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Home / Equine Research Bank / PLoS One / Mitochondrial phylogenomics of modern and ancient equids.
PloS one2013; 8(2); e55950; doi: 10.1371/journal.pone.0055950

Mitochondrial phylogenomics of modern and ancient equids.

Abstract: The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy's zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya).
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Publication Date: 2013-02-20 PubMed ID: 23437078PubMed Central: PMC3577844DOI: 10.1371/journal.pone.0055950Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research focused on examining the evolutionary relationships within the genus Equus, which includes modern horses, zebras, asses, and donkeys, using mitochondrial phylogenomics from both modern and extinct species. The researchers drew from a data set of complete mitochondrial sequences from all seven existing lineages within the genus Equus.

Methodology

  • The researchers generated a comprehensive data set that included complete mitochondrial sequences derived from every extant or living lineage of the genus Equus.
  • Techniques for extracting and characterizing the complete mitochondrial genomes of extinct equid lineages were also implemented, specifically for the New World stilt-legged horses (NWSLH), the subgenus Sussemionus, and the Quagga (Equus quagga quagga).
  • Bayesian and Maximum Likelihood phylogenetic tools were used for data inference to estimate the phylogenetic relationships among the horses, zebras, asses, and donkeys.

Findings

  • Through the phylogenetic analysis, it was confirmed that zebras form a distinct group within the Equus genus. Moreover, the Plains and Grevy’s zebras specifically are in a well-supported monophyletic group, meaning they have a common ancestor that is not shared by any other species or group.
  • Results verified the New World stilt-legged horses as part of the caballines, a group which includes all modern horses.
  • The Quagga and Plains zebras were found to be conspecific, meaning they belong to the same species.
  • Despite the extensive data, the relationships among the non-caballine lineages, including the now extinct subgenus Sussemionus, remained unresolved due to assumptions of a rapid radiation within this group, meaning these species evolved quickly into distinct lineages.

Timeline and Molecular Clocks

  • There was an attempt to calibrate reliable molecular clocks using the closest living outgroups (rhinos and tapirs). However, these animal groups were found to be too genetically distant to provide accurate calibrations.
  • Despite this setback, the researchers were able to postulate that the modern equids may have shared a common ancestor up to as far as 4 Million years ago. However, a precise timeline of lineage radiation would require additional mitochondrial genome sequence data, which would preferably include radiocarbon-dated ancient equids.

Cite This Article

APA
Vilstrup JT, Seguin-Orlando A, Stiller M, Ginolhac A, Raghavan M, Nielsen SC, Weinstock J, Froese D, Vasiliev SK, Ovodov ND, Clary J, Helgen KM, Fleischer RC, Cooper A, Shapiro B, Orlando L. (2013). Mitochondrial phylogenomics of modern and ancient equids. PLoS One, 8(2), e55950. https://doi.org/10.1371/journal.pone.0055950

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 8
Issue: 2
Pages: e55950
PII: e55950

Researcher Affiliations

Vilstrup, Julia T
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
Seguin-Orlando, Andaine
    Stiller, Mathias
      Ginolhac, Aurelien
        Raghavan, Maanasa
          Nielsen, Sandra C A
            Weinstock, Jacobo
              Froese, Duane
                Vasiliev, Sergei K
                  Ovodov, Nikolai D
                    Clary, Joel
                      Helgen, Kristofer M
                        Fleischer, Robert C
                          Cooper, Alan
                            Shapiro, Beth
                              Orlando, Ludovic

                                MeSH Terms

                                • Animals
                                • Bayes Theorem
                                • Fossils
                                • Genome, Mitochondrial / genetics
                                • Genomics
                                • Horses / genetics
                                • Phylogeny
                                • Selection, Genetic / genetics
                                • Time Factors

                                Conflict of Interest Statement

                                The authors have declared that no competing interests exist.

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