Comparing Likelihood Ratios to Understand Genome-Wide Variation in Phylogenetic Support
Comparing Likelihood Ratios to Understand Genome-Wide Variation in Phylogenetic Support
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DOI：
10.1093/sysbio/syac014
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发表时间：
2022-03-22
影响因子：
6.5
通讯作者：
Brown, Jeremy M.
中科院分区：
文献类型：
--
作者：
Mount, Genevieve G.;Brown, Jeremy M.
基因组数据有时只能为生命树带来解答。大规模的基因组研究可能会对重要的关系得出相互矛盾的结论，相互排斥的假设得到强有力的支持。要确定这些差异，需要详细了解系统发育信号在数据集之间的变化。两个互补的策略，以更好地了解基因组冲突的支持，在一个位点的基础上，通过位点的基础上，并使用支持值，捕捉更大范围的变化，在系统发育信息，如似然比。似然比可以使用最大似然或边际似然来计算。尽管在概念上是相似的，但在如何计算和解释这些比率方面的差异尚未在基因组学中仔细研究。在这里，我们比较的行为时，最大和边际似然比评估替代决议的主要有鳞动物谱系之间的关系。我们发现，这些比率是广泛相关的基因座之间，但相关性是由极端值。因此，支持假设的基因座的比例可以根据使用哪个比率以及是否丢弃较小的值而改变。此外，最大似然比经常表现出相同的支持替代假设，使冲突解决的挑战。我们发现令人惊讶的支持蛇和鬣蜥之间的姐妹关系，在四个不同的基因组数据集与以前的实证研究。[贝叶斯因子;似然比;边际似然;最大似然;基因组学;有鳞动物。]
Genomic data have only sometimes brought resolution to the tree of life. Large phylogenomic studies can reach conflicting conclusions about important relationships, with mutually exclusive hypotheses receiving strong support. Reconciling such differences requires a detailed understanding of how phylogenetic signal varies among data sets. Two complementary strategies for better understanding phylogenomic conflicts are to examine support on a locus-by-locus basis and use support values that capture a larger range of variation in phylogenetic information, such as likelihood ratios. Likelihood ratios can be calculated using either maximum or marginal likelihoods. Despite being conceptually similar, differences in how these ratios are calculated and interpreted have not been closely examined in phylogenomics. Here, we compare the behavior of maximum and marginal likelihood ratios when evaluating alternate resolutions of recalcitrant relationships among major squamate lineages. We find that these ratios are broadly correlated between loci, but the correlation is driven by extreme values. As a consequence, the proportion of loci that support a hypothesis can change depending on which ratio is used and whether smaller values are discarded. In addition, maximum likelihood ratios frequently exhibit identical support for alternate hypotheses, making conflict resolution a challenge. We find surprising support for a sister relationship between snakes and iguanians across four different phylogenomic data sets in contrast to previous empirical studies. [Bayes factors; likelihood ratios; marginal likelihood; maximum likelihood; phylogenomics; squamates.]