@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={Abstract}, 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_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={Abstract}, number={2}, journal={SYSTEMATIC BIOLOGY}, author={Zhou, Wenbin and Soghigian, John and Xiang, Qiu-Yun Jenny}, year={2022}, month={Feb}, pages={410–425} }
 @article{liu_ren_kwak_hodel_xu_he_zhou_huang_ma_qian_et al._2022, title={Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere}, volume={64}, ISSN={["1744-7909"]}, DOI={10.1111/jipb.13246}, abstractNote={Abstract}, number={5}, journal={JOURNAL OF INTEGRATIVE PLANT BIOLOGY}, author={Liu, Bin-Bin and Ren, Chen and Kwak, Myounghai and Hodel, Richard G. J. and Xu, Chao and He, Jian and Zhou, Wen-Bin and Huang, Chien-Hsun and Ma, Hong and Qian, Guan-Ze and et al.}, year={2022}, month={May}, pages={1020–1043} }
 @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={Abstract}, journal={JOURNAL OF SYSTEMATICS AND EVOLUTION}, publisher={Wiley}, author={Zhou, Wenbin and Harris, A. J. and Xiang, Qiu-Yun}, year={2022}, month={May} }
 @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={Abstract}, 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{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={Abstract}, 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{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{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} }