadziabdic_xiang_molnar_huff_staton_zhao_trigiano_et al._2018, title={Haplotyping of Cornus florida and C. kousa chloroplasts: Insights into species-level differences and patterns of plastic DNA variation in cultivars}, volume={13}, ISSN={1932-6203}, url={http://dx.plos.org/10.1371/journal.pone.0205407}, DOI={10.1371/journal.pone.0205407}, abstractNote={Chloroplast DNA is a part of plant non-nuclear genome, and is of particular interest for lineage studies. Moreover, the non-coding regions of cpDNA display higher mutation rates than the conserved coding cpDNA, which has been employed for phylogenetic and population research. We analyzed the cpDNA of 332 gDNA samples from collections of Cornus florida and C. kousa (commercial cultivars, breeding selections, and wild kousa accessions from Asia), using the chlorotyping system developed on North America-native, wild accessions of C. florida. Our results indicated significant differences in chlorotype frequencies between the two species. Cornus florida samples were represented by all major chlorotypes previously described, whereas all C. kousa samples analyzed had only one of the chlorotype patterns shown by C. florida. The chlorotyping analytic panel was then expanded by sequencing the targeted three non-coding cpDNA regions. Results indicated a major difference in the maternally-inherited cpDNA between the two closely related Big-Bracted Cornus species. Chlorotype diversity and differences in the proportion of informative sites in the cpDNA regions of focus emphasized the importance of proper loci choice for cpDNA-based comparative studies between the closely related dogwood species. Phylogenetic analyses of the retrieved sequences for the other species of Cornus provided information on the relative utility of the cpDNA regions studied and helped delineate the groups (Big-Bracted, Cornelian Cherries, Blue/White-Fruited) within the genus. Genealogical relationships based on the cpDNA sequences and the inferred chlorotype networks indicated the need for continued analyses across further non-coding cpDNA regions to improve the phylogenetic resolution of dogwoods.}, number={10}, journal={PLOS ONE}, author={Nowicki, Marcin and Boggess, Sarah L. and Saxton, Arnold M. and Hadziabdic, Denita and Xiang, Qiu-Yun and Molnar, Thomas and Huff, Matthew L. and Staton, Margaret E. and Zhao, Yichen and Trigiano, Robert N. and et al.}, editor={Heinze, BertholdEditor}, year={2018}, month={Oct} }
 @article{zhou_ji_obata_pais_dong_peet_xiang_2018, title={Resolving relationships and phylogeographic history of the Nyssa sylvatica complex using data from RAD-seq and species distribution modeling}, volume={126}, ISSN={1055-7903}, url={http://dx.doi.org/10.1016/j.ympev.2018.04.001}, DOI={10.1016/j.ympev.2018.04.001}, abstractNote={Nyssa sylvatica complex consists of several woody taxa occurring in eastern North America. These taxa were recognized as two or three species including three or four varieties by different authors. Due to high morphological similarities and complexity of morphological variation, classification and delineation of taxa in the group have been difficult and controversial. Here we employ data from RAD-seq to elucidate the genetic structure and phylogenetic relationships within the group. Using the genetic evidence, we evaluate previous classifications and delineate species. We also employ Species Distribution Modeling (SDM) to evaluate impacts of climatic changes on the ranges of the taxa and to gain insights into the relevant refugia in eastern North America. Results from Molecular Variance Analysis (AMOVA), STRUCTURE, phylogenetic analyses using Maximum likelihood, Bayesian Inference, and Splittree methods of RAD-seq data strongly support a two-clade pattern, largely separating samples of N. sylvatica from those of N. biflora-N. ursina mix. Divergence time analysis with BEAST suggests the two clades diverged in the mid Miocene. The ancestor of the present trees of N. sylvatica was suggested to be in the Pliocene and that of N. biflora-N. ursina mix in the end of the Miocene. Results from SDM predicted a smaller range in the southern part of the species present range of each clade during the Last Glacial Maximum (LGM). A northward expansion of the ranges during interglacial period and a northward shift of the ranges in the future under a model of global warming were also predicted. Our results support the recognition of two species in the complex, N. sylvatica and N. biflora, following the phylogenetic species concept. We found no genetic evidence supporting recognitions of intraspecific taxa. However, we propose subsp. ursina and subsp. biflora within N. biflora due to their distinction in habits, distributions, and habitats. Our results further support movements of trees in eastern North America in response to climatic changes. Finally, our study demonstrates that RAD-seq data and a combination of population genomics and SDM are valuable in resolving relationship and biogeographic history of closely related species that are taxonomically difficult.}, journal={Molecular Phylogenetics and Evolution}, publisher={Elsevier BV}, author={Zhou, Wenbin and Ji, Xiang and Obata, Shihori and Pais, Andrew and Dong, Yibo and Peet, Robert and Xiang, Qiu-Yun (Jenny)}, year={2018}, month={Sep}, pages={1–16} }
 @inbook{plunkett_xiang_lowery_schutzs_2018, place={Switzerland}, title={Toricelliaceae}, volume={XV}, booktitle={The Families and Genera of Vascular Plants : Flowering Plants Eudicots-Apiales, Gentianales (Except Rubiaceae)}, publisher={Springer}, author={Plunkett, G.R. and Xiang, Q-Y(J) and Lowery, P.P. and Schutzs, G.E.}, editor={Kubitzki, K. and Kadereit, J.W. and Bittrich, V.Editors}, year={2018}, pages={549–556} }
 @article{liu_li_jenny xiang_2017, title={Down regulation of APETALA 3 homolog resulted in defect of floral structure critical to explosive pollen release in Cornus canadensis: The role of APETALA3 homolog in Cornus}, volume={55}, ISSN={16744918}, url={http://doi.wiley.com/10.1111/jse.12272}, DOI={10.1111/jse.12272}, abstractNote={AbstractIn mature buds of the dwarf dogwood lineage (DW) of Cornus, petals and filaments form an “x”‐like box containing mechanical energy from the filaments to allow explosive pollen dispersal. As a start to understand the molecular mechanisms responsible for the origin of this unique structure in Cornus, we cloned and characterized the sequences of APETALA3 (AP3) homologs from Cornus canadensis of the DW lineage and five other Cornus species, given the function of AP3 on petal and stamen development in Arabidopsis, and tested the function of CorcanAP3 using a stable Agrobacterium‐mediated transformation system. The cloned CorAP3s (AP3‐like genes in Cornus) were confirmed to belong to the euAP3 lineage. qRT‐PCR analysis indicated strong increase of CorcanAP3 expression in floral buds of wildtype C. canadensis. A hairpin construct of CorcanAP3 was successfully introduced into wild type plants of C. canadensis, resulting in significant reduction of CorcanAP3 expression and abnormal floral development. The abnormal floral buds lost the “x” form and opened immaturely due to delay or retard of petal and stamen elongation and the push of style elongation. The results suggested CorcanAP3 may function to regulate the coordinated rate of development of petals and stamens in C. canadensis, necessary for the x‐structure formation, although the exact molecular mechanism remains unclear. Comparison among six Cornus species indicated a greater ratio of stamen to petal and style growth in C. canadensis, suggesting an evolutionary change of CorAP3 expression pattern in the DW lineage, leading to the greater growth of filaments to form the “x”‐box.}, number={6}, journal={Journal of Systematics and Evolution}, publisher={Wiley}, author={Liu, Xiang and Li, Lu and Jenny Xiang, Qiu-Yun}, year={2017}, month={Nov}, pages={566–580} }
 @article{ma_zhang_jenny xiang_2017, title={Evolution and developmental genetics of floral display-A review of progress: A review of progress in evo-devo of floral display}, volume={55}, ISSN={16744918}, url={http://doi.wiley.com/10.1111/jse.12259}, DOI={10.1111/jse.12259}, abstractNote={AbstractAngiosperms evolved a great diversity of ways to display their flowers for reproductive success by variation in floral color, size, shape, scent, arrangements, and flowering time. The various innovations in floral forms and the aggregation of flowers into different kinds of inflorescences can drive new ecological adaptations, speciation, and angiosperm diversification. Evolutionary developmental biology (evo‐devo) seeks to uncover the developmental and genetic basis underlying morphological diversification. Advances in the developmental genetics of floral display have provided a foundation for insights into the genetic basis of floral and inflorescence evolution. A number of regulatory genes controlling floral and inflorescence development have been identified in model plants (e.g., Arabidopsis thaliana, Antirrhinum majus) using forward genetics and conserved functions of many of these genes across diverse non‐model species have been revealed by reverse genetics. Gene‐regulatory networks that mediated the developmental progresses of floral and inflorescence development have also been established in some plant species. Meanwhile, phylogeny‐based comparative analysis of morphological and genetic character has enabled the identification of key evolutionary events that lead to morphological complexity and diversification. Here we review the recent progress on evo‐devo studies of floral display including floral symmetry, petal fusion, floral color, floral scent, and inflorescences. We also review the molecular genetic approaches applied to plant evo‐devo studies and highlight the future directions of evo‐devo.}, number={6}, journal={Journal of Systematics and Evolution}, publisher={Wiley}, author={Ma, Qing and Zhang, Wenheng and Jenny Xiang, Qiu-Yun}, year={2017}, month={Nov}, pages={487–515} }
 @article{zhang_xiang_wen_2017, title={Evolution, development, and genetics of floral display-form, size, and arrangement}, volume={55}, ISSN={["1759-6831"]}, DOI={10.1111/jse.12274}, abstractNote={The flower, frequently arranged in clusters known as inflorescences, is one of the most fascinating outcomes through evolution (Endress, 2010). The dimensions of floral diversity in angiosperms are enormous through variations, such as, in floral size, color, shape, scent, and flowering time.}, number={6}, journal={JOURNAL OF SYSTEMATICS AND EVOLUTION}, author={Zhang, Wenheng and Xiang, Qiu-Yun and Wen, Jun}, year={2017}, month={Nov}, pages={485–486} }
 @article{yu_xiang_manos_soltis_soltis_song_cheng_liu_wong_2017, title={Whole genome duplication and acceleration of molecular evolution is associated with the early diversification of the genus Cornus L. (Cornaceae): Insights from De Novo Assembled Transcriptome Sequences}, volume={12}, ISSN={1932-6203}, url={http://dx.plos.org/10.1371/journal.pone.0171361}, DOI={10.1371/journal.pone.0171361}, abstractNote={The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework. Here we compare ten de novo-assembled transcriptomes representing the major lineages of the angiosperm genus Cornus (dogwood) and relevant outgroups using a customized pipeline for analyses. Using three distinct approaches, molecular dating of orthologous genes, analyses of the distribution of synonymous substitutions between paralogous genes, and examination of substitution rates through time, we detected a shared WGD event in the late Cretaceous across all taxa sampled. The inferred doubling event coincides temporally with the paleoclimatic changes associated with the initial divergence of the genus into three major lineages. Analyses also showed an acceleration of rates of molecular evolution after WGD. The highest rates of molecular evolution were observed in the transcriptome of the herbaceous lineage, C. canadensis, a species commonly found at higher latitudes, including the Arctic. Our study demonstrates the value of transcriptome data for understanding genome evolution in closely related species. The results suggest dramatic increase in sea surface temperature in the late Cretaceous may have contributed to the evolution and diversification of flowering plants.}, number={2}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Yu, Yan and Xiang, Qiuyun and Manos, Paul S. and Soltis, Douglas E. and Soltis, Pamela S. and Song, Bao-Hua and Cheng, Shifeng and Liu, Xin and Wong, Gane}, editor={Chiang, Tzen-YuhEditor}, year={2017}, month={Feb}, pages={e0171361} }
 @article{ma_liu_franks_xiang_2016, title={Alterations of CorTFL1 and CorAP1 expression correlate with major evolutionary shifts of inflorescence architecture in Cornus (Cornaceae) - a proposed model for variation of closed inflorescence forms}, volume={216}, ISSN={0028646X}, url={http://doi.wiley.com/10.1111/nph.14197}, DOI={10.1111/nph.14197}, abstractNote={Summary


TFL1‐, AP1‐ and LFY‐like genes are known to be key regulators of inflorescence development. However, it remains to be tested whether the evolutionary modifications of inflorescence morphology result from shifts in their expression patterns.

We compared the spatiotemporal expression patterns of CorTFL1, CorAP1 and CorLFY in six closely related Cornus species that display four types of closed inflorescence morphology using quantitative real‐time polymerase chain reaction (qRT‐PCR) and RNA in situ hybridization. Character mapping on the phylogeny was conducted to identify evolutionary changes and to assess the correlation between changes in gene expression and inflorescence morphology.

Results demonstrated variation of gene expression patterns among species and a strong correlation between CorTFL1 expression and the branch index of the inflorescence type. Evolutionary changes in CorTFL1 and CorAP1 expression co‐occurred on the phylogeny with the morphological changes underpinning inflorescence divergence.

The study found a clear correlation between the expression patterns of CorTFL1 and CorAP1 and the inflorescence architecture in a natural system displaying closed inflorescences. The results suggest a role for the alteration in CorTFL1 and CorAP1 expression during the evolutionary modification of inflorescences in Cornus. We propose that a TFL1‐like and AP1‐like gene‐based model may explain variation of closed inflorescences in Cornus and other lineages.

