Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

Abstract

Phylogenomics offers the potential to fully resolve the Tree of Life, but increasing genomic coverage also reveals conflicting evolutionary histories among genes, demanding new analytical strategies for elucidating a single history of life. Here, we outline a phylogenomic approach using a novel class of phylogenetic markers derived from ultraconserved elements and flanking DNA. Using species-tree analysis that accounts for discord among hundreds of independent loci, we show that this class of marker is useful for recovering deep-level phylogeny in placental mammals. In broad outline, our phylogeny agrees with recent phylogenomic studies of mammals, including several formerly controversial relationships. Our results also inform two outstanding questions in placental mammal phylogeny involving rapid speciation, where species-tree methods are particularly needed. Contrary to most phylogenomic studies, our study supports a first-diverging placental mammal lineage that includes elephants and tenrecs (Afrotheria). The level of conflict among gene histories is consistent with this basal divergence occurring in or near a phylogenetic "anomaly zone" where a failure to account for coalescent stochasticity will mislead phylogenetic inference. Addressing a long-standing phylogenetic mystery, we find some support from a high genomic coverage data set for a traditional placement of bats (Chiroptera) sister to a clade containing Perissodactyla, Cetartiodactyla, and Carnivora, and not nested within the latter clade, as has been suggested recently, although other results were conflicting. One of the most remarkable findings of our study is that ultraconserved elements and their flanking DNA are a rich source of phylogenetic information with strong potential for application across Amniotes.

Figure 1.

Variability and saturation of UCE core and flanking regions compared to exons. (A) High variability in exons from Springer et al. (2007) is driven largely by third positions of codons, whereas variability in first and second position codons is more similar to UCE flanking regions. (B) UCEs have low saturation indexes, whereas saturation is highest among third positions of codons of exons. Box plots show the mean (line within box), 25th to 75th percentiles (box), fifth to 95th percentiles (whiskers), and outliers (dots).

Figure 2.

Evolutionary history of placental mammals resolved from conflicting gene histories. (A) Summary of STAR species trees generated from 183-locus and 917-locus data sets (Supplemental Table S1), in addition to the 444-locus data set that included UCEs from Stephen et al. (2008) and a 485-locus data set that included 41 exons (see Discussion). Note that STAR trees contain no branch length information. (B) Discord among four representative gene trees from the 183-locus data set. In general, gene trees were highly discordant, although some similarities emerged, such as the sister relationship between rat and mouse (shaded box 1) and monophyly of primates (shaded box 2). Discord among all gene trees is depicted in Supplemental Figure S7. (C) Widespread consensus among 1000 species-tree bootstrap replicates of the same 183-locus data set. STEAC trees (see Methods) are depicted because the branch lengths allow for better visualization of branching patterns, but STAR results supported the same topology. Cones emanating from terminal tips of species trees (red arrows) indicate disagreement among bootstrap replicates, for example, in the placement of the sloth and tree shrew. Colored squares indicate terminal taxa from A.

Figure 3.

Basal divergence of placental mammals near the phylogenetic “anomaly zone.” Expected regions of gene-tree agreement (green) and discordance (pink) under a range of possible demographic parameters at the time of the divergence of the three placental mammal superorders. The phylogenetic “anomaly zone” where concatenation will fail (red) expands as speciation intervals shorten from 5 Mya (A), to 1 Mya (B), to 0.5 Mya (C). Empirical estimates of gene-tree discord (Table 1) from retroposons (Nishihara et al. 2009) are shown with yellow tiles, whereas estimates observed in our study would occur well within the anomaly zone. Speciation intervals for this divergence are thought to be closer to 2 Mya (Murphy et al. 2004).

Figure 4.

Species trees and concatenated trees from high genomic coverage data sets for two rapid radiations in placental mammals. (A) Species tree from a 591-locus analysis identifies Afrotheria as the first-diverging lineage of placental mammals, whereas alternate topologies had less than half the bootstrap support (Table 1). A Bayesian analysis based on concatenated data places Afrotheria and Xenarthra together with high PP. Data on gene-tree discordance from Figure 2 suggest that this may be because the basal divergence of placental mammals lies close to the phylogenetic anomaly zone. (B) Species tree of taxa in the Laurasiatheria based on 683 loci places bats (Chiroptera) in a traditional location sister to Perissodactyla, Cetartiodactyla, and Carnivora. Bayesian analysis based on concatenated data produced an unusual tree with bats grouping sister to Perissodactyla, but with Carnivora grouping with Cetartiodactyla. The species tree and concatenated analysis of the 183 locus data set produced a different topology, more supportive of the hypothesized clade Pegasoferae (see text), suggesting that a robust understanding of this divergence event will require further investigation incorporating additional taxa and loci. Note that STAR trees do not contain branch length information.