A Phylogenomic Supertree of Birds
A Phylogenomic Supertree of Birds
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DOI：
10.3390/d11070109
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发表时间：
2019-07-01
期刊：
影响因子：
2.4
通讯作者：
Braun, Edward L.
中科院分区：
文献类型：
--
作者：
Kimball, Rebecca T.;Oliveros, Carl H.;Braun, Edward L.
长期以来人们已经认识到，基因组数据的分析（例如，全基因组测序或序列捕获）具有揭示生命树的潜力，但从序列数据转向对进化历史的清晰理解仍然具有挑战性，部分原因是使用基因组规模数据进行系统发育估计的计算挑战。超树方法解决了这一挑战，因为它们通过以计算高效的方式集成较小的子树，促进了大规模同源推理的分治方法。在这里，我们使用超树方法将序列捕获和全基因组同源性分析的信息结合起来。然而，可用的多基因组树具有有限的重叠，因此我们使用分类丰富的（但不是多基因组的）巨葡萄球菌将它们编织在一起。这使我们能够构建一个包含707种鸟类（类似于鸟类物种多样性的7%）的基因组超树。我们使用线粒体序列数据估计了分支长度，并使用这些分支长度来估计分歧时间。我们的时间校准的超级树支持辐射的所有三个主要的鸟类分支（Palaeognathae，Galloanseres和Neoaves）附近的古近纪（K-PG）边界。我们所使用的方法将允许继续增加分类群，这个超级树作为新的基因组数据发表，它也可以适用于其他分类群。
It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (similar to 7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.