UNLABELLED: There are only about 7,100 adolescent and adult cheetahs (Acinonyx jubatus) remaining in the wild. With the majority occurring outside protected areas, their numbers are rapidly declining. Evidence-based conservation measures are essential for the survival of this species. Genetic data is routinely used to inform conservation strategies, e.g., by establishing conservation units (CU). A commonly used marker in conservation genetics is mitochondrial DNA (mtDNA). Here, we investigated the cheetah's phylogeography using a large-scale mtDNA data set to refine subspecies distributions and better assign individuals to CUs. Our dataset mostly consisted of historic samples to cover the cheetah's whole range as the species has been extinct in most of its former distribution. While our genetic data largely agree with geography-based subspecies assignments, several geographic regions show conflicting mtDNA signals. Our analyses support previous findings that evolutionary forces such as incomplete lineage sorting or mitochondrial capture likely confound the mitochondrial phylogeography of this species, especially in East and, to some extent, in Northeast Africa. We caution that subspecies assignments solely based on mtDNA should be treated carefully and argue for an additional standardized nuclear single nucleotide polymorphism (SNP) marker set for subspecies identification and monitoring. However, the detection of the A. j. soemmeringii specific haplogroup by a newly designed Amplification-Refractory Mutation System (ARMS) can already provide support for conservation measures. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10592-022-01483-1.

BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Campus de Vairão 4485‑661 Vairão Portugal

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 1749 016 Lisboa Portugal

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

Centro de Investigação Em Biodiversidade e Recursos Genéticos CIBIO InBIO Laboratório Associado Campus de Vairão Universidade Do Porto Vairão Portugal

Department of Animal Genetics University of Veterinary Sciences Brno Czech Republic

Department of Behavioral and Cognitive Biology University of Vienna Djerassiplatz 1 1030 Vienna Austria

Faculdade de Psicologia Universidade de Lisboa Alameda da Universidade 1649 013 Lisboa Portugal

Institute for Ecology Evolution and Diversity Goethe University Max von Laue Straße 13 60438 Frankfurt am Main Germany

Kölner Zoo AG Riehler Straße 173 50735 Cologne Germany

Konrad Lorenz Institute of Ethology Savoyenstraße 1 1160 Vienna Austria

LOEWE Centre for Translational Biodiversity Genomics Senckenberganlage 25 60325 Frankfurt am Main Germany

Mohitban Society No 91 Moghaddas Ardebili str Tehran Iran

Natural History Museum Central Research Laboratories Burgring 7 1010 Vienna Austria

Opel Zoo von Opel Hessische Zoostiftung Königsteinerstrasse 35 61476 Kronberg im Taunus Germany

Research Institute of Wildlife Ecology University of Veterinary Medicine Savoyenstraße 1 1160 Vienna Austria

Rex Foundation White Rock House 2 Whipsnade Road LU6 2NB Dunstable UK

School of Life Sciences University of KwaZulu Natal Durban South Africa

South African National Biodiversity Institute National Zoological Garden 232 Boom Street 0002 Pretoria South Africa

Wildlife Conservation Society New York NY USA

Zoological Institute Russian Academy of Sciences Saint Petersburg Russia

Zobrazit více v PubMed

Allendorf FW, Funk WC, Aitken SN et al (2022). In: Conservation and the Genomics of Populations.Oxford University Press, p280

Balint P, Billerbeck R, Bright P et al (1997) (1997) Lyke, J., McAllister, N., and Steinberg, J. A New Conservation Strategy for the Namibian Cheetah (Acinonyx jubatus). Repor: 1–20. The 1997 Problem Solving Team, Graduate Program in Sustainable Development and Conservation Biology, University of Maryland

Bertola LD, Miller SM, Williams VL et al (2022) Genetic guidelines for translocations: Maintaining intraspecific diversity in the lion (Panthera leo) Evolutionary Applications 15:22–39. 10.1111/eva.13318 PubMed PMC

Brito JC, Durant SM, Pettorelli N et al (2018) Armed conflicts and wildlife decline: Challenges and recommendations for effective conservation policy in the Sahara-Sahel Conservation Letters 11:e12446https://doi.org/10.1111/conl.12446

Charruau P, Fernandes C, Orozco-terWengel P et al (2011) Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates Molecular Ecology 20:706–724https://doi.org/10.1111/j.1365-294X.2010.04986.x PubMed PMC

