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.

Animal Ecology Department of Ecology and Genetics Evolutionary Biology Centre Science for Life Laboratory Uppsala Universitet Uppsala Sweden

Breeding Centre for Endangered Arabian Wildlife Sharjah United Arab Emirates

CE3C Centre for Ecology Evolution and Environmental Changes and CHANGE Global Change and Sustainability Institute Departamento de Biologia Animal Faculdade de Ciências Universidade de Lisboa Lisbon Portugal

Central European Institute of Technology University of Veterinary Sciences Brno Brno Czech Republic

Department of Animal Genetics University of Veterinary Sciences Brno Czech Republic

Department of Ecology and Evolution University of Lausanne Lausanne Switzerland

Department of Natural History NTNU University Museum Norwegian University of Science and Technology Trondheim Norway

Faculdade de Psicologia Universidade de Lisboa Alameda da Universidade Lisbon Portugal

Genetics Department University of the Free State Bloemfontein South Africa

Institute for Ecology Evolution and Diversity Goethe University Frankfurt Germany

Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK

LOEWE Center for Translational Biodiversity Genomics Senckenberg Museum Frankfurt Germany

Research Institute of Wildlife Ecology Vetmeduni Vienna Vienna Austria

Rex Foundation Dunstable UK

School of Life Sciences University of KwaZulu Natal Durban South Africa

South African National Biodiversity Institute Pretoria South Africa

Wildlife Conservation Society New York New York USA

Zoological Institute Russian Academy of Sciences Saint Petersburg Russia

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Altschul, S. F. , Gish, W. , Miller, W. , Myers, E. W. , & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410. 10.1016/S0022-2836(05)80360-2 PubMed DOI

Belbachir, F. (2008). Acinonyx jubatus ssp. Hecki. The IUCN red list of threatened species 2008 , e.T221A13035738. 10.2305/IUCN.UK.2008.RLTS.T221A13035738.en DOI

Bertola, L. D. , Jongbloed, H. , van der Gaag, K. J. , de Knijff, P. , Yamaguchi, N. , Hooghiemstra, H. , Bauer, H. , Henschel, P. , White, P. A. , Driscoll, C. A. , Tende, T. , Ottosson, U. , Saidu, Y. , Vrieling, K. , & de Longh, H. H. (2016). Phylogeographic patterns in Africa and high resolution delineation of genetic clades in the lion (Panthera leo). Scientific Reports, 6(1), 1–11. 10.1038/srep30807 PubMed DOI PMC

Beschta, R. L. , & Ripple, W. J. (2009). Large predators and trophic cascades in terrestrial ecosystems of the western United States. Biological Conservation, 142(11), 2401–2414. 10.1016/j.biocon.2009.06.015 DOI

Boast, L. K. , Chelysheva, E. V. , van der Merwe, V. , Schmidt‐Küntzel, A. , Walker, E. H. , Cilliers, D. , Gusset, M. , & Marker, L. (2018). Chapter 20—Cheetah translocation and reintroduction programs: Past, present, and future. In Nyhus P. J., Marker L., Boast L. K., & Schmidt‐Küntzel A. (Eds.), Cheetahs: Biology and conservation (pp. 275–289). Academic Press. 10.1016/B978-0-12-804088-1.00020-4 DOI

Briers‐Louw, W. D. , Verschueren, S. , & Leslie, A. J. (2019). Big cats return to Majete wildlife reserve, Malawi: Evaluating reintroduction success. African Journal of Wildlife Research, 49(1), 34–50. 10.3957/056.049.0034 DOI

Burger, P. A. , Steinborn, R. , Walzer, C. , Petit, T. , Mueller, M. , & Schwarzenberger, F. (2004). Analysis of the mitochondrial genome of cheetahs (Acinonyx jubatus) with neurodegenerative disease. Gene, 338(1), 111–119. 10.1016/j.gene.2004.05.020 PubMed DOI PMC

Castro‐Prieto, A. , Wachter, B. , Melzheimer, J. , Thalwitzer, S. , & Sommer, S. (2011). Diversity and evolutionary patterns of immune genes in free‐ranging Namibian leopards (Panthera pardus pardus). Journal of Heredity, 102(6), 653–665. 10.1093/jhered/esr097 PubMed DOI

