The genetic tale of a recovering lion population (Panthera leo) in the Save Valley region (Zimbabwe): A better understanding of the history and managing the future.
ABSTRACT: The rapid decline of the African lion (Panthera leo) has raised conservation concerns. In the Savé Valley Conservancy (SVC), in the Lowveld of Zimbabwe, lions were presumably reduced to approximately 5 to 10 individuals. After ten lions were reintroduced in 2005, the population has recovered to over 200 lions in 2016. Although the increase of lions in the SVC seems promising, a question remains whether the population is genetically viable, considering their small founding population. In this study, we document the genetic diversity in the SVC lion population using both mitochondrial and nuclear genetic markers, and compare our results to literature from other lion populations across Africa. We also tested whether genetic diversity is spatially structured between lion populations residing on several reserves in the Lowveld of Zimbabwe. A total of 42 lions were genotyped successfully for 11 microsatellite loci. We confirmed that the loss of allelic richness (probably resulting from genetic drift and small number of founders) has resulted in low genetic diversity and inbreeding. The SVC lion population was also found to be genetically differentiated from surrounding population, as a result of genetic drift and restricted natural dispersal due to anthropogenic barriers. From a conservation perspective, it is important to avoid further loss of genetic variability in the SVC lion population and maintain evolutionary potential required for future survival. Genetic restoration through the introduction of unrelated individuals is recommended, as this will increase genetic heterozygosity and improve survival and reproductive fitness in populations.
Project description:We compiled all credible repeated lion surveys and present time series data for 47 lion (Panthera leo) populations. We used a Bayesian state space model to estimate growth rate-? for each population and summed these into three regional sets to provide conservation-relevant estimates of trends since 1990. We found a striking geographical pattern: African lion populations are declining everywhere, except in four southern countries (Botswana, Namibia, South Africa, and Zimbabwe). Population models indicate a 67% chance that lions in West and Central Africa decline by one-half, while estimating a 37% chance that lions in East Africa also decline by one-half over two decades. We recommend separate regional assessments of the lion in the World Conservation Union (IUCN) Red List of Threatened Species: already recognized as critically endangered in West Africa, our analysis supports listing as regionally endangered in Central and East Africa and least concern in southern Africa. Almost all lion populations that historically exceeded ? 500 individuals are declining, but lion conservation is successful in southern Africa, in part because of the proliferation of reintroduced lions in small, fenced, intensively managed, and funded reserves. If management budgets for wild lands cannot keep pace with mounting levels of threat, the species may rely increasingly on these southern African areas and may no longer be a flagship species of the once vast natural ecosystems across the rest of the continent.
Project description:The lion Panthera leo is one of the world's most charismatic carnivores and is one of Africa's key predators. Here, we used a large dataset from 357 lions comprehending 1.13 megabases of sequence data and genotypes from 22 microsatellite loci to characterize its recent evolutionary history. Patterns of molecular genetic variation in multiple maternal (mtDNA), paternal (Y-chromosome), and biparental nuclear (nDNA) genetic markers were compared with patterns of sequence and subtype variation of the lion feline immunodeficiency virus (FIV(Ple)), a lentivirus analogous to human immunodeficiency virus (HIV). In spite of the ability of lions to disperse long distances, patterns of lion genetic diversity suggest substantial population subdivision (mtDNA Phi(ST) = 0.92; nDNA F(ST) = 0.18), and reduced gene flow, which, along with large differences in sero-prevalence of six distinct FIV(Ple) subtypes among lion populations, refute the hypothesis that African lions consist of a single panmictic population. Our results suggest that extant lion populations derive from several Pleistocene refugia in East and Southern Africa ( approximately 324,000-169,000 years ago), which expanded during the Late Pleistocene ( approximately 100,000 years ago) into Central and North Africa and into Asia. During the Pleistocene/Holocene transition ( approximately 14,000-7,000 years), another expansion occurred from southern refugia northwards towards East Africa, causing population interbreeding. In particular, lion and FIV(Ple) variation affirms that the large, well-studied lion population occupying the greater Serengeti Ecosystem is derived from three distinct populations that admixed recently.
Project description:Feline immunodeficiency virus (FIV) is a novel lentivirus that is genetically homologous and functionally analogous to the human AIDS viruses, human immunodeficiency virus types 1 and 2. FIV causes immunosuppression in domestic cats by destroying the CD4 T-lymphocyte subsets in infected hosts. A serological survey of over 400 free-ranging African and Asian lions (Panthera leo) for antibodies to FIV revealed endemic lentivirus prevalence with an incidence of seropositivity as high as 90%. A lion lentivirus (FIV-Ple) was isolated by infection of lion lymphocytes in vitro. Seroconversion was documented in two Serengeti lions, and discordance of mother-cub serological status argues against maternal transmission (in favor of horizontal spread) as a major route of infection among lions. A phylogenetic analysis of cloned FIV-Ple pol gene sequences from 27 lions from four African populations (from the Serengeti reserve, Ngorongoro Crater, Lake Manyara, and Kruger Park) revealed remarkably high intra- and interindividual genetic diversity at the sequence level. Three FIV-Ple phylogenetic clusters or clades were resolved with phenetic, parsimony, and likelihood analytical procedures. The three clades, which occurred not only together in the same population but throughout Africa, were as divergent from each other as were homologous pol sequences of lentivirus isolated from distinct feline species, i.e., puma and domestic cat. The FIV-Ple clades, however, were more closely related to each other than to other feline lentiviruses (monophyletic for lion species), suggesting that the ancestors of FIV-Ple evolved in allopatric (geographically isolated) lion populations that converged recently. To date, there is no clear evidence of FIV-Ple-associated pathology, raising the possibility of a historic genetic accommodation of the lion lentivirus and its host leading to a coevolved host-parasite symbiosis (or commensalism) in the population similar to that hypothesized for endemic simian immunodeficiency virus without pathology in free-ranging African monkey species.