De Volo SB, Reynolds RT, Douglas MR, Antolin MF ((2008)) An Improved Extraction Method to Increase DNA Yield from Molted Feathers The Condor 110:762–766https://doi.org/10.1525/cond.2008.8586

Durant, SM (2000) Living with the enemy: avoidance of hyenas and lions by cheetahs in the Serengeti. Behavioral ecology, 11(6), 624-632. 10.1093/beheco/11.6.624

Durant SM, Mitchell N, Groom R et al (2017) The global decline of cheetah Acinonyx jubatus and what it means for conservation Proceedings of the National Academy of Sciences 114:528–533https://doi.org/10.1073/pnas.1611122114 PubMed PMC

Farhadinia MS, Gholikhani N, Behnoud P et al (2016) Wandering the barren deserts of Iran: Illuminating high mobility of the Asiatic cheetah with sparse data Journal of Arid Environments 134:145–149https://doi.org/10.1016/j.jaridenv.2016.06.011

Farhadinia MS, Hunter LTB, Jourabchian A et al (2017) The critically endangered Asiatic cheetah Acinonyx jubatus venaticus in Iran: a review of recent distribution, and conservation status Biodivers Conserv 26:1027–1046https://doi.org/10.1007/s10531-017-1298-8

Gaber A, Hassan MM, Boland C et al (2020) Molecular identification of Todiramphus chloris subspecies on the Arabian Peninsula using three mitochondrial barcoding genes and ISSR markers Saudi Journal of Biological Sciences 27:480–488https://doi.org/10.1016/j.sjbs.2019.11.014 PubMed PMC

Hahn MW ((2019) ). In: Molecular Population Genetics.Oxford University Press, pp240–245

Hunter JS, Durant SM, Caro TM (2007) To flee or not too flee: predator avoidance by cheetahs at kills. Behavioral Ecology and Sociobiology, 61(7), 1033-1042. 10.1007/s00265-006-0336-4

Jacobs MJ, Schloeder CA ((2001)) Impacts of conflict on biodiversity and protected areas in Ethiopia Washington, DC:Biodiversity support program

Khalatbari L, Yusefi GH, MartínezFreirí F et al ((2018)) Availability of prey and natural habitats are related with temporal dynamics in range and habitat suitability for Asiatic Cheetah Hystrix, 29(1),145

Khalatbari L, Jowkar H, Yusefi GH et al(2018) The current status of Asiatic cheetah in Iran. https://library.wcs.org/doi/ctl/view/mid/33065/pubid/PUB22375.aspx

Kitchener AC, Breitenmoser-Würsten C, Eizirik E et al ((2017)) A revised taxonomy of the Felidae: The final report of the Cat ClassificationTask Force of the IUCN Cat Specialist Group

Klaassen B, Broekhuis F ((2018)) Living on the edge: Multiscale habitat selection by cheetahs in a human-wildlife landscape Ecology and Evolution 8:7611–7623https://doi.org/10.1002/ece3.4269 PubMed PMC

Korneliussen TS, Albrechtsen A, Nielsen R (2014) ANGSD: Analysis of Next Generation Sequencing Data.BMC Bioinformatics15:356. https://doi.org/10.1186/s12859-014-0356-4 PubMed PMC

Krausman PR, Morales SM ((2005)) Acinonyx jubatus mmsp 2005:1–6https://doi.org/10.1644/1545-1410(2005)771[i>0001:AJ]2.0.CO;2

Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows–Wheeler transform Bioinformatics 26:589–595https://doi.org/10.1093/bioinformatics/btp698 PubMed PMC

Li H, Handsaker B, Wysoker A et al (2009) The Sequence Alignment/Map format and SAMtools Bioinformatics 25:2078–(2079). https://doi.org/10.1093/bioinformatics/btp352 PubMed PMC

Liu Y-C, Sun X, Driscoll C et al (2018) Genome-Wide Evolutionary Analysis of Natural History and Adaptation in the World’s Tigers Current Biology 28:3840–3849.e6https://doi.org/10.1016/j.cub.2018.09.019 PubMed

Magliolo M, Prost S, Orozco-terWengel P et al (2021) Unlocking the potential of a validated single nucleotide polymorphism array for genomic monitoring of trade in cheetahs (Acinonyx jubatus) Mol Biol Rep 48:171–181https://doi.org/10.1007/s11033-020-06030-0 PubMed

Marker L (2019) Cheetahs race for survival: ecology and conservation. In: Wildlife population monitoring. IntechOpen

