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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The morphology of the eutherian ethmoidal region and its implications for higher‐order phylogeny
TL;DR: It is shown that the ethmoidal region is highly variable within eutherians and its structural elements display a strong tendency towards homoplasy, therefore, this cranial region is not suitable for use in mammalian superordinal systematics except as support for monophyletic Tethytheria.
Journal ArticleDOI
Immunohistochemical demonstration of keratins in the epidermal layers of the Malayan pangolin (Manis javanica), with remarks on the evolution of the integumental scale armour.
Wilfried Meyer,Maleewan Liumsiricharoen,Apinun Suprasert,L.-G. Fleischer,M. Hewicker-Trautwein +4 more
TL;DR: Using immunohistochemistry, the authors in this paper demonstrated the distribution of pan-keratin, with body region-dependent negative to very strong reaction intensities in the Malayan pangolin epidermis.
Journal ArticleDOI
Association and evolutionary studies of the melatonin receptor 1B gene (MTNR1B) in the self-contained population of Sorbs from Germany.
Kerstin Dietrich,S. Birkmeier,Dorit Schleinitz,Jana Breitfeld,B. Enigk,I Müller,Yvonne Böttcher,T. Lindner,Michael Stumvoll,Anke Tönjes,Peter Kovacs +10 more
TL;DR: In this article, the effects of MTNR1B variants on traits related to the metabolic syndrome in the self-contained population of Sorbs from Germany were assessed by regression analyses, the conservation between species was investigated with phylogenetic analysis by maximum likelihood (PAML).
Journal ArticleDOI
Not so pseudo: the evolutionary history of protein phosphatase 1 regulatory subunit 2 and related pseudogenes.
Luís Korrodi-Gregório,Joana Abrantes,Joana Abrantes,Thorsten Müller,José Melo-Ferreira,Katrin Marcus,Odete A. B. da Cruz e Silva,Margarida Fardilha,Pedro J. Esteves +8 more
TL;DR: The results show that contrary to initial observations PPP1R2-related pseudogenes are not simple bystanders of the evolutionary process but may rather be at the origin of genes with novel functions.
Journal ArticleDOI
Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics
TL;DR: The results suggest that SWS1 may be a good marker for vertebrate phylogenetics due to the variable yet consistent patterns of sequence evolution exhibited across fairly wide taxonomic groups.
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.