Literature DB >> 22628470

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

Mario dos Reis1, Jun Inoue, Masami Hasegawa, Robert J Asher, Philip C J Donoghue, Ziheng Yang.   

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.

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Mesh:

Year:  2012        PMID: 22628470      PMCID: PMC3396900          DOI: 10.1098/rspb.2012.0683

Source DB:  PubMed          Journal:  Proc Biol Sci        ISSN: 0962-8452            Impact factor:   5.349


  43 in total

1.  A radiation of arboreal basal eutherian mammals beginning in the Late Cretaceous of India.

Authors:  Anjali Goswami; Guntupalli V R Prasad; Paul Upchurch; Doug M Boyer; Erik R Seiffert; Omkar Verma; Emmanuel Gheerbrant; John J Flynn
Journal:  Proc Natl Acad Sci U S A       Date:  2011-09-19       Impact factor: 11.205

2.  Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals.

Authors:  M Foote; J P Hunter; C M Janis; J J Sepkoski
Journal:  Science       Date:  1999-02-26       Impact factor: 47.728

3.  PAML 4: phylogenetic analysis by maximum likelihood.

Authors:  Ziheng Yang
Journal:  Mol Biol Evol       Date:  2007-05-04       Impact factor: 16.240

4.  Models of amino acid substitution and applications to mitochondrial protein evolution.

Authors:  Z Yang; R Nielsen; M Hasegawa
Journal:  Mol Biol Evol       Date:  1998-12       Impact factor: 16.240

5.  Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times.

Authors:  Mario dos Reis; Ziheng Yang
Journal:  Mol Biol Evol       Date:  2011-02-10       Impact factor: 16.240

6.  Bayesian estimation of divergence times from large sequence alignments.

Authors:  Stéphane Guindon
Journal:  Mol Biol Evol       Date:  2010-03-01       Impact factor: 16.240

7.  Evolutionary explosions and the phylogenetic fuse.

Authors:  A Cooper; R Fortey
Journal:  Trends Ecol Evol       Date:  1998-04-01       Impact factor: 17.712

8.  A Jurassic eutherian mammal and divergence of marsupials and placentals.

Authors:  Zhe-Xi Luo; Chong-Xi Yuan; Qing-Jin Meng; Qiang Ji
Journal:  Nature       Date:  2011-08-24       Impact factor: 49.962

9.  Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods.

Authors:  Z Yang
Journal:  J Mol Evol       Date:  1994-09       Impact factor: 2.395

10.  Tracking marsupial evolution using archaic genomic retroposon insertions.

Authors:  Maria A Nilsson; Gennady Churakov; Mirjam Sommer; Ngoc Van Tran; Anja Zemann; Jürgen Brosius; Jürgen Schmitz
Journal:  PLoS Biol       Date:  2010-07-27       Impact factor: 8.029

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  165 in total

1.  Phylogeny: Rewriting evolution.

Authors:  Elie Dolgin
Journal:  Nature       Date:  2012-06-27       Impact factor: 49.962

Review 2.  A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome.

Authors:  Bastian Fromm; Tyler Billipp; Liam E Peck; Morten Johansen; James E Tarver; Benjamin L King; James M Newcomb; Lorenzo F Sempere; Kjersti Flatmark; Eivind Hovig; Kevin J Peterson
Journal:  Annu Rev Genet       Date:  2015-10-14       Impact factor: 16.830

Review 3.  Contextualising primate origins--an ecomorphological framework.

Authors:  Christophe Soligo; Jeroen B Smaers
Journal:  J Anat       Date:  2016-02-02       Impact factor: 2.610

4.  Genomic analysis of snub-nosed monkeys (Rhinopithecus) identifies genes and processes related to high-altitude adaptation.

Authors:  Li Yu; Guo-Dong Wang; Jue Ruan; Yong-Bin Chen; Cui-Ping Yang; Xue Cao; Hong Wu; Yan-Hu Liu; Zheng-Lin Du; Xiao-Ping Wang; Jing Yang; Shao-Chen Cheng; Li Zhong; Lu Wang; Xuan Wang; Jing-Yang Hu; Lu Fang; Bing Bai; Kai-Le Wang; Na Yuan; Shi-Fang Wu; Bao-Guo Li; Jin-Guo Zhang; Ye-Qin Yang; Cheng-Lin Zhang; Yong-Cheng Long; Hai-Shu Li; Jing-Yuan Yang; David M Irwin; Oliver A Ryder; Ying Li; Chung-I Wu; Ya-Ping Zhang
Journal:  Nat Genet       Date:  2016-07-11       Impact factor: 38.330

5.  Searching for efficient Markov chain Monte Carlo proposal kernels.

Authors:  Ziheng Yang; Carlos E Rodríguez
Journal:  Proc Natl Acad Sci U S A       Date:  2013-11-11       Impact factor: 11.205

6.  Bamboo Specialists from Two Mammalian Orders (Primates, Carnivora) Share a High Number of Low-Abundance Gut Microbes.

Authors:  Erin A McKenney; Michael Maslanka; Allen Rodrigo; Anne D Yoder
Journal:  Microb Ecol       Date:  2017-11-29       Impact factor: 4.552

Review 7.  Exploring macroevolution using modern and fossil data.

Authors:  Michael J Benton
Journal:  Proc Biol Sci       Date:  2015-07-07       Impact factor: 5.349

8.  Biogeography of worm lizards (Amphisbaenia) driven by end-Cretaceous mass extinction.

Authors:  Nicholas R Longrich; Jakob Vinther; R Alexander Pyron; Davide Pisani; Jacques A Gauthier
Journal:  Proc Biol Sci       Date:  2015-05-07       Impact factor: 5.349

9.  Evolutionary conservation and modulation of a juvenile growth-regulating genetic program.

Authors:  Angela Delaney; Vasantha Padmanabhan; Geoffrey Rezvani; Weiping Chen; Patricia Forcinito; Crystal S F Cheung; Jeffrey Baron; Julian C K Lui
Journal:  J Mol Endocrinol       Date:  2014-04-28       Impact factor: 5.098

10.  PhyloCore: A phylogenetic approach to identifying core taxa in microbial communities.

Authors:  Tiantian Ren; Martin Wu
Journal:  Gene       Date:  2016-08-24       Impact factor: 3.688

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