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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The Secondary Structure of Mammalian Mitochondrial 16S rRNA Molecules: Refinements Based on a Comparative Phylogenetic Approach
TL;DR: This work uses the criteria of potential base-pairing and positional covariance to make refinements in these models for mammalian 16S rRNA molecules, and suggests a mammalian secondary structure model with deletions as well as additions to the Gutell et al. (1993) and De Rijk (1999) models for cow.
Journal ArticleDOI
Evolution, expression and effectiveness in a cluster of novel bovine beta-defensins.
Paul Cormican,Kieran G. Meade,Sarah Cahalane,Fernando Narciandi,Aspinas Chapwanya,Andrew T. Lloyd,Cliona O'Farrelly +6 more
TL;DR: A systematic search of the sequenced bovine genome is described to characterise this extensive gene family in Bos taurus, providing an insight into the pattern of conservation of β-defensin genes between species.
Journal ArticleDOI
Phylogeny and conservation priorities of afrotherian mammals (Afrotheria, Mammalia)
TL;DR: Kuntner, M., May‐Collado, L. J. & Agnarsson, I. (2010) Phylogeny and conservation priorities of afrotherian mammals (Afrotheria, Mammalia).
Journal ArticleDOI
Architectonic Subdivisions of Neocortex in the Tree Shrew (Tupaia belangeri)
Peiyan Wong,Jon H. Kaas +1 more
TL;DR: The presence of well‐differentiated cortical areas in tree shrews indicates their usefulness in studies of cortical organization and function.
Journal ArticleDOI
Automated Removal of Noisy Data in Phylogenomic Analyses
TL;DR: An automated procedure involving the step-wise removal of the most variable positions in a given data set coupled with a stopping criterion derived from correlation analyses of pairwise ML distances calculated from the deleted and the remaining subsets of the alignment.
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.