Castro‐Prieto, A. , Wachter, B. , & Sommer, S. (2011). Cheetah paradigm revisited: MHC diversity in the World's largest free‐ranging population. Molecular Biology and Evolution, 28(4), 1455–1468. 10.1093/molbev/msq330 PubMed DOI PMC

Charruau, P. , Fernandes, C. , Orozco‐terWengel, P. , Peters, J. , Hunter, L. , Ziaie, H. , Jourabchian, A. , Jowkar, H. , Schaller, G. , Ostrowski, S. , Vercammen, P. , Grange, T. , Schlötterer, C. , Kotze, A. , Geigl, E.‐M. , Walzer, C. , & Burger, P. A. (2011). Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: Evidence for long‐term geographic isolates. Molecular Ecology, 20(4), 706–724. 10.1111/j.1365-294X.2010.04986.x PubMed DOI PMC

Cheng, B. S. , Komoroske, L. M. , & Grosholz, E. D. (2017). Trophic sensitivity of invasive predator and native prey interactions: Integrating environmental context and climate change. Functional Ecology, 31(3), 642–652. 10.1111/1365-2435.12759 DOI

Colwell, R. K. , & Elsensohn, J. E. (2014). EstimateS turns 20: Statistical estimation of species richness and shared species from samples, with non‐parametric extrapolation. Ecography, 37(6), 609–613.

Dabney, J. , Knapp, M. , Glocke, I. , Gansauge, M.‐T. , Weihmann, A. , Nickel, B. , Valdiosera, C. , García, N. , Pääbo, S. , Arsuaga, J.‐L. , & Meyer, M. (2013). Complete mitochondrial genome sequence of a middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proceedings of the National Academy of Sciences, 110(39), 15758–15763. 10.1073/pnas.1314445110 PubMed DOI PMC

de Manuel, M. , Barnett, R. , Sandoval‐Velasco, M. , Yamaguchi, N. , Vieira, F. G. , Mendoza, M. L. Z. , Liu, S. , Martin, M. D. , Sinding, M.‐H. S. , Mak, S. S. T. , Carøe, C. , Liu, S. , Guo, C. , Zheng, J. , Zazula, G. , Baryshnikov, G. , Eizirik, E. , Koepfli, K.‐P. , Johnson, W. E. , … Gilbert, M. T. P. (2020). The evolutionary history of extinct and living lions. Proceedings of the National Academy of Sciences, 117(20), 10927–10934. 10.1073/pnas.1919423117 PubMed DOI PMC

Díaz, S. , Settele, J. , Brondízio, E. S. , Ngo, H. T. , Agard, J. , Arneth, A. , Balvanera, P. , Brauman, K. A. , Butchart, S. H. M. , Chan, K. M. A. , Garibaldi, L. A. , Ichii, K. , Liu, J. , Subramanian, S. M. , Midgley, G. F. , Miloslavich, P. , Molnár, Z. , Obura, D. , Pfaff, A. , … Zayas, C. N. (2019). Pervasive human‐driven decline of life on earth points to the need for transformative change. Science, 366(6471). 10.1126/science.aax3100 PubMed DOI

Divyabhanusinh, G. . (1999). The end of a trail: The cheetah in India. Oxford University Press.

Dobrynin, P. , Liu, S. , Tamazian, G. , Xiong, Z. , Yurchenko, A. A. , Krasheninnikova, K. , Kliver, S. , Schmidt‐Küntzel, A. , Koepfli, K.‐P. , Johnson, W. , Kuderna, L. F. K. , García‐Pérez, R. , Manuel, M. , de Godinez, R. , Komissarov, A. , Makunin, A. , Brukhin, V. , Qiu, W. , Zhou, L. , … O'Brien, S. J. (2015). Genomic legacy of the African cheetah, Acinonyx jubatus. Genome Biology, 16(1), 277. 10.1186/s13059-015-0837-4 PubMed DOI PMC

Drake, G. J. C. , Kennedy, L. J. , Auty, H. K. , Ryvar, R. , Ollier, W. E. R. , Kitchener, A. C. , Freeman, A. R. , & Radford, A. D. (2004). The use of reference strand‐mediated conformational analysis for the study of cheetah (Acinonyx jubatus) feline leucocyte antigen class II DRB polymorphisms. Molecular Ecology, 13(1), 221–229. 10.1046/j.1365-294X.2003.02027.x PubMed DOI

