A genetic legacy of introgression confounds phylogeny and biogeography in oaks

Oaks (Quercus L.) have long been suspected to hybridize in nature, and widespread genetic exchange between morphologically defined species is well documented in two- to six-species systems, but the phylogenetic consequences of hybridization in oaks have never been demonstrated in a phylogenetically diverse sample. Here, we present phylogenomic analyses of a ca 30 Myr clade that strongly support morphologically defined species and the resolution of novel clades of white oaks; however, historical hybridization across clade boundaries is detectable and, undiagnosed, would obscure the imprint of biogeographic history in the phylogeny. Phylogenetic estimation from restriction-site-associated DNA sequencing data for 156 individuals representing 81 species supports two successive intercontinental disjunctions of white oaks: an early vicariance between the Eurasian and American white oaks, and a second, independent radiation represented by two relictual species. A suite of subsampled and partit...

橡树（栎属Quercus L.）长期以来被推测可在自然环境中发生杂交，且在仅包含2至6个物种的类群中，基于形态特征界定的栎树物种间广泛存在的遗传交流已有充分的文献报道。然而，栎属植物杂交所带来的系统发育演化后果，从未在具有系统发育多样性的研究样本中得到验证。本研究对一个约30百万年（30 Myr）的演化支开展系统基因组学分析，结果强烈支持形态学界定的物种，并解析出白栎类群的全新演化支；不过，跨演化支边界的历史杂交事件仍可被检测到，若未被识别，这类杂交事件将掩盖系统发育树中生物地理历史的印记。基于对81个物种共156个个体的限制性酶切位点相关DNA测序（restriction-site-associated DNA sequencing）数据进行的系统发育推断，结果支持白栎类群存在两次连续的洲际间断分布事件：一次为欧亚白栎与美洲白栎间的早期地理隔离分化，另一次则是以两个孑遗物种为代表的独立辐射演化。一系列经子采样与分...