Freeman AR, Machugh DE, McKeown S, Walzer C, McConnell DJ, Bradley DG. 2001. Sequence variation in the mitochondrial DNA control region of wild African cheetahs (Acinonyx jubatus). Heredity 86, 355-362.

Five hundred and twenty-five bp of mitochondrial control region were sequenced and analyzed for 20 Acinonyx jubatus and one Felis catus. These sequences were compared with published sequences from another domestic cat, 20 ocelots (Leopardus pardalis) and 11 margays (Leopardus weidii). The intraspecific population divergence in cheetahs was found to be less than in the other cats. However, variation was present and distinct groups of cheetahs were discernible. The 80 bp RS2 repetitive sequence motif previously described in other felids was found in four copies in cheetah. The repeat units probably have the ability to form secondary structure and may have some function in the regulation of control region replication. The two central repeat units in cheetah show homogenization that may have arisen by convergent evolution.

Freeman_et_al_2001_Genetic_variation_in_wild_cheetahs.pdf

During a five months stay in Namibia, we helped with the completion of CCF's education centre consisting of the History of the Cheetah, Biology of the Cheetah, Ecology of Namibia's Cheetah Habitat; and the Future of the Cheetah.

Gottelli_et_al_2007_Promiscuity_among_cheetah_females.pdf

Hedrick PW. 1987. Genetic bottleneck. Science 237(28 August 1987), 963.

The article by R. Lewin about genetic bottlenecks in house flies and supposed genetic bottlenecks in cheetahs may be misleading, particularly when applied to conservation genetics. It appears that captive conditions also contribute to poor breeding quality in cheetahs. Caution is the best approach when interpreting research results for application to conservation genetics.

Hedrick_1987_Genetic_bottleneck.pdf

Hedrick PW. 1996. Bottleneck(s) or metapopulation in cheetahs. Conservation Biology 10(3):897-9.

The "cheetah paradigm" proposes that a low level of genetic variation has resulted in a high probability of extinction for this species, a connection that has recently been questioned. I do not wish to address this controversy further but to suggest that the extent of genetic variation observed in cheetahs, including the recent minisatellite and microsatellite data, is consistent with the equilibrium heterozygosity expected from the small effective population size that may occur because of  metapopulation dynamics, that is, because of extinction and re-colonization of habitat patches. In other words, a severe, ancient population bottleneck or a series of ancient bottlenecks "over time, over space or both, with small populations being founded and surviving, while the larger parent populations died out" at the end of Pleistocene (10,000 to 12,000 years ago) are not the only explanations for the observed pattern of genetic variation in cheetahs. Alternative possibilities are presented.

Hedrick_1996_Bottleneck(s)_or_metapopulation_in_cheetahs.pdf

Hedrick PW, Lacy RC, Allendorf FW, Soulé ME. 1996. Directions in Conservation Biology: Comments on Caughley. Conservation Biology 10(5):1312-20.

The recent review by Caughley (1994) on approaches used in conservation biology suggested that there are two: the small population paradigm and the declining population paradigm. We believe that this division is overly simplistic and that it should not be perpetuated. Both the deterministic factors that reduce population size and the stochastic factors that lead to the final extinction of a small population are critical to consider in preventing extinction. Only through an overall and comprehensive effort, which we call inclusive population viability analysis, can extinction  processes be understood and mitigated. In this context we discuss Caughley's comments about genetics, demography, and general population viability, with particular attention to cheetahs (Acinonyx jubatus) and Pacific salmon (Oncorhynchus sp.).

Hedrick_et_al_1996_Directions_in_Conservation_Biology.pdf

Kat PW. 1993. Genetics of the cheetah: What we know and how we should use this knowledge. Swara 16:13.

The number of people the author met that are conversant with the genetics of cheetahs is amazing. The wisdom of programmes that propose to curve a variety of ills merely by increasing genetic variation, however, are unconvincing, and have largely resulted from a lack of understanding of complexities involved.

Kat_1993_Genetics_of_the_cheetah.pdf

Kelly MJ. 2001. Lineage loss in Serengeti cheetahs: consequences of high reproductive variance and heritability of fitness on effective population size. Conservation Biology 15(1):137-47.

