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
More filters
Journal ArticleDOI
Genome-Wide Scan for Bats and Dolphin to Detect Their Genetic Basis for New Locomotive Styles
Yongyi Shen,Wei-Ping Zhou,Wei-Ping Zhou,Tai-Cheng Zhou,Yan-Ni Zeng,Yan-Ni Zeng,Gui-Mei Li,David M. Irwin,David M. Irwin,Ya-Ping Zhang,Ya-Ping Zhang +10 more
TL;DR: A genome-wide comparative analysis showed that on the dolphin and bat lineages, genes associated with locomotion not only both show a greater propensity to adaptively evolve, but also show evidence of sequence convergence, which likely reflects a response to a common requirement during their development of these two drastic locomotive styles.
Patent
System and method for sequence distance measure for phylogenetic tree construction
TL;DR: In this article, the authors proposed an ab initio approach with the potential for rapid identification of biological materials of unknown origin using standard techniques by comparing a mathematical characterization of the unknown sequence with DNA sequences of known genera and species.
Journal ArticleDOI
The ink4a/arf Locus Evolution in Primates: Characterization of Three ARF Sequences
TL;DR: This work characterized the exon 1beta of ARF in 12 different species of primates and suggests that when the radiation human/simian appeared or after, a selection of threonine occurred, which could play a role in different interactions between ARF and other proteins to stabilize or not these complexes.
Book ChapterDOI
Animal phylogenomics: multiple interspecific genome comparisons.
TL;DR: This chapter focuses on fundamental approaches and techniques that implement the collection of DNA sequence data for comparative phylogenetic purposes in a genomic context (phylogenomics), and addresses how genomics has made it more important for a clear understanding of orthology of gene regions in comparative biology.
Journal ArticleDOI
Tracing the Evolution of Novel Features of Human Toll-like Receptor 4
TL;DR: This work has polarized this set of transitions and sets up work to study the mechanistic underpinnings for the evolution of new functions in TLR4.
References
More filters
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.