}, number={2}, journal={New Phytologist}, publisher={Wiley}, author={Ma, Qing and Liu, Xiang and Franks, Robert G. and Xiang, Qiu-Yun Jenny}, year={2016}, pages={519–535} }
 @article{liu_zhang_abuahmad_franks_xie_xiang_2016, title={Analysis of two TFL1 homologs of dogwood species (Cornus L.) indicates functional conservation in control of transition to flowering}, volume={243}, ISSN={0032-0935, 1432-2048}, url={http://link.springer.com/10.1007/s00425-016-2466-x}, DOI={10.1007/s00425-016-2466-x}, abstractNote={Two TFL1 -like genes, CorfloTFL1 and CorcanTFL1 cloned from Cornus florida and C. canadensis, function in regulating the transition to reproductive development in Arabidopsis. TERMINAL FLOWER 1 (TFL1) is known to regulate inflorescence development in Arabidopsis thaliana and to inhibit the transition from a vegetative to reproductive phase within the shoot apical meristem. Despite the importance, TFL1 homologs have been functionally characterized in only a handful eudicots. Here we report the role of TFL1 homologs of Cornus L. in asterid clade of eudicots. Two TFL1-like genes, CorfloTFL1 and CorcanTFL1, were cloned from Cornus florida (a tree) and C. canadensis (a subshrub), respectively. Both are deduced to encode proteins of 175 amino acids. The amino acid sequences of these two Cornus TFL1 homologs share a high similarity to Arabidopsis TFL1 and phylogenetically more close to TFL1 paralogous copy ATC (Arabidopsis thaliana CENTRORADIALIS homologue). Two genes are overexpressed in wild-type and tfl1 mutant plants of A. thaliana. The over-expression of each gene in wild-type Arabidopsis plants results in delaying flowering time, increase of plant height and cauline and rosette leaf numbers, excessive shoot buds, and secondary inflorescence branches. The over-expression of each gene in the tfl1 mutant rescued developmental defects, such as the early determinate inflorescence development, early flowering time, and other vegetative growth defects, to normal phenotypes of wild-type plants. These transgenic phenotypes are inherited in progenies. All data indicate that CorfloTFL1 and CorcanTFL1 have conserved the ancestral function of TFL1 and CEN regulating flowering time and inflorescence determinacy.}, number={5}, journal={Planta}, publisher={Springer Science and Business Media LLC}, author={Liu, Xiang and Zhang, Jian and Abuahmad, Ahmad and Franks, Robert G. and Xie, De-Yu and Xiang, Qiu-Yun}, year={2016}, month={May}, pages={1129–1141} }
 @inbook{xiang_2016, series={Flowering Plants. Eudicots}, title={Aucubaceae}, volume={XIV}, DOI={10.1007/978-3-319-28534-4_4}, booktitle={The Families and Genera of Vascular Plants}, publisher={Springer Nature, AG Switzerland}, author={Xiang, Q.Y.}, editor={W., Kadereit J. and Bitterich, VolkerEditors}, year={2016}, pages={37–40}, collection={Flowering Plants. Eudicots} }
 @article{pais_whetten_xiang_2016, title={Ecological genomics of local adaptation in Cornus florida L. by genotyping by sequencing}, volume={7}, ISSN={2045-7758}, url={http://dx.doi.org/10.1002/ece3.2623}, DOI={10.1002/ece3.2623}, abstractNote={AbstractDiscovering local adaptation, its genetic underpinnings, and environmental drivers is important for conserving forest species. Ecological genomic approaches coupled with next‐generation sequencing are useful means to detect local adaptation and uncover its underlying genetic basis in nonmodel species. We report results from a study on flowering dogwood trees (Cornus florida L.) using genotyping by sequencing (GBS). This species is ecologically important to eastern US forests but is severely threatened by fungal diseases. We analyzed subpopulations in divergent ecological habitats within North Carolina to uncover loci under local selection and associated with environmental–functional traits or disease infection. At this scale, we tested the effect of incorporating additional sequencing before scaling for a broader examination of the entire range. To test for biases of GBS, we sequenced two similarly sampled libraries independently from six populations of three ecological habitats. We obtained environmental–functional traits for each subpopulation to identify associations with genotypes via latent factor mixed modeling (LFMM) and gradient forests analysis. To test whether heterogeneity of abiotic pressures resulted in genetic differentiation indicative of local adaptation, we evaluated Fst per locus while accounting for genetic differentiation between coastal subpopulations and Piedmont‐Mountain subpopulations. Of the 54 candidate loci with sufficient evidence of being under selection among both libraries, 28–39 were Arlequin–BayeScan Fst outliers. For LFMM, 45 candidates were associated with climate (of 54), 30 were associated with soil properties, and four were associated with plant health. Reanalysis of combined libraries showed that 42 candidate loci still showed evidence of being under selection. We conclude environment‐driven selection on specific loci has resulted in local adaptation in response to potassium deficiencies, temperature, precipitation, and (to a marginal extent) disease. High allele turnover along ecological gradients further supports the adaptive significance of loci speculated to be under selection.}, number={1}, journal={Ecology and Evolution}, publisher={Wiley}, author={Pais, Andrew L. and Whetten, Ross W. and Xiang, Qiu-Yun Jenny}, year={2016}, month={Dec}, pages={441–465} }
 @article{geng_liu_ji_hoffmann_grunden_xiang_2016, title={Enhancing Heat Tolerance of the Little Dogwood Cornus canadensis L. f. with Introduction of a Superoxide Reductase Gene from the Hyperthermophilic Archaeon Pyrococcus furiosus}, volume={7}, ISSN={1664-462X}, url={http://dx.doi.org/10.3389/fpls.2016.00026}, DOI={10.3389/fpls.2016.00026}, abstractNote={Production of reactive oxygen species (ROS) can be accelerated under various biotic and abiotic stresses causing lipid peroxidation, protein degradation, enzyme inactivation, and DNA damage. Superoxide reductase (SOR) is a novel antioxidant enzyme from Pyrococcus furiosus and is employed by this anaerobic hyperthermophilic archaeon for efficient detoxification of ROS. In this study, SOR was introduced into a flowering plant Cornus canadensis to enhance its heat tolerance and reduce heat induced damage. A fusion construct of the SOR gene and Green Fluorescent Protein gene (GFP) was introduced into C. canadensis using Agrobacterium-mediated transformation. Heat tolerance of the GFP-SOR expressing transgenic plants was investigated by observing morphological symptoms of heat injury and by examining changes in photosynthesis, malondialdehyde (MDA), and proline levels in the plants. Our results indicate that the expression of the P. furiosus SOR gene in the transgenic plants alleviated lipid peroxidation of cell membranes and photoinhibition of PS II, and decreased the accumulation of proline at 40°C. After a series of exposures to increasing temperatures, the SOR transgenic plants remained healthy and green whereas most of the non-transgenic plants dried up and were unable to recover. While it had previously been reported that expression of SOR in Arabidopsis enhanced heat tolerance, this is the first report of the successful demonstration of improved heat tolerance in a non-model plant resulting from the introduction of P. furiosus SOR. The study demonstrates the potential of SOR for crop improvement and that inherent limitations of plant heat tolerance can be ameliorated with P. furiosus SOR.}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Geng, Xing-Min and Liu, Xiang and Ji, Mikyoung and Hoffmann, William A. and Grunden, Amy and Xiang, Qiu-Yun J.}, year={2016}, month={Jan} }
 @inbook{xiang_2016, series={Flowering Plants. Eudicots.}, title={Helwingiaceae}, volume={XIV}, DOI={10.1007/978-3-319-28534-4_18}, booktitle={The Families and Genera of Vascular Plants}, author={Xiang, Q.Y.}, editor={K.KubitzkiEditor}, year={2016}, pages={213–216}, collection={Flowering Plants. Eudicots.} }
 @article{harris_fu_xiang_holland_wen_2016, title={Testing the monophyly of Aesculus L. and Billia Peyr., woody genera of tribe Hippocastaneae of the Sapindaceae}, volume={102}, ISSN={1055-7903}, url={http://dx.doi.org/10.1016/j.ympev.2016.06.001}, DOI={10.1016/j.ympev.2016.06.001}, abstractNote={Hippocastaneae is a well-supported clade in Sapindaceae that comprises 15+ species; 12+ in Aesculus, two in Billia, and one in Handeliodendron Rehder. The monophyly of Aesculus and Billia were widely assumed, but a recent molecular phylogenetic study of Sapindanceae used seven species of Aesculus and one each of Billia and Handeliodendron and showed that Billia and Handeliodendron were nested within Aesculus. Here, we tested the hypothesis that Aesculus and Billia are mutually monophyletic using phylogenetic analyses of seven molecular markers and 31 accessions of Hippocastaneae representing 14 species. We performed phylogenetic analyses using a dataset of concatenated genes as well as with coalescent method for constructing a species tree from individual gene trees. The analysis of seven concatenated markers and the species tree strongly supported the mutual monophyly of Aesculus and Billia. We also recovered support for the traditional arrangement of genera within Hippocastaneae: Aesculus and Billia comprising a clade that is sister to Handeliodendron. However, the relationships among the genera remain incompletely resolved.}, journal={Molecular Phylogenetics and Evolution}, publisher={Elsevier BV}, author={Harris, AJ and Fu, Chengxin and Xiang, Qiu-Yun (Jenny) and Holland, LaRinda and Wen, Jun}, year={2016}, month={Sep}, pages={145–151} }
 @article{call_sun_yu_pearman_thomas_trigiano_carbone_xiang_2016, title={Genetic structure and post-glacial expansion of Cornus florida L. (Cornaceae): integrative evidence from phylogeography, population demographic history, and species distribution modeling}, volume={54}, ISSN={16744918}, url={http://doi.wiley.com/10.1111/jse.12171}, DOI={10.1111/jse.12171}, abstractNote={AbstractRepeated global climatic cooling and warming cycles during the Pleistocene played a major role in the distribution and evolution of the Earth biota. Here, we integrate phylogeography, coalescent‐based Bayesian estimation of demographic history, and species distribution modeling (SDM) to understand the genetic patterns and biogeography of the flowering dogwood, Cornus florida subsp. florida L., since the Last Glacial Maximum (LGM). Natural populations of the species are severely threatened by dogwood anthracnose. We genotyped 306 plants from 73 locations of the species across most of its native distribution with three DNA regions from the plastid genome, ndhF‐rpl32, rps16 and trnQ‐rps16. The genealogy and haplotype network reconstruction revealed two haplotype lineages diverging ≈3.70 million years ago. We detected no clear geographic structuring of genetic variation, although significant local structure appeared to be evident, likely due to a combination of substantial localized seed dispersal by small mammals and small population size/limited sampling at a location. The spatial distribution of haplotype frequencies, estimated population demographic history, and results from hindcasting analysis using SDM suggested refugia in southeastern North America and population reduction during the LGM, followed by rapid post‐glacial expansion to the north. Forecasting analysis using SDM predicted range shifts to the north under ongoing global warming. Our results further suggested that gene flow via seed dispersal has been high but insufficient to counter the effect of genetic drift. This study demonstrates the benefit of integrating genetic data and species distribution modeling to obtain corroborative evidence in elucidating recent biogeographic history and understanding of genetic patterns and species evolution.}, number={2}, journal={Journal of Systematics and Evolution}, publisher={Wiley}, author={Call, Ashley and Sun, Yan-Xia and Yu, Yan and Pearman, Peter B. and Thomas, David T. and Trigiano, Robert N. and Carbone, Ignazio and Xiang, Qiu-Yun Jenny}, year={2016}, month={Mar}, pages={136–151} }
 @article{wen_liu_ge_xiang_zimmer_2015, title={Phylogenomic approaches to deciphering the tree of life}, volume={53}, ISSN={["1759-6831"]}, DOI={10.1111/jse.12175}, abstractNote={Phylogenomics comprises an interdisciplinary field of comparative biology that uses genomic data to produce phylogenetic relationships among organisms (Philippe et al., 2005; Chan & Ragan, 2013). The term “phylogenomics” was initially applied to studies on gene functions (Eisen, 1998) but subsequently has been widely used to infer the tree of life (Philippe et al., 2004,2005; Pennisi, 2008; Zou et al., 2008; Dos Reis et al., 2012; Liu et al., 2015a, 2015b). With the advent and rapid development of next-generation sequencing (NGS), phylogenomics has gained more popularity in the last few years and is now being employed by many members of the evolutionary and systematics community (Lemmon & Lemmon, 2013; Wen et al., 2013, 2015; Jarvis et al., 2014; Weitemier et al., 2014; Wickett et al., 2014; Zeng et al., 2014).}, number={5}, journal={JOURNAL OF SYSTEMATICS AND EVOLUTION}, author={Wen, Jun and Liu, Jianquan and Ge, Song and Xiang, Qiu-Yun and Zimmer, Elizabeth A.}, year={2015}, month={Sep}, pages={369–370} }
 @article{qi_yu_liu_pais_ranney_whetten_xiang_2015, title={Phylogenomics of polyploidy Fothergilla (Hamamelidaceae) by RAD-tag based GBS—Insights into species origin and effects of software pipelines}, volume={53}, ISSN={16744918}, url={http://doi.wiley.com/10.1111/jse.12176}, DOI={10.1111/jse.12176}, abstractNote={AbstractFothergilla (Hamamelidaceae) consists of Fothergilla gardenii (4x) from the coastal plains of the southeastern USA, F. major (6x) from the piedmont and mountains of the same region, and a few allopatric diploid populations of unknown taxonomic status. The objective of this study was to explore the relationships of the polyploid species with the diploid plants. Genotyping by sequencing (GBS) was applied to generate genome‐wide molecular markers for phylogenetic and genetic structure analyses of 36 accessions of Fothergilla. Sanger sequencing of three plastid and one nuclear regions provided data for comparison with GBS‐based results. Phylogenetic outcomes were compared using data from different sequencing runs and different software workflows. The different data sets showed substantial differences in inferred phylogenies, but all supported a genetically distinct 6x F. major and two lineages of the diploid populations closely associated with the 4x F. gardenii. We hypothesize that the 4x F. gardenii originated through hybridization between the Gulf coastal 2x and an extinct (or undiscovered) 2x lineage, followed by backcrosses to the Atlantic coastal 2x before chromosome doubling, and the 6x F. major also originated from the “extinct” 2x lineage. Alternative scenarios are possible but are not as well supported. The origins and divergence of the polyploid species likely occurred during the Pleistocene cycles of glaciation, although fossil evidence indicates the genus might have existed for a much longer time with a wider past distribution. Our study demonstrates the power of combining GBS data with Sanger sequencing in reconstructing the evolutionary network of polyploid lineages.}, number={5}, journal={Journal of Systematics and Evolution}, publisher={Wiley}, author={Qi, Zhe-Chen and Yu, Yi and Liu, Xiang and Pais, Andrew and Ranney, Thomas and Whetten, Ross and Xiang, Qiu-Yun Jenny}, year={2015}, month={Sep}, pages={432–447} }
 @article{kang_tao_wang_ren_qi_xiang_huang_2014, title={Adaptive and nonadaptive genome size evolution in Karst endemic flora of China}, volume={202}, ISSN={0028-646X}, url={http://dx.doi.org/10.1111/nph.12726}, DOI={10.1111/nph.12726}, abstractNote={Summary


Genome size variation is of fundamental biological importance and has been a longstanding puzzle in evolutionary biology. Several hypotheses for genome size evolution including neutral, maladaptive, and adaptive models have been proposed, but the relative importance of these models remains controversial.

Primulina is a genus that is highly diversified in the Karst region of southern China, where genome size variation and the underlying evolutionary mechanisms are poorly understood. We reconstructed the phylogeny of Primulina using DNA sequences for 104 species and determined the genome sizes of 101 species. We examined the phylogenetic signal in genome size variation, and tested the fit to different evolutionary models and for correlations with variation in latitude and specific leaf area (SLA).

The results showed that genome size, SLA and latitudinal variation all displayed strong phylogenetic signals, but were best explained by different evolutionary models. Furthermore, significant positive relationships were detected between genome size and SLA and between genome size and latitude.

Our study is the first to investigate genome size evolution on such a comprehensive scale and in the Karst region flora. We conclude that genome size in Primulina is phylogenetically conserved but its variation among species is a combined outcome of both neutral and adaptive evolution.

}, number={4}, journal={New Phytologist}, publisher={Wiley}, author={Kang, Ming and Tao, Junjie and Wang, Jing and Ren, Chen and Qi, Qingwen and Xiang, Qiu-Yun and Huang, Hongwen}, year={2014}, month={Feb}, pages={1371–1381} }
 @article{liu_franks_feng_liu_fu_(jenny) xiang_2013, title={Characterization of the sequence and expression pattern of LFY homologues from dogwood species (Cornus) with divergent inflorescence architectures}, volume={112}, ISSN={0305-7364, 1095-8290}, url={https://academic.oup.com/aob/article-lookup/doi/10.1093/aob/mct202}, DOI={10.1093/aob/mct202}, abstractNote={BACKGROUND AND AIMS
LFY homologues encode transcription factors that regulate the transition from vegetative to reproductive growth in flowering plants and have been shown to control inflorescence patterning in model species. This study investigated the expression patterns of LFY homologues within the diverse inflorescence types (head-like, umbel-like and inflorescences with elongated internodes) in closely related lineages in the dogwood genus (Cornus s.l.). The study sought to determine whether LFY homologues in Cornus species are expressed during floral and inflorescence development and if the pattern of expression is consistent with a function in regulating floral development and inflorescence architectures in the genus.


METHODS
Total RNAs were extracted using the CTAB method and the first-strand cDNA was synthesized using the SuperScript III first-strand synthesis system kit (Invitrogen). Expression of CorLFY was investigated by RT-PCR and RNA in situ hybridization. Phylogenetic analyses were conducted using the maximum likelihood methods implemented in RAxML-HPC v7.2.8.


KEY RESULTS
cDNA clones of LFY homologues (designated CorLFY) were isolated from six Cornus species bearing different types of inflorescence. CorLFY cDNAs were predicted to encode proteins of approximately 375 amino acids. The detection of CorLFY expression patterns using in situ RNA hybridization demonstrated the expression of CorLFY within the inflorescence meristems, inflorescence branch meristems, floral meristems and developing floral organ primordia. PCR analyses for cDNA libraries derived from reverse transcription of total RNAs showed that CorLFY was also expressed during the late-stage development of flowers and inflorescences, as well as in bracts and developing leaves. Consistent differences in the CorLFY expression patterns were not detected among the distinct inflorescence types.


CONCLUSIONS
The results suggest a role for CorLFY genes during floral and inflorescence development in dogwoods. However, the failure to detect expression differences between the inflorescence types in the Cornus species analysed suggests that the evolutionary shift between major inflorescence types in the genus is not controlled by dramatic alterations in the levels of CorLFY gene transcript accumulation. However, due to spatial, temporal and quantitative limitations of the expression data, it cannot be ruled out that subtle differences in the level or location of CorLFY transcripts may underlie the different inflorescence architectures that are observed across these species. Alternatively, differences in CorLFY protein function or the expression or function of other regulators (e.g. TFL1 and UFO homologues) may support the divergent developmental trajectories.}, number={8}, journal={Annals of Botany}, publisher={Oxford University Press (OUP)}, author={Liu, Juan and Franks, Robert G. and Feng, Chun-Miao and Liu, Xiang and Fu, Cheng-Xin and (Jenny) Xiang, Qiu-Yun}, year={2013}, month={Nov}, pages={1629–1641} }
 @article{zhao_qi_ma_dai_li_cameron_lee_xiang_fu_2013, title={Comparative phylogeography of the Smilax hispida group (Smilacaceae) in eastern Asia and North America – Implications for allopatric speciation, causes of diversity disparity, and origins of temperate elements in Mexico}, volume={68}, ISSN={10557903}, url={https://linkinghub.elsevier.com/retrieve/pii/S1055790313001346}, DOI={10.1016/j.ympev.2013.03.025}, abstractNote={The Smilax hispida group (Smilacaceae) exhibits a discontinuous distribution in eastern Asia, eastern and western United States, and Mexico. A broad scale phylogeographic analysis was conducted for this group to evaluate the hypotheses of accelerated allopatric divergence in eastern Asia and a northern origin of the temperate elements in Mexico. Phylogeny was inferred using seven plastid and nuclear DNA sequences. Species delineation was assessed using genealogical sorting indices (GSI). Lineage divergence time, haplotype diversification rates, and ancestral distributions were estimated using Bayesian methods. Phylogeographic patterns in eastern Asia and North America were compared by analyzing 539 individuals from 64 populations to assess allopatric diversification. Results strongly supported delineation of six allopatric species, the origin of this group from a Mexican ancestor around 11.42 mya, and Mexican origins of the temperate species in Mexico. Significant geographic structure of haplotypes was found in eastern Asia, and greater haplotype diversification rate was observed for the North American lineage. Our data support allopatric speciation in eastern Asia but do not find evidence of an elevated diversification rate. Greater species diversity of the study system in eastern Asia may be due to a longer evolutionary history. Our results do not support northern origins of the Mexican temperate species.}, number={2}, journal={Molecular Phylogenetics and Evolution}, author={Zhao, Yunpeng and Qi, Zhechen and Ma, Weiwei and Dai, Qiongyan and Li, Pan and Cameron, Kenneth M. and Lee, Joongku and Xiang, Qiu-Yun (Jenny) and Fu, Chengxin}, year={2013}, month={Aug}, pages={300–311} }
 @inbook{xiang_2013, place={Chichester, UK}, title={Cornales (Dogwood)}, ISBN={978-0-470-01590-2 978-0-470-01617-6}, url={http://doi.wiley.com/10.1002/9780470015902.a0003729.pub2}, DOI={10.1002/9780470015902.a0003729.pub2}, abstractNote={Abstract
          
            
            
              Cornales, a relatively small, but morphologically diverse, order of flowering plants, consist of trees, shrubs, lianas, rhizomatous herbs and rarely aquatic herbs. The order represents an early divergent lineage in the Asterid clade and has a cosmopolitan distribution, occurring from cold temperate regions to the tropics, rarely in subarctic zones. Four to ten families, depending on how Cornaceae are circumscribed, comprise the order. Recent molecular phylogenetic studies supported a classification of 10 families that diverged during the late Cretaceous and early Tertiary. Many of the 10 families are small and with restricted, modern distributions, but have fossils occurring in areas outside their present distribution. Common representatives include the dogwoods (e.g.,
              
                Cornus florida
              
              (flowering dogwood),
              
                Cornus kousa
              
              (kousa dogwood),
              
                Cornus canadensis
              
              (bunchberry),
              
                Cornus mas
              
              (European cornelian cherry),
              
                Cornus sericea
              
              (red‐osier dogwood),
              
                Nyssa sylvatica
              
              (black gum),
              
                Davidia involucrata
              
              (dove tree),
              
                Hydrangea macrophylla
              
              (Hydrangea),
              Deutzia
              spp. (deutzias) and
              Philadelphus
              spp. (mock oranges)), which are widely cultivated as ornamentals. Several species are medicinally important, including
              
                Cornus officinalis
              
              (cornelian cherry),
              
                Camptotheca acuminata
              
              (Happy tree),
              
                Curtisia dentata
              
              (assegai tree) and
              
                Alangium salvifolium
              
              (sage‐leaved alangium).
            
          
          
            Key Concepts:
            
              
                
                  Phylogenetic studies are essential to understanding and conserving biodiversity.
                
                
                  Phylogeny depicts evolutionary relationships of species and speciation events, providing the basis for classification and understanding macro‐ and microevolution.
                
                
                  Including more species and molecular data in phylogenetic studies can help to clarify relationships that were obscured by morphology and difficult to resolve due to rapid radiation.
                
                
                  The age of a lineage on a phylogeny can be estimated using molecular data with a relaxed molecular clock calibrated from fossils (referred to as divergence time estimation).
                
                
                  Time estimation for a given lineage is substantially affected by molecular data, taxon sampling and the phylogenetic nodes calibrated by the fossils.
                
                
                  Dated phylogeny provides the temporal framework to understand diversification patterns and speciation events in absolute historical time that can be linked to specific events in the Earth's history.
                
                
                  Fossils are important records of past distributions of a lineage, providing data on extinction, speciation, and morphological evolution through time.
                
