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Ancient genomes revisit the ancestry of domestic and Przewalski’s horses

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Science  06 Apr 2018:
Vol. 360, Issue 6384, pp. 111-114
DOI: 10.1126/science.aao3297

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  • RE: The mystery wild Przewalski’s horse and its alleged feralisation: neglected alternative hypotheses and overstatements in Gaunitz et al.’s article and the press release.
    • Claudia Feh, Reintroduction director, Association pour le cheval de Przewalski : TAKH
    • Other Contributors:
      • Frédéric Joly, Director, Association pour le cheval de Przewalski : TAKH
      • Hannah Davie, School of Animal, Rural and Environmental Sciences, Nottingham Trent University
      • Florian Drouard, Association pour le cheval de Przewalski : TAKH

    COMPREHENSIVE SUMMARY
    Ever since Nicolai Przewalski brought the skin and skull of an unknown equid back from one of his expeditions to Central Asia in 1879, the status of the Przewalski’s horse (PH) has been hotly debated: Was it a new species? A crossbreed with the wild ass, Equus hemionus? Was it a wild horse? (1, 2). Gaunitz et al. (3) therefore renew an old argument. Nevertheless, the authors’ conclusion that PH are feral descendants of the allegedly domesticated Botai/Borly horse population that existed 5,500 BP in northern Kazakhstan is based on the genetic analyses of a highly selective sample choice, previously contested (4) archaeological studies (5) and no conclusive evidence for a feralisation process.
    As Orlando and Outram state in their press release, the subject of the study was to identify the origin of domestic horses, not the phylogeny of wild versus domesticated horses. Besides, ever since the establishment of the Przewalski’s horse pedigree (6) and recent genetic analyses (7), we know that ancient and recent introgression between PH and domestic horses occurred over several thousand years. Furthermore, genetic bottlenecks and potential other changes affecting PH due to their 10 generations of life in captivity before being reintroduced 26 years ago may have had an unconscious and unverifiable influence on their genome, making comparative studies on ‘domestic’ or ‘feral’ selective forces inconclusive (8). However, persons familiar with PH know...

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    Competing Interests: None declared.
  • RE: Przewalski’s horses may be wild, despite close relationship with early domestic horses
    • Chris Walzer, Exec. Director Wildlife Health, Wildlife Conservation Society Bronx, USA, and University of Veterinary Medicine, Vienna, Austria,
    • Other Contributors:
      • Pamela Burger, Conservation Geneticist, Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
      • Oyunsaikhan Ganbaatar, Director, Greater Gobi B Strictly Protected Area, Takhiin Tal, Mongolia
      • Petra Kaczensky, Ecologist, Norwegian Institute for Nature Research, Trondheim, Norway, and University of Veterinary Medicine, Vienna, Austria
      • Peter Kistler, Zoologist, Science Communication, International Takhi Group, ITG, c/o Stiftung Wildnispark Zürich, Sihlwald, Switzerland
      • Reinhard Schnidrig, Zoologist, President ITG, International Takhi Group, ITG, c/o Stiftung Wildnispark Zürich, Sihlwald, Switzerland
      • Jaroslav Šimek, PH International Studbook Keeper, Deputy Director, Prague Zoo, Prague, Czech Republic
      • Steve Smith, Head Genetics Unit, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, Austria
      • Christian Stauffer, ITG Board Member, General Manager, Swiss Parks Network, Bern, Switzerland
      • Claus Vogl, Geneticist, Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria

    C. Gaunitz et al. (1) conclude from their comprehensive analysis of ancient horse genomes that extant Przewalski’s horses (PH) are feral descendants of previously domesticated Botai horses. While this might be one possible scenario considering the currently available genetic data, from a population genetics point of view we favor an alternative interpretation. PH could actually derive from an unsampled horse population that is closely related to the Botai population but was never domesticated and might never have carried putatively (2) domestic signatures such as the TRPM1 allele. It is not possible to establish relationships accurately enough with 5000-year-old data (several hundred horse generations), that is by its very nature patchy in sample coverage, to claim actual ancestry of a sequenced ancient horse to an extant free-roaming wild horse. In fact, principal component analysis reveals PH and the archaic Botai/Borly horses as two independent clusters (1), although this might be explained by genetic drift due to the extreme genetic pressure from relentless hunting of PH, culminating in their extinction in the wild in the 1960s. One could consider the Botai herd as corralled PH and on their way to domestication, but not making it into later populations of domesticated horses and not necessarily making it into any wild populations of PH that likely existed in numbers before, during, and after the Botai horse herds. Regardless of the interpretation (related or feral), PH...

