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
DOI：
10.1093/molbev/msac276
复制
发表时间：
2023-01-04
影响因子：
10.7
通讯作者：
O'Connell, Mary J.
中科院分区：
文献类型：
--
作者：
McCarthy, Charley G. P.;Mulhair, Peter O.;Siu-Ting, Karen;Creevey, Christopher J.;O'Connell, Mary J.
关于海绵属(Porifera)和梳状水母属(Ctenophora)是否构成动物系统发育的根源，有相互矛盾的证据。在模式选择、分类单元抽样和外群选择的背景下，对Porifera姐妹树或Ctenopore姐妹树的支持已经得到了广泛的研究。而对数据集构造的影响研究相对较少。我们使用一种旨在丰富系统发育数据集中的同源信号的方法，重新检查了支持这两种假说之一的五个动物系统发育数据集。我们发现，动物数据集中的许多成分正群都无法将主要谱系恢复为单系系，但Ctenophora除外，无论支持的根是什么。丰富这些数据集以保留恢复≥3主要谱系的正群，可将数据集大小减少高达50%，同时保留潜在的系统发育信息和分类单元采样。对这些丰富的数据集的位置异质性系统基因组分析恢复了Porifera姐妹和Ctenophora姐妹的位置，即使对外群抽样有额外的限制。两个先前支持Ctenophora-SISTER的数据集在浓缩后支持Porifera-SISTER。在后验预测分析下，所有丰富的数据集都显示出改进的模型适应性。虽然在Porifera或Ctenophora没有确定动物的根，但我们确实看到Porifera-SISTER的信号增加，而当数据被过滤以获得同源信号时，Porifera-SISTER的信号减少。我们的结果表明，数据集的大小和结构以及模型的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.
登录
查看更多内容
影响因子：
9.2
作者：
Feuda, Roberto;Dohrmann, Martin;Pisani, Davide
通讯作者：
Pisani, Davide
影响因子：
16.8
作者：
Fernandez, Rosa;Gabaldon, Toni
通讯作者：
Gabaldon, Toni
影响因子：
4.4
作者：
Belahbib H;Renard E;Santini S;Jourda C;Claverie JM;Borchiellini C;Le Bivic A
通讯作者：
Le Bivic A
影响因子：
10.7
作者：
Bollback, JP
通讯作者：
Bollback, JP
影响因子：
6.5
作者：
Brown, Jeremy M.;Thomson, Robert C.
通讯作者：
Thomson, Robert C.