Acinonyx jubatus

Bayesian Prediction of Multivariate Ecology from Phenotypic Data Yields New Insights into the Diets of Extant and Extinct Taxa

AbstractMorphology often reflects ecology, enabling the prediction of ecological roles for taxa that lack direct observations, such as fossils. In comparative analyses, ecological traits, like diet, are often treated as categorical, which may aid prediction and simplify analyses but ignores the multivariate nature of ecological niches. Furthermore, methods for quantifying and predicting multivariate ecology remain rare. Here, we ranked the relative importance of 13 food items for a sample of 88 extant carnivoran mammals and then used Bayesian multilevel modeling to assess whether those rankings could be predicted from dental morphology and body size. Traditional diet categories fail to capture the true multivariate nature of carnivoran diets, but Bayesian regression models derived from living taxa have good predictive accuracy for importance ranks. Using our models to predict the importance of individual food items, the multivariate dietary niche, and the nearest extant analogs for a set of data-deficient extant and extinct carnivoran species confirms long-standing ideas for some taxa but yields new insights into the fundamental dietary niches of others. Our approach provides a promising alternative to traditional dietary classifications. Importantly, this approach need not be limited to diet but serves as a general framework for predicting multivariate ecology from phenotypic traits.

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

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.

The brain of the North American cheetah-like cat Miracinonyx trumani

The cheetah Acinonyx jubatus, the fastest living land mammal, is an atypical member of the family Felidae. The extinct feline Miracinonyx trumani, known as the North American cheetah, is thought to have convergently evolved with Acinonyx to pursue fast and open-country prey across prairies and steppe environments of the North American Pleistocene. The brain of Acinonyx is unique among the living felids, but it is unknown whether the brain of the extinct M. trumani is convergent to that of Acinonyx. Here, we investigate the brain of M. trumani from a cranium endocast, using a comparative sample of other big cats. We demonstrate that the brain of M. trumani was different from that of the living A. jubatus. Indeed, its brain shows a unique combination of traits among living cats. This suggests that the case of extreme convergence between Miracinonyx and its living Old World vicar should be reconsidered.

The cheetah optimizer: a nature-inspired metaheuristic algorithm for large-scale optimization problems

Motivated by the hunting strategies of cheetahs, this paper proposes a nature-inspired algorithm called the cheetah optimizer (CO). Cheetahs generally utilize three main strategies for hunting prey, i.e., searching, sitting-and-waiting, and attacking. These strategies are adopted in this work. Additionally, the leave the pray and go back home strategy is also incorporated in the hunting process to improve the proposed framework's population diversification, convergence performance, and robustness. We perform intensive testing over 14 shifted-rotated CEC-2005 benchmark functions to evaluate the performance of the proposed CO in comparison to state-of-the-art algorithms. Moreover, to test the power of the proposed CO algorithm over large-scale optimization problems, the CEC2010 and the CEC2013 benchmarks are considered. The proposed algorithm is also tested in solving one of the well-known and complex engineering problems, i.e., the economic load dispatch problem. For all considered problems, the results are shown to outperform those obtained using other conventional and improved algorithms. The simulation results demonstrate that the CO algorithm can successfully solve large-scale and challenging optimization problems and offers a significant advantage over different standards and improved and hybrid existing algorithms. Note that the source code of the CO algorithm is publicly available at https://www.optim-app.com/projects/co .

