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A southern African origin and cryptic structure in the highly mobile plains zebra

Nature Ecology & Evolution volume 2, pages 491–498 (2018)Cite this article

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Abstract

The plains zebra (Equus quagga) is an ecologically important species of the African savannah. It is also one of the most numerous and widely distributed ungulates, and six subspecies have been described based on morphological variation. However, the within-species evolutionary processes have been difficult to resolve due to its high mobility and a lack of consensus regarding the population structure. We obtained genome-wide DNA polymorphism data from more than 167,000 loci for 59 plains zebras from across the species range, encompassing all recognized extant subspecies, as well as three mountain zebras (Equus zebra) and three Grevy’s zebras (Equus grevyi). Surprisingly, the population genetic structure does not mirror the morphology-based subspecies delineation, underlining the dangers of basing management units exclusively on morphological variation. We use demographic modelling to provide insights into the past phylogeography of the species. The results identify a southern African location as the most likely source region from which all extant populations expanded around 370,000 years ago. We show evidence for inclusion of the extinct and phenotypically divergent quagga (Equus quagga quagga) in the plains zebra variation and reveal that it was less divergent from the other subspecies than the northernmost (Ugandan) extant population.

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Fig. 1: Sampling areas for the identified plains zebra populations.
Fig. 2: Estimating effective migration surfaces and directionality index.
Fig. 3: Admixture proportions using NGSadmix.
Fig. 4: Principal component analysis plot showing clustering in the plains zebras using the 60 individuals in dataset 2.
Fig. 5: Maximum likelihood tree obtained using TreeMix without migration edges for the 67 individuals in dataset 1.
Fig. 6: Stairway plots for the seven plains zebra populations with at least three samples.

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Acknowledgements

The authors thank A. al-Cher for laboratory work in connection with this study. The work was funded by research grants from the The Danish Council for Independent Research | Natural Sciences, the Lundbeck Foundation and the Villum Foundation.

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Authors and Affiliations

  1. Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, Denmark

    Casper-Emil T. Pedersen, Anders Albrechtsen, Hans R. Siegismund & Rasmus Heller

  2. Institute of Molecular Biology, University of Oregon, Eugene, OR, USA

    Paul D. Etter & Eric A. Johnson

  3. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark

    Ludovic Orlando

  4. Instituto Gulbenkian de Ciência, Oeiras, Portugal

    Lounes Chikhi

  5. Centre National de la Recherche Scientifique, Université Paul Sabatier, École Nationale de Formation Agronomique, UMR 5174 Laboratoire Évolution et Diversité Biologique, Toulouse, France

    Lounes Chikhi

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Contributions

C.-E.T.P and R.H. designed and performed the experiments, analysed the data and wrote the paper. A.A. developed the analytical tools and analysed the data. H.R.S., P.D.E., E.A.J., L.O. and L.C. analysed the data and wrote the paper.

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Correspondence to Casper-Emil T. Pedersen or Rasmus Heller.

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Pedersen, CE.T., Albrechtsen, A., Etter, P.D. et al. A southern African origin and cryptic structure in the highly mobile plains zebra. Nat Ecol Evol 2, 491–498 (2018). https://doi.org/10.1038/s41559-017-0453-7

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