A species-level timeline of mammal evolution integrating phylogenomic data
A species-level timeline of mammal evolution integrating phylogenomic data
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DOI：
10.1038/s41586-021-04341-1
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发表时间：
2021-12-22
期刊：
影响因子：
64.8
通讯作者：
dos Reis, Mario
中科院分区：
文献类型：
--
作者：
Alvarez-Carretero, Sandra;Tamuri, Asif U.;dos Reis, Mario
高通量测序项目为物种水平的系统发育生成基因组规模的序列数据(1-3)。然而，用于推断时间表的最先进的贝叶斯方法在计算上仅限于较小的数据集，不能利用不断增加的可用基因组(4)。就哺乳动物而言，对有限数据集的分子时钟分析产生了具有很大不确定性的支系年龄的相互矛盾的估计(5，6)，因此胎盘哺乳动物进化的时间尺度仍然存在争议(7-10)。在这里，我们开发了一种贝叶斯分子时钟测年方法来估计来自72个哺乳动物基因组的信息，以估计4705个哺乳动物物种的时间表。我们表明，越来越大的系统基因组数据集产生的多样化时间估计具有逐渐较小的不确定性，有助于对宏观进化假说的精确测试。例如，我们自信地拒绝了胎盘哺乳动物起源于古近纪的爆炸性模型(8)，并表明皇冠胎盘起源于晚白垩世，在古新世/始新世具有明确的有序多样性。我们的贝叶斯方法便于在一个综合框架内分析完整的基因组和数千个物种，从而有可能解决物种多样性方面迄今难以解决的研究问题。这种方法可以用来处理其他有争议的动植物多样化案例，这些案例需要对物种水平的系统基因组数据集进行分析。
High-throughput sequencing projects generate genome-scale sequence data for species-level phylogenies(1-3). However, state-of-the-art Bayesian methods for inferring timetrees are computationally limited to small datasets and cannot exploit the growing number of available genomes(4). In the case of mammals, molecular-clock analyses of limited datasets have produced conflicting estimates of clade ages with large uncertainties(5,6), and thus the timescale of placental mammal evolution remains contentious(7-10). Here we develop a Bayesian molecular-clock dating approach to estimate a timetree of 4,705 mammal species integrating information from 72 mammal genomes. We show that increasingly larger phylogenomic datasets produce diversification time estimates with progressively smaller uncertainties, facilitating precise tests of macroevolutionary hypotheses. For example, we confidently reject an explosive model of placental mammal origination in the Palaeogene(8) and show that crown Placentalia originated in the Late Cretaceous with unambiguous ordinal diversification in the Palaeocene/Eocene. Our Bayesian methodology facilitates analysis of complete genomes and thousands of species within an integrated framework, making it possible to address hitherto intractable research questions on species diversifications. This approach can be used to address other contentious cases of animal and plant diversifications that require analysis of species-level phylogenomic datasets.