Marker L Dickman A (2004) Human Aspects of Cheetah Conservation: Lessons Learned from the Namibian Farmlands Human Dimensions of Wildlife 9:297–305https://doi.org/10.1080/10871200490505729

Merola M (1994) A Reassessment of Homozygosity and the Case for Inbreeding Depression in the Cheetah, Acinonyx jubatus: Implications for Conservation Conservation Biology 8:961–971https://doi.org/10.1046/j.1523-1739.1994.08040961.x

Mills MGL, Broomhall LS, Toit JT (2004) du (2004) Cheetah Acinonyx jubatus feeding ecology in the Kruger National Park and a comparison across African savanna habitats: is the cheetah only a successful hunter on open grassland plains? wbio 10:177–186https://doi.org/10.2981/wlb.024

Myers N Resources IU for C of N and N (1975) The Cheetah Acinonyx Jubatus in Africa: Report of a Survey in Africa from the Sahara Southwards,IUCN/WWF Joint Project. IUCN

Newton CR, Graham A, Heptinstall LE et al (1989) analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS).Nucleic Acids Research17:2503–2516. 10.1093/nar/17.7.2503 PubMed PMC

Nowell K, Jackson P (1996) Wild cats: status survey and conservation action plan.IUCN Gland

O’Brien SJ Roelke ME, Marker L, (1985) Genetic Basis for Species Vulnerability in the Cheetah Science 227:1428–1434https://doi.org/10.1126/science.2983425 PubMed

O’Brien SJ, Wildt DE, Bush M. The Cheetah in genetic peril . Scientific American. 1986;254:84–95. doi: 10.1038/scientificamerican0586-84. PubMed DOI

Paradis E, Schliep K ((2019)) ape 5.0: an environment for modern phylogenetics and evolutionary analysesin R. Bioinformatics35:526–528. 10.1093/bioinformatics/bty633 PubMed

Prost S, Machado AP, Zumbroich J et al (2022) Genomic Analyses Show Extremely Perilous Conservation Status of African and Asiatic cheetahs (Acinonyx jubatus) Molecular Ecology n/a: 10.1111/mec.16577 PubMed PMC

RStudio Team ((2022)) RStudio: Integrated Development Environment for R. Boston, MA. Retrieved fromhttp://www.rstudio.com/

Schmidt-Küntzel A, Dalton DL, Menotti-Raymond M et al ((2018)) Conservation Genetics of the Cheetah: Genetic History and Implications for Conservation Cheetahs: Biology and Conservation 71–92. 10.1016/B978-0-12-804088-1.00006-X

Sharp NCC ((1997)) Timed running speed of a cheetah (Acinonyx jubatus)Journal of Zoology241:493–494. 10.1111/j.1469-7998.1997.tb04840.x

Soares S, Grazina L, Mafra I et al (2019) Towards honey authentication: Differentiation of Apis mellifera subspecies in European honeys based on mitochondrial DNA markers Food Chemistry 283:294–301https://doi.org/10.1016/j.foodchem.2018.12.119 PubMed

Spee LB, Hazel SJ, Dal Grande E et al (2019) Endangered Exotic Pets on Social Media in the Middle East: Presence and Impact Animals 9:480https://doi.org/10.3390/ani9080480 PubMed PMC

Tavares ES, Baker AJ ((2008)) Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds.BMC Evolutionary Biology8:81https://doi.org/10.1186/1471-2148-8-81 PubMed PMC

Toews DPL, Brelsford A. The biogeography of mitochondrial and nuclear discordance in animals. Mol Ecol. 2012;21:3907–3930. doi: 10.1111/j.1365-294X.2012.05664.x. PubMed DOI

Tricorache P, Nowell K, Wirth G et al ((2018)) Pets and pelts: Understanding and combating poaching and trafficking in cheetahs Biodiversity of the World—Cheetahs: Biology and Conservation 1st ed San Diego: Elsevier 191–205

Tricorache P, Yashphe S, Marker L ((2021)) Global dataset for seized and non-intercepted illegal cheetah trade (Acinonyx jubatus) 2010–2019Data in Brief35:106848. 10.1016/j.dib.2021.106848 PubMed PMC

Wickham H, Chang W (2016) Package ‘ggplot2’: create elegant data visualisations using the grammar of graphics description. CRAN Repos

Diversity of selected toll-like receptor genes in cheetahs (Acinonyx jubatus) and African leopards (Panthera pardus pardus)