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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Selection and the Cell Cycle: Positive Darwinian Selection in a Well-Known DNA Damage Response Pathway
TL;DR: It is shown here that modern human populations display evidence of an ongoing selective sweep in 9 of these DNA damage repair proteins, and those proteins where human and mouse have undergone lineage-specific functional shift are highlighted.
Journal ArticleDOI
Primate sociality in evolutionary context.
TL;DR: Results show sociality to be most strongly associated with large-bodied arboreal species that include a significant portion of fruit in their diet, and is likely to have played an important role in maintaining the presence of a social lifestyle throughout primate evolution.
Journal ArticleDOI
Integration of the mammalian shoulder girdle within populations and over evolutionary time.
TL;DR: It is suggested that shoulder girdle elements tended to vary and evolve independently during the origin of mammals and subsequent radiation of placentals, consistent with the elements’ distinct developmental and evolutionary origins and suggests that skeletal element correlations can be conserved over large taxonomic and temporal scales.
Journal ArticleDOI
A genomic timescale for placental mammal evolution
Nicole M. Foley,Victor C. Mason,Andrew J. Harris,Kevin R. Bredemeyer,Joana Damas,Harris A. Lewin,Eduardo Eizirik,John Gatesy,Mark S. Springer,William J. Murphy +9 more
TL;DR: A comprehensive whole genome phylogeny of extant placental mammals reveals timing and patterns of ordinal diversification and compares neutral genome-wide phylogenomic signal using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes and analyzed extensive catalogs of structural variants.
Posted Content
Measuring Fit of Sequence Data to Phylogenetic Model: Gain of Power using Marginal Tests
TL;DR: In this paper, the authors compare the general log-likelihood ratio (the G or G2 statistic) statistic between the evolutionary tree model and the multinomial model with that of marginalized tests applied to an alignment (using placental mammal coding sequence data).
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.
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.