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

This review summarizes the current knowledge on the major histocompatibility complex (MHC) of the family Felidae. This family comprises an important domestic species, the cat, as well as a variety of free-living felids, including several endangered species. As such, the Felidae have the potential to be an informative model for studying different aspects of the biological functions of MHC genes, such as their role in disease mechanisms and adaptation to different environments, as well as the importance of genetic diversity for conservation issues in free-ranging or captive populations. Despite this potential, the current knowledge on the MHC in the family as a whole is fragmentary and based mostly on studies of the domestic cat and selected species of big cats. The overall structure of the domestic cat MHC is similar to other mammalian MHCs following the general scheme "centromere-MHC class I-MHC class III-MHC class II" with some differences in the gene contents. An unambiguously defined orthologue of the non-classical class I HLA-E gene has not been identified so far and the class II DQ and DP genes are missing or pseudogenized, respectively. A comparison with available genomes of other felids showed a generally high level of structural and sequence conservation of the MHC region. Very little and fragmentary information on in vitro and/or in vivo biological functions of felid MHC genes is available. So far, no association studies have indicated effects of MHC genetic diversity on a particular disease. No information is available on the role of MHC class I molecules in interactions with Natural Killer (NK) cell receptors or on the putative evolutionary interactions (co-evolution) of the underlying genes. A comparison of complex genomic regions encoding NK cell receptors (the Leukocyte Receptor Complex, LRC and the Natural Killer Cell Complex, NKC) in the available felid genomes showed a higher variability in the NKC compared to the LRC and the MHC regions. Studies of the genetic diversity of domestic cat populations and/or specific breeds have focused mainly on DRB genes. Not surprisingly, higher levels of MHC diversity were observed in stray cats compared to pure breeds, as evaluated by DRB sequencing as well as by MHC-linked microsatellite typing. Immunogenetic analysis in wild felids has only been performed on MHC class I and II loci in tigers, Namibian leopards and cheetahs. This information is important as part of current conservation tasks to assess the adaptive potential of endangered wild species at the human-wildlife interface, which will be essential for preserving biodiversity in a functional ecosystem.

Evolutionary Pathways to Communal and Cooperative Breeding in Carnivores

In animal societies, individuals can cooperate in a variety of tasks, including rearing young. Such cooperation is observed in complex social systems, including communal and cooperative breeding. In mammals, both these social systems are characterized by delayed dispersal and alloparenting, whereas only cooperative breeding involves reproductive suppression. While the evolution of communal breeding has been linked to direct fitness benefits of alloparenting, the direct fitness cost of reproductive suppression has led to the hypothesis that the evolution of cooperative breeding is driven by indirect fitness benefits accrued through raising the offspring of related individuals. To decipher between the evolutionary scenarios leading to communal and cooperative breeding in carnivores, we investigated the coevolution among delayed dispersal, reproductive suppression, and alloparenting. We reconstructed ancestral states and transition rates between these traits. We found that cooperative breeding and communal breeding evolved along separate pathways, with delayed dispersal as the first step for both. The three traits coevolved, enhancing and stabilizing one another, which resulted in cooperative social systems as opposed to intermediate configurations being stable. These findings promote the key role of coevolution among traits to stabilize cooperative social systems and highlight the specificities of evolutionary patterns of sociality in carnivores.

Recent inner ear specialization for high-speed hunting in cheetahs

The cheetah, Acinonyx jubatus, is the fastest living land mammal. Because of its specialized hunting strategy, this species evolved a series of specialized morphological and functional body features to increase its exceptional predatory performance during high-speed hunting. Using high-resolution X-ray computed micro-tomography (μCT), we provide the first analyses of the size and shape of the vestibular system of the inner ear in cats, an organ essential for maintaining body balance and adapting head posture and gaze direction during movement in most vertebrates. We demonstrate that the vestibular system of modern cheetahs is extremely different in shape and proportions relative to other cats analysed (12 modern and two fossil felid species), including a closely-related fossil cheetah species. These distinctive attributes (i.e., one of the greatest volumes of the vestibular system, dorsal extension of the anterior and posterior semicircular canals) correlate with a greater afferent sensitivity of the inner ear to head motions, facilitating postural and visual stability during high-speed prey pursuit and capture. These features are not present in the fossil cheetah A. pardinensis, that went extinct about 126,000 years ago, demonstrating that the unique and highly specialized inner ear of the sole living species of cheetah likely evolved extremely recently, possibly later than the middle Pleistocene.

Conservation Genetics of the Cheetah: Genetic History and Implications for Conservation

From allozymes in 1983 to whole genomes in 2015, genetic studies of the cheetah have been extensive. In this chapter we provide an overview of the available literature. Overall, patterns of genetic variation provided evidence of low variability and suggest this loss occurred thousands of years ago. Differences between published subspecies were supported genetically. At a local scale, populations were generally considered panmictic with minor genetic structure. Although cheetahs have persisted despite low genetic variability, important questions arise from these findings: Does the cheetah have the ability to adapt to and evolve with future changes in environmental and infectious pressure? How would cheetahs cope with further loss of genetic diversity? Connectivity in the wild should be maintained via prevention of habitat loss, while management of small isolated populations may require reestablishing gene flow. Genetics could assist captive-breeding decisions and provide forensic evidence as to the geographical origin of illegally traded animals.

