小柯机器人

科学家解析犀科动物系统进化史
2019-09-12 15:59

丹麦哥本哈根大学Eske Willerslev、Jesper V. Olsen、Enrico Cappellini等研究人员,合作利用德马尼西(Dmanisi)地区更新世早期牙釉质蛋白组解决了犀科动物(Stephanorhinus)系统进化史。2019年9月11日,《自然》在线发表了这一成果。

研究人员使用来自德马尼西考古遗址的犀科动物牙齿的牙釉质蛋白质组(大约177万年前),讨论了更新世时期的欧亚犀科的系统发育关系。分子系统发育分析将这种犀科动物作为姐妹群体放置在由披毛犀(Coelodonta antiquitatis)和Stephanorhinus kirchbergensis形成的分支中。研究人员发现Coelodonta从早期的Stephanorhinus谱系进化而来,这后者属包括至少两个不同的进化系。因此,Stephanorhinus属目前属于并系类群,需要进行系统修订。研究人员证明对早更新世牙釉质的蛋白质组进行测序克服了基于古代胶原蛋白或DNA的系统发育推断的局限性。这个方法还提供了有关德马尼西其他标本的性别和分类学分配的更多信息。

这项研究结果表明,古代牙釉质(这是脊椎动物中最难的组织,并且在化石记录中非常丰富)的蛋白质组学研究可以推动分子进化的重建进一步回到更新世早期,超出了目前已知的古代DNA保存极限。

据介绍,对古代DNA进行测序能够重建物种形成、迁移和灭绝类群的混合事件。然而,到目前为止古代DNA不可逆转的死后降解限制了对不超过50万年样本的恢复(永久冻土除外)。相比之下,串联质谱法已经能够对大约150万年的I型胶原进行测序,并且表明白垩纪时期化石中存在蛋白质残留物,尽管在系统发育中的使用有限。在没有分子证据的情况下,早期和中更新世时期几种已灭绝物种的形态仍然存在争议。

附:英文原文

Title:Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny

Author:Enrico Cappellini, Frido Welker, Luca Pandolfi, Jazmín Ramos-Madrigal, Diana Samodova, Patrick L. Rüther, Anna K. Fotakis, David Lyon, J. Víctor Moreno-Mayar, Maia Bukhsianidze, Rosa Rakownikow Jersie-Christensen, Meaghan Mackie, Aurélien Ginolhac, Reid Ferring, Martha Tappen, Eleftheria Palkopoulou, Marc R. Dickinson, Thomas W. Stafford Jr, Yvonne L. Chan, Anders Götherström, Senthilvel K. S. S. Nathan, Peter D. Heintzman, Joshua D. Kapp, Irina Kirillova, Yoshan Moodley, Jordi Agusti, Ralf-Dietrich Kahlke, Gocha Kiladze, Bienvenido Martínez-Navarro, Shanlin Liu, Marcela Sandoval Velasco, Mikkel-Holger S. Sinding, Christian D. Kelstrup, Morten E. Allentoft, Ludovic Orlando, Kirsty Penkman, Beth Shapiro, Lorenzo Rook, Love Dalén, M. Thomas P. Gilbert, Jesper V. Olsen, David Lordkipanidze, Eske Willerslev

Issue&Volume: 2019-09-11

Abstract:

The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa1. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its recovery—outside permafrost areas—to specimens that are not older than approximately 0.5 million years (Myr)3. By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I4, and suggested the presence of protein residues in fossils of the Cretaceous period5—although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch7,8,9, using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)10. Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck’s rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel—which is the hardest tissue in vertebrates11, and is highly abundant in the fossil record—can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.

DOI: 10.1038/s41586-019-1555-y

Source:https://www.nature.com/articles/s41586-019-1555-y

Nature:《自然》,创刊于1869年。隶属于施普林格·自然出版集团,最新IF:43.07
官方网址:http://www.nature.com/
投稿链接:http://www.nature.com/authors/submit_manuscript.html


本期文章:《自然》:Online/在线发表

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