Dataset Information

Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (Panthera pardus nimr).

ABSTRACT: In endangered species, low-genetic variation and inbreeding result from recent population declines. Genetic screenings in endangered populations help to assess their vulnerability to extinction and to create informed management actions toward their conservation efforts. The leopard, Panthera pardus, is a highly generalist predator with currently eight different subspecies. Yet, genomic data are still lacking for the Critically Endangered Arabian leopard (P. p. nimr). Here, we sequenced the whole genome of two Arabian leopards and assembled the most complete genomic dataset for leopards to date. Our phylogenomic analyses show that leopards are divided into two deeply divergent clades: the African and the Asian. Conservation genomic analyses indicate a prolonged population decline, which has led to an increase in inbreeding and runs of homozygosity, with consequent purging of deleterious mutations in both Arabian individuals. Our study represents the first attempt to genetically inform captive breeding programmes for this Critically Endangered subspecies.

SUBMITTER: Mochales-Riano G

PROVIDER: S-EPMC10432787 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature

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Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (Panthera pardus nimr).

Mochales-Riaño Gabriel G Fontsere Claudia C de Manuel Marc M Talavera Adrián A Burriel-Carranza Bernat B Tejero-Cicuéndez Héctor H AlGethami Raed Hamoud M RHM Shobrak Mohammed M Marques-Bonet Tomas T Carranza Salvador S

iScience 20230727 9

In endangered species, low-genetic variation and inbreeding result from recent population declines. Genetic screenings in endangered populations help to assess their vulnerability to extinction and to create informed management actions toward their conservation efforts. The leopard, Panthera pardus, is a highly generalist predator with currently eight different subspecies. Yet, genomic data are still lacking for the Critically Endangered Arabian leopard (P. p. nimr). Here, we seque ...[more]

PMID: 37601769

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Project description:The African leopard (Panthera pardus pardus) has lost a significant proportion of its historical range, notably in north-western Africa and South Africa. Recent studies have explored the genetic diversity and population structure of African leopards across the continent. A notable genetic observation is the presence of two divergent mitochondrial lineages, PAR-I and PAR-II. Both lineages appeared to be distributed widely, with PAR-II frequently found in southern Africa. Until now, no study has attempted to date the emergence of either lineage, assess haplotype distribution, or explore their evolutionary histories in any detail. To investigate these underappreciated questions, we compiled the largest and most geographically representative leopard data set of the mitochondrial NADH-5 gene to date. We combined samples (n = 33) collected in an altitudinal transect across the Mpumalanga province of South Africa, where two populations of leopard are known to be in genetic contact, with previously published sequences of African leopard (n = 211). We estimate that the maternal PAR-I and PAR-II lineages diverged approximately 0.7051 (0.4477-0.9632) million years ago (Ma). Through spatial and demographic analyses, we show that while PAR-I underwent a mid-Pleistocene population expansion resulting in several closely related haplotypes with little geographic structure across much of its range, PAR-II remained at constant size and may even have declined slightly in the last 0.1 Ma. The higher genetic drift experienced within PAR-II drove a greater degree of structure with little haplotype sharing and unique haplotypes in central Africa, the Cape, KwaZulu-Natal and the South African Highveld. The phylogeographic structure of PAR-II, with its increasing frequency southward and its exclusive occurrence in south-eastern South Africa, suggests that this lineage may have been isolated in South Africa during the mid-Pleistocene. This hypothesis is supported by historical changes in paleoclimate that promoted intense aridification around the Limpopo Basin between 1.0-0.6 Ma, potentially reducing gene flow and promoting genetic drift. Interestingly, we ascertained that the two nuclear DNA populations identified by a previous study as East and West Mpumalanga correspond to PAR-I and PAR-II, respectively, and that they have come into secondary contact in the Lowveld region of South Africa. Our results suggest a subdivision of African leopard mtDNA into two clades, with one occurring almost exclusively in South Africa, and we identify the potential environmental drivers of this observed structure. We caution that our results are based on a single mtDNA locus, but it nevertheless provides a hypothesis that can be further tested with a dense sample of nuclear DNA data, preferably whole genomes. If our interpretation holds true, it would provide the first genetic explanation for the smaller observed size of leopards at the southernmost end of their range in Africa.

Project description:BackgroundResolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts?ResultsIn this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these.ConclusionsThe phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies.

Project description:BackgroundFeline Panleukopenia is an important disease of cats and has been reported worldwide. The disease is caused by a non-enveloped, single-stranded DNA virus; Feline Panleukopenia Virus (FPLV), belonging to the Parvoviridae family. The disease causes significant mortality in unvaccinated kittens. The disease has been well documented in companion animals. However, only a few reports have surfaced from the wild.Case presentationAn orphan leopard cub was presented to Wildlife Rescue Centre, Nagpur, for further care; the leopard was kept under quarantine. On day 22 of the quarantine, the leopard showed inappetence, lethargy and depression and did not consume the offered carabeef (Day 0 of treatment). The leopard was examined clinically and was found to have a temperature of 102°F; blood was collected and analysed. On day one, the leopard exhibited bloody diarrhoea, inappetence, fever and depression. The leopard was rationally treated with fluids, antibiotics, multi-vitamins, haemostatics and haematinics. To gain qualitative insights into the epidemiological aspect of the disease, molecular investigation, including Polymerase Chain Reaction (PCR) and qPCR (Quantitative Polymerase Chain Reaction), were utilized to confirm the infection. The amplicon was sequenced and was found to be similar to sequences of FPLV reported domestic cats and other wild felids from India and abroad. Phylogenetic analysis was performed to understand the evolutionary relationship of the virus with previously reported sequences of FPLV. Sequences were submitted to National Center for Biotechnology Information (NCBI) and were allotted accession numbers.ConclusionThe infection in endangered leopard cubs could be managed with prompt fluid therapy, antibiotics and support treatment, ensuring an uneventful recovery. Molecular investigation and sequencing efforts can provide valuable data on epidemiology and the evolutionary relationship of the virus with the circulating strains in the field. The study has implications in the preventive management of FPLV in captivity and the selection of strains for inclusion in vaccines meant for the wild felids.

Dataset Information

Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (Panthera pardus nimr).

Publications

Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (<i>Panthera pardus nimr</i>).

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