Durant, S. , Mitchell, N. , Groom, R. , Pettorelli, N. , Ipavec, A. , Jacobson, A. P. , Woodroffe, R. , Böhm, M. , Hunter, L. T. B. , Becker, M. S. , Broekhuis, F. , Bashir, S. , Andresen, L. , Aschenborn, O. , Beddiaf, M. , Belbachir, F. , Belbachir‐Bazi, A. , Berbash, A. , de Matos, B. , … Young‐Overton, K. (2017). The global decline of cheetah Acinonyx jubatus and what it means for conservation. Proceedings of the National Academy of Sciences, 114(3), 528–533. 10.1073/pnas.1611122114 PubMed DOI PMC

Durant, S. , Mitchell, N. , Ipavec, A. , & Groom, R. (2015). Acinonyx jubatus. The IUCN red list of threatened species 2015 , e.T219A50649567. 10.2305/IUCN.UK.2015-4.RLTS.T219A50649567.en DOI

Durant, S. M. , Wacher, T. , Bashir, S. , Woodroffe, R. , Ornellas, P. D. , Ransom, C. , Newby, J. , Abáigar, T. , Abdelgadir, M. , Alqamy, H. E. , Baillie, J. , Beddiaf, M. , Belbachir, F. , Belbachir‐Bazi, A. , Berbash, A. A. , Bemadjim, N. E. , Beudels‐Jamar, R. , Boitani, L. , Breitenmoser, C. , … Pettorelli, N. (2014). Fiddling in biodiversity hotspots while deserts burn? Collapse of the Sahara's megafauna. Diversity and Distributions, 20(1), 114–122. 10.1111/ddi.12157 DOI

Eichenberg, D. , Bowler, D. E. , Bonn, A. , Bruelheide, H. , Grescho, V. , Harter, D. , Jandt, U. , May, R. , Winter, M. , & Jansen, F. (2021). Widespread decline in central European plant diversity across six decades. Global Change Biology, 27(5), 1097–1110. 10.1111/gcb.15447 PubMed DOI

Estes, J. A. , Terborgh, J. , Brashares, J. S. , Power, M. E. , Berger, J. , Bond, W. J. , Carpenter, S. R. , Essington, T. E. , Holt, R. D. , Jackson, J. B. C. , Marquis, R. J. , Oksanen, L. , Oksanen, T. , Paine, R. T. , Pikitch, E. K. , Ripple, W. J. , Sandin, S. A. , Scheffer, M. , Schoener, T. W. , … Wardle, D. A. (2011). Trophic downgrading of planet earth. Science, 333(6040), 301–306. 10.1126/science.1205106 PubMed DOI

Excoffier, L. , & Lischer, H. E. (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and windows. Molecular Ecology Resources, 10(3), 564–567. PubMed

Farhadinia, M. S. , Hunter, L. T. B. , Jourabchian, A. , Hosseini‐Zavarei, F. , Akbari, H. , Ziaie, H. , Schaller, G. B. , & Jowkar, H. (2017). The critically endangered Asiatic cheetah Acinonyx jubatus venaticus in Iran: A review of recent distribution, and conservation status. Biodiversity and Conservation, 26(5), 1027–1046. 10.1007/s10531-017-1298-8 DOI

Frank, D. A. (2008). Evidence for top predator control of a grazing ecosystem. Oikos, 117(11), 1718–1724.

Frankham, R. , Briscoe, D. A. , & Ballou, J. D. (2002). Introduction to conservation genetics. Cambridge University Press.

Fukushima, C. S. , Mammola, S. , & Cardoso, P. (2020). Global wildlife trade permeates the tree of life. Biological Conservation, 247, 108503. PubMed PMC

Fumagalli, M. , Vieira, F. G. , Linderoth, T. , & Nielsen, R. (2014). ngsTools: Methods for population genetics analyses from next‐generation sequencing data. Bioinformatics, 30(10), 1486–1487. 10.1093/bioinformatics/btu041 PubMed DOI PMC

Garcia‐Erill, G. , & Albrechtsen, A. (2020). Evaluation of model fit of inferred admixture proportions. Molecular Ecology Resources, 20(4), 936–949. 10.1111/1755-0998.13171 PubMed DOI

Hanghøj, K. , Moltke, I. , Andersen, P. A. , Manica, A. , & Korneliussen, T. S. (2019). Fast and accurate relatedness estimation from high‐throughput sequencing data in the presence of inbreeding. GigaScience, 8(5), giz034. 10.1093/gigascience/giz034 PubMed DOI PMC

