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

Biology Letters
Clio Der SarkissianLudovic Orlando

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 reveals that 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.

References

Dec 26, 2001·Bioinformatics·H Shimodaira, M Hasegawa
Apr 10, 2008·Journal of Molecular Evolution·Ludovic OrlandoCatherine Hänni
Nov 21, 2008·Nature·Webb MillerStephan C Schuster
Dec 17, 2009·Proceedings of the National Academy of Sciences of the United States of America·Ludovic OrlandoAlan Cooper
Nov 26, 2010·PloS One·Tomislav MaricicSvante Pääbo
Mar 1, 2012·Molecular Biology and Evolution·Alexei J DrummondAndrew Rambaut
Feb 26, 2013·PloS One·Julia T VilstrupLudovic Orlando
Mar 26, 2013·Current Biology : CB·Qiaomei FuJohannes Krause
Jun 5, 2013·Cold Spring Harbor Perspectives in Biology·Jesse DabneySvante Pääbo
Dec 3, 2014·Proceedings of the National Academy of Sciences of the United States of America·Hákon JónssonLudovic Orlando

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Citations

Feb 18, 2016·Genome Biology and Evolution·Graham J SlaterAlex D Greenwood
Nov 29, 2017·ELife·Peter D HeintzmanBeth Shapiro
Sep 13, 2020·Science Advances·Tobias AndermannDaniele Silvestro
Oct 13, 2016·Genetics·Pablo LibradoLudovic Orlando
Nov 17, 2020·Annual Review of Animal Biosciences·Pablo Librado, Ludovic Orlando

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