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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Journal ArticleDOI
Placental mammal diversification and the Cretaceous–Tertiary boundary
TL;DR: The largest available molecular data set for placental mammals is investigated, which includes segments of 19 nuclear and three mitochondrial genes for representatives of all extant placental orders and permits simultaneous constraints from the fossil record and allows rates of molecular evolution to vary on different branches of a phylogenetic tree.
Book ChapterDOI
Estimating maximum likelihood phylogenies with PhyML.
TL;DR: This chapter focuses on phylogenetic tree estimation under the maximum likelihood (ML) principle, a software that implements recent ML phylogenetic methods and algorithms and illustrates the strengths and pitfalls of this program through the analysis of a real data set.
Journal ArticleDOI
Immunology of placentation in eutherian mammals.
Ashley Moffett,Charlie Loke +1 more
TL;DR: The traditional way to study the immunology of pregnancy follows the classical transplantation model, which views the fetus as an allograft, but a more recent approach focuses on the unique, local uterine immune response to the implanting placenta.
Journal ArticleDOI
Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution
Irina Solovei,Moritz Kreysing,Christian Lanctôt,Süleyman Kösem,Leo Peichl,Thomas Cremer,Thomas Cremer,Jochen Guck,Boris Joffe +8 more
TL;DR: It is shown that the nuclear architecture of rod photoreceptor cells differs fundamentally in nocturnal and diurnal mammals and suggests that the conventional architecture prevails in eukaryotic nuclei because it results in more flexible chromosome arrangements, facilitating positional regulation of nuclear functions.
Journal ArticleDOI
Comparative analyses of multi-species sequences from targeted genomic regions
James W. Thomas,James W. Thomas,Jeffrey W. Touchman,Robert W. Blakesley,Gerry Bouffard,Stephen M. Beckstrom-Sternberg,Elliott H. Margulies,Mathieu Blanchette,Adam Siepel,Pamela J. Thomas,Jenny McDowell,Baishali Maskeri,Nancy F. Hansen,M. S. Schwartz,R. J. Weber,W. J. Kent,Donna Karolchik,T. C. Bruen,R. Bevan,David J. Cutler,Scott Schwartz,Laura Elnitski,Jacquelyn R. Idol,Arjun B. Prasad,Shih-Queen Lee-Lin,Valerie Maduro,Tyrone J. Summers,Matthew E. Portnoy,Nicole Dietrich,N. Akhter,K. Ayele,Betty Benjamin,K. Cariaga,Charles P. Brinkley,Shelise Brooks,S. Granite,Xin-Yuan Guan,Jyoti Gupta,P. Haghighi,S. L. Ho,M. C. Huang,Eric Karlins,P. L. Laric,Richelle Legaspi,M. J. Lim,Quino Maduro,Cathy Masiello,Stephen D. Mastrian,J. C. McCloskey,R. Pearson,Sirintorn Stantripop,Emmanuelle Tiongson,J. T. Tran,C. Tsurgeon,Jennifer Vogt,M. A. Walker,Keith Wetherby,L. S. Wiggins,Alice C. Young,L. H. Zhang,Kazutoyo Osoegawa,Baoli Zhu,B. Zhao,C. L. Shu,P. J. De Jong,Charles E. Lawrence,Arian F.A. Smit,Aravinda Chakravarti,David Haussler,Philip Green,Webb Miller,Eric D. Green +71 more
TL;DR: The generation and analysis of over 12 megabases of sequence from 12 species, all derived from the genomic region orthologous to a segment of about 1.8 Mb on human chromosome 7 containing ten genes, show conservation reflecting both functional constraints and the neutral mutational events that shaped this genomic region.
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.