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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A molecular phylogeny of fleas (Insecta: Siphonaptera): origins and host associations
Michael F. Whiting,Alison S. Whiting,Michael W. Hastriter,Katharina Dittmar,Katharina Dittmar +4 more
TL;DR: This analysis supports Tungidae as the most basal flea lineage, sister group to the remainder of the extant fleas, and the first formal analysis of flea relationships based on a molecular matrix of four loci for 128 flea taxa from around the world.
Journal ArticleDOI
Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs)
Emmanouil T. Dermitzakis,Alexandre Reymond,Nathalie Scamuffa,Catherine Ucla,Ewen F. Kirkness,Colette Rossier,Stylianos E. Antonarakis +6 more
TL;DR: It is found that CNGs are significantly more conserved than protein-coding genes and noncoding RNAS (ncRNAs) within the mammalian class from primates to monotremes to marsupials.
Journal ArticleDOI
Arrival and diversification of caviomorph rodents and platyrrhine primates in South America.
TL;DR: Considering both the fossil record and these molecular datings, the favored scenarios are a trans-Atlantic migration of primates from Africa at the end of the Eocene or beginning of the Oligocene, and a colonization of South America by rodents during the Middle or Late Eocene.
Journal ArticleDOI
Comparative aspects of trophoblast development and placentation.
TL;DR: It is argued that a definitive epitheliochorial placenta is a secondary specialization and that it evolved twice,once in the Laurasiatheria and once in the lemurs and lorises.
Journal ArticleDOI
Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences.
Eduardo Eizirik,William J. Murphy,Klaus-Peter Koepfli,Warren E. Johnson,Jerry W. Dragoo,Robert K. Wayne,Stephen J. O'Brien +6 more
TL;DR: This study investigated the phylogenetic relationships among carnivoran families, and performed molecular dating analyses of the inferred nodes, leading to consistent and robust resolution of all supra-familial nodes in the carnivoran tree.
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.
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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.