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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Journal ArticleDOI
New Genes Originated via Multiple Recombinational Pathways in the β-Globin Gene Family of Rodents
TL;DR: Results of the comparative genomic analyses revealed that variation in gene family size among rodent species is mainly attributable to the differential gain and loss of later expressed beta-globin genes via unequal crossing-over, however, two distinct recombinational mechanisms were implicated in the creation of chimeric fusion genes.
Journal ArticleDOI
Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree.
Wilfried W. de Jong,Wilfried W. de Jong,Marjon A.M. van Dijk,Céline Poux,Guido Kappé,Teun van Rheede,Ole Madsen +6 more
TL;DR: The phylogenetic potential of indels in four nuclear protein-coding genes with regard to a possible rooting at the murid branch is explored, illustrating that indels can be convincing sources of independent molecular evidence to distinguish between alternative phylogenetic hypotheses.
Journal ArticleDOI
Rapid recovery from the effects of early monocular deprivation is enabled by temporary inactivation of the retinas
TL;DR: It is shown in two evolutionarily divergent species that experimental amblyopia can be rapidly corrected if binocular visual experience is restored after temporarily silencing the retinas with a local anesthetic, and that temporary retinal inactivation represents a highly efficacious means to promote recovery of function.
Book ChapterDOI
Pan-African Voyagers: The Phylogeography of Baboons
TL;DR: The authors used mitochondrial DNA (Brown region) sequence data obtained mainly from faecal samples collected across the geographical range of baboons to reconstruct their phylogenetic relationships, finding that West African olive and chacma baboons both comprise at least two deeply separated clades.
Journal ArticleDOI
A new tarkadectine primate from the Eocene of Inner Mongolia, China: phylogenetic and biogeographic implications
TL;DR: A new primate is described, Tarkops mckennai gen. et sp.
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.
Journal ArticleDOI
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.
Journal ArticleDOI
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.
Journal ArticleDOI
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.