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

Abstract

Low genetic variation and high levels of inbreeding are usually a consequence of recent population declines in endangered species. From a conservation point of view, it is essential to genetically screen endangered populations to help assess their vulnerability to extinction and to properly create informed management actions towards their conservation efforts. The leopard, Panthera pardus, is a highly generalist predator with currently eight different subspecies inhabiting a wide range of habitats. Yet, genomic data is still lacking for the Critically Endangered Arabian leopard (P. p. nimr). Here, we sequenced the whole genome of two specimens of Arabian leopard and assembled the most complete genomic dataset for leopards to date, including genomic data for all current subspecies. Our phylogenomic analyses show that leopards are divided into two deeply divergent clades, one including the only African subspecies and a second one including all seven subspecies of Asian leopards. Interestingly, the Arabian leopard represents a well-differentiated lineage sister to the rest of Asian subspecies. The demographic history, genomic diversity, Runs of Homozygosity (RoHs), and mutational load in the Arabian leopard indicate a prolonged population decline, which has led to an increase in inbreeding and RoHs, with consequent purging of deleterious mutations. Our study represents the first attempt to genetically inform captive breeding programs for this Critically Endangered subspecies. Still, more genomes, particularly from wild individuals, are needed to fully characterise the genetic makeup of this singular and iconic subspecies.

Niche conservatism in a generalist felid: low differentiation of the climatic niche among subspecies of the leopard(Panthera pardus)

“…Asian leopards show whole-genome monophyly and shallow genetic divergence, indicating a single founding dispersal from Africa, and exhibit strong isolation by distance and genetic structuring across Eurasia (Paijmans et al, 2021). This is in contrast to the highly diverse and admixed African leopard (Pečnerová et al, 2021), leading to suggestions that the greatest differentiation between leopard subspecies lies between the African leopard and all Asian populations (Paijmans et al, 2021; Riaño et al, 2022), which is not reflected in current taxonomy. The limited niche differentiation we describe here may support these patterns, implying that the genetic divergence observed between Asian leopards results mainly from dispersal patterns and founding effects, and does not reflect functional ecological differentiation between the subspecies – some of which might hence be biologically equivalent.…”

Can genetic rescue help save Arabia's last big cat?

“…Oman in 1976 (Spalton, Al Hikmani, Jahdhami, et al, 2006), Jordan in 1987 (Qarqz & Baker, 2006) and the UAE in 2001 (Edmonds et al, 2006). It is therefore reasonable to posit that the Arabian leopard has been subject to a prolonged genetic bottleneck (Mochales-Riaño et al, 2023), and that this likely resulted from a human-mediated population crash, which would explain the loss of genetic diversity.…”

“…The Critically Endangered Arabian leopard (Panthera pardus nimr) is endemic to the Arabian Peninsula (Al . This highly elusive subspecies is differentiated morphologically from other P. pardus subspecies by its pale coloration and smaller body size, and through molecular phylogenetic analysis (Khorozyan et al, 2006;Mochales-Riaño et al, 2023;Uphyrkina et al, 2001). The Arabian leopard was historically found across the Arabian Peninsula but has disappeared from most of its former range (Figure 1; Harrison & Bates, 1991;Breitenmoser et al, 2006).…”

Hidden in the sand: phylogenomics unravel an unexpected evolutionary history on the desert-adapted vipers of the genusCerastes

“…Traditionally, mitochondrial markers have been widely used in phylogenetic and/or phylogeographic approaches to infer the evolutionary history of species (Brown, 2002). However, mitonuclear discordances have been widely reported in many taxa (e.g., Dinis et al, 2019;Burriel-Carranza et al, 2023a;Hinojosa et al, 2019;Mochales-Riaño et al, 2023;Zaidi & Makova, 2019), mainly due to incomplete lineage sorting, sex-biased asymmetries, introgression, or different selection pressures on mitochondrial and nuclear genomes (Toews & Brelsford, 2012). Extensive discussion about this topic has led to the general agreement that the use of genomic data can efficiently resolve the evolutionary relationships of target species (e.g., Mao et al, 2019), as well as to infer other mechanisms, like introgression, which may influence the evolutionary trajectory of species (Cahill et al, 2015;Green et al, 2010).…”