title: Contributions of historical and contemporary geographic and environmental factors to phylogeographic structure in a Tertiary relict species, Emmenopterys henryi (Rubiaceae).
abstract: Examining how historical and contemporary geographic and environmental factors contribute to genetic divergence at different evolutionary scales is a central yet largely unexplored question in ecology and evolution. Here, we examine this key question by investigating how environmental and geographic factors across different epochs have driven genetic divergence at deeper (phylogeographic) and shallower (landscape genetic) evolutionary scales in the Chinese Tertiary relict tree Emmenopterys henryi. We found that geography played a predominant role at all levels - phylogeographic clades are broadly geographically structured, the deepest levels of divergence are associated with major geological or pre-Quaternary climatic events, and isolation by distance (IBD) primarily explained population genetic structure. However, environmental factors are clearly also important - climatic fluctuations since the Last Interglacial (LIG) have likely contributed to phylogeographic structure, and the population genetic structure (in our AFLP dataset) was partly explained by isolation by environment (IBE), which may have resulted from natural selection in environments with divergent climates. Thus, historical and contemporary geography and historical and contemporary environments have all shaped patterns of genetic structure in E. henryi, and, in fact, changes in the landscape through time have also been critical factors.
authors.affiliation: Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
authors.forename: Yong-Hua
authors.initials: YH
authors.lastname: Zhang
authors.affiliation: Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA.
authors.forename: Ian J
authors.initials: IJ
authors.lastname: Wang
authors.affiliation: Department of Ecology &Evolution, Salzburg University, A-5020 Salzburg, Austria.
authors.forename: Hans Peter
authors.initials: HP
authors.lastname: Comes
authors.affiliation: Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204, China.
authors.forename: Hua
authors.initials: H
authors.lastname: Peng
authors.affiliation: Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
authors.forename: Ying-Xiong
authors.initials: YX
authors.lastname: Qiu
mesh_terms: D054458:Amplified Fragment Length Polymorphism Analysis; D001499:Bayes Theorem; D002681:China; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004777:Environment; D005787:Gene Frequency; D059647:Gene-Environment Interaction; D056426:Genetic Loci; D014644:Genetic Variation; D005828:Genetics, Population; D006239:Haplotypes; D010802:Phylogeny; D058974:Phylogeography; D011110:Polymorphism, Genetic; D019666:Rubiaceae / Q000145:classification* / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant