Suppr超能文献

系统基因组数据集在估计胎盘哺乳动物系统发育的时间尺度方面提供了精确性和准确性。

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny.

机构信息

Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, UK.

出版信息

Proc Biol Sci. 2012 Sep 7;279(1742):3491-500. doi: 10.1098/rspb.2012.0683. Epub 2012 May 23.

Abstract

The fossil record suggests a rapid radiation of placental mammals following the Cretaceous-Paleogene (K-Pg) mass extinction 65 million years ago (Ma); nevertheless, molecular time estimates, while highly variable, are generally much older. Early molecular studies suffer from inadequate dating methods, reliance on the molecular clock, and simplistic and over-confident interpretations of the fossil record. More recent studies have used Bayesian dating methods that circumvent those issues, but the use of limited data has led to large estimation uncertainties, precluding a decisive conclusion on the timing of mammalian diversifications. Here we use a powerful Bayesian method to analyse 36 nuclear genomes and 274 mitochondrial genomes (20.6 million base pairs), combined with robust but flexible fossil calibrations. Our posterior time estimates suggest that marsupials diverged from eutherians 168-178 Ma, and crown Marsupialia diverged 64-84 Ma. Placentalia diverged 88-90 Ma, and present-day placental orders (except Primates and Xenarthra) originated in a ∼20 Myr window (45-65 Ma) after the K-Pg extinction. Therefore we reject a pre K-Pg model of placental ordinal diversification. We suggest other infamous instances of mismatch between molecular and palaeontological divergence time estimates will be resolved with this same approach.

摘要

化石记录表明,在 6500 万年前的白垩纪-古近纪(K-Pg)大灭绝之后,胎盘哺乳动物迅速辐射;然而,分子时间估计虽然高度可变,但通常要古老得多。早期的分子研究受到不充分的年代测定方法、对分子钟的依赖以及对化石记录的简单和过于自信的解释的影响。最近的研究使用了规避这些问题的贝叶斯测年方法,但有限数据的使用导致了估计不确定性很大,无法就哺乳动物多样化的时间做出决定性结论。在这里,我们使用一种强大的贝叶斯方法来分析 36 个核基因组和 274 个线粒体基因组(2060 万碱基对),同时结合了稳健但灵活的化石校准。我们的后验时间估计表明,有袋类动物与真兽类动物在 168-178 Ma 分化,有袋目动物在 64-84 Ma 分化。胎盘动物在 88-90 Ma 分化,而现今的胎盘类(除灵长类和贫齿目)起源于 K-Pg 灭绝后约 20 Myr 的窗口(45-65 Ma)。因此,我们拒绝胎盘类阶元多样化的预 K-Pg 模型。我们建议,同样的方法将解决其他分子和古生物学分歧时间估计之间不匹配的著名实例。

相似文献

1
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny.
Proc Biol Sci. 2012 Sep 7;279(1742):3491-500. doi: 10.1098/rspb.2012.0683. Epub 2012 May 23.
2
A timescale for placental mammal diversification based on Bayesian modeling of the fossil record.
Curr Biol. 2023 Aug 7;33(15):3073-3082.e3. doi: 10.1016/j.cub.2023.06.016. Epub 2023 Jun 27.
3
A species-level timeline of mammal evolution integrating phylogenomic data.
Nature. 2022 Feb;602(7896):263-267. doi: 10.1038/s41586-021-04341-1. Epub 2021 Dec 22.
4
A dating success story: genomes and fossils converge on placental mammal origins.
Evodevo. 2012 Aug 10;3(1):18. doi: 10.1186/2041-9139-3-18.
5
The placental mammal ancestor and the post-K-Pg radiation of placentals.
Science. 2013 Feb 8;339(6120):662-7. doi: 10.1126/science.1229237.
6
The soft explosive model of placental mammal evolution.
BMC Evol Biol. 2018 Jul 3;18(1):104. doi: 10.1186/s12862-018-1218-x.
7
Chitinase genes (s) provide genomic footprints of a post-Cretaceous dietary radiation in placental mammals.
Sci Adv. 2018 May 16;4(5):eaar6478. doi: 10.1126/sciadv.aar6478. eCollection 2018 May.
9
Geomolecular Dating and the Origin of Placental Mammals.
Syst Biol. 2016 May;65(3):546-57. doi: 10.1093/sysbio/syv115. Epub 2015 Dec 10.
10
Placental mammal diversification and the Cretaceous-Tertiary boundary.
Proc Natl Acad Sci U S A. 2003 Feb 4;100(3):1056-61. doi: 10.1073/pnas.0334222100. Epub 2003 Jan 27.

引用本文的文献

1
Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES.
Proc Natl Acad Sci U S A. 2025 May 13;122(19):e2500553122. doi: 10.1073/pnas.2500553122. Epub 2025 May 2.
2
Cathelicidin antimicrobial peptides mediate immune protection in marsupial neonates.
Sci Adv. 2025 Apr 18;11(16):eads6359. doi: 10.1126/sciadv.ads6359. Epub 2025 Apr 16.
4
Fish gills and human ears share the same genetic blueprint.
Nature. 2025 Mar;639(8055):579-580. doi: 10.1038/d41586-025-00342-6.
5
A comprehensive atlas of nuclear sequences of mitochondrial origin (NUMT) inserted into the pig genome.
Genet Sel Evol. 2024 Sep 16;56(1):64. doi: 10.1186/s12711-024-00930-6.
8
Dating Ammonia-Oxidizing Bacteria with Abundant Eukaryotic Fossils.
Mol Biol Evol. 2024 May 3;41(5). doi: 10.1093/molbev/msae096.
10
The decline and fall of the mammalian stem.
PeerJ. 2024 Feb 27;12:e17004. doi: 10.7717/peerj.17004. eCollection 2024.

本文引用的文献

1
Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification.
Science. 2011 Oct 28;334(6055):521-4. doi: 10.1126/science.1211028. Epub 2011 Sep 22.
2
A radiation of arboreal basal eutherian mammals beginning in the Late Cretaceous of India.
Proc Natl Acad Sci U S A. 2011 Sep 27;108(39):16333-8. doi: 10.1073/pnas.1108723108. Epub 2011 Sep 19.
3
A Jurassic eutherian mammal and divergence of marsupials and placentals.
Nature. 2011 Aug 24;476(7361):442-5. doi: 10.1038/nature10291.
4
Exploring uncertainty in the calibration of the molecular clock.
Biol Lett. 2012 Feb 23;8(1):156-9. doi: 10.1098/rsbl.2011.0710. Epub 2011 Aug 24.
5
The historical biogeography of Mammalia.
Philos Trans R Soc Lond B Biol Sci. 2011 Sep 12;366(1577):2478-502. doi: 10.1098/rstb.2011.0023.
6
Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times.
Mol Biol Evol. 2011 Jul;28(7):2161-72. doi: 10.1093/molbev/msr045. Epub 2011 Feb 10.
7
Evolutionary explosions and the phylogenetic fuse.
Trends Ecol Evol. 1998 Apr 1;13(4):151-6. doi: 10.1016/s0169-5347(97)01277-9.
8
Tracking marsupial evolution using archaic genomic retroposon insertions.
PLoS Biol. 2010 Jul 27;8(7):e1000436. doi: 10.1371/journal.pbio.1000436.
9
Mammalian evolution may not be strictly bifurcating.
Mol Biol Evol. 2010 Dec;27(12):2804-16. doi: 10.1093/molbev/msq166. Epub 2010 Jun 29.
10
The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times.
Syst Biol. 2010 Jan;59(1):74-89. doi: 10.1093/sysbio/syp078. Epub 2009 Nov 25.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验