The distribution and numbers of cheetah (Acinonyx jubatus) in southern Africa

Assessing the numbers and distribution of threatened species is a central challenge in conservation, often made difficult because the species of concern are rare and elusive. For some predators, this may be compounded by their being sparsely distributed over large areas. Such is the case with the cheetah Acinonyx jubatus. The IUCN Red List process solicits comments, is democratic, transparent, widely-used, and has recently assessed the species. Here, we present additional methods to that process and provide quantitative approaches that may afford greater detail and a benchmark against which to compare future assessments. The cheetah poses challenges, but also affords unique opportunities. It is photogenic, allowing the compilation of thousands of crowd-sourced data. It is also persecuted for killing livestock, enabling estimation of local population densities from the numbers persecuted. Documented instances of persecution in areas with known human and livestock density mean that these data can provide an estimate of where the species may or may not occur in areas without observational data. Compilations of extensive telemetry data coupled with nearly 20,000 additional observations from 39 sources show that free-ranging cheetahs were present across approximately 789,700 km2 of Namibia, Botswana, South Africa, and Zimbabwe (56%, 22%, 12% and 10% respectively) from 2010 to 2016, with an estimated adult population of 3,577 animals. We identified a further 742,800 km2 of potential cheetah habitat within the study region with low human and livestock densities, where another ∼3,250 cheetahs may occur. Unlike many previous estimates, we make the data available and provide explicit information on exactly where cheetahs occur, or are unlikely to occur. We stress the value of gathering data from public sources though these data were mostly from well-visited protected areas. There is a contiguous, transboundary population of cheetah in southern Africa, known to be the largest in the world. We suggest that this population is more threatened than believed due to the concentration of about 55% of free-ranging individuals in two ecoregions. This area overlaps with commercial farmland with high persecution risk; adult cheetahs were removed at the rate of 0.3 individuals per 100 km2 per year. Our population estimate for confirmed cheetah presence areas is 11% lower than the IUCN's current assessment for the same region, lending additional support to the recent call for the up-listing of this species from vulnerable to endangered status.

Theoretical considerations on maximum running speeds for large and small animals

Mechanical equations for fast running speeds are presented and analyzed. One of the equations and its associated model predict that animals tend to experience larger mechanical stresses in their limbs (muscles, tendons and bones) as a result of larger stride lengths, suggesting a structural restriction entailing the existence of an absolute maximum possible stride length. The consequence for big animals is that an increasingly larger body mass implies decreasing maximal speeds, given that the stride frequency generally decreases for increasingly larger animals. Another restriction, acting on small animals, is discussed only in preliminary terms, but it seems safe to assume from previous studies that for a given range of body masses of small animals, those which are bigger are faster. The difference between speed scaling trends for large and small animals implies the existence of a range of intermediate body masses corresponding to the fastest animals.

Using a Novel Absolute Ontogenetic Age Determination Technique to Calculate the Timing of Tooth Eruption in the Saber-Toothed Cat, Smilodon fatalis

Despite the superb fossil record of the saber-toothed cat, Smilodon fatalis, ontogenetic age determination for this and other ancient species remains a challenge. The present study utilizes a new technique, a combination of data from stable oxygen isotope analyses and micro-computed tomography, to establish the eruption rate for the permanent upper canines in Smilodon fatalis. The results imply an eruption rate of 6.0 millimeters per month, which is similar to a previously published average enamel growth rate of the S. fatalis upper canines (5.8 millimeters per month). Utilizing the upper canine growth rate, the upper canine eruption rate, and a previously published tooth replacement sequence, this study calculates absolute ontogenetic age ranges of tooth development and eruption in S. fatalis. The timing of tooth eruption is compared between S. fatalis and several extant conical-toothed felids, such as the African lion (Panthera leo). Results suggest that the permanent dentition of S. fatalis, except for the upper canines, was fully erupted by 14 to 22 months, and that the upper canines finished erupting at about 34 to 41 months. Based on these developmental age calculations, S. fatalis individuals less than 4 to 7 months of age were not typically preserved at Rancho La Brea. On the whole, S. fatalis appears to have had delayed dental development compared to dental development in similar-sized extant felids. This technique for absolute ontogenetic age determination can be replicated in other ancient species, including non-saber-toothed taxa, as long as the timing of growth initiation and growth rate can be determined for a specific feature, such as a tooth, and that growth period overlaps with the development of the other features under investigation.