In natural populations, many breeders do not leave surviving offspring, and as a result many potential genetic lineages are lost. I examined lineage extinction in Serengeti cheetahs (Acinonyx jubatus) and found that 76% of matrilines were lost over a 25-year period. Production of future breeders was nonrandom and generally confined to a few families. Five out of 63 matrilines accounted for 45% of the total cheetah population over the course of the study. Lineage persistence is perhaps best illustrated by the variance in lifetime reproductive success (LRS) and heritability in this parameter. In female cheetahs, variance in LRS was high, and new data show that this LRS was heritable. Variance in LRS and heritability in LRS have dramatic consequences for effective population size, Ne. I calculated Ne for cheetahs, taking into account fluctuating population size, unequal sex ratio, non-Poisson distribution of reproductive success, and heritability of fitness. The Ne was most strongly affected by variance in reproductive success and especially heritability in reproductive success. The variance Ne was 44% of the actual population size, and the inclusion of heritability further reduced Ne to only 15% of the actual population, a ratio similar to that of a social carnivore with reproductive suppression. The current cheetah population in the Serengeti is below numbers suggested by Ne estimates as sufficient to maintain sufficient genetic diversity.

Kelly_2001_Lineage_loss_in_Serengeti_Cheetahs.pdf

Kotze A, Ehlers K, Cilliers DC, Grobler JP. 2008. The power of resolution of microsatellite markers and assignment tests to determine the geographic origin of cheetah (Acinonyx jubatus) in Southern Africa. Mammalian Biology 73, 457-562.

Formerly found in 44 countries in Africa and Asia, cheetahs are currently confined to fragmented populations in 29 African countries, and remnant populations in Iran and Pakistan (Marker 2002). In southern Africa, cheetahs are at present found in Botswana, Namibia, South Africa and Zimbabwe. Trade in cheetah products and live export of cheetah from Namibia and Botswana is stringently controlled (CITES 1992). As a result, conservation authorities are constantly aware of potential illegal trade in cheetah over the Namibian and Botswana borders with South Africa. Where foul-play is involved, identification of source populations of confiscated animals will require implementation of identification techniques based on multilocus genotypes. Manel et al. (2002) demonstrated that genetic methods have high power of resolution to determine the geographic origin of population samples for sufficiently differentiated populations. Forensic science services for domesticated animals are well established in South Africa and have in recent years expanded to include game species, marine fish stock identification and ornamental fish (Grobler et al. 2005). In this paper, we describe the power of resolution of microsatellite markers and assignment tests to determine the geographic origin of cheetah (Acinonyx jubatus) confiscated in South Africa on suspicion of illegal import. Cheetah was formerly thought to be genetically highly monomorphic (presumably following a historic bottleneck), based on allozyme data (O'Brien et al. 1983). Subsequent studies (Menotti-Raymond and O'Brien 1993, 1995) have revealed genetic heterogeneity for microsatellite markers. This has been attributed to accumulated variation since the hypothetical bottleneck, resultant from the high mutation rates of microsatellite markers (Hedrick 1996). The presence of a moderate level of genetic diversity, comparable to other felids for some markers (Menotti-Raymond and O'Brien 1993), suggests that marker-based forensic identification in cheetah is feasible.

Kotze_et_al_2008_Genetic_determination_of_cheetah_origin_in_southern_Africa.pdf

Langley RJ, Hirsch VM, O'Brien SJ, Adger-Johnson D, Goeken RM, Olmsted RA. 1994. Nucleotide sequence analysis of puma lentivirus (PLV-14): Genomic organization and relationship to other lentiviruses. Virology 202: 853-64.