Heinrich, S. K. , Hofer, H. , Courtiol, A. , Melzheimer, J. , Dehnhard, M. , Czirják, G. Á. , & Wachter, B. (2017). Cheetahs have a stronger constitutive innate immunity than leopards. Scientific Reports, 7(1), 1–11. 10.1038/srep44837 PubMed DOI PMC

Huson, D. H. , Kloepper, T. , & Bryant, D. (2008). SplitsTree 4.0—Computation of phylogenetic trees and networks. 2008 , 14, 68–73.

Jowkar, H. , Hunter, L. , Ziaie, H. , Marker, L. , Breitenmoser‐Wursten, C. , & Durant, S. (2008). Acinonyx jubatus ssp. Venaticus. The IUCN red list of threatened species 2008 , e.T220A13035342. 10.2305/IUCN.UK.2008.RLTS.T220A13035342.en DOI

Katoh, K. , & Standley, D. M. (2013). MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution, 30(4), 772–780. 10.1093/molbev/mst010 PubMed DOI PMC

Kitchener, A. C. , Breitenmoser‐Würsten, C. , Eizirik, E. , Gentry, A. , Werdelin, L. , Wilting, A. , Yamaguchi, N. , Abramov, A. V. , Christiansen, P. , Driscoll, C. , Duckworth, J. W. , Johnson, W. E. , Luo, S. J. , Meijaard, E. , O'Donoghue, P. , Sanderson, J. , Seymour, K. , Bruford, M. , Groves, C. , … Tobe, S. (2017). A revised taxonomy of the Felidae: The final report of the Cat Classification Task Force of the IUCN Cat Specialist Group . http://repository.si.edu/xmlui/handle/10088/32616

Kopelman, N. M. , Mayzel, J. , Jakobsson, M. , Rosenberg, N. A. , & Mayrose, I. (2015). Clumpak: A program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecology Resources, 15(5), 1179–1191. 10.1111/1755-0998.12387 PubMed DOI PMC

Korneliussen, T. S. , Albrechtsen, A. , & Nielsen, R. (2014). ANGSD: Analysis of next generation sequencing data. BMC Bioinformatics, 15(1), 356. 10.1186/s12859-014-0356-4 PubMed DOI PMC

Korneliussen, T. S. , & Moltke, I. (2015). NgsRelate: A software tool for estimating pairwise relatedness from next‐generation sequencing data. Bioinformatics, 31(24), 4009–4011. 10.1093/bioinformatics/btv509 PubMed DOI PMC

Krausman, P. R. , & Morales, S. M. (2005). Acinonyx jubatus. Mammalian Species, 2005(771), 1–6. 10.1644/1545-1410(2005)771[0001:AJ]2.0.CO;2 DOI

Lange, V. , Böhme, I. , Hofmann, J. , Lang, K. , Sauter, J. , Schöne, B. , Paul, P. , Albrecht, V. , Andreas, J. M. , Baier, D. M. , Nething, J. , Ehninger, U. , Schwarzelt, C. , Pingel, J. , Ehninger, G. , & Schmidt, A. H. (2014). Cost‐efficient high‐throughput HLA typing by MiSeq amplicon sequencing. BMC Genomics, 15(1), 63. 10.1186/1471-2164-15-63 PubMed DOI PMC

Lefort, V. , Desper, R. , & Gascuel, O. (2015). FastME 2.0: A comprehensive, accurate, and fast distance‐based phylogeny inference program. Molecular Biology and Evolution, 32(10), 2798–2800. 10.1093/molbev/msv150 PubMed DOI PMC

Leigh, J. W. , & Bryant, D. (2015). Popart: Full‐feature software for haplotype network construction. Methods in Ecology and Evolution, 6(9), 1110–1116. 10.1111/2041-210X.12410 DOI

Li, H. , & Durbin, R. (2010). Fast and accurate long‐read alignment with burrows‐wheeler transform. Bioinformatics, 26(5), 589–595. 10.1093/bioinformatics/btp698 PubMed DOI PMC

Li, H. , Handsaker, B. , Wysoker, A. , Fennell, T. , Ruan, J. , Homer, N. , Marth, G. , Abecasis, G. , & Durbin, R. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25(16), 2078–2079. 10.1093/bioinformatics/btp352 PubMed DOI PMC