              
            
          }, booktitle={eLS}, publisher={John Wiley & Sons, Ltd}, author={Xiang, Qiu-Yun Jenny}, editor={Wiley, JohnEditor}, year={2013}, month={Sep} }
 @article{zhang_franks_liu_kang_keebler_schaff_huang_xiang_2013, title={De novo Sequencing, Characterization, and Comparison of Inflorescence Transcriptomes of Cornus canadensis and C. florida (Cornaceae)}, volume={8}, ISSN={1932-6203}, url={https://dx.plos.org/10.1371/journal.pone.0082674}, DOI={10.1371/journal.pone.0082674}, abstractNote={Background Transcriptome sequencing analysis is a powerful tool in molecular genetics and evolutionary biology. Here we report the results of de novo 454 sequencing, characterization, and comparison of inflorescence transcriptomes of two closely related dogwood species, Cornus canadensis and C. florida (Cornaceae). Our goals were to build a preliminary source of genome sequence data, and to identify genes potentially expressed differentially between the inflorescence transcriptomes for these important horticultural species. Results The sequencing of cDNAs from inflorescence buds of C. canadensis (cc) and C. florida (cf), and normalized cDNAs from leaves of C. canadensis resulted in 251799 (ccBud), 96245 (ccLeaf) and 114648 (cfBud) raw reads, respectively. The de novo assembly of the high quality (HQ) reads resulted in 36088, 17802 and 21210 unigenes for ccBud, ccLeaf and cfBud. A reference transcriptome for C. canadensis was built by assembling HQ reads of ccBud and ccLeaf, containing 40884 unigenes. Reference mapping and comparative analyses found 10926 sequences were putatively specific to ccBud, and 6979 putatively specific to cfBud. Putative differentially expressed genes between ccBud and cfBud that are related to flower development and/or stress response were identified among 7718 shared sequences by ccBud and cfBud. Bi-directional BLAST found 87 (41.83% of 208) of Arabidopsis genes related to inflorescence development had putative orthologs in the dogwood transcriptomes. Comparisons of the shared sequences by ccBud and cfBud yielded 65931 high quality SNPs between two species. The twenty unigenes with the most SNPs are listed as potential genetic markers for evolutionary studies. Conclusions The data provide an important, although preliminary, information platform for functional genomics and evolutionary developmental biology in Cornus. The study identified putative candidates potentially involved in the genetic regulation of inflorescence evolution and/or disease resistance in dogwoods for future analyses. Results of the study also provide markers useful for dogwood phylogenomic studies.}, number={12}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Zhang, Jian and Franks, Robert G. and Liu, Xiang and Kang, Ming and Keebler, Jonathan E. M. and Schaff, Jennifer E. and Huang, Hong-Wen and Xiang, Qiu-Yun (Jenny)}, editor={Wang, TingEditor}, year={2013}, month={Dec}, pages={e82674} }
 @article{wall_douglas_hoffmann_wentworth_gray_xiang_knaus_hohmann_g._2014, title={Evidence of population bottleneck in Astragalus michauxii (Fabaceae), a narrow endemic of the southeastern United States}, volume={15}, ISSN={1566-0621, 1572-9737}, url={http://link.springer.com/10.1007/s10592-013-0527-2}, DOI={10.1007/s10592-013-0527-2}, number={1}, journal={Conservation Genetics}, publisher={Springer Science and Business Media LLC}, author={Wall, W. A. and Douglas, N. A. and Hoffmann, W. A. and Wentworth, T. R. and Gray, J. B. and Xiang, Q. Y. J. and Knaus, B. K. and Hohmann and G., M.}, year={2014}, month={Feb}, pages={153–164} }
 @misc{harris_wen_xiang_2013, title={Inferring the biogeographic origins of inter-continental disjunct endemics using a Bayes-DIVA approach}, volume={51}, ISSN={["1759-6831"]}, DOI={10.1111/jse.12007}, abstractNote={AbstractThe arcto‐Tertiary relictual flora is comprised of many genera that occur non‐contiguously in the temperate zones of eastern Asia, Europe, eastern North America, and western North America. Within each distributional area, species are typically endemic and may thus be widely separated from closely related species within the other areas. It is widely accepted that this common pattern of distribution resulted from of the fragmentation of a once more‐continuous arcto‐Tertiary forest. The historical biogeographic events leading to the present‐day disjunction have often been investigated using a phylogenetic approach. Limitations to these previous studies have included phylogenetic uncertainty and uncertainty in ancestral range reconstructions. However, the recently described Bayes‐DIVA method handles both types of uncertainty. Thus, we used Bayes‐DIVA analysis to reconstruct the stem lineage distributions for 185 endemic lineages from 23 disjunct genera representing 17 vascular plant families. In particular, we asked whether endemic lineages within each of the four distributional areas more often evolved from (1) widespread ancestors, (2) ancestors dispersed from other areas, or (3) endemic ancestors. We also considered which of these three biogeographic mechanisms may best explain the origins of arcto‐Tertiary disjunct endemics in the neotropics. Our results show that eastern Asian endemics more often evolved from endemic ancestors compared to endemics in Europe and eastern and western North America. Present‐day endemic lineages in the latter areas more often arose from widespread ancestors. Our results also provide anecdotal evidence for the importance of dispersal in the biogeographic origins of arcto‐Tertiary species endemic in the neotropics.}, number={2}, journal={JOURNAL OF SYSTEMATICS AND EVOLUTION}, author={Harris, A. J. and Wen, Jun and Xiang, Qiu-Yun}, year={2013}, month={Mar}, pages={117–133} }
 @article{guo_pais_weakley_xiang_2013, title={Molecular phylogenetic analysis suggests paraphyly and early diversification of Philadelphus (Hydrangeaceae) in western North America: New insights into affinity with Carpenteria}, volume={51}, ISSN={1674-4918}, url={http://dx.doi.org/10.1111/jse.12041}, DOI={10.1111/jse.12041}, abstractNote={AbstractPhiladelphus (Hydrangeaceae) comprises 60 or fewer species distributed disjunctly in eastern Asia, eastern and western North America to Central America, and southeastern Europe and western Asia. The genus is highly valued in horticulture, but poorly understood regarding taxonomy, species relationships, and biogeographic history. The present study was the first phylogenetic and biogeographic analysis of Philadelphus using both nuclear and chloroplast DNA markers to evaluate classification schemes and to elucidate the biogeographic origin. Our results suggest that Philadelphus is a paraphyletic group with the monotypic genus Carpenteria nested within. Three major lineages were identified in the Philadelphus–Carpenteria clade, each strongly supported by the molecular data. Biogeographic analysis using the Bayes‐DIVA method (implemented in the newly developed RASP) and divergence time dating with BEAST resolved the origin and early diversification of Philadelphus s.l. (including Carpenteria) in western North America (including Mexico) in the Eocene. The lineage diversified and subsequently spread into Asia and other areas in the late Tertiary or Neogene to obtain a worldwide distribution. The study adds an additional example of an “out of western North America” migration in the phylogeographic history of the northern hemisphere.}, number={5}, journal={Journal of Systematics and Evolution}, publisher={Wiley}, author={Guo, Yue-Long and Pais, Andrew and Weakley, Alan S. and Xiang, Qiu-Yun Jenny}, year={2013}, month={Aug}, pages={545–563} }
 @article{liu_qi_zhao_fu_xiang_2012, title={Chloroplast DNA phylogenomics of Monocots – Insights into the placement of Liliales and influences of gene partitions}, volume={64}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2012.05.010}, abstractNote={The complete nucleotide sequence of the chloroplast genome (cpDNA) of Smilax china L. (Smilacaceae) is reported. It is the first complete cp genome sequence in Liliales. Genomic analyses were conducted to examine the rate and pattern of cpDNA genome evolution in Smilax relative to other major lineages of monocots. The cpDNA genomic sequences were combined with those available for Lilium to evaluate the phylogenetic position of Liliales and to investigate the influence of taxon sampling, gene sampling, gene function, natural selection, and substitution rate on phylogenetic inference in monocots. Phylogenetic analyses using sequence data of gene groups partitioned according to gene function, selection force, and total substitution rate demonstrated evident impacts of these factors on phylogenetic inference of monocots and the placement of Liliales, suggesting potential evolutionary convergence or adaptation of some cpDNA genes in monocots. Our study also demonstrated that reduced taxon sampling reduced the bootstrap support for the placement of Liliales in the cpDNA phylogenomic analysis. Analyses of sequences of 77 protein genes with some missing data and sequences of 81 genes (all protein genes plus the rRNA genes) support a sister relationship of Liliales to the commelinids–Asparagales clade, consistent with the APG III system. Analyses of 63 cpDNA protein genes for 32 taxa with few missing data, however, support a sister relationship of Liliales (represented by Smilax and Lilium) to Dioscoreales–Pandanales. Topology tests indicated that these two alignments do not significantly differ given any of these three cpDNA genomic sequence data sets. Furthermore, we found no saturation effect of the data, suggesting that the cpDNA genomic sequence data used in the study are appropriate for monocot phylogenetic study and long-branch attraction is unlikely to be the cause to explain the result of two well-supported, conflict placements of Liliales. Further analyses using sufficient nuclear data remain necessary to evaluate these two phylogenetic hypotheses regarding the position of Liliales and to address the causes of signal conflict among genes and partitions.}, number={3}, journal={Molecular Phylogenetics and Evolution}, author={Liu, J. and Qi, Z.C. and Zhao, Y.P. and Fu, C.X. and Xiang, Q.-Y.}, year={2012}, pages={545–562} }
 @article{feng_liu_yu_xie_franks_xiang_2012, title={Evolution of bract development and B‐class MADS box gene expression in petaloid bracts of
            Cornus
            s. l. (Cornaceae)}, volume={196}, ISSN={0028-646X 1469-8137}, url={http://dx.doi.org/10.1111/j.1469-8137.2012.04255.x}, DOI={10.1111/j.1469-8137.2012.04255.x}, abstractNote={Despite increasing interest in the molecular mechanisms of floral diversity, few studies have investigated the developmental and genetic bases of petaloid bracts. This study examined morphological patterns of bract initiation and expression patterns of B-class MADS-box genes in bracts of several Cornus species. We suggest that petaloid bracts in this genus may not share a single evolutionary origin. Developmental pathways of bracts and spatiotemporal expression of B-class genes in bracts and flowers were examined for four closely related dogwood species. Divergent morphological progressions and gene expression patterns were found in the two sister lineages with petaloid bracts, represented by Cornus florida and Cornus canadensis. Phylogeny-based analysis identified developmental and gene expression changes that are correlated with the evolution of petaloid bracts in C. florida and C. canadensis. Our data support the existence of independent evolutionary origins of petaloid bracts in C. canadensis and C. florida. Additionally, we suggest that functional transference within B-class gene families may have contributed to the origin of bract petaloidy in C. florida. However, the underlying mechanisms of petaloid bract development likely differ between C. florida and C. canadensis. In the future this hypothesis can be tested by functional analyses of Cornus B-class genes.}, number={2}, journal={New Phytologist}, publisher={Wiley}, author={Feng, Chun‐Miao and Liu, Xiang and Yu, Yi and Xie, Deyu and Franks, Robert G. and Xiang, Qiu‐Yun (Jenny)}, year={2012}, month={Aug}, pages={631–643} }
 @article{liu_feng_franks_qu_xie_xiang_2013, title={Plant regeneration and genetic transformation of C. canadensis: a non-model plant appropriate for investigation of flower development in Cornus (Cornaceae)}, volume={32}, ISSN={0721-7714, 1432-203X}, url={http://link.springer.com/10.1007/s00299-012-1341-x}, DOI={10.1007/s00299-012-1341-x}, abstractNote={KEY MESSAGE : Efficient Agrobacterium -mediated genetic transformation for investigation of genetic and molecular mechanisms involved in inflorescence architectures in Cornus species. Cornus canadensis is a subshrub species in Cornus, Cornaceae. It has recently become a favored non-model plant species to study genes involved in development and evolution of inflorescence architectures in Cornaceae. Here, we report an effective protocol of plant regeneration and genetic transformation of C. canadensis. We use young inflorescence buds as explants to efficiently induce calli and multiple adventitious shoots on an optimized induction medium consisting of basal MS medium supplemented with 1 mg/l of 6-benzylaminopurine and 0.1 mg/l of 1-naphthaleneacetic acid. On the same medium, primary adventitious shoots can produce a large number of secondary adventitious shoots. Using leaves of 8-week-old secondary shoots as explants, GFP as a reporter gene controlled by 35S promoter and hygromycin B as the selection antibiotic, a standard procedure including pre-culture of explants, infection, co-cultivation, resting and selection has been developed to transform C. canadensis via Agrobacterium strain EHA105-mediated transformation. Under a strict selection condition using 14 mg/l hygromycin B, approximately 5 % explants infected by Agrobacterium produce resistant calli, from which clusters of adventitious shoots are induced. On an optimized rooting medium consisting of basal MS medium supplemented with 0.1 mg/l of indole-3-butyric acid and 7 mg/l hygromycin B, most of the resistant shoots develop adventitious roots to form complete transgenic plantlets, which can grow normally in soil. RT-PCR analysis demonstrates the expression of GFP transgene. Green fluorescence emitted by GFP is observed in transgenic calli, roots and cells of transgenic leaves under both stereo fluorescence microscope and confocal microscope. The success of genetic transformation provides an appropriate platform to investigate the molecular mechanisms by which the various inflorescence forms are developed in Cornus plants.}, number={1}, journal={Plant Cell Reports}, publisher={Springer Science and Business Media LLC}, author={Liu, Xiang and Feng, Chun-Miao and Franks, Robert and Qu, Rongda and Xie, De-Yu and Xiang, Qiu-Yun Jenny}, year={2013}, month={Jan}, pages={77–87} }
 @article{post_ali_krings_xiang_sosinski_neal_2011, title={On the Identity of the Weedy Bittercresses (Cardamine: Brassicaceae) in United States Nurseries: Evidence from Molecules and Morphology}, volume={59}, ISSN={["1550-2759"]}, DOI={10.1614/ws-d-10-00063.1}, abstractNote={Bittercress (Brassicaceae) is one of the most prolific and costly weeds of the container nursery industry. Bittercress accessions from container nurseries throughout the major production zones in the United States were examined and compared with herbarium specimens. The identity of these weedy bittercress species were further explored using sequences of the nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) region and the nrDNA region for the COP1-interacting protein 7 (CIP7). Four species of bittercress were detected in the nursery industry of the United States, including New Zealand bittercress, hairy bittercress, flexuous bittercress, and little bittercress. The taxon referred to here as Cardamine flexuosa With. (flexuous bittercress) likely contains two genotypes previously reported as European C. flexuosa and Asian C. flexuosa. Phylogenetic relationships between the four species we examined, particularly in relationship to flexuous bittercress, were not fully resolved by the molecular evidence generated for this study. New Zealand bittercress is nonnative and does not appear in current keys to the species for the United States. Flexuous bittercress is also an alien species, which appears in some U.S. keys but not in all. To aid nurserymen and botanists in identification of these four closely related bittercress species, a key was developed and is accompanied by detailed descriptions and illustrations.}, number={1}, journal={WEED SCIENCE}, author={Post, Angela R. and Ali, Regina and Krings, Alexander and Xiang, Jenny and Sosinski, Brian R. and Neal, Joseph C.}, year={2011}, pages={123–135} }
 @article{feng_xiang_franks_2011, title={Phylogeny-based developmental analyses illuminate evolution of inflorescence architectures in dogwoods (Cornus s. l., Cornaceae)}, volume={191}, ISSN={["1469-8137"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79960555236&partnerID=MN8TOARS}, DOI={10.1111/j.1469-8137.2011.03716.x}, abstractNote={• Inflorescence architecture is important to angiosperm reproduction, but our knowledge of the developmental basis underlying the evolution of inflorescence architectures is limited. Using a phylogeny-based comparative analysis of developmental pathways, we tested the long-standing hypothesis that umbel evolved from elongated inflorescences by suppression of inflorescence branches, while head evolved from umbels by suppression of pedicels. • The developmental pathways of six species of Cornus producing different inflorescence types were characterized by scanning electron microscopy (SEM) and histological analysis. Critical developmental events were traced over the molecular phylogeny to identify evolutionary changes leading to the formation of umbels and heads using methods accounting for evolutionary time and phylogenetic uncertainty. • We defined 24 developmental events describing the developmental progression of the different inflorescence types. The evolutionary transition from paniculate cymes to umbels and heads required alterations of seven developmental events occurring at different evolutionary times. • Our results indicate that heads and umbels evolved independently in Cornus from elongated forms via an umbellate dichasium ancestor and this process involved several independent changes. Our findings shed novel insights into head and umbel evolution concealed by outer morphology. Our work illustrates the importance of combining developmental and phylogenetic data to better define morphological evolutionary processes.}, number={3}, journal={NEW PHYTOLOGIST}, author={Feng, Chun-Miao and Xiang, Qiu-Yun and Franks, Robert G.}, year={2011}, pages={850–869} }
 @article{douglas_wall_xiang_hoffmann_wentworth_gray_hohmann_2011, title={Recent vicariance and the origin of the rare, edaphically specialized Sandhills lily, Lilium pyrophilum (Liliaceae): evidence from phylogenetic and coalescent analyses}, volume={20}, ISSN={["0962-1083"]}, DOI={10.1111/j.1365-294x.2011.05151.x}, abstractNote={AbstractEstablishing the phylogenetic and demographic history of rare plants improves our understanding of mechanisms that have led to their origin and can lead to valuable insights that inform conservation decisions. The Atlantic coastal plain of eastern North America harbours many rare and endemic species, yet their evolution is poorly understood. We investigate the rare Sandhills lily (Lilium pyrophilum), which is endemic to seepage slopes in a restricted area of the Atlantic coastal plain of eastern North America. Using phylogenetic evidence from chloroplast, nuclear internal transcribed spacer and two low‐copy nuclear genes, we establish a close relationship between L. pyrophilum and the widespread Turk’s cap lily, L. superbum. Isolation‐with‐migration and coalescent simulation analyses suggest that (i) the divergence between these two species falls in the late Pleistocene or Holocene and almost certainly post‐dates the establishment of the edaphic conditions to which L. pyrophilum is presently restricted, (ii) vicariance is responsible for the present range disjunction between the two species, and that subsequent gene flow has been asymmetrical and (iii) L. pyrophilum harbours substantial genetic diversity in spite of its present rarity. This system provides an example of the role of edaphic specialization and climate change in promoting diversification in the Atlantic coastal plain.}, number={14}, journal={MOLECULAR ECOLOGY}, author={Douglas, Norman A. and Wall, Wade A. and Xiang, Qiu-Yun and Hoffmann, William A. and Wentworth, Thomas R. and Gray, Janet B. and Hohmann, Matthew G.}, year={2011}, month={Jul}, pages={2901–2915} }
