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

Gabriel Mochales-Riaño; Claudia Fontsere; Marc de Manuel; Adrián Talavera; Bernat Burriel-Carranza; Héctor Tejero-Cicuéndez; Raed Hamoud M AlGethami; Mohammed Shobrak; Tomas Marques-Bonet; Salvador Carranza

doi:10.1016/j.isci.2023.107481

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

iScience. 2023 Jul 27;26(9):107481. doi: 10.1016/j.isci.2023.107481. eCollection 2023 Sep 15.

Authors

Affiliations

¹ Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
² Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Øster Farimagsgade 5A, 1352 Copenhagen, Denmark.
³ Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain.
⁴ National Center for Wildlife, Prince Saud Al-Faisal for Wildlife Research, P. O Box 1086, Taif, Taif 21944, Saudi Arabia.
⁵ CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
⁶ Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
⁷ Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.

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.

Keywords: Genomics; Zoology.