Librado, P. , & Rozas, J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25(11), 1451–1452. 10.1093/bioinformatics/btp187 PubMed DOI

Lindsey, P. A. , Romañach, S. S. , Tambling, C. J. , Chartier, K. , & Groom, R. (2011). Ecological and financial impacts of illegal bushmeat trade in Zimbabwe. Oryx, 45(1), 96–111. 10.1017/S0030605310000153 DOI

Liu, Y.‐C. , Sun, X. , Driscoll, C. , Miquelle, D. G. , Xu, X. , Martelli, P. , Uphyrkina, O. , Smith, J. L. D. , O'Brien, S. J. , & Luo, S.‐J. (2018). Genome‐wide evolutionary analysis of natural history and adaptation in the World's tigers. Current Biology, 28(23), 3840–3849.e6. 10.1016/j.cub.2018.09.019 PubMed DOI

Magliolo, M. , Prost, S. , Orozco‐terWengel, P. , Burger, P. , Kropff, A. S. , Kotze, A. , Grobler, J. P. , & Dalton, D. L. (2021). Unlocking the potential of a validated single nucleotide polymorphism array for genomic monitoring of trade in cheetahs (Acinonyx jubatus). Molecular Biology Reports, 48(1), 171–181. 10.1007/s11033-020-06030-0 PubMed DOI

Maxwell, S. L. , Fuller, R. A. , Brooks, T. M. , & Watson, J. E. M. (2016). Biodiversity: The ravages of guns, nets and bulldozers. Nature News, 536(7615), 143–145. 10.1038/536143a PubMed DOI

McKenna, A. , Hanna, M. , Banks, E. , Sivachenko, A. , Cibulskis, K. , Kernytsky, A. , Garimella, K. , Altshuler, D. , Gabriel, S. , Daly, M. , & DePristo, M. A. (2010). The genome analysis toolkit: A MapReduce framework for analyzing next‐generation DNA sequencing data. Genome Research, 20(9), 1297–1303. 10.1101/gr.107524.110 PubMed DOI PMC

Meisner, J. , & Albrechtsen, A. (2018). Inferring population structure and admixture proportions in low‐depth NGS data. Genetics, 210(2), 719–731. 10.1534/genetics.118.301336 PubMed DOI PMC

Meyer, M. , & Kircher, M. (2010). Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harbor Protocols, 2010(6), pdb.prot5448. 10.1101/pdb.prot5448 PubMed DOI

Nazareno, A. G. , Bemmels, J. B. , Dick, C. W. , & Lohmann, L. G. (2017). Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species. Molecular Ecology Resources, 17(6), 1136–1147. 10.1111/1755-0998.12654 PubMed DOI

Nguyen, L.‐T. , Schmidt, H. A. , von Haeseler, A. , & Minh, B. Q. (2015). IQ‐TREE: A fast and effective stochastic algorithm for estimating maximum‐likelihood phylogenies. Molecular Biology and Evolution, 32(1), 268–274. 10.1093/molbev/msu300 PubMed DOI PMC

Nowell, K. (2014). An assessment of the conservation impacts of legal and illegal trade in cheetahs Acinonyx jubatus. In: IUCN SSC Cat Specialist Group report prepared forthe CITES Secretariat, 65th meeting of the CITES Standing Committee, Geneva, 7‐11 July. CITES SC65 Doc. 39. http://cites.org/sites/default/files/eng/com/sc/65/E‐SC65‐39.pdf

O'Brien, S. J. , Johnson, W. E. , Driscoll, C. A. , Dobrynin, P. , & Marker, L. (2017). Conservation genetics of the cheetah: Lessons learned and new opportunities. Journal of Heredity, 108(6), 671–677. 10.1093/jhered/esx047 PubMed DOI PMC

O'Brien, S. J. , Wildt, D. E. , Bush, M. , Caro, T. M. , FitzGibbon, C. , Aggundey, I. , & Leakey, R. E. (1987). East African cheetahs: Evidence for two population bottlenecks? Proceedings of the National Academy of Sciences, 84(2), 508–511. 10.1073/pnas.84.2.508 PubMed DOI PMC

