Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements - PubMed (original) (raw)

Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements

Jacob A Esselstyn et al. Genome Biol Evol. 2017.

Abstract

The phylogeny of eutherian mammals contains some of the most recalcitrant nodes in the tetrapod tree of life. We combined comprehensive taxon and character sampling to explore three of the most debated interordinal relationships among placental mammals. We performed in silico extraction of ultraconserved element loci from 72 published genomes and invitro enrichment and sequencing of ultraconserved elements from 28 additional mammals, resulting in alignments of 3,787 loci. We analyzed these data using concatenated and multispecies coalescent phylogenetic approaches, topological tests, and exploration of support among individual loci to identify the root of Eutheria and the sister groups of tree shrews (Scandentia) and horses (Perissodactyla). Individual loci provided weak, but often consistent support for topological hypotheses. Although many gene trees lacked accepted species-tree relationships, summary coalescent topologies were largely consistent with inferences from concatenation. At the root of Eutheria, we identified consistent support for a sister relationship between Xenarthra and Afrotheria (i.e., Atlantogenata). At the other nodes of interest, support was less consistent. We suggest Scandentia is the sister of Primatomorpha (Euarchonta), but we failed to reject a sister relationship between Scandentia and Glires. Similarly, we suggest Perissodactyla is sister to Cetartiodactyla (Euungulata), but a sister relationship between Perissodactyla and Chiroptera remains plausible.

Keywords: Atlantogenata; Eutheria; Perissodactyla; Scandentia; phylogenomics.

© The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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Figures

<sc>Fig</sc>. 1.

Fig. 1.

—Maximum likelihood estimate of mammalian phylogeny from 3,787 concatenated ultraconserved elements. Clades discussed in the text are labeled. Branches between Metatheria (marsupials), Eutheria (placentals), and Prototheria (platypus; not shown) were truncated for ease of presentation. Bootstrap support values are 100 unless otherwise noted. Taxa with an asterisk after the specific epithet are those we enriched and sequenced.

<sc>Fig</sc>. 2.

Fig. 2.

—Species tree estimates of eutherian relationships derived from analysis of 3,787 ultraconserved elements in (A) ASTRAL and ASTRID, and (B) SVDquartets. The topology is collapsed to the ordinal level or higher. Bootstrap support values are 100 unless otherwise noted.

<sc>Fig</sc>. 3.

Fig. 3.

—Summary of the consistency of individual gene trees with competing topological hypotheses for species relationships. (A) Hypotheses regarding earliest divergence among placentals, (B) relationships of Scandentia, and (C) relationships of Perissodactyla. The percentage of gene trees consistent with a multi-constraint topological filter is shown above each topology (e.g., 24.7% of gene trees contain monophyletic Afrotheria, Xenarthra, and Afrotheria + Xenarthra). The percentage of gene trees consistent with a single-constraint topological filter is shown to the right of the relevant node (e.g., 26.3% contain a monophyletic Afrotheria + Xenarthra). Average bootstrap support (BS) at a particular bifurcation are shown to the left of each node (e.g., 33.8% mean BS for Afrotheria + Xenarthra). In each panel, relevant tip labels include the percent of gene trees containing that clade, followed by their average BS at that node among those gene trees (e.g., Afrotheria found in 73% of gene trees with mean of 59% BS).

<sc>Fig</sc>. 4.

Fig. 4.

—Plots of per gene ΔlnL against the number of parsimony informative sites for our maximum likelihood (ML) tree (Hypothesis 1) versus 2–4 alternative hypotheses (Hypotheses 2–5). Each topological hypothesis is defined in the gray box at center right. The following orders are abbreviated: Perissodactyla (Per); Cetartiodactyla (Cet); Chiroptera (Chir); and Carnivora (Carn).

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