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    Competing Interests: None declared.
  • Domestication rather than taming is required to explain Botai phenomenon
    • Ludovic Orlando, Professor of Molecular Archaeology, Research Director, Centre for GeoGenetics, SNM, Copenhagen, Denmark; Laboratoire AMIS CNRS UMR 5288, Université de Toulouse, UPS, Toulouse, France
    • Other Contributors:
      • Alan K Outram, Head of Archaeology, Professor of Archaeological Science, Department of Archaeology, University of Exeter, Exeter, UK

    Comparing Botai horse herding with elephant taming is inappropriate. The Botai culture manifests a sudden, extreme focus on horses as its subsistence base across at least a 1,000km swathe of the Central Asian forest steppe for at least ~500 years (1, 2). Control of the horse resource is evidenced by corrals (1, 3), poleaxing and absence of ‘Schlepp effect’ (3), suggesting slaughter at settlements. Exploitation includes harnessing and milking, evidenced through three types of ‘bit-wear’ and ceramic lipid residues, respectively (4).

    Demographic modelling and drift estimates indicate collapsing wild horse populations prior to domestication (1). Advocating that hunter-gatherers, faced with this, would simultaneously increase dependency on that species whilst reducing mobility clashes with accepted models of diet breadth (5), territoriality and mobility (6). Reduced mobility and specialization are instead commonly associated with domestication (7).

    Holistically the evidence supports increasing control to intensively exploit a diminishing resource. Ancient human genomes (8, 9) demonstrate Sintashta-Andronovo-related migrations from the West replacing Botai-like populations without admixture in the later Bronze Age. This highlights a strong pressure to translocate eastwards, consistent with the presence of Botai horse’s direct feral descendants in Mongolia when discovered by Colonel Przewalski.

    PH conservation has been tremendously successful following their...

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    Competing Interests: None declared.
  • Przewalski’s horses and earliest domesticates are not sister populations but descend from one another
    • Ludovic Orlando, Professor of Molecular Archaeology, Research Director, Centre for GeoGenetics, SNM, Copenhagen, Denmark; Laboratoire AMIS CNRS UMR 5288, Université de Toulouse, UPS, Toulouse, France
    • Other Contributors:
      • Alan K Outram, Head of Archaeology, Professor of Archaeological Science, Department of Archaeology, University of Exeter, Exeter, UK

    If ‘BB and PH descended from a common ancestor’, they should form two reciprocally monophyletic clades. This is ruled out in phylogenies showing strong temporal structure within a single lineage where Botai horses branch out first, followed by Borly4, one 19th century PH paratype and finally modern PH horses (1). This receives maximal bootstrap support at key nodes and is robust to the method considered, post-mortem damage (as transitions were disregarded (2)) and incomplete lineage sorting (as not based on single markers but ~3.7-14.0 million transversion sites across the genome).

    Direct-ancestry tests contrast a scenario where two lineages diverge from a common ancestor and another where they are placed along the same evolutionary branch, with the oldest directly ancestral to the youngest (3). Seven out of nine such tests support Botai horses as the direct ancestors of the PH paratype, which represents the only pre-captivity PH specimen sequenced with limited transversion errors (4). Rejecting direct ancestry is difficult close to split times (5), however, replacing Botai with Borly4 horses, which differentiated for ~500 additional years (~50-100 generations), still supported direct ancestry in all five tests implemented.

    Rejection of half the tests between the paratype and modern PH horses illustrates the significant introgression of domestic DOM2 genes during the 20th century, representing ~7% of the genome in the subset of modern PH horses considered in...

