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.].

中文翻译：

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比较似然比以了解系统发育支持的全基因组变异。

基因组数据有时只会为生命之树带来解决方案。大型系统基因组学研究可能会就重要关系得出相互矛盾的结论，而相互排斥的假设得到了强有力的支持。调和这些差异需要详细了解系统发育信号在数据集之间是如何变化的。为了更好地理解系统发育冲突，两个互补的策略是逐个位点检查支持，并使用支持值来捕获系统发育信息中更大范围的变化，例如似然比。似然比可以使用最大似然或边际似然来计算。尽管在概念上相似，但在系统基因组学中尚未仔细检查这些比率的计算和解释方式的差异。这里，在评估主要鳞状动物谱系之间顽固关系的替代解决方案时，我们比较了最大似然比和边际似然比的行为。我们发现这些比率在基因座之间具有广泛的相关性，但相关性是由极值驱动的。因此，支持假设的基因座比例可能会根据使用的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对替代假设的相同支持，使解决冲突成为一项挑战。与之前的实证研究相比，我们发现在四个不同的系统基因组数据集中对蛇和鬣蜥之间的姐妹关系提供了令人惊讶的支持。[贝叶斯因子；似然比；边际可能性；最大似然; 系统基因组学；鳞片。]。