Journal ArticleDOI
Resolution of the early placental mammal radiation using Bayesian phylogenetics
William J. Murphy,Eduardo Eizirik,Eduardo Eizirik,Stephen J. O'Brien,Ole Madsen,Mark Scally,Mark Scally,Christophe J. Douady,Christophe J. Douady,Emma C. Teeling,Emma C. Teeling,Oliver A. Ryder,Michael J. Stanhope,Michael J. Stanhope,Wilfried W. de Jong,Mark S. Springer +15 more
TLDR
Crown-group Eutheria may have their most recent common ancestry in the Southern Hemisphere (Gondwana), and placental phylogeny is investigated using Bayesian and maximum-likelihood methods and a 16.4-kilobase molecular data set.Abstract:
Molecular phylogenetic studies have resolved placental mammals into four major groups, but have not established the full hierarchy of interordinal relationships, including the position of the root. The latter is critical for understanding the early biogeographic history of placentals. We investigated placental phylogeny using Bayesian and maximum-likelihood methods and a 16.4-kilobase molecular data set. Interordinal relationships are almost entirely resolved. The basal split is between Afrotheria and other placentals, at about 103 million years, and may be accounted for by the separation of South America and Africa in the Cretaceous. Crown-group Eutheria may have their most recent common ancestry in the Southern Hemisphere (Gondwana).read more
Citations
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Why are some human disease-associated mutations fixed in mice?
Li-Zhi Gao,Jianzhi Zhang +1 more
TL;DR: It is found that except for one case, the fixations of the disease-associated mutations occurred before the separation of Mus musculus and Mus spretus at least 1 million years ago and that thefixations are not attributable to a founder effect during the recent history of mouse breeding.
Journal ArticleDOI
A chromosome painting test of the basal eutherian karyotype.
TL;DR: The chromosomes of an Afrotherian species, the short-eared elephant shrew Macroscelides proboscideus, are studied with traditional banding techniques and the homology to human chromosomes are mapped by in-situ hybridization of human chromosome paints.
Journal ArticleDOI
MOLECULAR PALAEOBIOLOGY: PETERSON Et al.: MOLECULAR PALAEOBIOLOGY
Journal ArticleDOI
Sodium taurocholate cotransporting polypeptide mediates woolly monkey hepatitis B virus infection of Tupaia hepatocytes
Guocai Zhong,Huan Yan,Haiming Wang,Wenhui He,Zhiyi Jing,Yonghe Qi,Liran Fu,Zhenchao Gao,Yi Huang,Guangwei Xu,Xiaofeng Feng,Jianhua Sui,Wenhui Li +12 more
TL;DR: It is demonstrated that tsNTCP is a functional receptor for WMHBV infection of PTHs and that NTCP's orthologs likely act as a common cellular receptor for all known primate hepadnaviruses.
Journal ArticleDOI
Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression.
Dan Vanderpool,Bui Quang Minh,Robert Lanfear,Daniel S.T. Hughes,Shwetha C. Murali,R. Alan Harris,Muthuswamy Raveendran,Donna M. Muzny,Mark S. Hibbins,Robert J. Williamson,Richard A. Gibbs,Kim C. Worley,Jeffrey Rogers,Matthew W. Hahn +13 more
TL;DR: New reference genome assemblies for 3 Old World monkey species are presented and strongly asymmetric patterns of gene tree discordance around specific branches are used to identify multiple instances of introgression between ancestral primate lineages.
References
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Journal ArticleDOI
MRBAYES: Bayesian inference of phylogenetic trees
TL;DR: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo, and an executable is available at http://brahms.rochester.edu/software.html.
Journal ArticleDOI
MODELTEST: testing the model of DNA substitution.
David Posada,Keith A. Crandall +1 more
TL;DR: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.
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An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis
David M. Hillis,James J. Bull +1 more
TL;DR: This work uses computer simulations and a laboratory-generated phylogeny to test bootstrapping results of parsimony analyses, and indicates that any given bootstrap proportion provides an unbiased but highly imprecise measure of repeatability, unless the actual probability of replicating the relevant result is nearly one.
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A molecular timescale for vertebrate evolution
Sudhir Kumar,S. Blair Hedges +1 more
TL;DR: The clock-like accumulation of sequence differences in some genes provides an alternative method by which the mean divergence time can be estimated, and the molecular times agree with most early and late fossil-based times, but indicate major gaps in the Mesozoic fossil record.
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Markov Chasin Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees
Bret Larget,DL Simon +1 more
TL;DR: The Bayesian framework for analyzing aligned nucleotide sequence data to reconstruct phylogenies, assess uncertainty in the reconstructions, and perform other statistical inferences is developed and a Markov chain Monte Carlo sampler is employed to sample trees and model parameter values from their joint posterior distribution.