Evolutionary Adaptive Genomics, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany.
Evolutionary Adaptive Genomics, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany.
Mol Phylogenet Evol. 2023 Jun;183:107756. doi: 10.1016/j.ympev.2023.107756. Epub 2023 Mar 9.
Sengis (order Macroscelidea) are small mammals endemic to Africa. The taxonomy and phylogeny of sengis has been difficult to resolve due to a lack of clear morphological apomorphies. Molecular phylogenies have already significantly revised sengi systematics, but until now no molecular phylogeny has included all 20 extant species. In addition, the age of origin of the sengi crown clade and the divergence age of its two extant families remain unclear. Two recently published studies based on different datasets and age-calibration parameters (DNA type, outgroup selection, fossil calibration points) proposed highly different divergent age estimates and evolutionary scenarios. We obtained nuclear and mitochondrial DNA from mainly museum specimens using target enrichment of single-stranded DNA libraries to generate the first phylogeny of all extant macroscelidean species. We then explored the effects of different parameters (type of DNA, ratio of ingroup to outgroup sampling, number and type of fossil calibration points) and their resulting impacts on age estimates for the origin and initial diversification of Macroscelidea. We show that, even after correcting for substitution saturation, both using mitochondrial DNA in conjunction with nuclear DNA or alone results in much older ages and different branch lengths than when using nuclear DNA alone. We further show that the former effect can be attributed to insufficient amounts of nuclear data. If multiple calibration points are included, the age of the sengi crown group fossil prior has minimal impact on the estimated time frame of sengi evolution. In contrast, the inclusion or exclusion of outgroup fossil priors has a major effect on the resulting node ages. We also find that a reduced sampling of ingroup species does not significantly affect overall age estimates and that terminal specific substitution rates can serve as a means to evaluate the biological likeliness of the produced temporal estimates. Our study demonstrates how commonly varied parameters in temporal calibration of phylogenies affect age estimates. Dated phylogenies should therefore always be seen in the context of the dataset which was used to produce them.
穿山甲（鳞甲目）是非洲特有的小型哺乳动物。由于缺乏明显的形态特征，穿山甲的分类和系统发育一直难以解决。分子系统发育已经极大地修正了穿山甲的系统发育，但到目前为止，还没有分子系统发育包括所有 20 种现存的物种。此外，穿山甲冠群的起源年龄和其两个现存科的分化年龄仍然不清楚。最近发表的两项研究基于不同的数据集和年龄校准参数（DNA 类型、外群选择、化石校准点），提出了高度不同的分歧年龄估计和进化情景。我们使用单链 DNA 文库的靶向富集从主要的博物馆标本中获得了核和线粒体 DNA，以生成所有现存鳞甲目物种的第一个系统发育。然后，我们探索了不同参数（DNA 类型、内群与外群采样比例、化石校准点的数量和类型）的影响及其对鳞甲目起源和初始多样化的年龄估计的影响。我们表明，即使在纠正替代饱和后，与单独使用核 DNA 相比，同时使用线粒体 DNA 与核 DNA 或单独使用核 DNA 会导致更老的年龄和不同的分支长度。我们进一步表明，前一种效应可归因于核数据量不足。如果包括多个校准点，那么穿山甲冠群化石的年龄对估计的穿山甲进化时间框架的影响最小。相比之下，外群化石先验的包含或排除对产生的节点年龄有重大影响。我们还发现，内群物种采样的减少不会显著影响总体年龄估计，并且末端特定的替代率可以作为评估所产生时间估计的生物学可能性的手段。我们的研究表明，系统发育学中时间校准中常见的变化参数如何影响年龄估计。因此，应始终根据产生它们的数据集来看待有时间校准的系统发育树。
