Morphological Convergence in Hippidion and Equus (Amerhippus) South American Equids Elucidated by Ancient DNA Analysis

Abstract

Unusual equids named hippidions inhabited South America for more than 2 MY (million years). Like many other animals they succumbed to the worldwide climatic change that occurred 10 KY (thousand years) ago and completely disappeared during the great late Pleistocene megafaunal extinction. According to fossil records and numerous dental, cranial, and postcranial characters, Hippidion and Equus lineages are known to have diverged prior to 10 MY. Some equid bones from Rio Verde and Ultima Esperanza (Patagonia, Chile) dating back to the late Pleistocene period (8-13 KY) have been identified as Hippidion saldiasi, while a few teeth have been assigned to Equus. Six samples of those remains have been obtained from the Zoological Museum of Amsterdam for ancient DNA analysis to try to place Hippidion in the evolutive tree of Perissodactyla. Two samples of Hippidion and one sample of Equus yielded 241-394 bp of the mtDNA control region and 172-296 bp of the cytochrome b gene. Unexpectedly, all the sequences clustered deep inside the Equus genus, casting doubt on the initial identification of the bones. For paleontologists, one of the striking and classical diagnostic characters of Hippidion is their extremely short and massive metapodials, a probable locomotory adaptation to the Andine steep slopes. However, our DNA analysis reveals that a very Hippidion-like metapod might also have been possessed by another South American equid, i.e., Equus (Amerhippus), an interpretation supported by complementary anatomical observations. This adaptive convergence between members of the two South American equid genera may lead paleontologists to limb bone misidentification.

Revising the recent evolutionary history of equids using ancient DNA

“…Both the maximum likelihood and Bayesian phylogenetic analyses ( Fig. 1) of the mtDNA HVR sequences identified three monophyletic New World groups: caballine horses (node G); NWSL horses (node F); and hippidiforms (node C2), in agreement with earlier studies (15,16,18). The exact branching order of the three groups (relative to the Old World noncaballine horses) could not be resolved with either the HVR-1 dataset alone (node B shows weak supports in Fig.…”

“…It is noteworthy that no modern equid DNA was stored in the aDNA laboratories, and though modern Grevy's zebra hairs were analyzed in the Lyon post-PCR laboratory, this haplotype was not found in any ancient sample. Of the new sequences, the mtDNA HVR-I sequences of the Patagonian Hippidion saldiasi specimens were highly similar to previously reported Hippidion sequences (15)(16)(17) (Fig. 1).…”

“…Similarly, although the strongest support was obtained for the placement of hippidiforms within a larger paraphyletic group of Equus (with merged datasets, Table S2, and with marginal support from SH tests: P values ϭ 0.065-0.083; Table S5, topologies R-V), likelihood-based topological tests cannot significantly reject alternative topologies and the exact position of the root, previously reported between nodes A and H ( Fig. 1) (15,16) should be considered preliminary. The lack of resolution is complicated by the short divergence time among caballines and New World horses (circa 0.5 MY; nodes A and B/B1/B2; Table S4) and the lack of a close outgroup, as has been noted with mammoths (30,31).…”

“…Hippidions exhibited a similar distinctive nasal morphology to Pliohippines, and appeared in the South American fossil record Ϸ2.5 MYA (20). However, mitochondrial sequences of hippidions from Patagonia and the Buenos Aires Province form a tight clade within a larger paraphyletic group of Equus, suggesting either that hippidions and living equids belong to the same genus or that living equids should be split into several genera (15,16,18,21). Similarly, the South American subgenus (Amerhippus), which was contemporaneous with hippidion but quite Equus-like (22), was shown by aDNA sequences to actually be conspecific with caballines and did not form a separate subgenus within living Equus (18).…”

“…Indeed, the field of aDNA started with the publication of mitochondrial DNA sequences from a museum specimen of the quagga (13), an equid related to Plains zebras that became extinct in the wild in the late 1870s. Over recent decades, aDNA sequences have been reported from other extinct members of the Equidae family (11,(14)(15)(16)(17)(18) and have revealed unexpected patterns in equid evolution with varying degrees of conflict to morphological and paleontological phylogenies. For instance, the morphologically distinct South American hippidions were formerly considered to be descendants of the Pliohippines, a basal North American group that diverged from the lineage that gave rise to the genus Equus before 10 MYA (19).…”