Crowl Andrew A, Manos Paul S, McVay John D, Lemmon Alan R, Lemmon Emily Moriarty, Hipp Andrew L
Department of Biology, Duke University, Durham, NC, 27708, USA.
Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32317, USA.
New Phytol. 2020 May;226(4):1158-1170. doi: 10.1111/nph.15842. Epub 2019 May 9.
Botanists have long recognised interspecific gene flow as a common occurrence within white oaks (Quercus section Quercus). Historical allele exchange, however, has not been fully characterised and the complex genomic signals resulting from the combination of vertical and horizontal gene transmission may confound phylogenetic inference and obscure our ability to accurately infer the deep evolutionary history of oaks. Using anchored enrichment, we obtained a phylogenomic dataset consisting of hundreds of single-copy nuclear loci. Concatenation, species-tree and network analyses were carried out in an attempt to uncover the genomic signal of ancient introgression and infer the divergent phylogenetic topology for the white oak clade. Locus and site-level likelihood comparisons were then conducted to further explore the introgressed signal within our dataset. Historical, intersectional gene flow is suggested to have occurred between an ancestor of the Eurasian Roburoid lineage and Quercus pontica and North American Dumosae and Prinoideae lineages. Despite extensive time past, our approach proved successful in detecting the genomic signature of ancient introgression. Our results, however, highlight the importance of sampling and the use of a plurality of analytical tools and methods to sufficiently explore genomic datasets, uncover this signal, and accurately infer evolutionary history.
长期以来，植物学家一直认为种间基因流动在白栎属（栎亚属）中很常见。然而，历史上的等位基因交换尚未得到充分描述，垂直和水平基因传递相结合所产生的复杂基因组信号可能会混淆系统发育推断，并模糊我们准确推断栎树深层进化历史的能力。利用锚定富集技术，我们获得了一个由数百个单拷贝核基因座组成的系统基因组数据集。我们进行了串联分析、物种树分析和网络分析，试图揭示古代基因渗入的基因组信号，并推断白栎进化枝的不同系统发育拓扑结构。然后进行基因座和位点水平的似然性比较，以进一步探索数据集中的渗入信号。研究表明，欧亚大陆的硬叶栎谱系的一个祖先与 Pontica 栎以及北美 Dumosae 和 Prinoideae 谱系之间发生了历史上的、跨谱系的基因流动。尽管时间已经过去很久，但我们的方法在检测古代基因渗入的基因组特征方面被证明是成功的。然而，我们的结果强调了采样以及使用多种分析工具和方法的重要性，以便充分探索基因组数据集、揭示这种信号并准确推断进化历史。