The complete nucleotide sequence of an isolate of puma lentivirus (PLV-14) was obtained by an inverse polymerase chain reaction (I-PCR) technique and confirmed by conventional PCR. Both methods were used to amplify overlapping regions of proviral DNA, for cloning and sequencing, from genomic DNA isolated from PLV-14 infected Florida puma (Felis concolor coryi) peripheral blood mononuclear cells (PBMC). The provirus has a total length of 9100 nucleotides and the genomic organization of presumed protein coding regions are similar to those seen in other members of the lentivirus family, i.e., three large open reading frames gag, pol, and env as well as smaller intergenic regions that apparently encode regulatory proteins vif and 3' rev by positional and sequence similarity to those seen in other lentiviruses. Two additional open reading frames were identified in the env region and their function (if any) is unknown. The length of the PLV-14 long terminal repeat (LTR) was found to be shorter than the LTRs of feline immunodeficiency virus (FIV). The sequence homology between PLV-14 and other lentiviruses demonstrates that PLV-14 is most closely related to FIV from domestic cats. However, the extent of sequence divergence of each retroviral gene segment is large (e.g., percentage sequence similarity between FIV and PLV-14 env is 8% amino acid and 37% nucleotide similarity), indicating relatively ancient divergence of these feline lentiviral genomes.The complete nucleotide sequence of an isolate of puma lentivirus (PLV-14) was obtained by an inverse polymerase chain reaction (I-PCR) technique and confirmed by conventional PCR.

Langley_et_al_1994_Puma_lentivirus_sequence.pdf

Laurenson MK, Caro TM, Gros PM, Wielebnowski N. 1995. Controversial cheetahs? Nature 377(5.October 1995):392.

May has discussed some of recent reappraisals of O'Brien and colleagues' evidence that the cheetah's generic impoverishment is threatening the species' persistence. Some comments, however, particularly those of O'Brien, may be misleading, according to the author's opinion. Particularly, are discussed the causes of cub mortality and the thesis of the vulnerability of the cheetah to pathogens, pointing out that intrinsic source of mortality are apparently insignificant compared with extrinsic source, both in the wild and in captivity. Ecology can be as important as genetics, and interdisciplinary cooperation in conservation problems is essential.

Laurenson_et_al_1995_Controversial_cheetahs.pdf

Marker-Kraus L.  Focus on the Cheetah: Technical innovations in species conservation Washington D.C.: NOAHS; 19 pp.

A recently drafted Master Plan developed by the cheetah propagation group of the Species Survival Plan of the American Association of Zoological Parks and Aquarium has listed basic research in reproduction as a primary end of the SSP. This research is to be conducted by NOAHS Center scientists and will include: (1) fundamental studies of the reproductive physiology, and endocrinology of the species; (2) assessing, understanding and combating infertility; (3) germ plasm storage of sperm, and embryos for conservation and biodiversity; and (4) artificial breeding strategies including in vitro fertilization and artificial insemination. Considering the combined results of the genetics, physiology, structure and natural history of the captive population of the cheetah there are several recommendations that are important to improve the demographic pattern: First, the outbreeding of individuals within the captive population, second, the increasing of the breeding population's size and finally, the continually increasing of the research on captive and free-ranging cheetahs.

Marker-Kraus_-_Focus_on_cheetah_-_Technical_innovations.pdf

Marker LL, Pearks Wilkerson AJ, Sarno RJ, Martenson J, Breitenmoser-Würsten Ch, O'Brien SJ, Johnson WE. 2008. Molecular genetics insights on cheetah (Acinonyx jubatus) ecology and conservationn in Namibia.
Journal of Heredity 99(1):2-13.

The extent and geographic patterns of molecular genetic diversity of the largest remaining free-ranging cheetah population were described in a survey of 313 individuals from throughout Namibia. Levels of relatedness, including paternity/maternity (parentage), were assessed across all individuals using 19 polymorphic microsatellite loci, and unrelated cheetahs (n = 89) from 7 regions were genotyped at 38 loci to document broad geographical patterns. There was limited differentiation among regions, evidence that this is a generally panmictic population. Measures of genetic variation were similar among all regions and were comparable with Eastern African cheetah populations. Parentage analyses confirmed several observations based on field studies, including 21 of 23 previously hypothesized family groups, 40 probable parent/offspring pairs, and 8 sibling groups. These results also verified the successful integration and reproduction of several cheetahs following natural dispersal or translocation. Animals within social groups (family groups, male coalitions, or sibling groups) were generally related. Within the main study area, radio-collared female cheetahs were more closely interrelated than similarly compared males, a pattern consistent with greater male dispersal. The long-term maintenance of current patterns of genetic variation in Namibia depends on retaining habitat characteristics that promote natural dispersal and gene flow of cheetahs.

