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
Deciphering ancient rapid radiations
TL;DR: The underlying causes of difficulty in determining the branching patterns of diversification in ancient rapid radiations are reviewed, and novel data exploration tools are reviewed that can facilitate understanding of these radiations.
Journal ArticleDOI
Mammalian mitogenomic relationships and the root of the eutherian tree.
Ulfur Arnason,Joseph A. Adegoke,Kristina Bodin,Erik W. Born,Yuzine Esa,Anette Gullberg,Maria Nilsson,Roger V. Short,Xiufeng Xu,Axel Janke +9 more
TL;DR: A mitogenomic study based on the set of protein-coding genes from complete mt genomes of 60 mammalian species finds that the previously unrepresented order Dermoptera (flying lemurs) fell within Primates as the sister group of Anthropoidea, making Primates paraphyletic.
Journal ArticleDOI
Genome-wide patterns and properties of de novo mutations in humans
Laurent C. Francioli,Paz Polak,Amnon Koren,Androniki Menelaou,Sung Chun,Ivo Renkens,Cornelia M. van Duijn,Morris A. Swertz,Cisca Wijmenga,Gert-Jan B. van Ommen,P. Eline Slagboom,Dorret I. Boomsma,Kai Ye,Kai Ye,Victor Guryev,Peter F. Arndt,Wigard P. Kloosterman,Paul I.W. de Bakker,Shamil R. Sunyaev +18 more
TL;DR: It is shown that de novo mutations in the offspring of older fathers are not only more numerous but also occur more frequently in early-replicating, genic regions, providing a genome-wide mutation rate map for medical and population genetics applications.
Journal ArticleDOI
The evolution of fungus-growing termites and their mutualistic fungal symbionts.
Duur K. Aanen,Paul Eggleton,Corinne Rouland-Lefèvre,Tobias Guldberg-Frøslev,Søren Rosendahl,Jacobus J. Boomsma +5 more
TL;DR: This study shows that the symbiosis has a single African origin and that secondary domestication of other fungi or reversal of mutualistic fungi to a free-living state has not occurred, and identifies common characteristics of fungus-farming evolution in termites and ants, which apply despite the major differences between these two insect agricultural systems.
Journal ArticleDOI
Estimation of Divergence Times for Major Lineages of Primate Species
Galina V. Glazko,Masatoshi Nei +1 more
TL;DR: It is advisable to concatenate many gene sequences and use a multigene gamma distance for estimating divergence times rather than using the individual gene approach, and nuclear proteins are generally more suitable than mitochondrial proteins for time estimation.
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.
Journal ArticleDOI
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.