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
Extensive Gains and Losses of Olfactory Receptor Genes in Mammalian Evolution
TL;DR: It appears that the number of OR genes is determined primarily by the functional requirement for each species, but once the number reaches the required level, it fluctuates by random duplication and deletion of genes, aided by the stochastic nature of OR gene expression.
Journal ArticleDOI
Molecular and Genomic Data Identify the Closest Living Relative of Primates
Jan E. Janecka,Webb Miller,Thomas H. Pringle,Frank Wiens,Annette Zitzmann,Kristofer M. Helgen,Mark S. Springer,William J. Murphy +7 more
TL;DR: The data show that colugos are the closest living relatives of primates and indicate that their divergence occurred in the Cretaceous, and suggest that treeshrews arose approximately 63 million years ago.
Journal ArticleDOI
Evolution of the mammalian placenta revealed by phylogenetic analysis
Derek E. Wildman,Caoyi Chen,Offer Erez,Offer Erez,Lawrence I. Grossman,Morris Goodman,Roberto Romero,Roberto Romero +7 more
TL;DR: Using phylogenetic and statistical analyses of molecular and morphological data, it is demonstrated that the ancestral eutherian mammalian placenta had the distinctive features of (i) hemochorial placental interface, (ii) a discoid shape, and (iii) a labyrinthine maternofetal interdigitation.
Journal ArticleDOI
Rodent Phylogeny and a Timescale for the Evolution of Glires: Evidence from an Extensive Taxon Sampling Using Three Nuclear Genes
Dorothée Huchon,Ole Madsen,Mark J. J. B. Sibbald,Kai Ament,Michael J. Stanhope,François Catzeflis,Wilfried W. de Jong,Emmanuel J. P. Douzery +7 more
TL;DR: Rodentia is the largest order of placental mammals, with approximately 2,050 species divided into 28 families as discussed by the authors, and it is also one of the most controversial with respect to its monophyly, relationships between families, and divergence dates.
Journal ArticleDOI
Detecting and overcoming systematic errors in genome-scale phylogenies.
Naiara Rodríguez-Ezpeleta,Henner Brinkmann,Béatrice Roure,Nicolas Lartillot,B. Franz Lang,Hervé Philippe +5 more
TL;DR: The impact of systematic errors on the resolution of the eukaryotic phylogeny is explored using a data set of 143 nuclear-encoded proteins from 37 species, and removing fast-evolving positions, recoding amino acids into functional categories, and using a site-heterogeneous mixture model (CAT) are three effective means of increasing the ratio of phylogenetic to nonphylogenetic signal.
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.