New Approaches for Inferring Phylogenies in the Presence of Paralogs
New Approaches for Inferring Phylogenies in the Presence of Paralogs
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存在旁系同源物时推断系统发育的新方法
DOI：
10.1016/j.tig.2020.08.012
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发表时间：
2021
影响因子：
11.4
通讯作者：
Hahn, Matthew W.
中科院分区：
文献类型：
--
作者：
Smith, Megan L.;Hahn, Matthew W.
全基因组序列的可用性预计将为遗传学提供基本上无限的数据。然而，严格依赖单拷贝基因用于此目的极大地限制了可以使用的数据量。在这里，我们回顾了几种方法，增加用于系统发育推断的数据量，重点是方法，允许包括重复的基因（旁系同源）。最近开发的方法，是强大的高水平的不完整的谱系排序也似乎是强大的包括旁系同源，这表明一个有前途的方式，充分利用基因组数据。我们讨论这些方法的陷阱，以及进一步的研究途径。
The availability of whole genome sequences was expected to supply essentially unlimited data for phylogenetics. However, strict reliance on single-copy genes for this purpose has drastically limited the amount of data that can be used. Here, we review several approaches for increasing the amount of data used for phylogenetic inference, focusing on methods that allow for the inclusion of duplicated genes (paralogs). Recently developed methods that are robust to high levels of incomplete lineage sorting also appear to be robust to the inclusion of paralogs, suggesting a promising way to take full advantage of genomic data. We discuss the pitfalls of these approaches, as well as further avenues for research.