Project description:Analysis of DNA sequence diversity at the 12S to 16S mitochondrial genes of 165 African lions (Panthera leo) from five main areas in Zambia has uncovered haplotypes which link Southern Africa with East Africa. Phylogenetic analysis suggests Zambia may serve as a bridge connecting the lion populations in southern Africa to eastern Africa, supporting earlier hypotheses that eastern-southern Africa may represent the evolutionary cradle for the species. Overall gene diversity throughout the Zambian lion population was 0.7319 +/- 0.0174 with eight haplotypes found; three haplotypes previously described and the remaining five novel. The addition of these five novel haplotypes, so far only found within Zambia, nearly doubles the number of haplotypes previously reported for any given geographic location of wild lions. However, based on an AMOVA analysis of these haplotypes, there is little to no matrilineal gene flow (Fst = 0.47) when the eastern and western regions of Zambia are considered as two regional sub-populations. Crossover haplotypes (H9, H11, and Z1) appear in both populations as rare in one but common in the other. This pattern is a possible result of the lion mating system in which predominately males disperse, as all individuals with crossover haplotypes were male. The determination and characterization of lion sub-populations, such as done in this study for Zambia, represent a higher-resolution of knowledge regarding both the genetic health and connectivity of lion populations, which can serve to inform conservation and management of this iconic species.
Project description:The African lion has declined to <35,000 individuals occupying 25% of its historic range. The situation is most critical for the geographically isolated populations in West Africa, where the species is considered regionally endangered. Elevating their conservation significance, recent molecular studies establish the genetic distinctiveness of West and Central African lions from other extant African populations. Interventions to save West African lions are urgently required. However formulating effective conservation strategies has been hampered by a lack of data on the species' current distribution, status, and potential management deficiencies of protected areas (PAs) harboring lions. Our study synthesized available expert opinion and field data to close this knowledge gap, and formulate recommendations for the conservation of West African lions. We undertook lion surveys in 13 large (>500 km²) PAs and compiled evidence of lion presence/absence for a further eight PAs. All PAs were situated within Lion Conservation Units, geographical units designated as priority lion areas by wildlife experts at a regional lion conservation workshop in 2005. Lions were confirmed in only 4 PAs, and our results suggest that only 406 (273-605) lions remain in West Africa, representing <250 mature individuals. Confirmed lion range is estimated at 49,000 km², or 1.1% of historical range in West Africa. PAs retaining lions were larger than PAs without lions and had significantly higher management budgets. We encourage revision of lion taxonomy, to recognize the genetic distinctiveness of West African lions and highlight their potentially unique conservation value. Further, we call for listing of the lion as critically endangered in West Africa, under criterion C2a(ii) for populations with <250 mature individuals. Finally, considering the relative poverty of lion range states in West Africa, we call for urgent mobilization of investment from the international community to assist range states to increase management effectiveness of PAs retaining lions.
Project description:BACKGROUND: Understanding the demographic history of a population is critical to conservation and to our broader understanding of evolutionary processes. For many tropical large mammals, however, this aim is confounded by the absence of fossil material and by the misleading signal obtained from genetic data of recently fragmented and isolated populations. This is particularly true for the lion which as a consequence of millennia of human persecution, has large gaps in its natural distribution and several recently extinct populations. RESULTS: We sequenced mitochondrial DNA from museum-preserved individuals, including the extinct Barbary lion (Panthera leo leo) and Iranian lion (P. l. persica), as well as lions from West and Central Africa. We added these to a broader sample of lion sequences, resulting in a data set spanning the historical range of lions. Our Bayesian phylogeographical analyses provide evidence for highly supported, reciprocally monophyletic lion clades. Using a molecular clock, we estimated that recent lion lineages began to diverge in the Late Pleistocene. Expanding equatorial rainforest probably separated lions in South and East Africa from other populations. West African lions then expanded into Central Africa during periods of rainforest contraction. Lastly, we found evidence of two separate incursions into Asia from North Africa, first into India and later into the Middle East. CONCLUSIONS: We have identified deep, well-supported splits within the mitochondrial phylogeny of African lions, arguing for recognition of some regional populations as worthy of independent conservation. More morphological and nuclear DNA data are now needed to test these subdivisions.
