The Frequency and Topology of Pseudoorthologs
The Frequency and Topology of Pseudoorthologs
复制标题
伪同系物的频率和拓扑
DOI：
10.1093/sysbio/syab097
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发表时间：
2021
影响因子：
6.5
通讯作者：
Smith, ed., Stephen
中科院分区：
文献类型：
--
作者：
Smith, Megan L.;Hahn, Matthew W.;Smith, ed., Stephen
系统发生学长期以来依赖于使用直系同源物，或通过物种形成事件相关的基因，以推断物种关系。然而，识别直系同源物很困难，因为基因复制会模糊基因之间的关系。研究人员一直特别关注伪直系同源物的潜在影响，这些复制的基因被误认为是直系同源物，因为它们在每个样本物种中都存在于一个拷贝中。由于伪直系同源物的基因树拓扑结构可能与物种树拓扑结构不同，因此它们经常被引用为遗传学中违反直觉的结果的原因。尽管这些感知的问题，没有以前的工作已经计算出的概率pseudortholog拓扑结构或已能够外切的区域参数空间中的pseudortholog是最有可能发生。在这里，我们介绍了一个模型，用于计算的概率和分支长度的直系同源物和pseudorthologs，包括一致和不一致的pseudorthologs的拓扑结构，在一个有根的三个类群的物种树。我们表明，直向同源物的概率是高的相对于合理的区域的参数空间的伪直向同源物的概率。此外，两个不一致拓扑的概率相等，并且永远不会超过一致拓扑的概率，通常要低得多。我们描述了最容易产生pseudorthologs的物种树拓扑结构，发现它们很可能会出现问题，无论pseudorthologs的存在，系统发育推断。总的来说，我们的研究结果表明，pseudorthologs是不太可能误导推断的物种关系的生物场景下考虑在这里。[死亡模型;直系同源物;旁系同源物;遗传学。]
Phylogenetics has long relied on the use of orthologs, or genes related through speciation events, to infer species relationships. However, identifying orthologs is difficult because gene duplication can obscure relationships among genes. Researchers have been particularly concerned with the insidious effects of pseudoorthologs—duplicated genes that are mistaken for orthologs because they are present in a single copy in each sampled species. Because gene tree topologies of pseudoorthologs may differ from the species tree topology, they have often been invoked as the cause of counterintuitive results in phylogenetics. Despite these perceived problems, no previous work has calculated the probabilities of pseudoortholog topologies or has been able to circumscribe the regions of parameter space in which pseudoorthologs are most likely to occur. Here, we introduce a model for calculating the probabilities and branch lengths of orthologs and pseudoorthologs, including concordant and discordant pseudoortholog topologies, on a rooted three-taxon species tree. We show that the probability of orthologs is high relative to the probability of pseudoorthologs across reasonable regions of parameter space. Furthermore, the probabilities of the two discordant topologies are equal and never exceed that of the concordant topology, generally being much lower. We describe the species tree topologies most prone to generating pseudoorthologs, finding that they are likely to present problems to phylogenetic inference irrespective of the presence of pseudoorthologs. Overall, our results suggest that pseudoorthologs are unlikely to mislead inferences of species relationships under the biological scenarios considered here.[Birth–death model; orthologs; paralogs; phylogenetics.]