O'Brien, S. J. , & Yuhki, N. (1999). Comparative genome organization of the major histocompatibility complex: Lessons from the Felidae. Immunological Reviews, 167(1), 133–144. 10.1111/j.1600-065X.1999.tb01387.x PubMed DOI PMC

O'Brien, S. J. , Wildt, D. E. , Goldman, D. , Merril, C. R. , & Bush, M. (1983). The cheetah is depauperate in genetic variation. Science, 221(4609), 459–462. 10.1126/science.221.4609.459 PubMed DOI

Okonechnikov, K. , Conesa, A. , & García‐Alcalde, F. (2016). Qualimap 2: Advanced multi‐sample quality control for high‐throughput sequencing data. Bioinformatics, 32(2), 292–294. 10.1093/bioinformatics/btv566 PubMed DOI PMC

Pečnerová, P. , Garcia‐Erill, G. , Liu, X. , Nursyifa, C. , Waples, R. K. , Santander, C. G. , Quinn, L. , Frandsen, P. , Meisner, J. , Stæger, F. F. , Rasmussen, M. S. , Brüniche‐Olsen, A. , Hviid Friis Jørgensen, C. , da Fonseca, R. R. , Siegismund, H. R. , Albrechtsen, A. , Heller, R. , Moltke, I. , & Hanghøj, K. (2021). High genetic diversity and low differentiation reflect the ecological versatility of the African leopard. Current Biology, 31, 1862–1871.e5. 10.1016/j.cub.2021.01.064 PubMed DOI

Peterson, B. K. , Weber, J. N. , Kay, E. H. , Fisher, H. S. , & Hoekstra, H. E. (2012). Double digest RADseq: An inexpensive method for De novo SNP discovery and genotyping in model and non‐model species. PLoS One, 7(5), e37135. 10.1371/journal.pone.0037135 PubMed DOI PMC

Petkova, D. , Novembre, J. , & Stephens, M. (2016). Visualizing spatial population structure with estimated effective migration surfaces. Nature Genetics, 48(1), 94–100. 10.1038/ng.3464 PubMed DOI PMC

Pocock, R. I. (1939). The Fauna of British India including Ceylon and Burma Vol‐1 . http://krishikosh.egranth.ac.in/handle/1/19065

Pokorny, I. , Sharma, R. , Goyal, S. P. , Mishra, S. , & Tiedemann, R. (2010). MHC class I and MHC class II DRB gene variability in wild and captive Bengal tigers (Panthera tigris tigris). Immunogenetics, 62(10), 667–679. 10.1007/s00251-010-0475-7 PubMed DOI

Puechmaille, S. J. (2016). The program structure does not reliably recover the correct population structure when sampling is uneven: Subsampling and new estimators alleviate the problem. Molecular Ecology Resources, 16(3), 608–627. 10.1111/1755-0998.12512 PubMed DOI

Rai, N. , Verma, S. K. , Gaur, A. , Iliescu, F. M. , Thakur, M. , Golla, T. R. , Chandra, K. , Prakash, S. , Tabasum, W. , Ara, S. , Singh, L. , Thangaraj, K. , & Jacobs, G. S. (2020). Ancient mtDNA from the extinct Indian cheetah supports unexpectedly deep divergence from African cheetahs. Scientific Reports, 10(1), 1–11. 10.1038/s41598-020-60751-7 PubMed DOI PMC

Ranjitsinh, M. K. , & Jhala, Y. V. (2010). Assessing the potential for reintroducing the cheetah in India. Wildlife Trust of India, Noida, & the wildlife Institute of India, Dehradun, TR2010/001.

Raven, P. H. , & Wagner, D. L. (2021). Agricultural intensification and climate change are rapidly decreasing insect biodiversity. Proceedings of the National Academy of Sciences, 118(2), e2002548117. 10.1073/pnas.2002548117 PubMed DOI PMC

Ray, J. C. (2005). Setting conservation and research priorities for larger African carnivores. Wildlife Conservation Society.

