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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Superior Colliculus Connections With Visual Thalamus in Gray Squirrels (Sciurus carolinensis): Evidence for Four Subdivisions Within the Pulvinar Complex
TL;DR: The anatomical results support the conclusion that the pulvinar complex of squirrels consists of four distinct nuclei, and comparisons with other rodents suggest that a variously named caudal nucleus, which relays visual inputs from the SC to temporal visual cortex, is common to all rodents and possibly most mammals.
Journal ArticleDOI
Molecular phylogeny and systematics of anoplocephaline cestodes in rodents and lagomorphs.
TL;DR: The results contradict the view of uterine morphology being the primary determinant of deeper phylogenetic splits within Anoplocephalinae and indicate a rapid radiation involving a nearly simultaneous diversification of many lineages, a scenario also proposed for the arvicoline hosts.
Journal ArticleDOI
B1 and related SINEs in mammalian genomes.
TL;DR: The revealed common pattern of microenvironment of some rearrangement hot spots in SINEs (internal duplications and deletions) suggests involvement of short direct repeats in the mechanism of such rearrangements, which allows us to explain short rearrangments in these and other short retroposons.
Journal ArticleDOI
A phylogenetic study of cytochrome b561 proteins
Wim Verelst,Han Asard +1 more
TL;DR: All cytochromes b561 have probably evolved from a common ancestral protein before the separation of plants and animals, and their phyletic distribution mirrors the use of ascorbate as primary antioxidant, indicating their role in asCorbate homeostasis and antioxidative defense.
Journal ArticleDOI
Mitochondrial phylogeny of hedgehogs and monophyly of Eulipotyphla
TL;DR: The long-eared hedgehog Hemiechinus auritus, the Japanese mole Mogera wogura, and the greater Japanese shrew-mole Urotrichus talpoides genomes are sequenced and the Erinaceoidea-Eulipotyphla tree emerges as the bestTree or as a tree with a log-likelihood score indistinguishable from that of the best tree.
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.