Saharan cheetah Acinonyx jubatus hecki, a ghostly dweller on Niger's Termit massif

The Saharan cheetah Acinonyx jubatus hecki, once broadly distributed across north-western Africa, now occurs in only 9% of its former range and is categorized as Critically Endangered on the IUCN Red List. The Saharan cheetah is rare and threatened but there is a lack of reliable data on its population status and distribution. We report sightings of cheetahs in the Termit & Tin Toumma National Nature and Cultural Reserve of Niger, recorded using three methods: camera-trap surveys, sign surveys and interviews with local people. We recorded three individuals in camera-traps, three direct sightings of lone individuals, 43 distinct cheetah tracks, and one cheetah scat, which suggest a resident population. Most respondents had negative attitudes towards carnivores, including the cheetah. Paradoxically, local nomads reported no conflict with the cheetah and perceived that the number of cheetahs was declining. Attitudes towards carnivores were correlated with respondents’ age and level of education. Efforts to reduce killing of carnivores and their prey are needed but it is equally important for conservation initiatives to focus on increasing local knowledge about wildlife through education, particularly targeted at the younger generation. Our findings highlight the benefits of using various techniques for recording the presence of a rare carnivore.

A three-dimensional analysis of morphological evolution and locomotor performance of the carnivoran forelimb

In this study, three-dimensional landmark-based methods of geometric morphometrics are used for estimating the influence of phylogeny, allometry and locomotor performance on forelimb shape in living and extinct carnivorans (Mammalia, Carnivora). The main objective is to investigate morphological convergences towards similar locomotor strategies in the shape of the major forelimb bones. Results indicate that both size and phylogeny have strong effects on the anatomy of all forelimb bones. In contrast, bone shape does not correlate in the living taxa with maximum running speed or daily movement distance, two proxies closely related to locomotor performance. A phylomorphospace approach showed that shape variation in forelimb bones mainly relates to changes in bone robustness. This indicates the presence of biomechanical constraints resulting from opposite demands for energetic efficiency in locomotion -which would require a slender forelimb- and resistance to stress -which would be satisfied by a robust forelimb-. Thus, we interpret that the need of maintaining a trade-off between both functional demands would limit shape variability in forelimb bones. Given that different situations can lead to one or another morphological solution, depending on the specific ecology of taxa, the evolution of forelimb morphology represents a remarkable "one-to-many mapping" case between anatomy and ecology.

Panthera pardus(Carnivora: Felidae)

Panthera pardus (leopard; Linnaeus, 1758) is the smallest of the 4 large felids in the genus Panthera. A solitary and adaptable species, P. pardus is the widest ranging of all wild felids, inhabiting rain forests, mountains, semiarid environments, and suburban areas throughout sub-Saharan Africa, the Middle East, and South Asia to the Russian Far East. Despite this distribution, P. pardus is listed as “Near Threatened” by the International Union for Conservation of Nature and Natural Resources and several Asian subspecies are listed as endangered. P. pardus primarily feeds on small to medium-sized ungulates, but has a varied diet including fish, reptiles, birds, and small mammals.

Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates

The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya using an average mammalian microsatellite mutation rate and at 4700–44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70–110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity.

Feline immunodeficiency virus (FIV) in wild Pallas' cats

Feline immunodeficiency virus (FIV), a feline lentivirus related to HIV, causes immune dysfunction in domestic and wild cats. The Pallas' cat is the only species from Asia known to harbor a species-specific strain of FIV designated FIV(Oma) in natural populations. Here, a 25% seroprevalence of FIV is reported from 28 wild Mongolian Pallas' cats sampled from 2000 to 2008. Phylogenetic analysis of proviral RT-Pol from eight FIV(Oma) isolates from Mongolia, Russia, China and Kazakhstan reveals a unique monophyletic lineage of the virus within the Pallas' cat population, most closely related to the African cheetah and leopard FIV strains. Histopathological examination of lymph node and spleen from infected and uninfected Pallas' cats suggests that FIV(Oma) causes immune depletion in its' native host.