 @article{(jenny) xiang_thomas_xiang_2011, title={Resolving and dating the phylogeny of Cornales – Effects of taxon sampling, data partitions, and fossil calibrations}, volume={59}, ISSN={10557903}, url={https://linkinghub.elsevier.com/retrieve/pii/S1055790311000340}, DOI={10.1016/j.ympev.2011.01.016}, abstractNote={The order Cornales descends from the earliest split in the Asterid clade of flowering plants. Despite a few phylogenetic studies, relationships among families within Cornales remain unclear. In the present study, we increased taxon and character sampling to further resolve the relationships and to date the early diversification events of the order. We conducted phylogenetic analyses of sequence data from 26S rDNA and six chloroplast DNA (cpDNA) regions using parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI) methods with different partition models and different data sets. We employed relaxed, uncorrelated molecular clocks on BEAST to date the phylogeny and examined the effects of different taxon sampling, fossil calibration, and data partitions. Our results from ML and BI analyses of the combined cpDNA sequences and combined cpDNA and 26S rDNA data suggested the monophyly of each family and the following familial relationships ((Cornaceae-Alangiaceae)-(Curtisiaceae-Grubbiaceae))-(((Nyssaceae-Davidiaceae)-Mastixiaceae)-((Hydrostachyaceae-(Hydrangeaceae-Loasaceae))). These relationships were strongly supported by posterior probability and bootstrap values, except for the sister relationship between the N-D-M and H-H-L clades. The 26S rDNA data and some MP trees from cpDNA and total evidence suggested some alternative alignments for Hydrostachyaceae within Cornales, but results of SH tests indicated that these trees were significantly worse explanations of the total data. Phylogenetic dating with simultaneous calibration of multiple nodes suggested that the crown group of Cornales originated around the middle Cretaceous and rapidly radiated into several major clades. The origins of most families dated back to the late Cretaceous except for Curtisiaceae and Grubbiaceae which may have diverged in the very early Tertiary. We found that reducing sampling density within families and analyzing partitioned data sets from coding and noncoding cpDNA, 26S rDNA, and combined data sets produced congruent estimation of divergence times, but reducing the number and changing positions of calibration points resulted in very different estimations.}, number={1}, journal={Molecular Phylogenetics and Evolution}, author={(Jenny) Xiang, Qiu-Yun and Thomas, David T. and Xiang, Qiao Ping}, year={2011}, month={Apr}, pages={123–138} }
 @article{wall_douglas_xiang_hoffmann_wentworth_hohmann_2010, title={Evidence for range stasis during the latter Pleistocene for the Atlantic Coastal Plain endemic genus, Pyxidanthera Michaux}, volume={19}, ISSN={["1365-294X"]}, DOI={10.1111/j.1365-294x.2010.04793.x}, abstractNote={The general phylogeographical paradigm for eastern North America (ENA) is that many plant and animal species retreated into southern refugia during the last glacial period, then expanded northward after the last glacial maximum (LGM). However, some taxa of the Gulf and Atlantic Coastal Plain (GACP) demonstrate complex yet recurrent distributional patterns that cannot be explained by this model. For example, eight co‐occurring endemic plant taxa with ranges from New York to South Carolina exhibit a large disjunction separating northern and southern populations by >300 km. Pyxidanthera (Diapensiaceae), a plant genus that exhibits this pattern, consists of two taxa recognized as either species or varieties. We investigated the taxonomy and phylogeography of Pyxidanthera using morphological data, cpDNA sequences, and amplified fragment length polymorphism markers. Morphological characters thought to be important in distinguishing Pyxidanthera barbulata and P. brevifolia demonstrate substantial overlap with no clear discontinuities. Genetic differentiation is minimal and diversity estimates for northern and southern populations of Pxyidanthera are similar, with no decrease in rare alleles in northern populations. In addition, the northern populations harbour several unique cpDNA haplotypes. Pyxidanthera appears to consist of one morphologically variable species that persisted in or near its present range at least through the latter Pleistocene, while the vicariance of the northern and southern populations may be comparatively recent. This work demonstrates that the refugial paradigm is not always appropriate and GACP endemic plants, in particular, may exhibit phylogeographical patterns qualitatively different from those of other ENA plant species.}, number={19}, journal={MOLECULAR ECOLOGY}, author={Wall, Wade A. and Douglas, Norman A. and Xiang, Qiu-Yun and Hoffmann, William A. and Wentworth, Thomas R. and Hohmann, Matthew G.}, year={2010}, month={Oct}, pages={4302–4314} }
 @article{manchester_xiang_xiang_2010, title={FRUITS OF CORNELIAN CHERRIES (CORNACEAE: CORNUS SUBG. CORNUS) IN THE PALEOCENE AND EOCENE OF THE NORTHERN HEMISPHERE}, volume={171}, ISSN={["1537-5315"]}, DOI={10.1086/655771}, abstractNote={Fossil fruits confirm that cornelian cherries (Cornus, subgenus Cornus) were established in the Northern Hemisphere in the Early Tertiary. We describe the oldest known member of the subgenus, Cornus piggae sp. n., on the basis of well‐preserved silicified endocarps from the late Paleocene of North Dakota. The endocarps are ellipsoidal, thin walled, and two to three locular, and they lack an axial longitudinal bundle. The septa and external walls of the fruit stone are riddled with cavities, a feature diagnostic of extant subgenus Cornus. For comparison, we sectioned fruits of each of the extant species and reexamined fossil fruits from the Early Eocene London Clay of southern England. These London Clay fossils differ from C. piggae by much thicker external walls (Cornus ettingshausenii [Gardner] Eyde) and higher locule number (up to 6 in Cornus multilocularis [Gardner] Eyde). Comparison with fruits of extant cornelian cherries indicates that the morphological range among the modern species is narrower than that seen in the Paleogene.}, number={8}, journal={INTERNATIONAL JOURNAL OF PLANT SCIENCES}, author={Manchester, Steven R. and Xiang, Xiao-Ping and Xiang, Qiu-Yun}, year={2010}, month={Oct}, pages={882–891} }
 @article{boufford_fu_xiang_zhao_2010, title={Observations on Buckleya (Thesiaceae ) in China}, volume={4}, journal={J. Bot. Res. Inst. Texas}, author={Boufford, D.E. and Fu, C.X. and Xiang, Q.Y. and Zhao, Y.P.}, year={2010}, pages={281–286} }
 @article{group_2009, title={An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III}, volume={161}, ISSN={00244074, 10958339}, url={https://academic.oup.com/botlinnean/article-lookup/doi/10.1111/j.1095-8339.2009.00996.x}, DOI={10.1111/j.1095-8339.2009.00996.x}, abstractNote={A revised and updated classification for the families of flowering plants is provided. Many recent studies have yielded increasingly detailed evidence for the positions of formerly unplaced families, resulting in a number of newly adopted orders, including Amborellales, Berberidopsidales, Bruniales, Buxales, Chloranthales, Escalloniales, Huerteales, Nymphaeales, Paracryphiales, Petrosaviales, Picramniales, Trochodendrales, Vitales and Zygophylla-les. A number of previously unplaced genera and families are included here in orders, greatly reducing the number of unplaced taxa; these include Hydatellaceae (Nymphaeales), Haptanthaceae (Buxales), Peridiscaceae (Saxifragales), Huaceae (Oxalidales), Centroplacaceae and Rafflesiaceae (both Malpighiales), Aphloiaceae, Geisso-lomataceae and Strasburgeriaceae (all Crossosomatales), Picramniaceae (Picramniales), Dipentodontaceae and Gerrardinaceae (both Huerteales), Cytinaceae (Malvales), Balanophoraceae (Santalales), Mitrastemonaceae (Ericales) and Boraginaceae (now at least known to be a member of lamiid clade). Newly segregated families for genera previously understood to be in other APG-recognized families include Petermanniaceae (Liliales), Calophyllaceae (Malpighiales), Capparaceae and Cleomaceae (both Brassicales), Schoepfiaceae (Santalales), Anacampserotaceae, Limeaceae, Lophiocarpaceae, Montiaceae and Talinaceae (all Caryophyllales) and Linder-niaceae and Thomandersiaceae (both Lamiales). Use of bracketed families is abandoned because of its unpopu-larity, and in most cases the broader circumscriptions are retained; these include Amaryllidaceae, Asparagaceace and Xanthorrheaceae (all Asparagales), Passifloraceae (Malpighiales), Primulaceae (Ericales) and several other smaller families. linear order APG, subfamilial}, number={2}, journal={Botanical Journal of the Linnean Society}, author={GROUP, THE ANGIOSPERM PHYLOGENY}, year={2009}, month={Oct}, pages={105–121} }
 @inbook{xiang_2009, place={Beijing, China}, series={Catalogue of Life, China: 2009 Annual Checklist}, title={Cornaceae}, url={http://www.sp2000.cn/}, booktitle={China Checklist of Higher Plants, In the Biodiversity Committeee of Chinese Academy of Sciences}, publisher={Species 2000 China Node}, author={Xiang, Q.-Y.}, editor={Qin, H.N.Editor}, year={2009}, collection={Catalogue of Life, China: 2009 Annual Checklist} }
 @article{harris_xiang_2009, title={Estimating ancestral distributions of lineages with uncertain sister groups: a statistical approach to Dispersal-Vicariance Analysis and a case using Aesculus L. (Sapindaceae) including fossils}, volume={47}, ISSN={16744918}, url={http://doi.wiley.com/10.1111/j.1759-6831.2009.00044.x}, DOI={10.1111/j.1759-6831.2009.00044.x}, abstractNote={Abstract  We propose a simple statistical approach for using Dispersal–Vicariance Analysis (DIVA) software to infer biogeographic histories without fully bifurcating trees. In this approach, ancestral ranges are first optimized for a sample of Bayesian trees. The probability P of an ancestral range r at a node is then calculated as  where Y is a node, and F(rY) is the frequency of range r among all the optimal solutions resulting from DIVA optimization at node Y, t is one of n topologies optimized, and Pt is the probability of topology t. Node Y is a hypothesized ancestor shared by a specific crown lineage and the sister of that lineage “x”, where x may vary due to phylogenetic uncertainty (polytomies and nodes with posterior probability <100%). Using this method, the ancestral distribution at Y can be estimated to provide inference of the geographic origins of the specific crown group of interest. This approach takes into account phylogenetic uncertainty as well as uncertainty from DIVA optimization. It is an extension of the previously described method called Bayes‐DIVA, which pairs Bayesian phylogenetic analysis with biogeographic analysis using DIVA. Further, we show that the probability P of an ancestral range at Y calculated using this method does not equate to pp*F(rY) on the Bayesian consensus tree when both variables are <100%, where pp is the posterior probability and F(rY) is the frequency of range r for the node containing the specific crown group. We tested our DIVA‐Bayes approach using Aesculus L., which has major lineages unresolved as a polytomy. We inferred the most probable geographic origins of the five traditional sections of Aesculus and of Aesculus californica Nutt. and examined range subdivisions at parental nodes of these lineages. Additionally, we used the DIVA‐Bayes data from Aesculus to quantify the effects on biogeographic inference of including two wildcard fossil taxa in phylogenetic analysis. Our analysis resolved the geographic ranges of the parental nodes of the lineages of Aesculus with moderate to high probabilities. The probabilities were greater than those estimated using the simple calculation of pp*F(ry) at a statistically significant level for two of the six lineages. We also found that adding fossil wildcard taxa in phylogenetic analysis generally increased P for ancestral ranges including the fossil's distribution area. The ΔP was more dramatic for ranges that include the area of a wildcard fossil with a distribution area underrepresented among extant taxa. This indicates the importance of including fossils in biogeographic analysis. Exmination of range subdivision at the parental nodes revealed potential range evolution (extinction and dispersal events) along the stems of A. californica and sect. Parryana.}, number={5}, journal={Journal of Systematics and Evolution}, author={Harris, A.J. and Xiang, Qiu-Yun Jenny}, year={2009}, month={Sep}, pages={349–368} }
 @article{wen_xiang_qian_li_wang_ickert-bond_2009, title={Intercontinental and intracontinental biogeography-patterns and methods}, volume={47}, ISSN={16744918}, url={http://doi.wiley.com/10.1111/j.1759-6831.2009.00052.x}, DOI={10.1111/j.1759-6831.2009.00052.x}, abstractNote={Intercontinental and intracontinental biogeography— patterns and methods 1Jun WEN∗ 2Qiu-Yun (Jenny) XIANG 3Hong QIAN 4Jianhua LI 5Xiao-Quan WANG 6Stefanie M. ICKERT-BOND 1(Department of Botany, MRC-166, Smithsonian Institution, PO Box 37012, Washington DC 20013-7012, USA) 2(Department of Plant Biology, North Carolina State University, Raleigh, NC 27695-7612, USA) 3(Research and Collections Center, Illinois State Museum, Springfield, IL 62703, USA) 4(Biology Department, Hope College, Holland, MI 49423, USA) 5(State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China) 6(UA Museum of the North Herbarium and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK 99775-6960, USA)}, number={5}, journal={Journal of Systematics and Evolution}, author={Wen, Jun and Xiang, Qiu-Yun Jenny and Qian, Hong and Li, Jianhua and Wang, Xiao-Quan and Ickert-Bond, Stefanie M.}, year={2009}, month={Sep}, pages={327–330} }
 @article{manchester_xiang_kodrul_akhmetiev_2009, title={LEAVES OF CORNUS (CORNACEAE) FROM THE PALEOCENE OF NORTH AMERICA AND ASIA CONFIRMED BY TRICHOME CHARACTERS}, volume={170}, ISSN={["1537-5315"]}, DOI={10.1086/593040}, abstractNote={The identification of Cornus foliage in the fossil record previously has relied primarily on similarities in venation, particularly the eucamptodromous secondary veins and widely spaced, transversely oriented tertiary veins. These features, while consistent with Cornus, are not by themselves diagnostic for the genus. Double‐armed, acicular trichomes mineralized with calcium carbonate are an additional characteristic feature found in all extant species of the genus. The presence of such trichomes provides a means of confirming leaf impression fossils attributed to Cornus. Reexamination of previously described Cornus leaves from the Paleocene of the Rocky Mountains and Great Plains region leads us to reject Cornus nebrascensis Schimper (=Cornus newberryi Hollick) from the genus. Another species, Cornus hyperborea Heer, is provisionally accepted as Cornus based on its venation, although we were unable to confirm the trichomes in the type material from Greenland or in the assigned specimens from North Dakota. We also review other Eurasian Paleocene Cornus‐like leaf remains, including Cornus platyphylla Saporta and Cornophyllum hebridicum (Johnson) Boulter and Kvaček. We recognize two new Paleocene species, whose identity as Cornus is confirmed by the presence of characteristic trichomes and venation: Cornus swingii sp. n., from the Paleocene of Wyoming, Montana, and North Dakota, and Cornus krassilovii sp. n., from the Paleocene Tsagayan flora of Russia. These occurrences, along with fruit records, indicate that the extant genus was well established in the Northern Hemisphere early in the Tertiary.}, number={1}, journal={INTERNATIONAL JOURNAL OF PLANT SCIENCES}, author={Manchester, Steven R. and Xiang, Qiu-Yun and Kodrul, Tatiana M. and Akhmetiev, Mikhail A.}, year={2009}, month={Jan}, pages={132–142} }
 @article{post_krings_xiang_sosinski_neal_2009, title={Lectotypification of Cardamine flexuosa (Brassicaceae).}, volume={3}, url={https://www.jstor.org/stable/41972157}, number={1}, journal={J. Bot. Res. Inst. Texas}, author={Post, A.R. and Krings, A. and Xiang, Q.Y. and Sosinski, B.R. and Neal, J.C.}, year={2009}, month={Jul}, pages={227–230} }
 @article{harris_xiang_thomas_2009, title={Molecular and morphological inference of the phylogeny, origin, and biogeographic History of Aesculus L. (Sapindaceae or Hippocastanaceae).}, volume={58}, journal={TAXON}, author={Harris, A.J. and Xiang, Q.Y. and Thomas, D.T.}, year={2009}, pages={1–19} }
 @article{post_neal_krings_sosinski_xiang_2009, title={New Zealand Bittercress (Cardamine corymbosa; Brassicaceae): New to the United States}, volume={23}, ISSN={["1550-2740"]}, DOI={10.1614/WT-09-017.1}, abstractNote={New Zealand bittercress is reported as new to the United States. While collecting specimens to determine what Cardamine species occur in the nursery trade, New Zealand bittercress was discovered in a container nursery in Wilkes County, North Carolina. The nursery tracked the shipment of contaminated plants to a wholesale nursery in Washington County, Oregon. It was subsequently confirmed that New Zealand bittercress also occurs in a nursery in Clackamas County, Oregon, and has likely been distributed throughout the United States as a contaminant in container grown ornamental plants. Thus far there have been no reports of naturalized populations outside of container nursery crop production facilities.}, number={4}, journal={WEED TECHNOLOGY}, author={Post, A. R. and Neal, J. C. and Krings, A. and Sosinski, B. R. and Xiang, Q.}, year={2009}, pages={604–607} }
 @article{feng_manchester_xiang_2009, title={Phylogeny and biogeography of Alangiaceae (Cornales) inferred from DNA sequences, morphology, and fossils}, volume={51}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2009.01.017}, abstractNote={Alangiaceae, in the basal Asterid clade Cornales, consists of only one genus, Alangium. The genus has approximately 24 species distributed mainly in tropical and subtropical regions of the Old World and is well represented in the Tertiary fossil record of the northern hemisphere. We conducted phylogenetic and biogeographic analyses for Alangium by integrating data from DNA sequences, morphology, and fossils to evaluate systematic and biogeographic hypotheses. The results largely agree with the traditional classification of four sections within the genus, and suggest sects. Conostigma and Rhytidandra are successive sister taxa to a clade containing sects. Marlea and Alangium. Our results also indicate that the widespread species A. chinense consists of at least two lineages meriting recognition as distinct species. Biogeographic analysis using DIVA and divergence time dating with the Bayesian method (MULTIDIVTIME) resolved the ancestor of Alangium as being in S.E. Asia in the Late Cretaceous. Several intercontinental migrations involving the margin of the Tethys seaway (TESW), the North Atlantic land bridge (NALB) or the Bering land bridge (BLB), and long-distance dispersals are suggested. The results support TESW for plant migration of thermophilic (including evergreen) taxa in the early Tertiary.}, number={2}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Feng, Chun-Miao and Manchester, Steven R. and Xiang, Qiu-Yun}, year={2009}, month={May}, pages={201–214} }
 @article{xiang_qy_guo_zhang_2009, title={Phylogeny of Abies (Pinaceae) inferred from ITS sequence data}, volume={58}, number={1}, journal={TAXON}, author={Xiang, Q.P. and Qy, Xiang and Guo, Y.Y. and Zhang, X.C.}, year={2009}, month={Feb}, pages={141–152} }
 @article{xiang_xiang_guo_zhang_2009, title={Phylogeny of Abies (Pinaceae) inferred from nrITS sequence data}, volume={58}, number={1}, journal={Taxon}, author={Xiang, Q. P. and Xiang, Q. Y. and Guo, Y. Y. and Zhang, X. C.}, year={2009}, pages={141–152} }
