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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A higher-level MRP supertree of placental mammals
Robin M. D. Beck,Robin M. D. Beck,Robin M. D. Beck,Olaf R. P. Bininda-Emonds,Olaf R. P. Bininda-Emonds,Marcel Cardillo,Fu Guo Robert Liu,Andy Purvis +7 more
TL;DR: The supertree is the first phylogeny to include all 113 extant families without making a priori assumptions of suprafamilial monophyly, and supports the idea that biogeography has played a crucial role in the evolution of placental mammals.
Journal ArticleDOI
Comparative analysis of ear-hole closure identifies epimorphic regeneration as a discrete trait in mammals
Thomas R. Gawriluk,Jennifer Simkin,Katherine L. Thompson,Shishir K. Biswas,Zak Clare-Salzler,John M. Kimani,Stephen G. Kiama,J. Joshua Smith,Vanessa O. Ezenwa,Ashley W. Seifert,Ashley W. Seifert +10 more
TL;DR: It is shown that several Acomys spp.
Journal ArticleDOI
Specificity and evolvability in eukaryotic protein interaction networks.
Pedro Beltrao,Luis Serrano +1 more
TL;DR: It is shown that eukaryotic species have rewired their interactomes at a fast rate of approximately 10−5 interactions changed per protein pair, per million years of divergence, and proposed that the power law distribution observed in protein interaction networks could be partly explained by the cell's requirement for different degrees of protein binding specificity.
Journal ArticleDOI
Molecular architecture of Pipistrellus pipistrellus/Pipistrellus pygmaeus complex (Chiroptera: Vespertilionidae): further cryptic species and Mediterranean origin of the divergence.
TL;DR: The phylogeographic patterns obtained and analysis of fossil records support the hypothesis of expansion of both species into Europe from the Mediterranean region during the Holocene, and the allopatric speciation model fits the data best.
Journal ArticleDOI
Divergence times, historical biogeography, and shifts in speciation rates of Myrtales
TL;DR: Divergence time estimates suggest Myrtales diverged from Geraniales ∼124Mya during the Aptian of the Early Cretaceous, and BioGeoBEARS showed significant improvement in the likelihood score when the "jump dispersal" parameter was added and issues with conducting diversification analyses more generally are examined.
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.