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Multispecies coalescent analysis of the early diversification of neotropical primates: phylogenetic inference under strong gene trees/species tree conflict.

Schrago CG, Menezes AN, Furtado C, Bonvicino CR, Seuanez HN - Genome Biol Evol (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Federal University of Rio de Janeiro, Brazil.

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(a) Size distribution of orthologous alignments; (b) distribution of orthologous alignments with human chromosomes; (c) distribution of the frequency of variable sites per alignment used; (d) average frequency of nucleotides on each species analyzed.
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evu244-F1: (a) Size distribution of orthologous alignments; (b) distribution of orthologous alignments with human chromosomes; (c) distribution of the frequency of variable sites per alignment used; (d) average frequency of nucleotides on each species analyzed.

Mentions: Genome assembly was conducted de novo with ABySS assembler using paired end libraries (Simpson et al. 2009). For each genome, assembly performance was optimized by scanning the best k-mer value from 25 to 55. Genome scaffolds were subsequently aligned against database of syntenic alignments from Homo sapiens, Pan troglodytes, and Callit. jacchus genomes available in the Ensembl’s Compara repository (ftp://ftp.ensembl.org/pub/release-67/emf/ensembl-compara; last accessed October 9, 2014) using the LAST software (Kielbasa et al. 2011). These newly generated syntenic alignments were subsequently scanned to obtain regions with small amounts of indels and missing data (fig. 1), and with full taxonomic coverage, resulting in 25,955 genome segments of approximately 3,500 bp. The final concatenated supermatrix of selected genome segments consisted of 92,496,904 bp. The length of genome segments was determined by scaffold length, and orthologous regions were identified by LAST. The average frequency of variable sites was 17.5% (standard deviation = 10.3%) and the percentage of nucleotides was very homogeneous between species (fig. 1).Fig. 1.—


Multispecies coalescent analysis of the early diversification of neotropical primates: phylogenetic inference under strong gene trees/species tree conflict.

Schrago CG, Menezes AN, Furtado C, Bonvicino CR, Seuanez HN - Genome Biol Evol (2014)

(a) Size distribution of orthologous alignments; (b) distribution of orthologous alignments with human chromosomes; (c) distribution of the frequency of variable sites per alignment used; (d) average frequency of nucleotides on each species analyzed.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4255775&req=5

evu244-F1: (a) Size distribution of orthologous alignments; (b) distribution of orthologous alignments with human chromosomes; (c) distribution of the frequency of variable sites per alignment used; (d) average frequency of nucleotides on each species analyzed.
Mentions: Genome assembly was conducted de novo with ABySS assembler using paired end libraries (Simpson et al. 2009). For each genome, assembly performance was optimized by scanning the best k-mer value from 25 to 55. Genome scaffolds were subsequently aligned against database of syntenic alignments from Homo sapiens, Pan troglodytes, and Callit. jacchus genomes available in the Ensembl’s Compara repository (ftp://ftp.ensembl.org/pub/release-67/emf/ensembl-compara; last accessed October 9, 2014) using the LAST software (Kielbasa et al. 2011). These newly generated syntenic alignments were subsequently scanned to obtain regions with small amounts of indels and missing data (fig. 1), and with full taxonomic coverage, resulting in 25,955 genome segments of approximately 3,500 bp. The final concatenated supermatrix of selected genome segments consisted of 92,496,904 bp. The length of genome segments was determined by scaffold length, and orthologous regions were identified by LAST. The average frequency of variable sites was 17.5% (standard deviation = 10.3%) and the percentage of nucleotides was very homogeneous between species (fig. 1).Fig. 1.—

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Federal University of Rio de Janeiro, Brazil.

Show MeSH
Related in: MedlinePlus