Journal of Molecular Evolution

, Volume 66, Issue 5, pp 533–538 | Cite as

Ancient DNA Clarifies the Evolutionary History of American Late Pleistocene Equids

  • Ludovic OrlandoEmail author
  • Dean Male
  • Maria Teresa Alberdi
  • Jose Luis Prado
  • Alfredo Prieto
  • Alan Cooper
  • Catherine Hänni


Hippidions are past members of the equid lineage which appeared in the South American fossil record around 2.5 Ma but then became extinct during the great late Pleistocene megafaunal extinction. According to fossil records and numerous dental, cranial, and postcranial characters, Hippidion and Equus lineages were expected to cluster in two distinct phylogenetic groups that diverged at least 10 MY, long before the emergence of the first Equus. However, the first DNA sequence information retrieved from Hippidion fossils supported a striking different phylogeny, with hippidions nesting inside a paraphyletic group of Equus. This result indicated either that the currently accepted phylogenetic tree of equids was incorrect regarding the timing of the evolutionary split between Hippidion and Equus or that the taxonomic identification of the hippidion fossils used for DNA analysis needed to be reexamined (and attributed to another extinct South American member of the equid lineage). The most likely candidate for the latter explanation is Equus (Amerhippus) neogeus. Here, we show by retrieving new ancient mtDNA sequences that hippidions and Equus (Amerhippus) neogeus were members of two distinct lineages. Furthermore, using a rigorous phylogenetic approach, we demonstrate that while formerly the largest equid from Southern America, Equus (Amerhippus) was just a member of the species Equus caballus. This new data increases the known phenotypic plasticity of horses and consequently casts doubt on the taxonomic validity of the subgenus Equus (Amerhippus).


Equid Lineage Megafaunal Extinction Postcranial Character Complete Sequence Identity Current Taxonomic Status 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Supplementary material

239_2008_9100_MOESM1_ESM.pdf (651 kb)
(PDF 650 kb)


  1. Alberdi MT, Cartelle C, Prado JL (2003) El registro Pleistoceno de Equus (Amerhippus) e Hippidion (Mammalia, Perissodactyla) de Brasil. Consideraciones paleoecológicas y biogeográficas. Ameghiniana 40:173–196Google Scholar
  2. Alberdi MT, Prado JL, Prieto A (2005) Considerations on the paper “Morphological Convergence in Hippidion and Equus (Amerhippus) South American Equids Elucidated by Ancient DNA Analysis,” by Ludovic Orlando, Véra Eisenmann, Frédéric Reynier, Paul Sondaar, and Catherine Hänni. J Mol Evol 61:145–147PubMedCrossRefGoogle Scholar
  3. Azzaroli A (1998) The genus Equus in North America. PalaeontographItal 85:1–60Google Scholar
  4. Bandelt H-J, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48PubMedGoogle Scholar
  5. Guindon S, Lethiec F, Duroux P, Gascuel O (2005) PHYML Online—a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 33:W557–W559PubMedCrossRefGoogle Scholar
  6. Hofreiter M, Jaenicke V, Serre D, Haeseler Av A, Pääbo S (2001) DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res 29:4793–4799PubMedCrossRefGoogle Scholar
  7. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755PubMedCrossRefGoogle Scholar
  8. MacFadden BJ (1997) Pleistocene horses from Tarija, Bolivia, and validity of the genus Onohippidium (Mammalia: Equidae). J Vertebr Paleontol 17:199–218Google Scholar
  9. Orlando L, Eisenmann V, Reynier F, Sondaar P, Hänni C (2003) Morphological convergence in Hippidion and Equus (Amerhippus) southern-american equids elucidated by ancient DNA analysis. J Mol Evol 57 (Suppl 1):S29–S40PubMedCrossRefGoogle Scholar
  10. Orlando L, Mashkour M, Burke A, Douady CJ, Eisenmann V, Hänni C (2006) Geographic distribution of an extinct equid (Equus hydruntinus: Mammalia, Equidae) revealed by morphological and genetical analyses of fossils. Mol Ecol 15:2083–2093PubMedCrossRefGoogle Scholar
  11. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817–818PubMedCrossRefGoogle Scholar
  12. Prado JL, Alberdi MT (1994) A quantitative review of the horse genus Equus from South America. Palaeontology 37:459–481Google Scholar
  13. Prado JL, Alberdi MT (1996) A cladistic analysis of the horses of the tribe Equini. Palaeontology 39:663–680Google Scholar
  14. Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497PubMedCrossRefGoogle Scholar
  15. Weinstock J, Willerslev E, Sher A, Tong W, Ho SY, Rubenstein D, Storer J, Burns J, Martin L, Bravi C, Prieto A, Froese D, Scott E, Xulong L, Cooper A (2005) Evolution, systematics, and phylogeography of pleistocene horses in the new world: a molecular perspective. PLoS Biol 3:e241PubMedCrossRefGoogle Scholar
  16. Winans MC (1989) A quantitative study of the North American fossil species of the genus Equus. In: Prothero DR, RM RM Schoch (eds) The evolution of Perissodactyls. Oxford University Press, New York, pp 262–297Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Ludovic Orlando
    • 1
    Email author
  • Dean Male
    • 2
  • Maria Teresa Alberdi
    • 3
  • Jose Luis Prado
    • 4
  • Alfredo Prieto
    • 5
  • Alan Cooper
    • 2
  • Catherine Hänni
    • 1
  1. 1.Université de Lyon, Paleogenetics and Molecular Evolution, Institut de Génomique Fonctionnelle de LyonCNRS UMR 5242 – INRA – Université Claude Bernard Lyon I–Ecole Normale Supérieure de LyonLyon Cedex 07France
  2. 2.Australian Centre for Ancient DNA (ACAD), School of Earth and Environmental SciencesUniversity of AdelaideAdelaideAustralia
  3. 3.Departamento de PaleobiologíaMuseo Nacional de Ciencias Naturales, CSICMadridSpain
  4. 4.INCUAPA, Departamento de ArqueologíaUniversidad Nacional del Centro Del ValleOlavarríaArgentina
  5. 5.Centro de Estudios del Cuaternario, Instituto de la PatagoniaUniversidad de MagallanesMagallanesChile

Personalised recommendations