Coalescent-based genome analyses resolve the early branches of the euarchontoglires - PubMed (original) (raw)

Coalescent-based genome analyses resolve the early branches of the euarchontoglires

Vikas Kumar et al. PLoS One. 2013.

Abstract

Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia) because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides) from all orders except Dermoptera (flying lemurs). Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. The ML tree of concatenated nucleotides data from 5,875 genes with all the branches being unanimously supported by TF.

Figure 2

Figure 2. The ML tree based on amino acid data from 5,875 genes representing the best option for a bifurcating topology.

Only the TF support values <99 are shown.

Figure 3

Figure 3. Species tree based on 1,006 gene trees with bootstrap support values (>99% not shown).

Above value indicates the STAR support value and MP-EST values are indicated below.

Figure 4

Figure 4. Consensus network in which at least 10% of the 1006 ML gene trees have common branches (threshold value 10%).

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Grants and funding

The present study was supported by the research funding program LOEWE: "Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz" of Hesse's Ministry of Higher Education, Research, and the Arts. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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