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完成灵长类动物的分子时间树。

Completing a molecular timetree of primates.

作者信息

Craig Jack M, Hedges S Blair, Kumar Sudhir

机构信息

Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States.

Department of Biology, Temple University, Philadelphia, PA, United States.

出版信息

Front Bioinform. 2024 Dec 16;4:1495417. doi: 10.3389/fbinf.2024.1495417. eCollection 2024.

Abstract

Primates, consisting of apes, monkeys, tarsiers, and lemurs, are among the most charismatic and well-studied animals on Earth, yet there is no taxonomically complete molecular timetree for the group. Combining the latest large-scale genomic primate phylogeny of 205 recognized species with the 400-species literature consensus tree available from TimeTree.org yields a phylogeny of just 405 primates, with 50 species still missing despite having molecular sequence data in the NCBI GenBank. In this study, we assemble a timetree of 455 primates, incorporating every species for which molecular data are available. We use a synthetic approach consisting of a literature review for published timetrees, dating of untimed trees, and assembly of timetrees from novel alignments. The resulting near-complete molecular timetree of primates allows testing of two long-standing alternate hypotheses for the origins of primate biodiversity: whether species richness arises at a constant rate, in which case older clades have more species, or whether some clades exhibit faster rates of speciation than others, in which case, these fast clades would be more species-rich. Consistent with other large-scale macroevolutionary analyses, we found that the speciation rate is similar across the primate tree of life, albeit with some variation in smaller clades.

摘要

灵长类动物包括猿、猴、跗猴和狐猴,是地球上最具魅力且研究充分的动物之一,但目前该类群尚无分类学上完整的分子时间树。将最新的包含205个已确认物种的大规模基因组灵长类系统发育树与可从TimeTree.org获取的400个物种的文献共识树相结合,得到的灵长类系统发育树仅包含405个物种,尽管NCBI基因库中有50个物种的分子序列数据,但仍缺失这50个物种。在本研究中,我们构建了一个包含455个灵长类物种的时间树,纳入了所有有分子数据的物种。我们采用了一种综合方法,包括对已发表的时间树进行文献综述、对未定时的树进行年代测定以及从新的序列比对中构建时间树。由此产生的近乎完整的灵长类分子时间树,使得我们能够检验关于灵长类生物多样性起源的两个长期存在的替代假说:物种丰富度是否以恒定速率增加,若是如此,较古老的分支物种更多;或者某些分支的物种形成速率是否比其他分支更快,若是这样,这些快速分支的物种会更丰富。与其他大规模宏观进化分析一致,我们发现整个灵长类生命树的物种形成速率相似,尽管在较小的分支中存在一些差异。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/afd5/11683086/1b3c0c31ca2a/fbinf-04-1495417-g001.jpg

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