Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes.
Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes.
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DOI：
10.1093/molbev/msaa288
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发表时间：
2021-04-13
影响因子：
10.7
通讯作者：
Robinson-Rechavi M
中科院分区：
文献类型：
--
作者：
Begum T;Robinson-Rechavi M
基因功能如何进化是进化生物学的核心问题。它可以通过比较物种之间和基因之间的功能基因组学结果来研究。大多数功能基因组学的比较研究使用成对比较。然而，已经表明，这可能会提供有偏见的结果，因为基因，像物种一样，是遗传相关的。系统发育比较方法应该用来纠正这一点，但它们依赖于强有力的假设，包括相对于被检验的假设的无偏树估计。这种方法最近被用来测试“直系同源猜想”，即旁系同源物的功能进化比直系同源物快的假设。虽然组织特异性的成对比较（）为直系同源推测提供了支持，但系统发育独立的对比没有。我们对相同基因树的重新分析发现了重复节点时间校准的问题。我们发现，所使用的基因树遭受重要的偏见，由于包括树没有重复节点，相对年龄的物种和重复，系统的差异分支长度，和非布朗运动的组织特异性在许多树木。我们发现，不正确的实施系统发育方法的经验基因树与重复的问题。控制偏差允许成功地使用系统发育方法来研究基因功能的进化，并提供了一些支持直系同源猜想使用三种不同的系统发育方法。
How gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise comparisons. Yet it has been shown that this can provide biased results, as genes, like species, are phylogenetically related. Phylogenetic comparative methods should be used to correct for this, but they depend on strong assumptions, including unbiased tree estimates relative to the hypothesis being tested. Such methods have recently been used to test the “ortholog conjecture,” the hypothesis that functional evolution is faster in paralogs than in orthologs. Although pairwise comparisons of tissue specificity () provided support for the ortholog conjecture, phylogenetic independent contrasts did not. Our reanalysis on the same gene trees identified problems with the time calibration of duplication nodes. We find that the gene trees used suffer from important biases, due to the inclusion of trees with no duplication nodes, to the relative age of speciations and duplications, to systematic differences in branch lengths, and to non-Brownian motion of tissue specificity on many trees. We find that incorrect implementation of phylogenetic method in empirical gene trees with duplications can be problematic. Controlling for biases allows successful use of phylogenetic methods to study the evolution of gene function and provides some support for the ortholog conjecture using three different phylogenetic approaches.
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