Rohland, N. , Siedel, H. , & Hofreiter, M. (2010). A rapid column‐based ancient DNA extraction method for increased sample throughput. Molecular Ecology Resources, 10(4), 677–683. 10.1111/j.1755-0998.2009.02824.x PubMed DOI

Sackett, L. C. , Seglund, A. , Guralnick, R. P. , Mazzella, M. N. , Wagner, D. M. , Busch, J. D. , & Martin, A. P. (2014). Evidence for two subspecies of Gunnison's prairie dogs (Cynomys gunnisoni), and the general importance of the subspecies concept. Biological Conservation, 174, 1–11. 10.1016/j.biocon.2014.03.010 DOI

Scheffers, B. R. , Oliveira, B. F. , Lamb, I. , & Edwards, D. P. (2019). Global wildlife trade across the tree of life. Science, 366(6461), 71–76. 10.1126/science.aav5327 PubMed DOI

Schmidt‐Kuntzel, A. , Dalton, D. L. , Menotti‐Raymond, M. , Fabiano, E. , Charruau, P. , Johnson, W. E. , Sommer, S. , Marker, L. , Kotze, A. , & O'Brien, S. J. (2018). Conservation genetics of the cheetah: Genetic history and implications for conservation. In Cheetahs: Biology and conservation: Biodiversity of the world: Conservation from genes to landscapes (pp. 71–92). Academic Press. 10.1016/B978-0-12-804088-1.00006-X DOI

Schubert, M. , Lindgreen, S. , & Orlando, L. (2016). AdapterRemoval v2: Rapid adapter trimming, identification, and read merging. BMC Research Notes, 9(1), 88. 10.1186/s13104-016-1900-2 PubMed DOI PMC

Skotte, L. , Korneliussen, T. S. , & Albrechtsen, A. (2013). Estimating individual admixture proportions from next generation sequencing data. Genetics, 195(3), 693–702. 10.1534/genetics.113.154138 PubMed DOI PMC

Smitz, N. , Jouvenet, O. , Ligate, F. A. , Crosmary, W.‐G. , Ikanda, D. , Chardonnet, P. , Fusari, A. , Meganck, K. , Gillet, F. , Melletti, M. , & Michaux, J. R. (2018). A genome‐wide data assessment of the African lion (Panthera leo) population genetic structure and diversity in Tanzania. PLoS One, 13(11), e0205395. 10.1371/journal.pone.0205395 PubMed DOI PMC

Tricorache, P. , Nowell, K. , Wirth, G. , Mitchell, N. , Boast, L. K. , & Marker, L. (2018). Chapter 14—Pets and pelts: Understanding and combating poaching and trafficking in cheetahs. In Nyhus P. J., Marker L., Boast L. K., & Schmidt‐Küntzel A. (Eds.), Cheetahs: Biology and conservation (pp. 191–205). Academic Press. 10.1016/B978-0-12-804088-1.00014-9 DOI

Tricorache, P. , Yashphe, S. , & Marker, L. (2021). Global dataset for seized and non‐intercepted illegal cheetah trade (Acinonyx jubatus) 2010–2019. Data in Brief, 35, 106848. 10.1016/j.dib.2021.106848 PubMed DOI PMC

Voigt, W. , Perner, J. , Davis, A. J. , Eggers, T. , Schumacher, J. , Bährmann, R. , Fabian, B. , Heinrich, W. , Köhler, G. , Lichter, D. , Marstaller, R. , & Sander, F. W. (2003). Trophic levels are differentially sensitive to climate. Ecology, 84(9), 2444–2453. 10.1890/02-0266 DOI

Wang, X. , Wei, K. , Zhang, Z. , Xu, X. , Zhang, W. , Shen, F. , Zhang, L. , & Yue, B. (2009). Major histocompatibility complex class II DRB exon‐2 diversity of the Eurasian lynx (Lynx lynx) in China. Journal of Natural History, 43(3–4), 245–257. 10.1080/00222930802478669 DOI

Willing, E.‐M. , Dreyer, C. , & van Oosterhout, C. (2012). Estimates of genetic differentiation measured by fst do not necessarily require large sample sizes when using many snp markers, PLoS ONE, 7(8), e42649. 10.1371/journal.pone.0042649 PubMed DOI PMC

Winter, S. , Fennessy, J. , & Janke, A. (2018). Limited introgression supports division of giraffe into four species. Ecology and Evolution, 8(20), 10156–10165. 10.1002/ece3.4490 PubMed DOI PMC

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The potential and shortcomings of mitochondrial DNA analysis for cheetah conservation management

A chromosome-scale high-contiguity genome assembly of the cheetah (Acinonyx jubatus)

Comparative genomics of the Leukocyte Receptor Complex in carnivores

Comparative Genomics of the Major Histocompatibility Complex (MHC) of Felids

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