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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Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals
TL;DR: It is proposed that near-simultaneous divisions of continents leading to isolated Africa, South America, and Laurasia caused nearly concomitant divergence of the ancient placental ancestor into 3 lineages, Afrotheria, Xenarthra, and Boreotheria, ≈120 Ma.
Journal ArticleDOI
Geologically ancient DNA: fact or artefact?
TL;DR: It remains doubtful whether amplifiable DNA sequences and viable bacteria can survive over geological timescales, so a rigorous set of authentication criteria is proposed for work with geologically ancient DNA.
Journal ArticleDOI
Analysis of missense variation in human BRCA1 in the context of interspecific sequence variation
Victor Abkevich,Andrey Zharkikh,Amie M. Deffenbaugh,David A. Frank,Yuan Chen,Donna Shattuck,Mark H. Skolnick,Alexander Gutin,Sean V. Tavtigian +8 more
TL;DR: This classification is tentative and does not have sufficient independent confirmation to serve as a clinically applicable stand alone method, but about 50% of the unclassified missense variants observed during clinical testing of BRCA1 are tentatively classified as probably deleterious.
Journal ArticleDOI
Von Economo Neurons in the Elephant Brain
Atiya Y. Hakeem,Chet C. Sherwood,Christopher J. Bonar,Camilla Butti,Camilla Butti,Patrick R. Hof,John M. Allman +6 more
TL;DR: The VEN morphology appears to have arisen independently in hominids, cetaceans, and elephants, and may reflect a specialization for the rapid transmission of crucial social information in very large brains.
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Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans
Gillian C. Gibb,Fabien L. Condamine,Melanie Kuch,Jacob Enk,Nadia Moraes-Barros,Mariella Superina,Hendrik N. Poinar,Frédéric Delsuc +7 more
TL;DR: Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction, and to split armadillos into two distinct families Dasypodidae and Chlamyphoridae to better reflect their ancient divergence.
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.