An ABBA-BABA Test for Introgression Using Retroposon Insertion Data

Abstract

DNA sequence alignments provide the majority of data for inferring phylogenetic relationships with both concatenation and coalescence methods. However, DNA sequences are susceptible to extensive homoplasy, especially for deep divergences in the Tree of Life. Retroposon insertions have emerged as a powerful alternative to sequences for deciphering evolutionary relationships because these data are nearly homoplasy-free.In addition, retroposon insertions satisfy the 'no intralocus recombination' assumption of summary coalescence methods because they are singular events and better approximate neutrality relative to DNA sequences commonly applied in phylogenomic work.Retroposons have traditionally been analyzed with phylogenetic methods that ignore incomplete lineage sorting (ILS). Here, we analyze three retroposon data sets for mammals (Placentalia, Laurasiatheria, Balaenopteroidea) with two different ILS-aware methods. The first approach constructs a species tree from retroposon bipartitions with ASTRAL, and the second is a modification of SVD-Quartets. We also develop a χ 2 Quartet-Asymmetry Test to detect hybridization using retroposon data. Both coalescence methods recovered the same topology for each of the three data sets. The ASTRAL species tree for Laurasiatheria has consecutive short branch lengths that are consistent with an anomaly zone situation. For the Balaenopteroidea data set, which includes rorquals (Balaenopteridae) and gray whale (Eschrichtiidae), both coalescence methods recovered a topology that supports the paraphyly of Balaenopteridae. Application of the χ 2 Quartet-Asymmetry Test to this data set detected 16 different quartets of species for which historical hybridization may be inferred, but significant asymmetry was not detected in the placental root and Laurasiatheria analyses.

Six reference-quality genomes reveal evolution of bat adaptations

“…This tree challenges the Pegasoferae hypothesis 31 , which groups bats with Perissodactyla, Carnivora and Pholidota, but agrees with a previous study of concatenated phylogenomic data 32 . Evolutionary studies of 102 retrotransposons, which considered incomplete lineage sorting, also supported a sister-group relationship between Chiroptera and Fereuungulata, but differ from the present study in supporting a sister-group relationship between Carnivora and Cetartiodactyla 25,26 .…”

“…However, the phylogeny of Laurasiatheria and-in particular-the origin of bats is a long-standing and unresolved phylogenetic question 24 , as multiple phylogenetic and systematic studies support alternative topologies 25 . These incongruent results have been attributed to the challenge of identifying the two (presumably short) internal branches that link the four key clades that diverged in the Late Cretaceous period 26 -that is, Chiroptera, Cetartiodactyla, Perissodactyla and (Carnivora + Pholidota) ( Fig. 2, Supplementary Table 1).…”

Six new reference-quality bat genomes illuminate the molecular basis and evolution of bat adaptations

“…This tree disagrees with the Pegasoferae hypothesis 40 , which groups bats with Perissodactyla, Carnivora and Pholidota, but agrees with concatenation analyses of phylogenomic data 41 . Evolutionary studies based on 102 retroposons, including ILS-aware analyses, also support a sister-group relationship between Chiroptera and Fereuungulata, but differ from the present analyses in supporting a sister-group relationship between Carnivora and Cetartiodactyla 34,35 . However, as the number of homologous sites increases in phylogenomic datasets, so too does bootstrap support 42 , even sometimes for an incorrect phylogeny 43 , and as non-coding sequences can produce a different topology than coding sequences 44 , we further explored the phylogenomic signal within our genomes.…”

“…However, the phylogeny of Laurasiatheria and, in particular, the position of bats has been a long-standing, unresolved phylogenetic question 14,34 . This is perhaps the most challenging interordinal problem in placental mammal phylogenetics, as multiple phylogenetic and systematic investigations using large nucleotide and genomic scale datasets or transposable element insertions support alternative topologies 35 . These incongruent results have been attributed to the challenge of identifying two, presumably short, internal branches linking four clades (Chiroptera, Cetartiodactyla, Perissodactyla, Carnivora + Pholidota) that diverged in the Late Cretaceous 35 .…”

“…However, even with similar support levels for several topologies, the phylogenetic position for Chiroptera is pectinate on the most common gene tree and does not qualify as anomalous. If the base of Scrotifera is in the anomaly zone, as suggested by coalescence analyses of retroposon insertions 35 , then we may expect the most common gene tree(s) to be symmetric rather than pectinate. We may also expect the species tree based on concatenation to be symmetric instead of pectinate 45 .…”