Marker_et_al_2008_Genetic_insight_on_cheetah_in_Namibia.pdf

May RM. 1995. The cheetah controversy. Nature 374:309-10.

In 1983, O'Brien et al. announced that cheetahs have remarkably little genetic variability. However, independent researchers, Caughley and Merola, studying 24 other carnivores, argued that cheetahs are not especially impoverished and deny that there is much evidence of any deleterious effects in the form of inbreeding depression. Current thinking may rightly recognize that lack of genetic diversity is not the primary factor for most endangered species. But O'Brien's concern nevertheless remains an important consideration for many conservation programmes, and particularly for cheetahs.

May_1995_The_cheetah_controversy.pdf

Menotti-Raymond M, O'Brien SJ. 1993. Dating the genetic bottleneck of the African cheetah. Proc Natl Acad Sci USA 90:3172-6.

The cheetah (Acinonyx jubatus) is unusual among felids in exhibiting near genetic uniformity at a variety of loci previously screened to measure population genetic diversity. It has been hypothesized that a demographic crash or population bottleneck in the recent history of the species is causal to the observed monomorphic profiles for nuclear coding loci. The timing of a bottleneck is difficult to assess, but certain aspects of the cheetah's natural history suggest it may have occurred near the end of the last ice age (late Pleistocene, approximately 10,000 years ago), when a remarkable extinction of large vertebrates occurred on several continents. To further define the timing of such a bottleneck, the character of genetic diversity for two rapidly evolving DNA sequences, mitochondrial DNA and hypervariable minisatellite loci, was examined. Moderate levels of genetic diversity were observed for both of these indices in surveys of two cheetah subspecies, one from South Africa and one from East Africa. Back calculation from the extent of accumulation of DNA diversity based on observed mutation rates for VNTR (variable number of tandem repeats) loci and mitochondrial DNA supports a hypothesis of an ancient Pleistocene bottleneck that rendered the cheetah depauperate in genetic variation for nuclear coding loci but would allow sufficient time for partial reconstitution of more rapidly evolving genomic DNA segments.

Menotti-Raymond_&_OBrien_1993_Genetic_bottleneck_of_the_African_cheetah.pdf

Menotti-Raymond M, O'Brien SJ. 1995. Hypervariable genomic variation to reconstruct the natural history of populations: Lessons from the big cats. Electrophoresis 16:1771-4.

The extent and nature of variation in hypervariable regions of DNA have been used in the past as a means to infer the natural histories of populations. We review the interpretation of the extent of genetic diversity for minisatellite DNA in the cheetah to estimate the timing of a population bottleneck in the species and the potential application of a second class of hypervariable DNA, microsatellite DNA, as a molecular tool to examine the natural histories of felid populations. A calibration curve relating the degree of allele fragment sharing in individuals to relatedness in a captive pedigree of cheetahs is presented. This measurement has important applications for management of potential matings in captive management situations.

Menotti-Raymond_&_OBrien_1995_Feline_DNA_fingerprinting.pdf

Menotti-Raymond M, O'Brien SJ. 1995. Evolutionary conservation of ten microsatellite loci in four species of Felidae. Journal of Heredity 86(4):319-22.

Short tandem repeat polymorphismus (STRP), or microsatellites, are widespread among vertebrate genomes and are useful in gene mapping and population studies due to their high level of length polymorphism. The authors describe the isolation, characterisation, and PCR amplification of 10 microsatellite loci from the domestic cat, Felis catus. The flanking primer sequences were conserved among other Felidae species, and amplification products demonstrated abundant polymorphism in puma, lion, cheetah, and domestic cat. The cheetah sample exhibited the lowest level of polymorphism for these loci among felid species.

Menotti-Raymond_&_OBrien_1995_Microsatellite_loci_in_felids.pdf

Mills LS. 1996. Cheetah extinction: Genetics or extrinsic factors? Conservation Biology 10(2):315.

In this article letter the author gives his opinion about the debate addressed by Laurenson et al  over the cheetah conservation strategy, on the Conservation Biology journal of 1996. He did not take a position in favour of genetic or extrinsic factors, on the contrary he pointed out that a view toward interactions between genetics and environmental, behavioural, and demographic factors would move us further toward helping small and isolated populations.

