Data from: 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 partitioned analyses, however, supports a more recent divergence of the Eurasian white oaks from within the American white oaks and suggests that historic introgression between the Eurasian white oaks and a now-relictual lineage biases concatenated phylogenetic estimates. We demonstrate how divergence and reticulation both influence our understanding of the timing and nature of diversification and global colonization in these ecologically and economically important taxa.

长期以来，学界一直推测栎属（Quercus L.）植物在自然界中存在天然杂交现象，且在包含2至6个物种的类群中，基于形态学特征界定的物种间广泛存在的遗传交换已有充分的文献记录，但栎属杂交所引发的系统发育效应，尚未在具有系统发育多样性的样本中得到证实。本研究针对一个约3000万年的演化支开展系统基因组学分析（phylogenomic analyses），结果强烈支持基于形态学特征界定的物种，并解析出白栎类的全新演化支；不过，跨演化支边界的历史杂交事件仍可被检测到，若未对这类事件进行甄别，将会掩盖系统发育树中生物地理历史的印记。基于涵盖81个物种的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，支持白栎类存在两次连续的洲际间断分布事件：一次是欧亚白栎与美洲白栎间的早期地理分替事件，另一次则是以两个孑遗物种为代表的独立辐射演化事件。然而，一系列亚采样与分区分析结果表明，欧亚白栎的分化时间晚于此前推断，其起源于美洲白栎类群内部；同时研究还揭示，欧亚白栎与现已孑遗的演化支间的历史基因渐渗，会对串联法系统发育推断产生偏倚。本研究阐明了物种分化与网状演化如何影响我们对这类兼具生态与经济重要性的类群的分化时间、多样化模式及全球定殖过程的认知。