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, 3 (8), e241

Evolution, Systematics, and Phylogeography of Pleistocene Horses in the New World: A Molecular Perspective


Evolution, Systematics, and Phylogeography of Pleistocene Horses in the New World: A Molecular Perspective

Jaco Weinstock et al. PLoS Biol.


The rich fossil record of horses has made them a classic example of evolutionary processes. However, while the overall picture of equid evolution is well known, the details are surprisingly poorly understood, especially for the later Pliocene and Pleistocene, c. 3 million to 0.01 million years (Ma) ago, and nowhere more so than in the Americas. There is no consensus on the number of equid species or even the number of lineages that existed in these continents. Likewise, the origin of the endemic South American genus Hippidion is unresolved, as is the phylogenetic position of the "stilt-legged" horses of North America. Using ancient DNA sequences, we show that, in contrast to current models based on morphology and a recent genetic study, Hippidion was phylogenetically close to the caballine (true) horses, with origins considerably more recent than the currently accepted date of c. 10 Ma. Furthermore, we show that stilt-legged horses, commonly regarded as Old World migrants related to the hemionid asses of Asia, were in fact an endemic North American lineage. Finally, our data suggest that there were fewer horse species in late Pleistocene North America than have been named on morphological grounds. Both caballine and stilt-legged lineages may each have comprised a single, wide-ranging species.


Figure 1
Figure 1. Metatarsal Shape and Size in Pleistocene and Extant Equids
(A) Bivariate plot showing metatarsal shape and size in extant and extinct horses. Modern asses: kiang (E. kiang) = light blue circles; onager (E. hemionus onager) = dark blue; kulan (E. hemionus kulan) = purple. Pleistocene equids: stilt-legged from Alaska and the Yukon = black; E. lambei (Alaska) = red; stilt-legged from Natural Trap Cave (Wyoming) = yellow; caballines from Natural Trap Cave = orange; caballines from Alberta = green; H. saldiasi from southern Patagonia = grey. “A” and “B” above/beside points of caballine horses denote the phylogenetic clade to which the specimens belong (Figure 5). Not all of the specimens were genetically analyzed. (B) Metatarsal shape in Pleistocene horses. From left to right: H. saldiasi (southern Patagonia); E. lambei (Yukon); NWSL (Yukon). Scale bar is 10 cm.
Figure 2
Figure 2. Diagrammatic Representation of North and South American Equid Taxonomy Superimposed on a Time Scale according to Paleontological (A, B) and Molecular Data (C)
(A) represents MacFadden's [13] view of hippidiform origins from a pliohippine, diversifying into two genera, Hippidion and Onohippidium, in North America during the Miocene. (B) shows Alberdi and Prado's [14,15] view of hippidiforms as descendants of a pliohippine during the Miocene; the single genus, Hippidion, originates only after dispersal into South America (they do not recognize the genus Onohippidium as valid [15]). (C) represents the results of the molecular data presented in the present study; it shows Hippidion as originating during the Pliocene, c. 3-3.5 Ma ago. The NWSL is possibly a sister species of Hippidion.
Figure 3
Figure 3. Provenance of Bone Samples Extracted and Sequenced for This Study
Details of each sample are given in Table S2.
Figure 4
Figure 4. Phylogeny of Recent and Pleistocene Equids
The maximum likelihood tree was constructed with two fragments of the mitochondrial control region (583 bp and 133 bp in the HVR1 and HVR2 regions, respectively). Bayesian analysis produced a similar topology. The general time-reversible substitution model was used in both techniques. Black numbers above/beside nodes are posterior probabilities and bootstrap values, respectively (only values > 50% are shown). White numbers on black background are divergence times as calculated from the molecular data. Numbers/letters in bold at the beginning of each specimen's name are sample numbers or GenBank accession numbers. Labels of prehistoric specimens are followed by their age, if available, in thousands of years. The outgroup (Rhinoceros and Ceratotherium) is not shown.
Figure 5
Figure 5. Maximum Likelihood Phylogenetic Tree of Recent, Historic, and Pleistocene Caballine Horses Based on 364 bp of the Mitochondrial Control Region (HVR1)
Posterior probabilities/bootstrap values are presented above or beside the main nodes only if either is > 50%. Labels of prehistoric specimens are followed by their age, if available, in thousands of years (k).

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    1. Winans MC. A quantitative study of North American fossil species of the genus Equus . In: Prothero DR, Schoch R, editors. The evolution of perissodactyls. Oxford: Oxford Univ. Press; 1989. pp. 262–297.
    1. Azzaroli A. The genus Equus in North America. Palaeontographica Italica. 1998;85:1–60.
    1. Guthrie RD. Paleobehavior in Alaskan Pleistocene horses: Social structure, maturation rates, uses of the landscape, and mortality patterns. In: Gerlach SC, Murray MS, editors. People and wildlife in northern North America: Essays in honor of R. Dale Guthrie. Oxford: BAR; 2001. pp. 32–49.
    1. Kurtén B, Anderson E. Pleistocene mammals of North America. New York: Columbia University Press; 1980. 442 pp.
    1. Dalquest WW. Phylogeny of American horses of Blancan and Pleistocene age. Ann Zool Fenn. 1978;15:191–199.

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