Project description:Due to anthropogenic pressures, African lion (Panthera leo) populations in Kenya and Tanzania are increasingly limited to fragmented populations. Lions living on isolated habitat patches exist in a matrix of less-preferred habitat. A framework of habitat patches within a less-suitable matrix describes a metapopulation. Metapopulation analysis can provide insight into the dynamics of each population patch in reference to the system as a whole, and these analyses often guide conservation planning. We present the first metapopulation analysis of African lions. We use a spatially-realistic model to investigate how sex-biased dispersal abilities of lions affect patch occupancy and also examine whether human densities surrounding the remaining lion populations affect the metapopulation as a whole. Our results indicate that male lion dispersal ability strongly contributes to population connectivity while the lesser dispersal ability of females could be a limiting factor. When populations go extinct, recolonization will not occur if distances between patches exceed female dispersal ability or if females are not able to survive moving across the matrix. This has profound implications for the overall metapopulation; the female models showed an intrinsic extinction rate from five-fold to a hundred-fold higher than the male models. Patch isolation is a consideration for even the largest lion populations. As lion populations continue to decline and with local extinctions occurring, female dispersal ability and the proximity to the nearest lion population are serious considerations for the recolonization of individual populations and for broader conservation efforts.
Project description:The African lion (Panthera Leo) has suffered drastic population and range declines over the last few decades and is listed by the IUCN as vulnerable to extinction. Conservation management requires reliable population estimates, however these data are lacking for many of the continent's remaining populations. It is possible to estimate lion abundance using a trophic scaling approach. However, such inferences assume that a predator population is subject only to bottom-up regulation, and are thus likely to produce biased estimates in systems experiencing top-down anthropogenic pressures. Here we provide baseline data on the status of lions in a developing National Park in Mozambique that is impacted by humans and livestock. We compare a direct density estimate with an estimate derived from trophic scaling. We then use replicated detection/non-detection surveys to estimate the proportion of area occupied by lions, and hierarchical ranking of covariates to provide inferences on the relative contribution of prey resources and anthropogenic factors influencing lion occurrence. The direct density estimate was less than 1/3 of the estimate derived from prey resources (0.99 lions/100 km² vs. 3.05 lions/100 km²). The proportion of area occupied by lions was ? = 0.439 (SE = 0.121), or approximately 44% of a 2,400 km2 sample of potential habitat. Although lions were strongly predicted by a greater probability of encountering prey resources, the greatest contributing factor to lion occurrence was a strong negative association with settlements. Finally, our empirical abundance estimate is approximately 1/3 of a published abundance estimate derived from opinion surveys. Altogether, our results describe a lion population held below resource-based carrying capacity by anthropogenic factors and highlight the limitations of trophic scaling and opinion surveys for estimating predator populations exposed to anthropogenic pressures. Our study provides the first empirical quantification of a population that future change can be measured against.
Project description:Understanding the phylogeographic processes affecting endangered species is crucial both to interpreting their evolutionary history and to the establishment of conservation strategies. Lions provide a key opportunity to explore such processes; however, a lack of genetic diversity and shortage of suitable samples has until now hindered such investigation. We used mitochondrial control region DNA (mtDNA) sequences to investigate the phylogeographic history of modern lions, using samples from across their entire range. We find the sub-Saharan African lions are basal among modern lions, supporting a single African origin model of modern lion evolution, equivalent to the 'recent African origin' model of modern human evolution. We also find the greatest variety of mtDNA haplotypes in the centre of Africa, which may be due to the distribution of physical barriers and continental-scale habitat changes caused by Pleistocene glacial oscillations. Our results suggest that the modern lion may currently consist of three geographic populations on the basis of their recent evolutionary history: North African-Asian, southern African and middle African. Future conservation strategies should take these evolutionary subdivisions into consideration.
Project description:This survey was conducted in two protected areas in Nigeria to genetically identify individual lions and to determine the genetic variation within and between the populations. We used faecal sample DNA, a non-invasive alternative to the risky and laborious task of taking samples directly from the animals, often preceded by catching and immobilization. Data collection in Yankari Game Reserve (YGR) spanned through a period of five years (2008 -2012), whereas data in Kainji Lake National Park (KLNP) was gathered for a period of three years (2009, 2010 and 2012). We identified a minimum of eight individuals (2 males, 3 females, 3 unknown) from YGR and a minimum of ten individuals (7 males, 3 females) from KLNP. The two populations were found to be genetically distinct as shown by the relatively high fixation index (FST ?= 0.17) with each population exhibiting signs of inbreeding (YGR FIS ?= 0.49, KLNP FIS ?= 0.38). The genetic differentiation between the Yankari and Kainji lions is assumed to result from large spatial geographic distance and physical barriers reducing gene flow between these two remaining wild lion populations in Nigeria. To mitigate the probable inbreeding depression in the lion populations within Nigeria it might be important to transfer lions between parks or reserves or to reintroduce lions from the zoos back to the wild.