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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Marsupials and monotremes sort genome treasures from junk
TL;DR: A recent landmark paper demonstrates the unique contribution of marsupials and monotremes to comparative genome analysis, filling an evolutionary gap between the eutherian mammals and more distant vertebrate species.
Journal ArticleDOI
Overlapping of MINK and CHRNE gene loci in the course of mammalian evolution
Ippeita Dan,Norinobu M. Watanabe,Eriko Kajikawa,Takafumi Ishida,Akhilesh Pandey,Akihiro Kusumi +5 more
TL;DR: Because CHRNE and MINK are differentially expressed, the potentially hazardous mutations responsible for the exon overlap seem to have escaped evolutionary pressures by differential temporo-spatial expression of the two genes.
Journal ArticleDOI
Random Wiring, Ganglion Cell Mosaics, and the Functional Architecture of the Visual Cortex.
TL;DR: It is concluded that V1 layout invariants are specific quantitative signatures of visual cortical optimization, which cannot be explained by generic random feedforward-wiring models.
Journal ArticleDOI
Characterization of California sea lion polyomavirus 1: Expansion of the known host range of the Polyomaviridae to Carnivora
James F. X. Wellehan,Rebecca Rivera,Linda L. Archer,Celeste Benham,Jennifer K. Muller,Kathleen M. Colegrove,Frances M.D. Gulland,Judy St. Leger,Stephanie Venn-Watson,Hendrik H. Nollens,Hendrik H. Nollens,Hendrik H. Nollens +11 more
TL;DR: The genome of a novel polyomavirus first identified in a proliferative tongue lesion of a California sea lion (Zalophus californianus) is reported and it is found that the laurasiatherianpolyomaviruses, together with Squirrel monkey polyomvirus and Murine pneumotropic virus, form a monophyletic clade.
Journal ArticleDOI
MOLECULAR EVOLUTION OF GPCRS: Ghrelin/ghrelin receptors
TL;DR: This work, focused on identifying the gh Relin receptor and its ligand ghrelin in laboratory animals, has provided new insights into the molecular evolution of theghrelin receptor.
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.