@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{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{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}, number={1}, journal={Taxon}, author={Harris, A. J. and Xiang, Q. Y. and Thomas, D. T.}, year={2009}, pages={108–126} }
 @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 stu...}, 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{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 involves Aesculus pavia, A. sylvatica, and A. flava, three cpDNA regions (matK, trnD-trnT, and trnH-trnK) were analyzed. The maternal inheritance of cpDNA in Aesculus was confirmed via sequencing of matK from 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 of A. pavia in 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{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={DNA 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} }
 @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{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} }