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Journal ArticleDOI

Resolution of the early placental mammal radiation using Bayesian phylogenetics

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).

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The relationship between the evolution of microRNA targets and the length of their UTRs

TL;DR: A systematic investigation of the relationship between miRNA regulation and their targets' evolution in two mammals: human and mouse finds genes with longer 3' UTRs are regulated by more distinct types of miRNAs.
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Retroposed Elements and Their Flanking Regions Resolve the Evolutionary History of Xenarthran Mammals (Armadillos, Anteaters, and Sloths)

TL;DR: The presence/absence patterns of phylogenetically informative retroposed elements and other RGCs were investigated, and multiple evidence supports the grouping of Chaetophractus and Zaedyus as a sister group to Euphractus within Euphractinae, an association that was not previously demonstrated.
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New views on tree shrews: The role of Tupaiids in primate supraordinal relationships

TL;DR: Whether or not tree shrews are the sister taxon to Primates, they are still crucial to primate supraordinal relationships and represent a critical outgroup in studies of primate phylogenetics.
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Radiation of Extant Marsupials After the K/T Boundary: Evidence from Complete Mitochondrial Genomes

TL;DR: Molecular estimates suggest that the deepest marsupial divergences took place 64–62 million years before present (MYBP), implying that the radiation of recent marsupials took place after the K/T (Cretaceous/Tertiary) boundary.
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Testing the Phylogenetic Position of a Parasitic Plant (Cuscuta, Convolvulaceae, Asteridae): Bayesian Inference and the Parametric Bootstrap on Data Drawn from Three Genomes

TL;DR: In this article, a new molecular data set consisting of mitochondrial (atpA and nuclear (RPB2) genes was generated and analyzed with an existing chloroplast data matrix (rbcL, atpB, trnL-F, and psbE-J), to which an additional chloroplayer gene (rpl2) was added.
References
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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.
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MODELTEST: testing the model of DNA substitution.

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

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

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

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.
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