Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids

Abstract

Hippidions were equids with very distinctive anatomical features. They lived in South America 2.5 million years ago (Ma) until their extinction approximately 10 000 years ago. The evolutionary origin of the three known Hippidion morphospecies is still disputed. Based on palaeontological data, Hippidion could have diverged from the lineage leading to modern equids before 10 Ma. In contrast, a much later divergence date, with Hippidion nesting within modern equids, was indicated by partial ancient mitochondrial DNA sequences. Here, we characterized eight Hippidion complete mitochondrial genomes at 3.4-386.3-fold coverage using target-enrichment capture and next-generation sequencing. Our dataset revealsthat the two morphospecies sequenced (H. saldiasi and H. principale) formed a monophyletic clade, basal to extant and extinct Equus lineages. This contrasts with previous genetic analyses and supports Hippidion as a distinct genus, in agreement with palaeontological models. We date the Hippidion split from Equus at 5.6-6.5 Ma, suggesting an early divergence in North America prior to the colonization of South America, after the formation of the Panamanian Isthmus 3.5 Ma and the Great American Biotic Interchange.

What Is Equus? Reconciling Taxonomy and Phylogenetic Analyses

“…francisci (= E. francisci) to extant Equus than primitive species of the genus, such as E. simplicidens (= E. shoshonensis) and E. stenonis, is also indicated by cranial proportions (Eisenmann and Baylac, 2000). Ancient mitochondrial DNA analyses suggested that the lineage which was later named Haringtonhippus was the sister species to extant and fossil caballine equids (Weinstock et al, 2005;Orlando et al, 2008;Vilstrup et al, 2013;Der Sarkissian et al, 2015;Barrón-Ortiz et al, 2017). In contrast to these results, a recent genomic analysis concluded that Ha.…”

Mitochondrial architecture rearrangements produce asymmetrical nonadaptive mutational pressures that subvert the phylogenetic reconstruction in Isopoda

“…Mitochondrial genomes (mitogenomes) generally provide much higher phylogenetic resolution than traditionally used morphological and single gene-based molecular markers (Nie et al, 2018), so mitochondrial phylogenomics is increasingly used to tackle phylogenetic controversies (Bourguignon et al, 2018; Cameron, 2014; Der Sarkissian et al, 2015; Lan et al, 2017; Li et al, 2017). Although the resolution of this approach is still limited by a very small number of available mitogenomes in isopods, overview of published studies shows that they also failed to produce results congruent with other approaches, failed to resolve the rogue taxa issues, and taken as a whole generated more questions than answers (Hua et al, 2018; Kilpert et al, 2012; Luana S.F.…”

The Evolutionary Origin and Genetic Makeup of Domestic Horses

“…These include the horse, but also the donkey (Kimura et al 2011), and a range of extinct equine species such as the hydruntine European ass, which flourished in Central and Western Europe at least until the Iron Age (Orlando et al 2006); the giant Cape zebra (Orlando et al 2009); as well as North and South American specimens (Vilà et al 2001;Weinstock et al 2005;Vilstrup et al 2013;Sarkissian et al 2015). The horse itself currently holds the world record for the oldest genome ever sequenced, which was characterized from bone material preserved in the Yukon permafrost and dated to 560-780 KYA .…”

“…In the near future, we expect that this approach will be superseded by target-enrichment methods coupled with high-throughput sequencing. In horses, such approaches have been applied to only a limited number of loci (Vilstrup et al 2013;Sarkissian et al 2015), but recent procedures enable genotyping millions of loci genome wide (Fu et al 2016), and even entire chromosomes (Fu et al 2013) and genomes (Carpenter et al 2013). This will likely facilitate the identification of the whole series of genetic modifications that have accompanied the recent evolutionary history of this family, domestication and extinction processes included.…”