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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Book ChapterDOI
The Biogeographic Origins of Primates and Euprimates: East, West, North, or South of Eden?
Journal ArticleDOI
A new genus and species of late Miocene inioid (Cetacea, Odontoceti) from the Meherrin River, North Carolina, U.S.A.
TL;DR: A cladistic analysis of morphological and molecular data supports a sister-group relationship between Meherrinia and Inia; thus this new taxon is tentatively assigned to the Iniidae, the first iniid represented by diagnostic remains from marine deposits and the second from North America.
Journal ArticleDOI
Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary.
TL;DR: The strengths and weaknesses of different timetree methods that may now be applied to estimate the timing of the placental radiation are examined and the complexities of timetree estimation when the signal of speciation times is impacted by incomplete lineage sorting (ILS) and hybridization.
Journal ArticleDOI
Statistical measures of uncertainty for branches in phylogenetic trees inferred from molecular sequences by using model-based methods
TL;DR: This paper reviews 3 approaches to assign support values to branches in trees obtained in the analysis of molecular sequences: the bootstrap, the Bayesian posterior probabilities for clades, and the interior branch tests.
Book ChapterDOI
Primate Brain Evolution in Phylogenetic Context
TL;DR: The evolution of anthropoid primates was accompanied by further increases in brain size, and the appearance of new areas, especially in higher-order and limbic regions, although it is not clear that the addition of new regions accounts for the increased encephalization of anthropoids.
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
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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.
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.