Improving orthologous signal and model fit in datasets addressing the root of the animal phylogeny
Improving orthologous signal and model fit in datasets addressing the root of the animal phylogeny
复制标题
改善数据集中的同源信号和模型拟合，解决动物系统发育的根源
DOI：
10.1101/2022.11.21.517274
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
McCarthy C
中科院分区：
文献类型：
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作者：
McCarthy C
关于Porifera（海绵）或Ctenophora（栉水母）是否构成动物系统发育的根源，存在相互矛盾的证据。在模式选择、分类单元取样和外群选择的背景下，对porifera -姐妹树或栉水母-姐妹树的支持已经得到了广泛的研究。数据集构建的影响研究相对较少。我们使用一种旨在丰富系统基因组数据集中的同源信号的方法重新检查了五个支持根假设的动物系统发育数据集。我们发现，在动物数据集中，除了栉虫外，许多成分正类群无法恢复主要的单系谱系，无论支持的根是什么。丰富这些数据集以保留恢复≥3个主要谱系的正类群，可减少数据集大小达50%，同时保留潜在的系统发育信息和分类单元抽样。这些丰富的数据集的位点异质系统基因组分析恢复了Porifera-sister和Ctenophora-sister的位置，即使有额外的外群采样限制。先前支持Ctenophora-sister的两个数据集在富集后支持Porifera-sister。在后验预测分析下，所有丰富的数据集都显示出更好的模型适应度。虽然没有确切的动物在Porifera或Ctenophora上生根，但当数据过滤了同源信号时，我们确实看到Porifera-sister的信号增加而ctenophote -sister的信号减少。我们的研究结果表明，数据集的大小和结构以及模型拟合都会影响动物根推理。
There is conflicting evidence as to whether Porifera (sponges) or Ctenophora (comb jellies) comprise the root of the animal phylogeny. Support for either a Porifera-sister or Ctenophore-sister tree has been extensively examined in the context of model selection, taxon sampling, and outgroup selection. The influence of dataset construction is comparatively understudied. We re-examine five animal phylogeny datasets that have supported either root hypothesis using an approach designed to enrich orthologous signal in phylogenomic datasets. We find that many component orthogroups in animal datasets fail to recover major lineages as monophyletic with the exception of Ctenophora, regardless of the supported root. Enriching these datasets to retain orthogroups recovering ≥3 major lineages reduces dataset size by up to 50% while retaining underlying phylogenetic information and taxon sampling. Site-heterogeneous phylogenomic analysis of these enriched datasets recovers both Porifera-sister and Ctenophora-sister positions, even with additional constraints on outgroup sampling. Two datasets which previously supported Ctenophora-sister support Porifera-sister upon enrichment. All enriched datasets display improved model fitness under posterior predictive analysis. While not conclusively rooting animals at either Porifera or Ctenophora, we do see an increase in signal for Porifera-sister and a decrease in signal for Ctenophore-sister when data are filtered for orthologous signal. Our results indicate that dataset size and construction as well as model fit influence animal root inference.