 @article{harris_xiang_thomas_2009, title={Phylogeny, origin, and biogeographic history of Aesculus L. (Sapindales) - an update from combined analysis of DNA sequences, morphology, and fossils}, volume={58}, ISSN={0040-0262}, url={http://dx.doi.org/10.1002/TAX.581012}, DOI={10.1002/TAX.581012}, abstractNote={AbstractConflicting phylogenies and biogeographic hypotheses for Aesculus L. were reevaluated using data integrating morphology, fossils, and DNA sequences. A more robust phylogeny of Aesculus was constructed by increasing taxon and character sampling to include 42 morphological characters and five DNA regions including rps16, trnHK, matK, ITS, and part of the LEAFY gene. Our analyses revealed three well‐supported major lineages in Aesculus. These are sect. Calothyrsus excluding A. californica, sect. Macrothyrsus + A. californica, and sect. Aesculus + sect. Pavia + sect. Parryana. The relationship of sect. Aesculus to sect. Parryana + sect. Pavia is strongly supported and previously unreported. Relationships among the three major clades remained incompletely resolved. Biogeographic and divergence time analyses using DIVA and Multidivtime support a Paleocene origin of Aesculus in eastern Asia and western North America, and showed that the genus subsequently dispersed into eastern North America, Central America, and Europe. Our results support that Aesculus originated as an element of the Paleogene mesophilic flora in the Beringian region with multiple eastward migrations characterizing the early spatial history of this genus. This biogeographic history supports Trans‐Beringian migration of plants in the very early Paleogene.}, number={1}, journal={TAXON}, publisher={Wiley}, author={Harris, AJ and Xiang, Qiu-Yunjenny and Thomas, David T.}, year={2009}, month={Feb}, pages={108–126} }
 @article{feng_qu_zhou_xie_xiang_2009, title={Shoot regeneration of dwarf dogwood (Cornus canadensis L.) and morphological characterization of the regenerated plants}, volume={97}, ISSN={["1573-5044"]}, DOI={10.1007/s11240-009-9495-0}, number={1}, journal={PLANT CELL TISSUE AND ORGAN CULTURE}, author={Feng, Chun-Miao and Qu, Rongda and Zhou, Li-Li and Xie, De-Yu and Xiang, Qiu-Yun}, year={2009}, month={Apr}, pages={27–37} }
 @article{peters_xiang_thomas_stucky_whiteman_2009, title={Genetic analyses of the federally endangered Echinacea laevigata using amplified fragment length polymorphisms (AFLP)—Inferences in population genetic structure and mating system}, volume={10}, ISSN={1566-0621, 1572-9737}, url={http://link.springer.com/10.1007/s10592-008-9509-1}, DOI={10.1007/s10592-008-9509-1}, abstractNote={Echinacea laevigata (Boynton and Beadle) Blake is a federally endangered flowering plant species restricted to four states in the southeastern United States. To determine the population structure and outcrossing rate across the range of the species, we conducted AFLP analysis using four primer combinations for 22 populations. The genetic diversity of this species was high based on the level of polymorphic loci (200 of 210 loci; 95.24%) and Nei's gene diversity (ranging from 0.1398 to 0.2606; overall 0.2611). There was significant population genetic differentiation (GST = 0.294; ӨII = 0.218 from the Bayesian f = 0 model). Results from the AMOVA analysis suggest that a majority of the genetic variance is attributed to variation within populations (70.26%), which is also evident from the PCoA. However, 82% of individuals were assigned back to the original population based on the results of the assignment test. An isolation by distance analysis indicated that genetic differentiation among populations was a function of geographic distance, although long-distance gene dispersal between some populations was suggested from an analysis of relatedness between populations using the neighbor-joining method. An estimate of the outcrossing rate based on genotypes of progenies from six of the 22 populations using the multilocus method from the program MLTR ranged from 0.780 to 0.912, suggesting that the species is predominantly outcrossing. These results are encouraging for conservation, signifying that populations may persist due to continued genetic exchange sustained by the outcrossing mating system of the species.}, number={1}, journal={Conservation Genetics}, author={Peters, Melinda D. and Xiang, Qiu-Yun (Jenny) and Thomas, David T. and Stucky, Jon and Whiteman, Noah K.}, year={2009}, month={Feb}, pages={1–14} }
 @article{thomas_ahedor_williams_depamphilis_crawford_xiang_2008, title={Microsatellite analysis of a broad hybrid zone in Aesculus (Sapindales) – Inferences in genetic structure and evolution}, volume={169}, ISSN={["1537-5315"]}, DOI={10.1086/533605}, abstractNote={The genetic structure of a broad hybrid zone involving three hybridizing Aesculus species, Aesculus flava, Aesculus pavia, and Aesculus sylvatica, was examined. The objectives were to assess genetic variability, to test previously reported hypotheses on patterns of gene flow, and to infer the genetic structure and evolutionary processes in the hybrid zone. Samples from 24 populations within parental ranges and the hybrid zone were analyzed for variation at microsatellite and intersimple sequence repeat loci. The results indicated that genetic variability was similar among parental and hybrid populations, indicating no evident increased diversity in the hybrid zone. Most hybrid individuals were genetically more similar to A. sylvatica than to the other two species, and the overall genetic structure of the hybrid zone is asymmetrically biased toward A. sylvatica. Our analyses supported occasional recurrent long‐distant gene flow from A. pavia and frequent gene flow from A. sylvatica into the hybrid zone, agreeing with results of a previous allozyme study. Collectively, the data from our study and previous allozyme and chloroplast DNA studies indicate that both historical localized gene flow and recurrent long‐distant gene flow have contributed to the existence of the hybrid zone, that is, its origin via historical localized gene flow, while its maintenance involves ongoing long‐distance pollen dispersal.}, number={5}, journal={International Journal of Plant Sciences}, author={Thomas, D.T. and Ahedor, A.R. and Williams, C.F. and DePamphilis, C. and Crawford, D.J. and Xiang, Q.Y.}, year={2008}, pages={647–657} }
 @misc{zhang_xiang_thomas_wiegmann_frohlich_soltis_2008, title={Molecular evolution of PISTILLATA-like genes in the dogwood genus Cornus (Cornaceae)}, volume={47}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2007.12.022}, abstractNote={The MADS-box gene family encodes critical regulators determining floral organ development. Understanding evolutionary patterns and processes of MADS-box genes is an important step toward unraveling the molecular basis of floral morphological evolution. In this study, we investigated the evolution of PI-like genes of the MADS-box family in the dogwood genus Cornus (Cornaceae). Cornus is a eudicot lineage in the asterids clade, and is intriguing in evolving petaloid bract morphology in two major lineages within the genus. The gene genealogy reconstructed using genomic DNA and cDNA sequences suggests multiple PI-like gene duplication events in Cornus. An ancient duplication event resulted in two ancient paralogs, CorPI-A and CorPI-B, which have highly diverged intron regions. Duplication of CorPI-A further resulted in two paralogs in one subgroup of Cornus, the BW group that does not produce modified bracts. Most species analyzed were found to contain more than one copy of the PI-like gene with most copies derived recently within species. Estimation and comparison of dN/dS ratios revealed relaxed selection in the PI-like gene in Cornus in comparison with the gene in the closely related outgroups Alangium and Davidia, and in other flowering plants. Selection also differed among major gene copies, CorPI-A and CorPI-B, and among different morphological subgroups of Cornus. Variation in selection pressures may indicate functional changes in PI-like genes after gene duplication and among different lineages. Strong positive selection at three amino acid sites of CorPI was also detected from a region critical for dimerization activity. Total substitution rates of the CorPI gene also differ among lineages of Cornus, showing a trend similar to that found in dN/dS ratios. We also found that the CorPI-A copy contains informative phylogenetic information when compared across species of Cornus.}, number={1}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Zhang, Wenheng and Xiang, Qiu-Yun and Thomas, David T. and Wiegmann, Brian M. and Frohlich, Michael W. and Soltis, Douglas E.}, year={2008}, month={Apr}, pages={175–195} }
 @article{krings_thomas_xiang_2008, title={On the Generic Circumscription of Gonolobus (Apocynaceae, Asclepiadoideae): Evidence from Molecules and Morphology}, volume={33}, ISSN={03636445, 15482324}, url={http://openurl.ingenta.com/content/xref?genre=article&issn=0363-6445&volume=33&issue=2&spage=403}, DOI={10.1600/036364408784571527}, abstractNote={Abstract Gonolobus (Apocynaceae, Asclepiadoideae) is a New World genus comprising an estimated 100–150 species. Variation in estimated species numbers is largely the result of still poorly known tropical taxa and differences regarding generic limits. Characters historically used to delimit genera such as Gonolobus within Gonolobinae—such as laminar dorsal anther appendages and various follicle morphologies—have been controversial and their evolution remains unknown, not having been explored in a phylogenetic framework. The primary objectives of the current study were to (1) test the monophyly of Gonolobus sensu Woodson in the context of a phylogeny of New World Asclepiadeae and (2) explore the evolution of laminar dorsal anther appendages and winged follicles with respect to their potential utility in generic circumscription. Chloroplast (trnL–F, rpsl6) data are newly presented for sixty-three taxa of Gonolobinae, representing an increased sampling of the subtribe from a maximum of seven taxa in prior studies. These data were combined with a previously published dataset to form a 183 taxa matrix of New World Asclepiadeae. Nuclear (LEAFY) data were newly generated for forty-nine taxa of Gonolobinae. Evidence from parsimony and Bayesian analyses of chloroplast and nuclear data presented here supports the monophyly of both the subtribe and the genus Gonolobus in a narrow or broad sense. Laminar dorsal anther appendages are restricted to Gonolobus s.l. or s.s., although parsimony remains equivocal on whether they evolved once or twice. A transversion in the trnL–F spacer is shown synapomorphic for Gonolobus s.s. Two indels in LEAFY, as well as winged follicles, are shown synapomorphic for Gonolobus s.l.}, number={2}, journal={Systematic Botany}, author={Krings, Alexander and Thomas, David T. and Xiang, Qiu-Yun}, year={2008}, month={Apr}, pages={403–415} }
 @article{xiang_thorne_seo_zhang_thomas_ricklefs_2008, title={Rates of nucleotide substitution in Cornaceae (Cornales)—Pattern of variation and underlying causal factors}, volume={49}, ISSN={10557903}, url={https://linkinghub.elsevier.com/retrieve/pii/S1055790308003606}, DOI={10.1016/j.ympev.2008.07.010}, abstractNote={Identifying causes of genetic divergence is a central goal in evolutionary biology. Although rates of nucleotide substitution vary among taxa and among genes, the causes of this variation tend to be poorly understood. In the present study, we examined the rate and pattern of molecular evolution for five DNA regions over a phylogeny of Cornus, the single genus of Cornaceae. To identify evolutionary mechanisms underlying the molecular variation, we employed Bayesian methods to estimate divergence times and to infer how absolute rates of synonymous and nonsynonymous substitutions and their ratios change over time. We found that the rates vary among genes, lineages, and through time, and differences in mutation rates, selection type and intensity, and possibly genetic drift all contributed to the variation of substitution rates observed among the major lineages of Cornus. We applied independent contrast analysis to explore whether speciation rates are linked to rates of molecular evolution. The results showed no relationships for individual genes, but suggested a possible localized link between species richness and rate of nonsynonymous nucleotide substitution for the combined cpDNA regions. Furthermore, we detected a positive correlation between rates of molecular evolution and morphological change in Cornus. This was particularly pronounced in the dwarf dogwood lineage, in which genome-wide acceleration in both molecular and morphological evolution has likely occurred.}, number={1}, journal={Molecular Phylogenetics and Evolution}, author={Xiang, Qiu-Yun (Jenny) and Thorne, Jeffrey L. and Seo, Tae-Kun and Zhang, Wenheng and Thomas, David T. and Ricklefs, Robert E.}, year={2008}, month={Oct}, pages={327–342} }
 @article{xiang_thomas_2008, title={Tracking character evolution and biogeographic history through time in Cornaceae - Does choice of methods matter?}, volume={46}, ISSN={["1759-6831"]}, DOI={10.3724/SP.J.1002.2008.08056}, number={3}, journal={JOURNAL OF SYSTEMATICS AND EVOLUTION}, author={Xiang, Qiu-Yun and Thomas, David T.}, year={2008}, month={May}, pages={349–374} }
 @article{qy_thomas_2008, title={Tracking character evolution and biogeographic history through time in Cornaceae – Does choice of methods matter?}, volume={46}, number={3}, journal={Journal of Systematics and Evolution}, author={Qy, Xiang and Thomas, D.T.}, year={2008}, pages={349–374} }
 @article{manchester_xiang_xiang_2007, title={Curtisia (Cornales) from the Eocene of Europe and its phytogeographical significance}, volume={155}, ISSN={1095-8339, 0024-4074}, url={https://academic.oup.com/botlinnean/article-lookup/doi/10.1111/j.1095-8339.2007.00680.x}, DOI={10.1111/j.1095-8339.2007.00680.x}, abstractNote={Fossil remains of Curtisia Aiton (Cornales) are recognized for the first time from the Tertiary of Europe, based on early Eocene anatomically preserved fruits from the London Clay and Poole Formations of southern England. The modern distribution of this monotypic genus is limited to the cape of South Africa. Curtisia quadrilocularis (Reid & Chandler) comb. nov. fruits have globose tetralocular endocarps composed of isodiametric sclereids with a single seed per locule, a prominent axial vascular canal, apical placentation, and four germination valves. All of these characters, as well as size, correspond to extant Curtisia. Although many fossil taxa from the Eocene of Europe have been shown to have their closest extant relatives in Asia, this occurrence of Curtisia highlights Tertiary floristic exchange between Europe and Africa. The newly recognized fossil occurrences suggest a Laurasian origin for Curtisia, in conformity with the fossil record for several other genera of the Cornales. In addition, our rejection of the former assignment of this species to Leucopogon causes us to question whether Epacridaceae were present in the Tertiary of Europe. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 155, 127‐134.}, number={1}, journal={Botanical Journal of the Linnean Society}, author={Manchester, Steven R. and Xiang, Qiu-Yun (Jenny) and Xiang, Qiao-Ping}, year={2007}, month={Sep}, pages={127–134} }
 @article{modliszewski_thomas_fan_crawford_depamphilis_xiang_2006, title={Ancestral chloroplast polymorphism and historical secondary contact in a broad hybrid zone of Aesculus (Sapindaceae)}, volume={93}, ISSN={["1537-2197"]}, DOI={10.3732/ajb.93.3.377}, abstractNote={Knowledge regarding the origin and maintenance of hybrid zones is critical for understanding the evolutionary outcomes of natural hybridization. To evaluate the contribution of historical contact vs. long‐distance gene flow in the formation of a broad hybrid zone in central and northern Georgia that involvesAesculus pavia,A. sylvatica, andA. flava, three cpDNA regions (matK,trnD‐trnT, andtrnH‐trnK) were analyzed. The maternal inheritance of cpDNA inAesculuswas confirmed via sequencing ofmatKfrom progeny of controlled crosses. Restriction site analyses identified 21 unique haplotypes among 248 individuals representing 29 populations from parental species and hybrids. Haplotypes were sequenced for all cpDNA regions. Restriction site and sequence data were subjected to phylogeographic and population genetic analyses. Considerable cpDNA variation was detected in the hybrid zone, as well as ancestral cpDNA polymorphism; furthermore, the distribution of haplotypes indicates limited interpopulation gene flow via seeds. The genealogy and structure of genetic variation further support the historical presence ofA. paviain the Piedmont, although they are at present locally extinct. In conjunction with previous allozyme studies, the cpDNA data suggest that the hybrid zone originated through historical local gene flow, yet is maintained by periodic long‐distance pollen dispersal.}, number={3}, journal={AMERICAN JOURNAL OF BOTANY}, author={Modliszewski, JL and Thomas, DT and Fan, CZ and Crawford, DJ and DePamphilis, CW and Xiang, QY}, year={2006}, month={Mar}, pages={377–388} }
 @article{fan_xiang_remington_purugganan_wiegmann_2007, title={Evolutionary patterns in the antR-Cor gene in the dwarf dogwood complex (Cornus, Cornaceae)}, volume={130}, ISSN={0016-6707, 1573-6857}, url={http://link.springer.com/10.1007/s10709-006-0016-3}, DOI={10.1007/s10709-006-0016-3}, abstractNote={The evolutionary pattern of the myc-like anthocyanin regulatory gene antR-Cor was examined in the dwarf dogwood species complex (Cornus Subgenus Arctocrania) that contains two diploid species (C. canadensis and C. suecica), their putative hybrids with intermediate phenotypes, and a tetraploid derivative (C. unalaschkensis). Full-length sequences of this gene ( approximately 4 kb) were sequenced and characterized for 47 dwarf dogwood samples representing all taxa categories from 43 sites in the Pacific Northwest. Analysis of nucleotide diversity indicated departures from neutral evolution, due most likely to local population structure. Neighbor-joining and haplotype network analyses show that sequences from the tetraploid and diploid intermediates are much more strongly diverged from C. suecica than from C. canadensis, and that the intermediate phenotypes may represent an ancestral group to C. canadensis rather than interspecific hybrids. Seven amino acid mutations that are potentially linked to myc-like anthocyanin regulatory gene function correlate with petal colors differences that characterize the divergence between two diploid species and the tetraploid species in this complex. The evidence provides a working hypothesis for testing the role of the gene in speciation and its link to the petal coloration. Sequencing and analysis of additional nuclear genes will be necessary to resolve questions about the evolution of the dwarf dogwood complex.}, number={1}, journal={Genetica}, author={Fan, Chuanzhu and Xiang, Qiu-Yun (Jenny) and Remington, David L. and Purugganan, Michael D. and Wiegmann, Brian M.}, year={2007}, month={Apr}, pages={19–34} }
