@article{8b4371642d124bc58f9b2003bdacc838,
title = "Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus)",
abstract = "We live in a world characterized by biodiversity loss and global environmental change. The extinction of large carnivores can have ramifying effects on ecosystems like an uncontrolled increase in wild herbivores, which in turn can have knock-on impacts on vegetation regeneration and communities. Cheetahs (Acinonyx jubatus) serve important ecosystem functions as apex predators; yet, they are quickly heading towards an uncertain future. Threatened by habitat loss, human-wildlife conflict and illegal trafficking, there are only approximately 7100 individuals remaining in nature. We present the most comprehensive genome-wide analysis of cheetah phylogeography and conservation genomics to date, assembling samples from nearly the entire current and past species' range. We show that their phylogeography is more complex than previously thought, and that East African cheetahs (A. j. raineyi) are genetically distinct from Southern African individuals (A. j. jubatus), warranting their recognition as a distinct subspecies. We found strong genetic differentiation between all classically recognized subspecies, thus refuting earlier findings that cheetahs show only little differentiation. The strongest differentiation was observed between the Asiatic and all the African subspecies. We detected high inbreeding in the Critically Endangered Iranian (A. j. venaticus) and North-western (A. j. hecki) subspecies, and show that overall cheetahs, along with snow leopards, have the lowest genome-wide heterozygosity of all the big cats. This further emphasizes the cheetah's perilous conservation status. Our results provide novel and important information on cheetah phylogeography that can support evidence-based conservation policy decisions to help protect this species. This is especially relevant in light of ongoing and proposed translocations across subspecies boundaries, and the increasing threats of illegal trafficking.",
keywords = "acinonyx jubatus, cheetah, conservation genomics, double-digest restriction site associated DNA (ddRAD) sequencing, phylogeography",
author = "Stefan Prost and Machado, {Ana Paula} and Julia Zumbroich and Lisa Preier and Sarita Mahtani-Williams and Rene Meissner and Katerina Guschanski and Brealey, {Jaelle C.} and Fernandes, {Carlos Rodr{\'i}guez} and Paul Vercammen and Hunter, {Luke T.B.} and Abramov, {Alexei V.} and Martin Plasil and Petr Horin and Lena Godsall-Bottriell and Paul Bottriell and Dalton, {Desire Lee} and Antoinette Kotze and Burger, {Pamela Anna}",
note = "Funding Information: For assistance with samples, we are very grateful to the Iranian Department of Environment, the CACP (Conservation of Asiatic Cheetah Project) and especially its former directors, Houman Jowkar, Alireza Jourabchian, Akbar Hamedanian and Hooshang Ziae. Thanks also to Stephane Ostrowski and Chris Walzer (WCS) for their assistance in Iran. We thank the curators of the Natural History Museums of London, Vienna, Berlin, Paris, Copenhagen, Stuttgart and Senckenberg, the Alexander Koenig Research Museum, the Harrison Institute, the Royal Museum of Scotland and the Royal Museum for Central Africa (Tervuren), and the Zoological Institute of the Russian Academy of Sciences (ZIN‐1021051302397‐6). We appreciate the support from the veterinarians and keepers of DECAN Rescue Centre Djibouti, Vienna Zoo, Salzburg Zoo, La Palmyre Zoo and the Zoological Garden of Montpellier. Thanks to the REX Foundation for access to their extensive collection. The authors further acknowledge support from the Central European Institute of Technology (CEITEC) in Brno (CZ; Jan Oppelt), the National Genomics Infrastructure in Stockholm funded by Science for Life Laboratory, the Knut and Alice Wallenberg Foundation and the Swedish Research Council, and SNIC/Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. The authors also thank Henrique Leit{\~a}o and Thijs Hofstede for assisting with processing the museum specimens in the aDNA laboratory. We thank Christine and Urs Breitenmoser, Sven Winter and Menno de‐Jong for their helpful comments on the manuscript, and Patricia Pe{\v c}nerov{\'a} for help plotting the EEMS results. PB and PH acknowledge funding from the Central European Science Partnership (CEUS) project Austrian Science Fund (FWF) I5081‐B/GACR Czech Republic 21‐28637L, as well as the Scientific & Technology Cooperation Austria, South Africa grant ZA02/2019 from the Austrian Agency for Education and Internationalization (OeAD) and the National Research Foundation, South Africa to PB and DLD. CRF thanks the support of cE3c through an assistant researcher contract (FCi{\^e}ncia.ID contract no. 366) and FCT (Funda{\c c}{\~a}o para a Ci{\^e}ncia e a Tecnologia) for Portuguese National Funds attributed to cE3c within the strategic project UID/BIA/00329/2020; CF also thanks FPUL for a contract of invited assistant professor. We thank Sara Durant and Mark Holden for the photographs used in Figure 1 . Photograph credits: ({\textcopyright}ZSL‐RWCP/Panthera/IUCN Cat SG in collaboration with APN), ({\textcopyright} Sarah Durant), ({\textcopyright}Sarah Durant), ({\textcopyright} Mark Holden) and ({\textcopyright} Sarah Durant). A. j. hecki A. j. jubatus A. j. venaticus A. j. soemmeringii A. j. raineyi Publisher Copyright: {\textcopyright} 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.",
year = "2022",
month = aug,
day = "1",
doi = "10.1111/mec.16577",
language = "English",
volume = "31",
pages = "4208--4223",
journal = "Molecular Ecology",
issn = "0962-1083",
publisher = "Wiley-Blackwell",
number = "16",
}