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, 106 (51), 21754-9

Revising the Recent Evolutionary History of Equids Using Ancient DNA


Revising the Recent Evolutionary History of Equids Using Ancient DNA

Ludovic Orlando et al. Proc Natl Acad Sci U S A.


The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.

Conflict of interest statement

The authors declare no conflict of interest.


Fig. 1.
Fig. 1.
Phylogenetic relationships among equids. Unrooted phylogenetic tree based on maximum likelihood analysis of the HVR-1 dataset. Sequences generated in this study are highlighted in gray. Numbers above/below branches correspond to node bootstrap values, approximate likelihood ratio test (aLRT SH-like), and Bayesian posterior probabilities. Δ28: 28-bp deletion in the mitochondrial HVR-1 (positions 15533–15560 according to the complete horse mitochondrial genome; GenBank accession no. X79547) (Fig. 2A). The potential locations of the root are reported with gray (alternative)/black (most likely) triangles according to likelihood-based topological tests (Fig. S4 and Table S5) and previous reports (15, 16). C1 and C2 nodes have been used as calibration points for molecular dating. Two radiocarbon dates were retrieved at the University of Colorado Laboratory for AMS Radiocarbon Preparation and Research (CURL) and the University of California-Irvine Accelerator Mass Spectrometry (UCIAMS) Facility for sussemione samples ACAD2303 and ACAD2305 (see SI Text).
Fig. 2.
Fig. 2.
Intra- and interspecific corrected (GTR+Γ+I) pairwise distances among equids. The dataset consisted of 1,544 sequences encompassing positions 15518 and 15818 from the complete horse mitochondrial genome (GenBank accession no. X79547). Numeric values are reported on Table S3A. A complete list of accession numbers used for defining each taxonomic group is provided as SI Text. Parameters and distances were estimated using PhyML 3.0 and PAUP* 4.0, respectively. Bar, median; box, 50% quantiles; bars, 75% quantiles; CAB, E. caballus; ASI, E. asinus; QUA, E. quagga (all Plain zebras, including E. quagga quagga); QUAJ2, node J2 is defined on Fig. 1 and includes samples ACAD226 and ACAD230; QUAALL-J2, QUA but excluding samples for node J2; GRE, E. grevyi; ZEB, E. hartmannae; HEM, E. hemionus; KIA, E. kiang; HIP, Hippidion saldiasi/principale; ONO, Hippidion devillei (Peruvian hippidions; ACAD3615, ACAD3625, ACAD3627, ACAD3628, and ACAD3629); STL, New World Stilt-Legged horses; SUS, Sussemiones (Khakassia, SW Siberia; ACAD2302, ACAD2303, and ACAD2305). Only two distributions (GRE/ZEB and HEM/KIA) are shown for the intergroup genetic distances, given that all others are included within these two.

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