Mills_1996_Cheetah_extinction_by_genetic_or_extrinsic_factors.pdf

Mishra MK. 1996. Re-introduction of "cheetah" into the wild in India - is there a case? Zoo's Print Ten Years(January 1996):11-2.

 To see the cheetah back into the Indian wilds has been a fond hope and dream with many an Indian wildlifer and conservationist. Cheetah is the only large mammal of India to have gone extinct within historical times. According to the Journal of the Bombay Natural History Society, it was only in 1947 that the last cheetah was shot in the Ramgarh area of north-east Madhya Pradesh. During the seventies and eighties of the 20th century a serious attempt was made by the Government of India, to procure some numbers of cheetahs from the relict free-ranging population in Iran. the scheme, for some reasons, failed to materialize, but does there exist a case for yet another attempt now?

Mishra_1996_Cheetah_re-introduction_in_India.pdf

O'Brien SJ. 1991. The genetic peril of the cheetah. In Seidensticker J, Lumpkin S. (eds). Great Cats: Majestic Creatures of the Wild. Sydney: Weldon Owen; pp. 146-147.

The cheetah is descended from a handful of survivors of a global extinction that occurred at the end of the last Ice Age, more than 10'000 years ago. They have 10-100 times less variation in their intrinsic genetic material. The species as a whole is suffering from the effects of what we call inbreeding depression. This causes an increase in the incidence of two unhealthy genes in the same individual. This causes the entire species to be susceptible to infectious disease agents, viruses or pathogens, which periodically evolve. But the cheetah has survived and even increased to tens of thousands since its ancestors passed through the ancient population bottleneck. The cheetah's future may be in our hands. The only long-term prospects for survival are in areas with effective protection against shooting, hunting and also high densities of predators.

OBrien_1991_The_genetic_peril_of_the_cheetah.pdf

O'Brien SJ, Goldman D, Merril CR, Bush ME. 1983. The cheetah is depauperate in genetic variation.
Science 221, 459-462.

A sample of 55 South African cheetahs (Acinonyx jubatus jubatus) from two geographically isolated populations in South Africa were found to be genetically monomorphic at each of 47 allozyme (allelic isozyme) loci. Two-dimensional gel electrophoresis of about 155 abundant soluble proteins from cheetah fibroblasts also revealed a low frequency of polymorphism (average heterozygosity, 0.013). Both estimates are dramatically lower than levels of variation reported in other cats and mammals in general. The extreme monomorphism may be a consequence of a demographic contraction of the cheetah (a population bottleneck) in association with a reduced rate of increase in the recent natural history of this endangered species.

OBrien_1983_Cheetah_is_depauperate_in_genetic_variation.pdf

O'Brien SJ. 1994. The cheetah's conservation controversy. Conservation Biology 8, 1153-1155.

In 1994 Merola reviewed the results that have been collected over the last decade relative to the population genetic structure of the African cheetah and the implications for survival. Synthesizing the data in a critical manner, this work brought into question the relevance of previous observations that the cheetah has a remarkably reduced complement of genomic variation and is suffering a physiological fitness cost as a consequence. To respond to these criticisms O'Brien discusses in this article the major points of disagreement.

OBrien_1994_Cheetah_conservation_controversy.pdf

O'Brien SJ. 1994. A role for molecular genetics in biological conservation. Proceedings of the National Academy of Sciences of the United States of America 91, 5748-5755.

The recognition of recent accelerated depletion of species as a consequence of human industrial development has spawned a wide interest in identifying threats to endangered species. In addition to ecological and demographic perils, it has become clear that small populations that narrowly survive demographic contraction may undergo close inbreeding genetic drift, and loss of overall genomic variation due to allelic loss or reduction to homozygosity. I review here the consequences of such genetic depletion revealed by applying molecular population genetic analysis to four endangered mammals: African cheetah, lion, Florida panther, and humpback whale. The accumulated genetic results, combined with physiological, ecological, and ethological data, provide a multifaceted perspective of the process of species diminution. An emerging role of population genetics, phylogenetics, and phylogeography as indicators of a population's natural history and its future prognosis provides valuable data of use in the development of conservation management plans for endangered species.

