Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States of America.
PLoS One. 2021 Sep 17;16(9):e0257338. doi: 10.1371/journal.pone.0257338. eCollection 2021.
Pseudoextinction analyses, which simulate extinction in extant taxa, use molecular phylogenetics to assess the accuracy of morphological phylogenetics. Previous pseudoextinction analyses have shown a failure of morphological phylogenetics to place some individual placental orders in the correct superordinal clade. Recent work suggests that the inclusion of hypothetical ancestors of extant placental clades, estimated by ancestral state reconstructions of morphological characters, may increase the accuracy of morphological phylogenetic analyses. However, these studies reconstructed direct hypothetical ancestors for each extant taxon based on a well-corroborated molecular phylogeny, which is not possible for extinct taxa that lack molecular data. It remains to be determined if pseudoextinct taxa, and by proxy extinct taxa, can be accurately placed when their immediate hypothetical ancestors are unknown. To investigate this, we employed molecular scaffolds with the largest available morphological data set for placental mammals. Each placental order was sequentially treated as pseudoextinct by exempting it from the molecular scaffold and recoding soft morphological characters as missing for all its constituent species. For each pseudoextinct data set, we omitted the pseudoextinct taxon and performed a parsimony ancestral state reconstruction to obtain hypothetical predicted ancestors. Each pseudoextinct order was then evaluated in seven parsimony analyses that employed combinations of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold. In treatments that included fossils, hypothetical predicted ancestors, and a molecular scaffold, only 8 of 19 pseudoextinct placental orders (42%) retained the same interordinal placement as on the molecular scaffold. In treatments that included hypothetical predicted ancestors but not fossils or a scaffold, only four placental orders (21%) were recovered in positions that are congruent with the scaffold. These results indicate that hypothetical predicted ancestors do not increase the accuracy of pseudoextinct taxon placement when the immediate hypothetical ancestor of the taxon is unknown. Hypothetical predicted ancestors are not a panacea for morphological phylogenetics.
拟灭绝分析模拟现存分类单元的灭绝，使用分子系统发生学来评估形态系统发生学的准确性。以前的拟灭绝分析表明，形态系统发生学未能将一些个别胎盘类群置于正确的超类群分支中。最近的研究表明，通过对形态特征的祖先状态重建来包含现存胎盘类群的假设祖先，可能会提高形态系统发生分析的准确性。然而，这些研究是根据经过充分证实的分子系统发生重建了每个现存分类单元的直接假设祖先，对于缺乏分子数据的灭绝类群来说，这是不可能的。仍然需要确定当未知灭绝类群的直接假设祖先时，是否可以准确地对拟灭绝类群和间接灭绝类群进行分类。为了研究这个问题，我们使用了胎盘哺乳动物最大的形态数据集的分子支架。每个胎盘类群依次被视为拟灭绝，从分子支架中排除，并对其所有组成物种的软形态特征进行重新编码为缺失。对于每个拟灭绝数据集，我们忽略了拟灭绝的分类单元，并进行了简约祖先状态重建以获得假设的预测祖先。然后，在七个简约分析中评估每个拟灭绝的胎盘类群，这些分析采用了化石类群、假设的预测祖先和分子支架的组合。在包含化石、假设的预测祖先和分子支架的处理中，只有 19 个拟灭绝的胎盘类群中的 8 个（42%）保留了与分子支架相同的类间位置。在包含假设的预测祖先但不包含化石或支架的处理中，只有四个胎盘类群（21%）恢复到与支架一致的位置。这些结果表明，当未知分类单元的直接假设祖先时，假设的预测祖先并不能提高拟灭绝分类单元的分类准确性。假设的预测祖先并不是形态系统发生学的万能药。
