Data from: Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach

The nature and timing of evolution of niche differentiation among closely related species remains an important question in ecology and evolution. The American live oak clade, Virentes, which spans the unglaciated temperate and tropical regions of North America and Mesoamerica, provides an instructive system in which to examine speciation and niche evolution. We generated a fossil-calibrated phylogeny of Virentes using RADseq data to estimate divergence times and used nuclear microsatellites, chloroplast sequences and an intron region of nitrate reductase (NIA-i3) to examine genetic diversity within species, rates of gene flow among species and ancestral population size of disjunct sister species. Transitions in functional and morphological traits associated with ecological and climatic niche axes were examined across the phylogeny. We found the Virentes to be monophyletic with three subclades, including a southwest clade, a southeastern US clade and a Central American/Cuban clade. Despite high leaf morphological variation within species and transpecific chloroplast haplotypes, RADseq and nuclear SSR data showed genetic coherence of species. We estimated a crown date for Virentes of 11 Ma and implicated the formation of the Sea of Cortés in a speciation event ~5 Ma. Tree height at maturity, associated with fire tolerance, differs among the sympatric species, while freezing tolerance appears to have diverged repeatedly across the tropical–temperate divide. Sympatric species thus show evidence of ecological niche differentiation but share climatic niches, while allopatric and parapatric species conserve ecological niches, but diverge in climatic niches. The mode of speciation and/or degree of co-occurrence may thus influence which niche axis plants diverge along.

近缘物种间生态位分化的演化本质与时间节点，始终是生态学与进化生物学领域的核心研究课题。分布于北美及中美洲未受冰川覆盖的温带与热带区域的美洲活栎支系（Virentes），为物种形成与生态位演化研究提供了极具指导意义的实验体系。本研究利用限制性位点关联DNA测序（RADseq）数据构建了美洲活栎支系的化石校准系统发育树以估算分化时间，并借助核微卫星、叶绿体序列以及硝酸还原酶内含子区域（NIA-i3），分析了物种内遗传多样性、物种间基因流速率以及间断分布姊妹物种的祖先种群规模。研究团队针对系统发育树各分支，解析了与生态位及气候生态位轴相关的功能性状与形态性状的演化转变。本研究发现美洲活栎支系（Virentes）为单系群，包含三个亚支系：西南亚支、美国东南部亚支以及中美洲/古巴亚支。尽管物种内叶片形态变异较大且存在跨物种叶绿体单倍型，但RADseq数据与核SSR数据均显示各物种具有遗传一致性。本研究估算得到美洲活栎支系的冠群分化时间为1100万年前（11 Ma），并指出科尔特斯海的形成与约500万年前（~5 Ma）的一次物种形成事件相关。同域分布物种间与耐火性相关的成熟树高存在显著差异，而耐寒性则在热带-温带分界处多次发生演化分化。由此可见，同域分布物种表现出生态位分化特征，但共享气候生态位；而异域及邻域分布物种则保留了相似的生态位，却在气候生态位上发生了分化。因此，物种形成模式以及（或）物种共现程度，可能会决定植物沿何种生态位轴发生演化分化。