Multispecies coalescent analysis of the early diversification of neotropical primates: phylogenetic inference under strong gene trees/species tree conflict.
Bottom Line: However, despite major efforts, the phylogenetic relationship between these three major clades and the age of their last common ancestor are still controversial because these inferences were based on limited numbers of loci and dating analyses that did not consider the evolutionary variation associated with the distribution of gene trees within the proposed phylogenies.We show, by multispecies coalescent analyses of selected genome segments, spanning along 92,496,904 bp that the early diversification of extant NP was marked by a 2-fold increase of their effective population size and that Atelids and Cebids are more closely related respective to Pitheciids.This approach, based on extensive genomic data provided by new generation DNA sequencing, provides more accurate reconstructions of phylogenies and timescales for all organisms.
Affiliation: Department of Genetics, Federal University of Rio de Janeiro, Brazil.Show MeSH
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Mentions: Coalescent-based phylogenetic analyses inferred the Brachyteles/Callithrix topology as the NP species tree (fig. 2). The majority of ML and Bayesian inferred gene trees (∼47%) supported a topology with Brachyteles as the sister lineage of Callithrix whereas the second most common topology associated Callithrix with Callicebus (29%), followed by the association of Brachyteles and Callicebus (24%). The estimated length of the branch separating the Callicebus offshoot from Brachyteles/Callithrix varied from 0.255 to 0.447 coalescent units (table 1). The traditional ML method and Bayesian inference also positioned Brachyteles as a sister lineage of Callithrix when a concatenated supermatrix of all genes was used. Bayesian concordance analysis inferred a concordance factor of 0.541 for the Brachyteles/Callithrix topology, whereas both alternative topologies showed concordance factors higher than 5%: 0.255 for the Callithrix/Callicebus tree and 0.204 for Brachyteles/Callicebus. The distributions of statistical supports for each topology along gene trees also indicated a high gene tree/species tree conflict. For example, the average aLRT support for the Brachyteles/Callithrix clade was approximately 80% (fig. 3), with an average Bayesian posterior probability for this clade of approximately 95%. The distribution of Bayesian posterior probabilities of full topologies also showed a large amount of mismatching between gene trees and the species tree. The average posterior probability of topologies matching the species tree accounted for 46% (fig. 3d).Fig. 2.—
Affiliation: Department of Genetics, Federal University of Rio de Janeiro, Brazil.