@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={AbstractPhylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single‐copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian‐western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.}, 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_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{guo_fei_potter_liebhold_wen_2019, title={Tree diversity regulates forest pest invasion}, volume={116}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1821039116}, DOI={10.1073/pnas.1821039116}, abstractNote={Nonnative pests often cause cascading ecological impacts, leading to detrimental socioeconomic consequences; however, how plant diversity may influence insect and disease invasions remains unclear. High species diversity in host communities may promote pest invasions by providing more niches (i.e., facilitation), but it can also diminish invasion success because low host dominance may make it more difficult for pests to establish (i.e., dilution). Most studies to date have focused on small-scale, experimental, or individual pest/disease species, while large-scale empirical studies, especially in natural ecosystems, are extremely rare. Using subcontinental-level data, we examined the role of tree diversity on pest invasion across the conterminous United States and found that the tree-pest diversity relationships are hump-shaped. Pest diversity increases with tree diversity at low tree diversity (because of facilitation or amplification) and is reduced at higher tree diversity (as a result of dilution). Thus, tree diversity likely regulates forest pest invasion through both facilitation and dilution that operate simultaneously, but their relative strengths vary with overall diversity. Our findings suggest the role of native species diversity in regulating nonnative pest invasions.}, number={15}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Guo, Qinfeng and Fei, Songlin and Potter, Kevin M. and Liebhold, Andrew M. and Wen, Jun}, year={2019}, month={Mar}, pages={7382–7386} }