OBrien_1994_A_role_for_molecular_genetics_in_conservation.pdf

O'Brien SJ. 1994. Genetic and phylogenetic analyses of endangered species. Annual Review of Genetics 28:467-89.

Several reviews have chronicled the application of genetic principles to conservation management and summarized the state of genetic data on the few studied species. The goal here is to review some lessons learned by applying empirical population genetic approaches to define the factors that imperil fragile populations. Both the limitations of the inference and the conclusions reached as a community of conservation scientists are summarized. Several examples will illustrate the synthesis of genetic interpretation with demographic, ecological, and life-history data to draw a cohesive picture of the threatened taxon. Most of the examples are endangered large charismatic carnivore species selected for two reasons. First, large carnivore species occupy the top position of a trophic chain for their ecosystem. They are often highly specialized and provide a sensitive barometer of an ecosystem's condition. Second, charismatic species attract long-term field studies that lay the groundwork for formulating falsifiable ecological and life-history hypotheses. On of the presented examples is the cheetah.

OBrien_1994_Genetic_and_phylogenetic_analyses_of_endangered_species.pdf

Sanjayan MA, Crooks KR. 1996. Skin grafts and cheetahs. Nature 381.

Since the publication of the landmark study by O'Brien et al. on the lack of genetic variation in cheetahs, a flurry of reports have questioned this work. This skepticism is due, in part, to the acceptance of reciprocal skin grafts between unrelated cheetahs reported by O'Brien et al., a phenomenon not previously observed in wild mammals. We performed skin-graft experiments in Thomomys bottae, the pocket gopher, in order to repeat this test on an other wild species. Our results indicate that individuals from populations with low levels of genetic variation can have similar major histocompatibility complex (MHC) genotypes, and we believe that the earlier cheetah results, because of their concordance with our work, were real phenomena.

Sanjayan_&_Crooks_1996_Skin_grafts_and_cheetahs.pdf

Sullivan W. 1983. Rare genetic uniformity found in cheetahs. New York Times, 24 July 1983.

In the New York Times of July 1983, the author mentions the rare genetic uniformity found in cheetahs, the bottleneck theory as the cause of this impoverishment, the problems with reproduction and man hunting, and its endangered status.

Sullivan_1983_Rare_genetic_uniformity_in_cheetahs.pdf

Wielebnowski N. 1996. Reassessing the relationship between juvenile mortality and genetic monomorphorism in captive cheetahs. Zoo Biology 15, 353-369.

Low levels of genetic heterozygosity are commonly considered a major threat to the survival of wild and captive populations. However, intense focus on genetic issues may obscure the importance of extrinsic factors influencing species' survival in wild and captive environments. A key example for this is the cheetah (Acinonyx jubatus), which is frequently cited as suffering from unusually high juvenile mortality and decreased fecundity in captivity due to genetic monomorphism at the species level. It has also been suggested that as a consequence of such extreme homozygosity, juvenile mortality rates of young from related vs. unrelated parents would not be expected to differ significantly. However, examination of current studbook data and breeding records of the North American captive population showed that juvenile mortality of young from related parents was significantly higher than that of young from unrelated parents, largely as a result of intrinsic causes, such as stillbirths and congenital defects, that may have a genetic basis. This indicates that in spite of the cheetah's homozygosity, effects of further inbreeding depression may still occur in the captive population, and deleterious recessive alleles are being segregated. Furthermore, juvenile mortality has declined over time and differs significantly among facilities, even when only young from unrelated parents are considered, suggesting that differences in management practices may be largely responsible for observed changes in mortality rate. Contrary to previous reports, cheetah juvenile mortality is not unusually high when compared to other captive-bred felids. In addition, cheetahs were found to have consistently higher litter sizes and the highest average number of surviving cubs per litter when compared to other captive-bred felid species. These findings cast doubt on the significance of overall homozygosity in this species for its juvenile survival and breeding performance and emphasize the key role of management practice in promoting breeding of endangered species.

Wielebnowski_1996_Juvenile_Mortality_in_Captive_Cheetahs.pdf