@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.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Pais, Andrew and Ristaino, Jean and Whetten, Ross and Xiang, Qiu-Yun}, year={2024}, month={Jan} }
 @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={Abstract}, 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{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} }
 @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={Abstract}, 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{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={Abstract}, 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{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={Abstract}, 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} }