Molecular phylogeny and evolution of the Perissodactyla

Abstract

The evolution of perissodactyls (rhinoceroses, tapirs, and horses) has been well studied primarily because of their extensive fossil record. Nevertheless, controversy persists regarding relationships of some of the extant taxa, reflecting inconsistencies between molecular and morphological studies. Here we examine the phylogenetic relationships of 16 living perissodactyl species by concatenating two mitochondrial and nine nuclear genes, and we estimate their divergence times using a relaxed Bayesian molecular clock approach. Our analyses recovered the monophyly of the suborders Ceratomorpha and Hippomorpha, and the families Rhinoceratidae, Tapiridae, and Equidae. We supported the early divergence of the Indian rhinoceros in the late Oligocene (26 Mya) relative to the Sumatran and African rhinoceroses, and the split of caballine (domestic horse and Przewalski's wild horse) and noncaballine equids (zebras and African and Asiatic asses) in the Pliocene (4 Mya). An important implication of this study is that Equus asinus, the African wild ass was found to be the sister taxon of Asiatic asses and zebras, diverging from the common ancestor with caballine horses 2 Mya. Rates of chromosome rearrangements were also evaluated in perissodactyls, placing a notably high rate of variation amongst equids, particularly within the zebra clade. The robust phylogenetic results presented here are relevant in terms of understanding the evolutionary history of this highly threatened group of mammals.

A new species of tapir from the Amazon

“…Our results concur partially with previous molecular phylogenies (Norman and Ashley 2000;de Thoisy et al 2010;Steiner and Ryder 2011). The mtDNA gene trees (Cytb, or Cytb þ COI þ COII) show strong support for a unique Neotropical clade, encompassing a strict South American tapir subclade (Fig.…”

“…Because the several fossil species included in the morphological matrix cannot be assessed genetically, a likely alternative would be a long-branch attraction causing T. bairdii to appear as sister taxon of T. indicus in the morphology analysis. Furthermore, many other genetic markers have shown T. bairdii as sister group of the South American tapirs (Steiner and Ryder 2011), the same topology we recover in our mtDNA analyses. Because no fossil tapirs from Asia are well known enough to be included in the morphological matrix, the position of T. indicus may change in future morphological analyses.…”

Speciation with gene flow in equids despite extensive chromosomal plasticity

“…Noncaballine equids were found to cluster into monophyletic zebras and asses, separating ∼1.69-1.99 Mya. This is significantly younger than previous estimates based on limited genetic information (10,11). African and Asiatic asses diverged soon after (∼1.47-1.75 Mya), in agreement with the appearance of donkeys in the fossil record (20).…”

“…In addition, the available genetic information is relatively limited, with complete genomes available only for the horse and the domestic donkey (2,8,9). Moreover, only a handful of mitochondrial genomes (10) and nuclear genes (11), along with limited genome-wide single nucleotide variants (SNVs) ascertained to horses (12), have been characterized. Although wild populations have been genetically monitored for mitochondrial variation (13,14) and microsatellite data (15), the amount of genetic information available is incompatible with detailed reconstructions of their population history.…”

Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages

“…Finally, mapping against the horse reference genome facilitates the identification of genetic variants segregating in horses versus other species. Aligning reads against an outgroup could reduce this bias, but is impracticable for equids since they diverged from their closest living phylogenetic relatives ∼55 myrs ago (Steiner and Ryder, 2011).…”