Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach

Understanding the factors promoting species formation is a major task in evolutionary research. Here, we employ an integrative approach to study the evolutionary history of the Californian scrub white oak species complex (genus Quercus). To infer the relative importance of geographical isolation and ecological divergence in driving the speciation process, we (i) analyzed inter- and intra-specific patterns of genetic differentiation and employed an approximate Bayesian computation (ABC) framework to evaluate different plausible scenarios of species divergence. In a second step, we (ii) linked the inferred divergence pathways with current and past species distribution models, and (iii) tested for niche differentiation and phylogenetic niche conservatism across taxa. ABC analyses showed that the most plausible scenario is the one considering the divergence of two main lineages followed by a more recent pulse of speciation. Genotypic data in conjunction with species distribution models and ...,
Simple Sequence Repeat Data
This file contains the genotypes for 16 nuclear (nuSSR) and 5 chloroplast (cpSSR) simple sequence repeat loci and 812 individuals from six Californian scrub oak species (Quercus berberidifolia, Quercus durata, Quercus cornelius-mulleri, Quercus john-tuckeri, Quercus dumosa and Quercus pacifica) collected in 87 localities.
GenotypicData.xlsx

Neighbor-joining phylogenetic trees
Neighbor-joining phylogenetic trees based on 16 nuclear (nuSSR) and 5 chloroplast (cpSSR) simple sequence repeat loci
PhylogeneticTrees.zip

Input files used for phylogenetic analyses in POPULATIONS
Input files used for neighbor-joining phylogenetic analyses implemented in the program POPULATIONS based on 16 nuclear (nuSSR) and 5 chloroplast (cpSSR) simple sequence repeat loci
PopulationsInputFiles.zip

Input files used for PCAs on genetic and environmental data
Input files for PCA analyses based on genetic (16 nuclear simple sequence repeat loci) and climatic data (Bio2, Bio3, Bio8...,

解析物种形成的促进因子是进化生物学研究的核心任务之一。
本研究采用整合分析方法，对加州灌丛白栎复合群（栎属*Quercus*）的进化历史展开研究。为解析地理隔离与生态分化在物种形成过程中的相对作用，我们：(1) 分析了种间与种内的遗传分化模式，并采用近似贝叶斯计算（approximate Bayesian computation, ABC）框架评估多种合理的物种分化情景；其次，(2) 将推断得到的分化路径与当前及历史物种分布模型进行关联；(3) 对不同类群开展生态位分化与系统发育生态位保守性检验。
近似贝叶斯计算分析结果显示，最符合数据的情景为：先分化出两个主要支系，随后在更近的时期发生一次物种形成脉冲事件。本研究结合基因型数据、物种分布模型及……

简单序列重复（Simple Sequence Repeat, SSR）数据集
本文件包含来自6种加州灌丛栎（*Quercus berberidifolia*、*Quercus durata*、*Quercus cornelius-mulleri*、*Quercus john-tuckeri*、*Quercus dumosa*及*Quercus pacifica*）的812个个体的基因型数据，涉及16个核基因组简单序列重复（nuSSR）位点与5个叶绿体基因组简单序列重复（cpSSR）位点，所有样本采自87个采样点。
GenotypicData.xlsx

邻接（Neighbor-joining, NJ）系统发育树
基于16个核基因组简单序列重复位点与5个叶绿体基因组简单序列重复位点构建的邻接系统发育树
PhylogeneticTrees.zip

POPULATIONS软件系统发育分析输入文件
基于16个核基因组简单序列重复位点与5个叶绿体基因组简单序列重复位点，采用POPULATIONS软件实现的邻接系统发育分析所用的输入文件
PopulationsInputFiles.zip

遗传与环境数据主成分分析（PCA）输入文件
基于遗传数据（16个核基因组简单序列重复位点）与气候数据（Bio2、Bio3、Bio8……）的主成分分析输入文件