 @article{xiang_thomas_zhang_manchester_murrell_2006, title={Species Level Phylogeny of the Genus Cornus (Cornaceae) Based on Molecular and Morphological Evidence-Implications for Taxonomy and Tertiary Intercontinental Migration}, volume={55}, ISSN={00400262}, url={http://doi.wiley.com/10.2307/25065525}, DOI={10.2307/25065525}, abstractNote={AbstractDNA sequences were generated for matK and ITS for 68 and 103 samples of Cornus to reconstruct a species level phylogeny of the genus. The results support the monophyly of most subgenera, except subg. Kraniopsis and subg. Cornus. Subgenus Kraniopsis was suggested to exclude C. peruviana from South America and subg. Afrocrania and subg. Sinocornus were nested within subg. Cornus. Four major clades corresponding to groups also recognizable by morphological differences were revealed: the big‐bracted dogwoods (BB) including subg. Cynoxylon, subg. Syncarpea, and subg. Discocrania, the dwarf dogwoods (DW) including subg. Arctocrania, the cornelian cherries (CC) including subg. Cornus, subg. Sinocornus, and subg. Afrocrania, and the blue‐ or white‐fruited dogwoods (BW) including subg. Kraniopsis, subg. Mesomora, and subg. Yinquania. This finding is consistent with previous studies with more limited sampling. The single South American species C. peruviana was found to be sister to the Asian C. oblonga of subg. Yinquania, adding a fourth intercontinental disjunction in the genus that was previously unknown. Species relationships within the subgenera were clearly resolved except for the relatively large subg. Syncarpea and subg. Kraniopsis. Phylogenetic analyses of total evidence combining morphology, matK, ITS, and previously published rbcL and 26S rDNA sequences resolved the relationships among subgenera as (BW(CC(BB, DW))). Biogeographic analyses using DIVA with or without fossils resulted in different inferences of biogeographic history of the genus, indicating the importance of fossil data in biogeographic analyses. The phylogeny based on the total evidence tree including fossils supports an origin and early Tertiary diversification of Cornus in Europe and multiple trans‐Atlantic migrations between Europe and North America by the early Tertiary. It also supports that distribution of the few species in the southern hemisphere was not ancestral, but a result of migration from the north. This evidence rejects a previous hypothesis of a southern hemispheric origin of the genus.}, number={1}, journal={Taxon}, author={Xiang, Qiu-Yun (Jenny) and Thomas, David T. and Zhang, Wenheng and Manchester, Steven R. and Murrell, Zack}, year={2006}, month={Feb}, pages={9} }
 @inbook{xiang_boufford_2005, title={Cornaceae, Mastixiaceae, Toricelliaceae, Helwingiacaee, Aucubaceae}, volume={14}, booktitle={Flora of China}, publisher={Science Press, Beijing, and Missouri botanical Garden Press, St. Louis}, author={Xiang, Q.-Y. and Boufford, D.E.}, editor={Wu, Z.Y. and Raven, P.H.Editors}, year={2005}, pages={206–234} }
 @article{houston_fan_xiang_schulze_jung_boston_2005, title={Phylogenetic analyses identify 10 classes of the protein disulfide isomerase family in plants, including single-domain protein disulfide isomerase-related proteins}, volume={137}, DOI={10.1104/pp.104.056507}, abstractNote={Abstract
               Protein disulfide isomerases (PDIs) are molecular chaperones that contain thioredoxin (TRX) domains and aid in the formation of proper disulfide bonds during protein folding. To identify plant PDI-like (PDIL) proteins, a genome-wide search of Arabidopsis (Arabidopsis thaliana) was carried out to produce a comprehensive list of 104 genes encoding proteins with TRX domains. Phylogenetic analysis was conducted for these sequences using Bayesian and maximum-likelihood methods. The resulting phylogenetic tree showed that evolutionary relationships of TRX domains alone were correlated with conserved enzymatic activities. From this tree, we identified a set of 22 PDIL proteins that constitute a well-supported clade containing orthologs of known PDIs. Using the Arabidopsis PDIL sequences in iterative BLAST searches of public and proprietary sequence databases, we further identified orthologous sets of 19 PDIL sequences in rice (Oryza sativa) and 22 PDIL sequences in maize (Zea mays), and resolved the PDIL phylogeny into 10 groups. Five groups (I–V) had two TRX domains and showed structural similarities to the PDIL proteins in other higher eukaryotes. The remaining five groups had a single TRX domain. Two of these (quiescin-sulfhydryl oxidase-like and adenosine 5′-phosphosulfate reductase-like) had putative nonisomerase enzymatic activities encoded by an additional domain. Two others (VI and VIII) resembled small single-domain PDIs from Giardia lamblia, a basal eukaryote, and from yeast. Mining of maize expressed sequence tag and RNA-profiling databases indicated that members of all of the single-domain PDIL groups were expressed throughout the plant. The group VI maize PDIL ZmPDIL5-1 accumulated during endoplasmic reticulum stress but was not found within the intracellular membrane fractions and may represent a new member of the molecular chaperone complement in the cell.}, number={2}, journal={Plant Physiology}, author={Houston, N. L. and Fan, C. Z. and Xiang, Qiu-Yun and Schulze, J. M. and Jung, R. and Boston, R. S.}, year={2005}, pages={762–778} }
 @article{xiang_sr_thomas_zhang_fan_2005, title={Phylogeny, biogeography, and molecular dating of cornelian cherries (Cornus, Cornaceae) – tracking Tertiary plant migration}, volume={59}, DOI={10.1554/03-763.1}, abstractNote={Data from four DNA regions (rbcL, matK, 26S rDNA, and ITS) as well as extant and fossil morphology were used to reconstruct the phylogeny and biogeographic history of an intercontinentally disjunct plant group, the cornelian cherries of Cornus (dogwoods). The study tests previous hypotheses on the relative roles of two Tertiary land bridges, the North Atlantic land bridge (NALB) and the Bering land bridge (BLB), in plant migration across continents. Three approaches, the Bayesian, nonparametric rate smoothing (NPRS), and penalized likelihood (PL) methods, were employed to estimate the times of geographic isolations of species. Dispersal and vicariance analysis (DIVA) was performed to infer the sequence and directionality of biogeographic pathways. Results of phylogenetic analyses suggest that among the six living species, C. sessilis from western North America represents the oldest lineage, followed by C. volkensii from Africa. The four Eurasian species form a clade consisting of two sister pairs, C. mas– C. officinalis and C. chinensis–C. eydeana. Results of DIVA and data from fossils and molecular dating indicate that the cornelian cherry subgroup arose in Europe as early as the Paleocene. Fossils confirm that the group was present in North America by the late Paleocene, consistent with the DIVA predictions that, by the end of the Eocene, it had diversified into several species and expanded its distribution to North America via the NALB and to Africa via the last direct connection between Eurasia and Africa prior to the Miocene, or via long-distance dispersal. The cornelian cherries in eastern Asia appear to be derived from two independent dispersal events from Europe. These events are inferred to have occurred during the Oligocene and Miocene. This study supports the hypothesis that the NALB served as an important land bridge connecting the North American and European floras, as well as connecting American and African floras via Europe during the early Tertiary.}, number={8}, journal={Evolution}, author={Xiang, Q.-Y and Sr, Manchester and Thomas, D. and Zhang, WH. and Fan, CZ}, year={2005}, pages={139–155} }
 @article{krings_xiang_2005, title={Taxonomy of the Gonolobus complex (Apocynaceae - Asclepiadoideae) in the southeastern US: ISSR evidence and parsimony analysis}, volume={10}, DOI={10.3100/1043-4534(2005)10[147:totgca]2.0.co;2}, abstractNote={ABSTRACT In a recent morphometric analysis of the Gonolobus complex (subgenus Gonolobus) in the southeastern United States, we found former specific concepts untenable as stated, as the diagnostic characters could not consistently assign individuals to one of two groups. However, our analysis showed a strong geographical component to the distribution of individuals delimited by uniformly and multicolored corollas, which we used as a basis for suggesting that two entities do appear to exist in the Southeast that may deserve recognition at some taxonomic rank. In the present study, we performed analysis of Inter-Simple Sequence Repeats (ISSR) to assess whether the two entities are genetically differentiated and, if so, to what level. We also conducted a cladistic analysis of morphological characters of the subgenus to determine whether the entities emerge as closest relatives. Our ISSR results showed substantial genetic differentiation at 18 loci between the two entities, although no fixed differences between them were detected. At 7 loci, the frequencies of band presence are significantly higher in the multicolored corolla group (MCCG) than in the uniformly colored corolla group (UCCG). At 11 loci they are significantly higher in the UCCG. Nineteen bands are unique to the MCCG, although at various frequencies (3.5–39.0%), whereas only a single band is unique to the UCCG, suggesting that the latter possesses a subset of the MCCG gene pool and is likely a derivative of it. Analysis of 61 parsimony-informative characters using Neighbor-Joining (NJ) and Unweighted Pair-Group Method using Arithmetic means (UPGMA) did not resolve the two groups, consistent with the view of a single species. In a parsimony analysis of morphological characters of 14 species of the subgenus, the two groups consistently appear as closest relatives. This evidence indicates that the complex represents a single evolutionary lineage with two incompletely differentiated morphological subgroups. On the basis of these results, we propose to treat the MCCG and UCCG as two varieties of Gonolobus suberosus. Gonolobus granulatus Scheele is neotypified in association with the required new combination for the UCCG variety. A key to the infraspecific taxa is provided.}, journal={Harvard Papers in Botany}, author={Krings, A. and Xiang, Qiu-Yun}, year={2005}, pages={147–159} }
 @article{fan_purugganan_thomas_wiegmann_xiang_2004, title={Heterogeneous evolution of the Myc-like Anthocyanin regulatory gene and its phylogenetic utility in Cornus L. (Cornaceae)}, volume={33}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2004.08.002}, abstractNote={Anthocyanin is a major pigment in vegetative and floral organs of most plants and plays an important role in plant evolution. The anthocyanin regulatory genes are responsible for regulating transcription of genes in the anthocyanin synthetic pathway. To assess evolutionary significance of sequence variation and evaluate the phylogenetic utility of an anthocyanin regulatory gene, we compared nucleotide sequences of the myc-like anthocyanin regulatory gene in the genus of dogwoods (Cornus: Cornaceae). Phylogenetic analyses demonstrate that the myc-like anthocyanin regulatory gene has potential as an informative phylogenetic marker at different taxonomic levels, depending on the data set considered (DNA or protein sequences) and regions applied (exons or introns). Pairwise nonsynonymous and synonymous substitution rate tests and codon-based substitution models were applied to characterize variation and to identify sites under diversifying selection. Mosaic evolution and heterogeneous rates among different domains and sites were detected.}, number={3}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Fan, CZ and Purugganan, MD and Thomas, DT and Wiegmann, BM and Xiang, QY}, year={2004}, month={Dec}, pages={580–594} }
 @article{karlson_xiang_stirm_shirazi_ashworth_2004, title={Phylogenetic analyses in Cornus substantiate ancestry of xylem supercooling freezing behavior and reveal lineage of desiccation related proteins}, volume={135}, ISSN={["0032-0889"]}, DOI={10.1104/pp.103.037473}, abstractNote={AbstractThe response of woody plant tissues to freezing temperature has evolved into two distinct behaviors: an avoidance strategy, in which intracellular water supercools, and a freeze-tolerance strategy, where cells tolerate the loss of water to extracellular ice. Although both strategies involve extracellular ice formation, supercooling cells are thought to resist freeze-induced dehydration. Dehydrin proteins, which accumulate during cold acclimation in numerous herbaceous and woody plants, have been speculated to provide, among other things, protection from desiccative extracellular ice formation. Here we use Cornus as a model system to provide the first phylogenetic characterization of xylem freezing behavior and dehydrin-like proteins. Our data suggest that both freezing behavior and the accumulation of dehydrin-like proteins in Cornus are lineage related; supercooling and nonaccumulation of dehydrin-like proteins are ancestral within the genus. The nonsupercooling strategy evolved within the blue- or white-fruited subgroup where representative species exhibit high levels of freeze tolerance. Within the blue- or white-fruited lineage, a single origin of dehydrin-like proteins was documented and displayed a trend for size increase in molecular mass. Phylogenetic analyses revealed that an early divergent group of red-fruited supercooling dogwoods lack a similar protein. Dehydrin-like proteins were limited to neither nonsupercooling species nor to those that possess extreme freeze tolerance.}, number={3}, journal={PLANT PHYSIOLOGY}, author={Karlson, DT and Xiang, QY and Stirm, VE and Shirazi, AM and Ashworth, EN}, year={2004}, month={Jul}, pages={1654–1665} }
 @article{xiang_xiang_liston_zhang_2004, title={Phylogenetic relationships in Abies (Pinaceae): evidence from PCR-RFLP of the nuclear ribosomal DNA internal transcribed spacer region}, volume={145}, ISSN={["1095-8339"]}, DOI={10.1111/j.1095-8339.2004.00286.x}, abstractNote={Phylogenetic analysis of restriction site data from the nuclear ribosomal DNA internal transcribed spacer region (ITS) was conducted for Abies to evaluate different infrageneric classification schemes. Twenty-eight species representing major morphological subgroups of the genus were included in this study. Thirty-three unambiguous restriction sites were scored from nine enzymes. The data were analysed using parsimony and neighbour-joining methods to infer phylogenetic relationships within the genus. Seven subclades that more or less correspond to previously recognized subgroups were resolved from these analyses: (1) sect. Bracteata, (2) sect. Balsamea (excluding A. kawakamii), (3) sect. Amabilis, (4) an eastern Asian group including sect. Momi, part of sect. Pseudopicea, and A. kawakamii, (5) core of sect. Pseudopicea, (6) a Mediterranean–south-western Asian group containing sect. Abies and sect. Piceaster and (7) sect. Nobilis. Lineages (4) and (5) are likely to be sisters, which are, in turn, sister to lineage (6). The results also suggest that this large Eurasian clade is most closely related to subclade (2) and the monotypic sect. Bracteata is most closely related to sect. Balsamea, but these relationships are supported by bootstrap values of less than 50%. These results indicate that the eastern Asian – North American disjunct section, sect. Balsamea, is monophyletic (96%) when A. kawakamii from Taiwan is excluded; species of sect. Abies and sect. Piceaster (Mediterranean and south-west Asia) are closely related, but the monophyly of each section remains unclear. The results also suggest that sect. Pseudopicea is not monophyletic; species from eastern China and the Qingling Mountains of this section appear to be more closely related to sect. Momi and A. kawakamii than to the other species of the same section. Species of sect. Grandis separate from the remaining species of Abies by having an approximately 500 base pairs longer ITS region. This study provides the first molecular-based phylogenetic hypothesis of Abies to be tested with additional data and broader sampling. © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society, 2004, 145, 425–435.}, number={4}, journal={BOTANICAL JOURNAL OF THE LINNEAN SOCIETY}, author={Xiang, QP and Xiang, QY and Liston, A and Zhang, XC}, year={2004}, month={Aug}, pages={425–435} }
 @article{xiang_zhang_ricklefs_qian_cheng_wen_li_2004, title={Regional differences in speciation and ITS Evolution: A comparison between eastern Asia and eastern North America}, volume={58}, ISSN={["1558-5646"]}, DOI={10.1111/j.0014-3820.2004.tb01596.x}, abstractNote={Abstract The eastern Asian (EAS)‐eastern North American (ENA) floristic disjunction is one of the best‐known biogeographic patterns in the Northern Hemisphere. Recent paleontological and molecular analyses have illuminated the origins of the biogeographic pattern, but subsequent diversification and evolution of the disjunct floras in each of the two continents after isolation remains poorly understood. Although similar in climate and floristic composition, EAS has twice as many species as ENA in genera occurring in both regions. Explaining such differences in species diversity between regions with similar environmental conditions (diversity anomalies) is an important goal of the study of the global patterns of biodiversity. We used a phylogenetic approach to compare rates of net speciation and molecular evolution between the two regions. We first identified EAS‐ENA disjunct sister clades from ten genera (Asarum, Buckleya, Carpinus, Carya, Cornus, Hamamelis, Illicium, Panax, Stewartia, and Styrax) that represent diverse angiosperm lineages using phylogenetic analyses of ITS (internal transcribed spacer of nuclear ribosomal DNA) sequence data. Species richness and substitution rate of ITS between sister clades were compared. The results revealed a pattern of greater species diversity in the EAS counterparts. A positive relationship between species diversity and ITS substitution rate was also documented. These results suggest greater net speciation and accelerated molecular evolution in EAS. The data support the idea that a regional difference in net speciation rate related to topographic heterogeneity contributes to the diversity anomaly between EAS and ENA. The close relationship between rates of ITS evolution and species richness further suggests that species production may be directly linked to rate of nucleotide substitution.}, number={10}, journal={Evolution}, author={Xiang, Q.Y. and Zhang, W.H. and Ricklefs, R.E. and Qian, H. and Cheng, Z.D. and Wen, J. and Li, J.H.}, year={2004}, pages={2175–2184} }
 @article{krings_xiang_2004, title={The Gonolobus complex (Apocynaceae - Asclepiadoideae) in the southeastern United States}, volume={21}, journal={SIDA, Contributions To Botany}, author={Krings, A. and Xiang, Q.-Y.}, year={2004}, pages={103–116} }
 @article{group*_2003, title={An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II}, volume={141}, ISSN={0024-4074, 1095-8339}, url={https://academic.oup.com/botlinnean/article-lookup/doi/10.1046/j.1095-8339.2003.t01-1-00158.x}, DOI={10.1046/j.1095-8339.2003.t01-1-00158.x}, abstractNote={A revised and updated classification for the families of the flowering plants is provided. Newly adopted orders include Austrobaileyales, Canellales, Gunnerales, Crossosomatales and Celastrales. Pertinent literature published since the first APG classification is included, such that many additional families are now placed in the phylogenetic scheme. Among these are Hydnoraceae (Piperales), Nartheciaceae (Dioscoreales), Corsiaceae (Liliales), Triuridaceae (Pan-danales), Hanguanaceae (Commelinales), Bromeliacae, Mayacaceae and Rapateaceae (all Poales), Barbeuiaceae and Gisekiaceae (both Caryophyllales), Geissolomataceae, Strasburgeriaceae and Vitaceae (unplaced to order, but included in the rosids), Zygophyllaceae (unplaced to order, but included in eurosids I), Bonnetiaceae, Ctenolophonaceae, Elatinaceae, Ixonanthaceae, Lophopyxidaceae, Podostemaceae (Malpighiales), Paracryphiaceae (unplaced in euasterid II), Sladeniaceae, Pentaphylacaceae (Ericales) and Cardiopteridaceae (Aquifoliales). Several major families are recircumscribed. Salicaceae are expanded to include a large part of Flacourtiaceae, including the type genus of that family; another portion of former Flacourtiaceae is assigned to an expanded circumscription of Achariaceae. Euphorbiaceae are restricted to the uniovulate subfamilies; Phyllanthoideae are recognized as Phyllanthaceae and Oldfieldioideae as Picrodendraceae. Scrophulariaceae are recircumscribed to include Buddlejaceae and Myoporaceae and exclude several former members; these are assigned to Calceolariaceae, Orobanchaceae and Plantaginaceae. We expand the use of bracketing families that could be included optionally in broader circumscriptions with other related families; these include Agapanthaceae and Amaryllidaceae in Alliaceae s.l. , Agavaceae, Hyacinthaceae and Ruscaceae (among many other Asparagales) in Asparagaceae s.l. , Dichapetalaceae in Chrysobalanaceae, Turneraceae in Passifloraceae, Erythroxylaceae in Rhizophoraceae, and Diervillaceae, Dipsacaceae, Linnaeaceae, Morinaceae and Valerianaceae in Caprifoliaceae s.l. © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 141 , 399–436.}, number={4}, journal={Botanical Journal of the Linnean Society}, author={GROUP*, THE ANGIOSPERM PHYLOGENY}, year={2003}, month={Apr}, pages={399–436} }
 @article{xiang_shui_murrell_2003, title={Cornus eydeana (Cornaceae), a new cornelian cherry from china - Notes on systematics and evolution}, volume={28}, number={4}, journal={Systematic Botany}, author={Xiang, Q. Y. and Shui, Y. M. and Murrell, Z.}, year={2003}, pages={757–764} }
 @misc{fan_xiang_2003, title={Phylogenetic analyses of Cornales based on 26S rRNA and combined 26S rDNA-matK-rbcL sequence data}, volume={90}, ISSN={["1537-2197"]}, DOI={10.3732/ajb.90.9.1357}, abstractNote={Nuclear 26S rDNA sequences were used to corroborate and test previously publishedmatK‐rbcL‐based hypotheses of phylogenetic relationships in Cornales. Sequences were generated for 53 taxa includingAlangium,Camptotheca,Cornus,Curtisia,Davidia,Diplopanax,Mastixia,Nyssa, and four families: Grubbiaceae, Hydrangeaceae, Hydrostachyaceae, and Loasaceae. Fifteen taxa from asterids were used as outgroups. The 26S rDNA sequences were initially analyzed separately and then combined withmatK‐rbcLsequences, using both parsimony and maximum likelihood methods. Eight strongly supported major clades were identified within Cornales by all analyses:Cornus,Alangium, nyssoids (Nyssa,Davidia, andCamptotheca), mastixioids (MastixiaandDiplopanax), Hydrangeaceae, Loasaceae,Grubbia‐Curtisia, andHydrostachys. However, relationships among the major lineages are not strongly supported in either 26S rDNA or combined 26S rDNA‐matK‐rbcLtopologies, except for the sister relationships betweenCornusandAlangiumand between nyssoids and mastixioids in the tree from combined data. Discrepancies in relationships among major lineages, especially the placement of the long‐branchedHydrostachys, were found between parsimony and maximum likelihood trees in all analyses. Incongruence between the 26S rDNA andmatK‐rbcLdata sets was suggested, where Hydrangeaceae was found to be largely responsible for the incongruence. The long branch ofHydrostachysrevealed in previous analyses was reduced significantly with more sampling. Maximum likelihood analysis of combined 26S rDNA‐matK‐rbcLsequences suggested thatHydrostachysmight be sister to the remainder of Cornales, thatCornus‐Alangiumare sisters, that nyssoids‐mastixioids are sisters, and that Hydrangeaceae‐Loasaceae are sisters, consistent with previous analyses ofmatK‐rbcLsequence data.}, number={9}, journal={AMERICAN JOURNAL OF BOTANY}, author={Fan, CZ and Xiang, QY}, year={2003}, month={Sep}, pages={1357–1372} }
 @article{xiang_moody_soltis_fan_soltis_2002, title={Relationships within Cornales and circumscription of Cornaceae – matK and rbcL sequence data and effects of outgroups and long branches}, volume={24}, ISSN={["1095-9513"]}, DOI={10.1016/S1055-7903(02)00267-1}, abstractNote={Phylogenetic relationships in Cornales were assessed using sequences rbcL and matK. Various combinations of outgroups were assessed for their suitability and the effects of long branches and outgroups on tree topology were examined using RASA 2.4 prior to conducting phylogenetic analyses. RASA identified several potentially problematic taxa having long branches in individual data sets that may have obscured phylogenetic signal, but when data sets were combined RASA no longer detected long branch problems. tRASA provides a more conservative measurement for phylogenetic signal than the PTP and skewness tests. The separate matK and rbcL sequence data sets were measured as the chloroplast DNA containing phylogenetic signal by RASA, but PTP and skewness tests suggested the reverse. Nonetheless, the matK and rbcL sequence data sets suggested relationships within Cornales largely congruent with those suggested by the combined matK–rbcL sequence data set that contains significant phylogenetic signal as measured by tRASA, PTP, and skewness tests. Our analyses also showed that a taxon having a long branch on the tree may not be identified as a “long-branched” taxon by RASA. The long branches identified by RASA had little effect on the arrangement of other taxa in the tree, but the placements of the long-branched taxa themselves were often problematic. Removing the long-branched taxa from analyses generally increased bootstrap support, often substantially. Use of non-optimal outgroups (as identified by RASA) decreased phylogenetic resolution in parsimony analyses and suggested different relationships in maximum likelihood analyses, although usually weakly supported clades (less than 50% support) were impacted. Our results do not recommend using tRASA as a sole criterion to discard data or taxa in phylogenetic analyses, but tRASA and the taxon variance ratio obtained from RASA may be useful as a guide for improved phylogenetic analyses. Results of parsimony and ML analyses of the sequence data using optimal outgroups suggested by RASA revealed four major clades within Cornales: (1) Curtisia–Grubbia, (2) Cornus–Alangium, (3) Nyssa–Camptotheca–Davidia–Mastixia–Diplopanax, and (4) Hydrangeaceae–Loasaceae, with clades (2) and (3) forming a monophyletic group sister to clade (4) and clade (1) sister to the remainder of Cornales. However, there was not strong bootstrap support for relationships among the major clades. The placement of Hydrostachys could not be reliably determined, although most analyses place the genus within Hydrangeaceae; ML analyses, for example, placed the genus as the sister of Hydrangeeae. Our results supported a Cornales including the systematically problematic Hydrostachys, a Cornaceae consisting of Cornus and Alangium, a Nyssaceae consisting of Nyssa and Camptotheca, a monogeneric Davidiaceae, a Mastixiaceae consisting of Mastixia and Diplopanax, and an expanded Grubbiaceae consisting of Grubbia and Curtisia, and two larger families, Hydrangeaceae and Loasaceae.}, number={1}, journal={Molecular Phylogeneics and Evolution}, author={Xiang, Q.Y. and Moody, M. and Soltis, D.E. and Fan, C.Z. and Soltis, P.S.}, year={2002}, pages={35–57} }
 @misc{xiang_2005, place={UK}, title={Cornales}, DOI={10.1002/9780470015902}, journal={Encyclopedia of Life Sciences}, publisher={John Wiley & Sons, Ltd.}, author={Xiang, Q.-Y.}, year={2005}, month={May} }
 @article{xiang_soltis_2001, title={Dispersal-vicariance analyses of intercontinental disjuncts: Historical biogeographical implications for angiosperms in the Northern Hemisphere}, volume={162}, ISSN={["1537-5315"]}, DOI={10.1086/323332}, abstractNote={Ten North Temperate taxa representing diverse angiosperm lineages were analyzed for biogeographic histories using the dispersal‐vicariance analysis method to gain insights into the origin and evolution of disjunct distributions in the Northern Hemisphere. Results indicate four general biogeographic patterns: (1) origin and speciation in eastern Asia with subsequent expansion into North America and/or Europe (e.g., Aralia sect. Aralia, Symplocarpus, and possibly Asarum, Aesculus, and Chrysosplenium); (2) origin in eastern Asia and western North America with subsequent spread into eastern North America (e.g., Calycanthus and Boykinia); (3) a disjunct origin in eastern Asia and eastern North America with subsequent dispersal from eastern Asia into eastern North America (e.g., Panax); and (4) a widespread origin in the Northern Hemisphere with subsequent fragmentation by intercontinental vicariance (e.g., Cornus and Trautvetteria). Although there are caveats, the results indicate that the disjunct distributions of angiosperm lineages in the Northern Hemisphere cannot be explained with a simple vicariance model. Most lineages may have been restricted ancestrally to one or two adjacent areas and then secondarily expanded their ranges via dispersal. A noteworthy finding was the one‐way intercontinental plant exchange from the Old World to the New World and biased dispersal within each continent. There was more dispersal from the west to the east in North America but more dispersal from the east to the west in Eurasia. Such asymmetrical dispersal has also been documented in animals. The results also indicate that eastern Asia and western North America were the centers of origin for a majority of lineages examined, implying that these two areas were important sources of temperate angiosperm evolution in the Northern Hemisphere. The results further support a complex evolutionary history of angiosperms in the Northern Hemisphere and suggest pseudocongruence among lineages in phylogenetic relationships and distributional patterns.}, number={2001 Nov}, journal={INTERNATIONAL JOURNAL OF PLANT SCIENCES}, author={Xiang, QYJ and Soltis, DE}, year={2001}, month={Nov}, pages={S29–S39} }
 @article{soltis_tago-nakazawa_xiang_kavano_murata_wakabayashi_hibsch-hetter_2001, title={Phylogenetic relationships in Chrysosplenium (Saxifragaceae) based on matK sequence data}, volume={88}, DOI={10.2307/2657040}, abstractNote={Chrysosplenium (Saxifragaceae) consists of 57 species widely distributed in temperate and arctic regions of the Northern Hemisphere, with two species restricted to the southern part of South America. Species relationships within the genus are highly problematic. The genus has traditionally been divided into two groups, sometimes recognized as sections (Oppositifolia and Alternifolia), based on leaf arrangement, or, alternatively, into 17 series. Based on morphological features, Hara suggested that the genus originated in South America and then subsequently migrated to the Northern Hemisphere. We conducted phylogenetic analyses of DNA sequences of the chloroplast gene matK for species of Chrysosplenium to elucidate relationships, test Hara's biogeographic hypothesis for the genus, and examine chromosomal and gynoecial diversification. These analyses revealed that both sections Oppositifolia and Alternifolia are monophyletic and form two large sister clades. Hence, leaf arrangement is a good indicator of relationships within this genus. Hara's series Pilosa and Macrostemon are each also monophyletic; however, series Oppositifolia, Alternifolia, and Nepalensia are clearly not monophyletic. MacClade reconstructions suggest that the genus arose in Eastern Asia, rather than in South America, with several independent migration events from Asia to the New World. In one well‐defined subclade, species from eastern and western North America form a discrete clade, with Old World species as their sister group, suggesting that the eastern and western North American taxa diverged following migration to that continent. The South American species forms a clade with species from eastern Asia; this disjunction may be the result of ancient long‐distance dispersal. Character mapping demonstrated that gynoecial diversification is dynamic, with reversals from inferior to half‐inferior ovaries, as well as to ovaries that appear superior. Chromosomal evolution also appears to be labile with several independent origins of n = 12 (from an original number of n = 11) and multiple episodes of aneuploidy.}, number={5}, journal={American Journal of Botany}, author={Soltis, D.E. and Tago-Nakazawa, M. and Xiang, Q.Y. and Kavano, S. and Murata, J. and Wakabayashi, M. and Hibsch-Hetter, C.}, year={2001}, pages={883–894} }
 @article{fan_xiang_2001, title={Phylogenetic relationships within Cornus (Cornaceae) based on 26S rDNA sequences}, volume={88}, ISSN={00029122}, url={http://doi.wiley.com/10.2307/2657096}, DOI={10.2307/2657096}, abstractNote={Phylogenetic relationships within the dogwood genus Cornus have been highly controversial due to the great morphological heterogeneity. Earlier phylogenetic analyses of Cornus using chloroplast DNA (cpDNA) data (including rbcL and matK sequences, as well as restriction sites) and morphological characters suggested incongruent relationships within the genus. The present study generated sequence data from the nuclear gene 26S rDNA for Cornus to test the phylogenetic hypotheses based on cpDNA and morphological data. The 26S rDNA sequence data obtained represent 16 species, 13 from Cornus and three from outgroups, having an aligned length of 3380 bp. Both parsimony and maximum likelihood analyses of these sequences were conducted. Trees resulting from these analyses suggest relationships among subgroups of Cornus consistent with those inferred from cpDNA data. That is, the dwarf dogwood (subg. Arctocrania) and the big‐bracted dogwood (subg. Cynoxylon and subg. Syncarpea) clades are sisters, which are, in turn, sister to the cornelian cherries (subg. Cornus and subg. Afrocrania). This red‐fruited clade is sister to the blue‐ or white‐fruited dogwoods (subg. Mesomora, subg. Kraniopsis, and subg. Yinquania). Within the blue‐ or white‐fruited clade, C. oblonga (subg. Yinquania) is sister to the remainder, and subg. Mesomora is sister to subg. Kraniopsis. These relationships were also suggested by the combined 26S rDNA and cpDNA data, but with higher bootstrap and Bremer support in the combined analysis. The 26S rDNA sequence data of Cornus consist of 12 expansion segments spanning 1034 bp. These expansion segments evolve approximately four times as fast as the conserved core regions. The study provides an example of phylogenetic utility of 26S rDNA sequences below the genus level.}, number={6}, journal={American Journal of Botany}, author={Fan, Chuanzhu and Xiang, Jenny Qiu-Yun}, year={2001}, month={Jun}, pages={1131–1138} }
 @article{xiang_xiang_liston_fu_fu_2000, title={Length variation of the nuclear ribosomal DNA internal transcribed spacer in the genus Abies, with references to its systematic utility in Pinaceae}, volume={42}, journal={Acta Botanica Sinica}, author={Xiang, Q.P. and Xiang, Q.Y. and Liston, A. and Fu, L.K. and Fu, D.Z.}, year={2000}, pages={946–951} }
 @article{xiang_soltis_soltis_manchester_crawford_2000, title={Timing the eastern Asian-Eastern North American floristic disjunction: Molecular clock corroborates paleontological estimates}, volume={15}, ISSN={["1095-9513"]}, DOI={10.1006/mpev.2000.0766}, abstractNote={Sequence data of the chloroplast gene rbcL were used to estimate the time of the well-known eastern Asian-eastern North American floristic disjunction. Sequence divergence of rbcL was examined for 22 species of 11 genera (Campsis, Caulophyllum, Cornus, Decumaria, Liriodendron, Menispermum, Mitchella, Pachysandra, Penthorum, Podophyllum, and Phryma) representing a diverse array of flowering plants occurring disjunctly in eastern Asia and eastern North America. Divergence times of putative disjunct species pairs were estimated from synonymous substitutions, using rbcL molecular clocks calibrated for Cornus. Relative rate tests were performed to assess rate constancy of rbcL evolution among lineages. Corrections of estimates of divergence times for each species pair were made based on rate differences of rbcL between Cornus and other species pairs. Results of these analyses indicate that the time of divergence of species pairs examined ranges from 12.56 +/- 4.30 million years to recent (<0.31 million years), with most within the last 10 million years (in the late Miocene and Pliocene). These results suggest that the isolation of most morphologically similar disjunct species in eastern Asia and eastern North America occurred during the global climatic cooling period that took place throughout the late Tertiary and Quaternary. This estimate is closely correlated with paleontological evidence and in agreement with the hypothesis that considers the eastern Asian-eastern North American floristic disjunction to be the result of the range restriction of a once more or less continuously distributed mixed mesophytic forest of the Northern Hemisphere that occurred during the late Tertiary and Quaternary. This implies that in most taxa the disjunction may have resulted from vicariance events. However, long-distance dispersal may explain the disjunct distribution of taxa with low divergence, such as Menispermum.}, number={3}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Xiang, QY and Soltis, DE and Soltis, PS and Manchester, SR and Crawford, DJ}, year={2000}, month={Jun}, pages={462–472} }
 @article{xiang_1999, title={Systematic affinities of Grubbiaceae and Hydrostachyaceae within Cornales - insights from rbcL sequences}, volume={4}, number={1999}, journal={Harvard Papers in Botany}, author={Xiang, Q.-Y.}, year={1999}, pages={527–542} }
 @article{wolfe_xiang_kephart_1998, title={Assessing hybridization in natural populations of Penstemon (Scrophulariaceae) using hypervariable intersimple sequence repeat (ISSR) bands}, volume={7}, ISSN={["1365-294X"]}, DOI={10.1046/j.1365-294x.1998.00425.x}, abstractNote={Inferences regarding hybridization rely on genetic markers to differentiate parental taxa from one another. Intersimple sequence repeat (ISSR) markers are based on single‐primer PCR reactions where the primer sequence is derived from di‐ and trinucleotide repeats. These markers have successfully been used to assay genetic variability among cultivated plants, but have not yet been tested in natural populations. We used genetic markers generated from eight ISSR primers to examine patterns of hybridization and purported examples of hybrid speciation in Penstemon (Scrophulariaceae) in a hybrid complex involving P. centranthifolius, P. grinnellii, P. spectabilis and P. clevelandii. This hybrid complex has previously been studied using three molecular data sets (allozymes, and restriction‐site variation of nuclear rDNA and chloroplast DNA). These studies revealed patterns of introgression involving P. centranthifolius, but were unsuccessful in determining whether gene flow occurs among the other species, and support for hypotheses of diploid hybrid speciation was also lacking. In this study, we were able to fingerprint each DNA accession sampled with one to three ISSR primers and most accessions could be identified with a single primer. We found population‐ and species‐specific markers for each taxon surveyed. Our results: (i) do not support the hybrid origin of P. spectabilis; (ii) do support the hypothesis that P. clevelandii is a diploid hybrid species derived from P. centranthifolius and P. spectabilis; and (iii) demonstrate that pollen‐mediated gene flow via hummingbird vectors is prevalent in the hybrid complex.}, number={9}, journal={MOLECULAR ECOLOGY}, author={Wolfe, AD and Xiang, QY and Kephart, SR}, year={1998}, month={Sep}, pages={1107–1125} }
 @article{wolfe_xiang_kephart_1998, title={Diploid hybrid speciation in Penstemon (Scrophulariaceae)}, volume={95}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.95.9.5112}, abstractNote={Hybrid speciation has played a significant role in the evolution of angiosperms at the polyploid level. However, relatively little is known about the importance of hybrid speciation at the diploid level. Two species ofPenstemonhave been proposed as diploid hybrid derivatives based on morphological data, artificial crossing studies, and pollinator behavior observations:Penstemon spectabilis(derived from hybridization betweenPenstemon centranthifoliusandPenstemon grinnellii) andPenstemon clevelandii(derived from hybridization betweenP. centranthifoliusandP. spectabilis). Previous studies were inconclusive regarding the purported hybrid nature of these species because of a lack of molecular markers sufficient to differentiate the parental taxa in the hybrid complex. We developed hypervariable nuclear markers using inter-simple sequence repeat banding patterns to test these classic hypotheses of diploid hybrid speciation inPenstemon. Each species in the hybrid complex was genetically distinct, separated by 10–42 species-specific inter-simple sequence repeat markers. Our data do not support the hybrid origin ofP. spectabilisbut clearly support the diploid hybrid origin ofP. clevelandii. Our results further suggest that the primary reason diploid hybrid speciation is so difficult to detect is the lack of molecular markers able to differentiate parental taxa from one another, particularly with recently diverged species.}, number={9}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Wolfe, AD and Xiang, QY and Kephart, SR}, year={1998}, month={Apr}, pages={5112–5115} }