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    Competing Interests: None declared.
  • As wild as they come: Study confirms that Przewalski’s horses are the best of the rest
    • Peter Leimgruber, Center Head & Conservation Biologist, Conservation Ecology Center, Smithsonian Conservation Biology Institute, Front Royal, VA 22630, USA.
    • Other Contributors:
      • Michael G. Campana, Computational Genomics Scientist, Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, D.C. 20008, USA.
      • Jesus E. Maldonado, Research Geneticist, Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, D.C. 20008, USA.
      • Tara R. Harris, Vice President for Conservation, Minnesota Zoo, Apple Valley, MN 55124, USA.
      • Nandintsetseg Dejid, PhD Candidate, Biodiversity and Climate Research Centre, Senckenberg Gesellschaft fur Naturforschung, Frankfurt 60325, Germany.
      • Qing Cao, PhD Candidate, Department of Ecology & Evolutionary Biology, Princeton, NJ 08544, USA.
      • Melissa A. Songer, Conservation Ecologist, Conservation Ecology Center, Smithsonian Conservation Biology Institute, Washington, D.C. 20008, USA.

    Przewalski’s horses (PH) have been considered the last surviving wild horse species (1). Gaunitz et al. provide new information on their phylogenetic origin, with PH more closely related to Botai than domestic horses (2). They concluded PH are not wild but feral because Botai horses are considered the first domesticated species by some (4). However, it is possible Botai horses were only tamed since they form a distinct clade from extant and ancient domesticated horses. Similar taming of a wild species occurred in Asian elephants which have never been domesticated but have been used as draft and war animals for thousands of years (5). Regardless, there is no strong evidence that PH are feral descendants of domestic ancestors. Rather, they are unique descendants of horses within the Botai/Borly clade, representing genetic diversity that no longer exists within other extant horses. Thus, while the new data highlights a close relationship with Botai horses, it does not confirm domestication or that PH are feral. In addition, the ‘ancient’ PH samples used were very recent and indicate little about PH diversity given genomic encroachment of the common domestic horse in the region. Twenty-five domestication experts warn against this type of assumption, and recommend that authors limit the definition of domestication to the “initial independent process”, consider whether more than one domestication has occurred, and do not apply the definition to admixtures that comprise genes an...

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    Competing Interests: None declared.
  • RE: Ancient genomes revisit the ancestry of domestic and Przewalski’s horses
    • Lee Boyd, IUCN/SSC Equid Specialist Group Przewalski's Horse Coordinator, Washburn University, Topeka, KS, 66621 USA
    • Other Contributors:
      • Sarah King, IUCN/SSCEquid Specialist Group co-chair, NREL, Warner College od Natural Resources, Colorado State University
      • Patricia Moehlman, IUCN/SSCEquid Specialist Group co-chair, Columbia University, NY
      • George Amato, IUCN/SSCEquid Specialist Group Population Genetics Coordinator, Sackler Institute for Comparative Genomics, American Museum of Natural History
      • Vera M. Warmuth, Faculty of Biology, Division of Evolutionary Biology, Ludwig-Maximilians-Universität München
      • Lkhagvasuren Badamjav, IUCN/SSC Equid Specialist Group Asiatic Wild Ass Coordinator, Mammalian Ecology Laboratory Institute of General & Experimental Biology, Mongolian Academy of Sciences

    Hold Your Horses

    In their February 22, 2018 article, Gaunitz et al.1 posit that Przewalski’s horses (PH) are feral descendants of Botai/Borly4 horses (BB). The genetic evidence provided by Gaunitz et al.1 for BB as direct ancestors of PH is weak. In drift-based ancestry tests only one of seven PH showed evidence of BB horse ancestry, and it is unclear how well test assumptions were met and damage errors typical of aDNA were accounted for. Second, the observation that PH are 'nested within BB horses' in some of the phylogenetic trees presented is equally compatible with PH being the never-domesticated descendants of the same wild horse population drawn upon by the Botai culture. If that were the case, the whole argument of PH being feral rather than wild collapses.

    According to Gaunitz et al. (2018) the leopard-spotting allele was present in BB. Due to the limited number of founders (n=13), and resultant inbreeding, this allele would be evident if it existed in the extant PH population. Gaunitz et al.1 hypothesize that the allele was subsequently selected against in the wild. Yet multiple unmanaged domestic horse populations contain thriving leopard-spotted individuals, and 5,000 years is a brief span in which to expect natural selection to eliminate this allele. It is more likely that PH do not carry this mutation because they are not direct descendants of BB.

    Genetic data from the extinct species that gave rise to modern horses and the exti...

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    Competing Interests: None declared.