 @article{brochmann_xiang_brunsfeld_soltis_soltis_1998, title={Molecular evidence for origins of polyploid Saxifraga (Saxifragaceae): the narrow arctic endemic S. svalbardensis and its widespread allies}, volume={85}, DOI={10.2307/2446562}, abstractNote={The recently described polyploid Saxifraga svalbardensis is endemic to the arctic archipelago of Svalbard. We investigated relationships among four closely related species of Saxifraga in Svalbard and tested three previously proposed hypotheses for the origin of S. svalbardensis: (1) differentiation from the morphologically and chromosomally variable polyploid S. cernua; (2) hybridization between the diploid S. hyperborea and S. cernua; and (3) hybridization between the tetraploid S. rivularis and S. cernua. Fifteen populations were analyzed using random amplified polymorphic DNAs (RAPDs) and nucleotide sequences of the chloroplast gene matK and the internal transcribed spacers (ITS) of nuclear ribosomal DNA (rDNA). RAPD and matK data suggest that S. svalbardensis has originated from a hybrid with S. rivularis as the maternal parent and S. cernua as the paternal parent, possibly a single time, whereas ITS data could not be used to discriminate among the hypotheses. The data also suggest that the diploid S. hyperborea is a progenitor of the tetraploid S. rivularis. The four populations examined of S. svalbardensis were virtually identical for RAPD and ITS markers, whereas S. cernua showed high levels of variation, suggesting that the latter polyploid either has formed recurrently or has undergone considerable differentiation since its origin.}, journal={American Journal of Botany}, author={Brochmann, C. and Xiang, Q.Y. and Brunsfeld, S.J. and Soltis, D.E. and Soltis, P.S.}, year={1998}, pages={135–143} }
 @article{xiang_crawford_wolfe_tang_depamphilis_1998, title={Origin and biogeography of Aesculus L. (Hippocastanaceae): a molecular phylogenetic perspective}, volume={52}, DOI={10.1111/j.1558-5646.1998.tb01828.x}, abstractNote={Sequences of chloroplast gene matK and internal transcribed spacers of nuclear ribosomal RNA genes were used for phylogenetic analyses of Aesculus, a genus currently distributed in eastern Asia, eastern and western North America, and southeastern Europe. Phylogenetic relationships inferred from these molecular data are highly correlated with the geographic distributions of species. The identified lineages closely correspond to the five sections previously recognized on the basis of morphology. Ancestral character‐state reconstruction, a molecular clock, and fossil evidence were used to infer the origin and biogeographic history of the genus within a phylogenetic framework. Based on the molecular phylogenetic reconstruction of the genus, sequence divergence, and paleontological evidence, we infer that the genus originated during the transition from the Cretaceous to the Tertiary (~65 M.Y.B.P.) at a high latitude in eastern Asia and spread into North America and Europe as an element of the “boreotropical flora”; the current disjunct distribution of the genus resulted from geological and climatic changes during the Tertiary.}, number={1998}, journal={Evolution}, author={Xiang, Qiu-Yun and Crawford, D. J. and Wolfe, A. D. and Tang, Y.-C. and DePamphilis, C. W.}, year={1998}, pages={988–997} }
 @article{xiang_soltis_soltis_1998, title={Phylogenetic relationships of cornaceae and close relatives inferred from matK and rbcL sequences}, volume={85}, ISSN={["1537-2197"]}, DOI={10.2307/2446317}, abstractNote={Phylogenetic relationships were inferred using nucleotide sequences of the chloroplast gene matK for members of Cornales, a well‐supported monophyletic group comprising Cornaceae and close relatives. The shortest trees resulting from this analysis were highly concordant with those based on previous phylogenetic analysis of rbcL sequences. Analysis of a combined matK and rbcL sequence data set (a total of 2652 bp [base pairs]) provided greater resolution of relationships and higher internal support for clades compared to the individual data sets. Four major clades (most inclusive monophyletic groups) of Cornales are indicated by both sets of genes: (1) Cornus‐Alangium, (2) nyssoids (Nyssa‐Davidia‐Camptotheca)‐mastixioids (Mastixia, Diplopanax), (3) Curtisia, and (4) Hydrangeaceae‐Loasaceae. The combined evidence indicates that clades 2 and 3 are sisters, with clade 4 sister to the remainder of Cornales. These relationships are also supported by other lines of evidence, including synapomorphies in fruit and pollen morphology and gynoecial vasculature. Comparisons of matK and rbcL sequences based on one of the most parsimonious rbcL‐matK trees indicate that matK has a much higher A‐T content (66.9% in matK vs. 55.8% in rbcL) and a lower transition:transversion ratio (1.23 in matK vs. 2.21 in rbcL). The total number of nucleotide substitutions per site for matK is 2.1 times that of rbcL in Cornales. These findings are similar to recent comparisons of matK and rbcL in other dicots. Variable sites of matK are almost evenly distributed among the three codon positions (1.0:1.0:1.3), whereas variable sites of rbcL are mostly at the third position (1.8:1.0:7.5). Among‐lineages rates of nucleotide substitutions in rbcL are basically homogeneous throughout Cornales, but are more heterogeneous in matK.}, number={2}, journal={AMERICAN JOURNAL OF BOTANY}, author={Xiang, QY and Soltis, DE and Soltis, PS}, year={1998}, month={Feb}, pages={285–297} }
 @article{xiang_soltis_soltis_1998, title={The eastern Asian and eastern and western North American floristic disjunction: Congruent phylogenetic patterns in seven diverse genera}, volume={10}, ISSN={["1095-9513"]}, DOI={10.1006/mpev.1998.0524}, abstractNote={One of the most remarkable examples of intercontinental disjunction of the North Temperate Flora involves eastern Asia and eastern and western North America. Although there has been considerable interest in this phytogeographic pattern for over 150 years (e.g., Gray, 1859; Li, 1952; Graham, 1972; Boufford and Spongberg, 1983; Wu, 1983; Tiffney, 1985a, 1985b), relationships among taxa displaying the disjunction remain obscure. Understanding phylogenetic relationships is, however, a prerequisite for historical biogeographic analyses of this distributional pattern. To understand better the relationships of taxa displaying this intercontinental disjunction, phylogenetic analyses were conducted using a variety of DNA data sets for species of four genera (Cornus, Boykinia, Tiarella, and Trautvetteria) that occur in eastern Asia, eastern North America, and western North America. An area cladogram was constructed for each of the four genera, all of which show a similar pattern of relationship: the eastern Asian species are sister to all North American species. An identical phylogenetic pattern is also found in three other taxa exhibiting this disjunction (Aralia sect. Aralia, Calycanthus, and Adiantum pedatum). The congruent phylogenetic pattern found in these seven diverse genera raises the possibility of a common origin of the eastern Asia, eastern and western North America disjunction. The data are in agreement with the long-standing hypothesis that this well-known floristic disjunction represents the fragmentation of a once continuous Mixed Mesophytic forest community and suggest that the disjunction may have involved only two major vicariance events: an initial split between Eurasia and North America, followed by the isolation of floras between eastern and western North America. However, congruence between phylogenies and geographic distributions does not necessarily indicate an identical phytogeographic history. Taxa exhibiting the same phylogenetic pattern may have originated at different geological times. Analysis of divergence times using the molecular clock indicates that species of Cornus, Boykinia, and Calycanthus may have diverged at different geological times, suggesting that the floristic disjunction involving eastern Asia and North America may not be simple; it may have involved multiple historical events at very different geological times in different genera.}, number={2}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Xiang, QY and Soltis, DE and Soltis, PS}, year={1998}, month={Oct}, pages={178–190} }
 @inbook{xiang_soltis_1998, place={Tokyo}, title={rbcL sequence divergence and phylogenetic relationships of Cornaceae sensu lato}, booktitle={Sino-Japanese Flora - Its Characteristics and Diversification}, publisher={The University of Tokyo Press}, author={Xiang, Q.-Y. and Soltis, D.E.}, editor={Boufford, D.E. and Ohba, H.Editors}, year={1998}, pages={123–139} }
 @article{xiang_brunsfeld_soltis_soltis_1996, title={Chloroplast DNA phylogeny of Cornus L. (Cornaceae) and its implications for biogeography and character evolution}, volume={21}, DOI={10.2307/2419612}, abstractNote={Chloroplast DNA (cpDNA) restriction site analysis was used to elucidate phylogenetic relationships within the taxonomically controversial genus, Cornus. Twenty-nine species representing all major morphological subgroups of the genus were analyzed with 21 restriction endonucleases. Major lineages within Cornus identified by the cpDNA restriction site data are highly concordant with those suggested by both rbcL sequences and morphology. Relationships among these lineages are well-resolved by the restriction site data. The genus diverged early into two major clades: the blue-fruited group bearing blue or white fruits and the red-fruited group bearing red fruits. The blue-fruited clade further comprises two lineages: the alternate-leaved group and the opposite-leaved group. The red-fruited clade is composed of three lineages: the cornelian cherries, the dwarf dogwoods, and the big-bracted dogwoods, with the latter two as sister- groups. The cpDNA restriction site data also correlate closely with the evolution of chromosome number, morphology, and phytochemistry. Most notably, the chromosome number of n = 10 evolved twice in Cornuis, and the small, non-petaloid bracts in C. disciflora apparently represent a reversal to the non-showy state. Furthermore, the presence of iridoids in the red-fruited dogwoods apparently is a retention of the plesiomor- phic condition.}, journal={Systematic Botany}, author={Xiang, Q.Y. and Brunsfeld, S.J. and Soltis, D.E. and Soltis, P.S.}, year={1996}, pages={515–534} }
 @article{xiang_edye_1995, title={Chromosome number of Cornus sessilis (Cornaceae): phylogenetic affinity and evolution of chromosome numbers in Cornus}, volume={16}, journal={Sida}, author={Xiang, Q.Y. and Edye, R.H.}, year={1995}, pages={765–768} }
 @article{soltis_xiang_hufford_1995, title={Relationships and Evolution of Hydrangeaceae Based on rbcL Sequence Data}, volume={82}, ISSN={00029122}, url={http://doi.wiley.com/10.1002/j.1537-2197.1995.tb15671.x}, DOI={10.2307/2445698}, abstractNote={Phylogenetic analyses of rbcL sequences were used to address both systematic and evolutionary questions posed by the angiosperm family Hydrangeaceae. Our analyses suggest the presence of a monophyletic Hydrangeaceae most closely allied with Loasaceae, a finding in agreement with other molecular as well as morphological analyses. Molecular data indicate that Hydrangeaceae comprise Decumaria, Pileostegia, Schizophragma, Hydrangea, Dichroa, Broussaisia, Platycrater, Cardiandra, Deinanthe, Carpenteria, Philadelphus, Deutzia, Fendlerella, Whipplea, Fendlera, Jamesia, and the enigmatic Kirengeshoma. A particularly close relationship of Kirengeshoma and Deutzia is indicated. Analysis of rbcL sequences suggests that Fendlera and Jamesia are sister to the remainder of the family, lending support to the hypothesis that at least some Carpenterieae are basal in the family and that Hydrangeaceae may have originated in xeric habitats. If this phylogenetic placement of Jamesia and Fendlera is correct, the rbcL trees also suggest that the level of epigyny has decreased in these genera, as well as in the Fendlerella- Whipplea clade and Carpenteria when compared to the outgroup taxa, which are wholly epigynous. Furthermore, the rbcL trees support proposed evolutionary trends in wood anatomy, suggesting, for example, that upland tropical taxa have evolved longer vessel elements with more numerous bars on scalariform perforation plates. The xerophytic basal members of Hydrangeaceae, like the closely related Loasaceae, have short, narrow vessel elements with scalariform perforation plates bearing few bars. Following Jamesia and Fendlera, the remaining hydrangeoids are divided into two large subclades that closely parallel the traditional division of the family into Philadelpheae and Hydrangeae. Both rbcL sequences and morphological data suggest close relationships between: 1) Fendlerella and Whipplea; 2) Decumaria, Pileostegia, and Schizophragma; 3) Carpenteria and Philadelphus; 4) Deinanthe and Cardiandra; 5) Dichroa, Broussaisia, and Hydrangea macrophylla. Molecular and morphological data also concur in demonstrating that the large genus Hydrangea is not a monophyletic assemblage.}, number={4}, journal={American Journal of Botany}, author={Soltis, Douglas E. and Xiang, Qiu-Yun and Hufford, Larry}, year={1995}, month={Apr}, pages={504} }
 @inbook{xiang_1993, place={Beijing}, title={Cornaceae}, volume={1}, booktitle={Vascular Flora of the Hengduan Mountains}, publisher={Science Press}, author={Xiang, Q.-Y.}, editor={Wang, W.T. and Wu, S.G. and Lang, K.Y. and Li, P.Q. and Pu, F.T. and Chen, S.K.Editors}, year={1993}, pages={1356–1363} }
 @article{xiang_soltis_morgan_soltis_1993, title={Phylogenetic Relationships of Cornus L. Sensu Lato and Putative Relatives Inferred from rbcL Sequence Data}, volume={80}, ISSN={00266493}, url={https://www.jstor.org/stable/2399856?origin=crossref}, DOI={10.2307/2399856}, abstractNote={A parsimony analysis of 46 rbcL sequences was performed to evaluate relationships among Cornus and putative relatives, as well as among subgroups within Cornus. Our results indicate that Alangium, nyssoids (Nyssa, Davidia, and Camptotheca), mastixioids (Diplopanax and Mastixia), Curtisia, and genera of Hydrangeaceae are the closest relatives of Cornus. These taxa, plus Cornus, constitute a «cornaceous clade,» which differs from all previously proposed Cornus alliances. Within this cornaceous clade, four major lineages were identified; (i) Cornus-Alangium, (ii) nyssoids-mastixioids, (iii) Curtisia, and (iv) hydrangeoids. The relationships among the four major lineages within the cornaceous clade remain unresolved}, number={3}, journal={Annals of the Missouri Botanical Garden}, author={Xiang, Qiu-Yun and Soltis, Douglas E. and Morgan, David R. and Soltis, Pamela S.}, year={1993}, pages={723} }
 @article{chase_soltis_olmstead_morgan_les_mishler_duvall_price_hills_qiu_et al._1993, title={Phylogenetics of Seed Plants: An Analysis of Nucleotide Sequences from the Plastid Gene rbcL}, volume={80}, ISSN={00266493}, url={https://www.jstor.org/stable/2399846?origin=crossref}, DOI={10.2307/2399846}, abstractNote={We present the results of two exploratory parsimony analyses of DNA sequences from 475 and 499 species of seed plants, respectively, representing all major taxonomic groups. The data are exclusively from the chloroplast gene rbcL, which codes for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO or RuBPCase). We used two different state-transformation assumptions resulting in two sets of cladograms: (i) equal-weighting for the 499-taxon analysis; and (ii) a procedure that differentially weights transversions over transitions within characters and codon positions among characters for the 475-taxon analysis. The degree of congruence between these results and other molecular, as well as morphological, cladistic studies indicates that rbcL sequence variation contains historical evidence appropriate for phylogenetic analysis at this taxonomic level of sampling. Because the topologies presented are necessarily approximate and cannot be evaluated adequately for internal support, these results should be assessed from the perspective of their predictive value and used to direct future studies, both molecular and morphological. In both analyses, the three genera of Gnetales are placed together as the sister group of the flowering plants, and the anomalous aquatic Ceratophyllum (Ceratophyllaceae) is sister to all other flowering plants. Several major lineages identified correspond well with at least some recent taxonomic schemes for angiosperms, particularly those of Dahlgren and Thorne. The basalmost clades within the angiosperms are orders of the apparently polyphyletic subclass Magnoliidae sensu Cronquist. The most conspicuous feature of the topology is that the major division is not monocot versus dicot, but rather one correlated with general pollen type: uniaperturate versus triaperturate. The Dilleniidae and Hamamelidae are the only subclasses that are grossly polyphyletic; an examination of the latter is presented as an example of the use of these broad analyses to focus more restricted studies. A broadly circumscribed Rosidae is paraphyletic to Asteridae and Dilleniidae. Subclass Caryophyllidae is monophyletic and derived from within Rosidae in the 475-taxon analysis but is sister to a group composed of broadly delineated Asteridae and Rosidae in the 499-taxon study.}, number={3}, journal={Annals of the Missouri Botanical Garden}, author={Chase, Mark W. and Soltis, Douglas E. and Olmstead, Richard G. and Morgan, David and Les, Donald H. and Mishler, Brent D. and Duvall, Melvin R. and Price, Robert A. and Hills, Harold G. and Qiu, Yin-Long and et al.}, year={1993}, pages={528} }
 @article{boufford_xiang_1992, series={Botanical Bulletin}, title={Pachysandra (Buxaceae) Reexamined}, volume={33}, journal={Academia Sinica}, year={1992}, pages={201–207}, collection={Botanical Bulletin} }
 @article{eyde_qiuyun_1990, title={Fossil mastixioid (Cornaceae) alive in Eastern Asia}, volume={77}, ISSN={00029122}, url={http://doi.wiley.com/10.1002/j.1537-2197.1990.tb14455.x}, DOI={10.1002/j.1537-2197.1990.tb14455.x}, abstractNote={The tree species Diplopanax stachyanthus, wrongly placed in the Araliaceae, belongs in fact to the mastixioid subfamily of Cornaceae. Fruit features make it congeneric with Mastixicarpum, part of a woody‐fruited complex known heretofore from Tertiary fossils.}, number={5}, journal={American Journal of Botany}, author={Eyde, Richard H. and Qiuyun, Xiang}, year={1990}, month={May}, pages={689–692} }
 @article{tang_xiang_1989, title={A reclassification of the genus Clematoclethra (Actinidiaceae) and further note on the methodology of plant taxonomy}, volume={27}, journal={Acta Phytotax. Sin.}, author={Tang, Y.C. and Xiang, Q.Y.}, year={1989}, pages={81–95} }
 @article{tang_xiang_1989, title={Cytological studies of Carex siderostricta Hance (Cyperaceae) and its importance in Phytogeography}, volume={1}, journal={Cathaya}, author={Tang, Y.C. and Xiang, Q.Y.}, year={1989}, pages={49–60} }
 @article{xiang_1989, title={Taxonomy of Cornus shindleri complex based on quantitative analysis of some characters}, volume={9}, number={1}, journal={Bulletin of Botanical Research}, author={Xiang, Q.Y.}, year={1989}, pages={125–138} }
 @article{xiang_1987, title={A neglected character of Cornus L. s. l. with special reference to a new subgenus -- Sinocornus}, volume={25}, journal={Acta Phytotax. Sin.}, author={Xiang, Q.Y.}, year={1987}, pages={25–131} }
 @article{tang_xiang_1987, title={Cytological studies on some plants of East China (I)}, volume={25}, journal={Acta Phytotax. Sin.}, author={Tang, Y.C. and Xiang, Q.Y.}, year={1987}, pages={1–8} }
 @article{tang_xiang_cao_1987, title={Cytological studies on some plants of Sichuan and its neighboring regions (I).}, volume={22}, journal={Acta Phytotax. Sin}, author={Tang, Y.C. and Xiang, Q.Y. and Cao, Y.L.}, year={1987}, pages={343–350} }
 @article{xiang_1987, title={System and synopsis of Cornus subgen. Syncarpea (Nakai) Q. Y. Xiang (Cornaceae)}, volume={7}, number={2}, journal={Bulletin of Botanical Research}, author={Xiang, Q.Y.}, year={1987}, pages={33–52} }