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

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

Swimming through the sands of the Sahara and Arabian deserts: Phylogeny of sandfish skinks (Scincidae, Scincus) reveals a recent and rapid diversification

Large parts of the Sahara Desert and Arabia are covered by sand seas and sand dunes, which are inhabited by specialized animal communities. For example, many lizards have developed adaptations to life in loose sand, including sand-swimming behavior. The best-known sand swimmers of the Saharo-Arabia are the sandfish skinks (genus Scincus). Although there are currently only four Scincus species recognized, their phylogenetic relationships have not yet been addressed in detail. We use eight genetic markers (three mitochondrial, five nuclear) and a complete sampling of species to infer the relationships within the genus. We employ multiple phylogenetic approaches to reconstruct the evolutionary history of these skinks and to assess the level of reticulation at the onset of their radiation. Our results indicate the presence of five strongly supported species-level lineages, four represented by the currently recognized species and the fifth by S. scincus conirostris, which does not form a clade with S. scincus. Based on these results we elevate the Iranian and northern Arabian S. conirostris to the species level. The two Saharan species, S. albifasciatus and S. scincus, are sister in all analyses. Deeper relationships within the genus, however, remained largely unresolved despite the extensive genetic data set. This basal polytomy, together with the fact that we detected no sign of hybridization in the history of the genus, indicates that the diversification of the five Scincus species was rapid, burst-like, and not followed by secondary hybridization events. Divergence time estimations show a Middle Pliocene crown radiation of the genus (3.3 Mya). We hypothesize that the aridification of the Saharo-Arabia that began in the Late Miocene triggered the initial diversification of Scincus, and that the subsequent expansion of sand deserts enabled their dispersal over the large Saharan and Arabian range. We discuss the evolution of body form in sand swimming lizards and ponder how Scincus retained their fully limbed morphology despite being sand swimmers that are typically limbless.We are thankful to Taif University, Saudi Arabia, for support under Researcher Supporting project number (TURSP-2020/06). Field work in Oman was carried out in collaboration with the Nature Conservation Department of the Ministry of Environment and Climate Affairs, MECA (Refs: 08/2005; 16/2008; 38/2010; 12/2011; 13/2013; 21/2013; 37/2014; 31/2016). The work of JŠ was supported by the Czech Science Foundation (GACR, project number 18–15286Y) and the Ministry of Culture of the Czech Republic (DKRVO 2019–2023/6.VII.c, 00023272). MU was supported by Charles University (SVV 260571/2020). SC was supported by grant PGC2018-098290-B-I00 (MCIU/AEI/FEDER, UE)

A new species of Pseudotrapelus (Reptilia: Squamata: Agamidae) from Central Arabia

Abstract A recent molecular phylogeny of the agamid genus Pseudotrapelus, distributed in the rocky areas of North Africa and the Arabian Peninsula, revealed the presence of a genetically distinct lineage around the city of Riyadh in central Saudi Arabia. With the inclusion of additional specimens, we were able to describe this lineage as a new species, P. tuwaiqensis sp. nov., confined to the Tuwaiq Escarpment, thus endemic to central Saudi Arabia. Our results of morphological examinations and molecular analyses, using three mitochondrial (COI, 16S, ND4-tRNAs) and two nuclear (c-mos, MC1R) gene fragments, show the new species is genetically differentiated and phylogenetically close to P. sinaitus and P. chlodnickii

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

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.This work was supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 864203), “Unidad de Excelencia María de Maeztu”, funded by the AEI (CEX2018-000792-M) to TMB, and grants PGC2018-098290-B-I00 (MCIU/AEI/FEDER, UE) Spain, PID2021-128901NB-I00 (MCIN/AEI/10.13039/501100011033 and by ERDF, A way of making Europe), Spain to SC. We acknowledge both Anders Albrechtsen and Nicolas Dussex for useful comments with introgression and mutational load analyses, respectively, and Núria Hermosilla for interesting comments about phylogenetic analysis. We further acknowledge Johanna Paijmans for helping during the downloading of some of the leopard genomes. We want to thank Prem Aguilar for his useful comments in a previous version of this manuscript as well as two anonymous reviewers. We are deeply thankful to Dr. Mohammed Qurban, chief executive officer of the National Center for Wildlife (NCW), and the former vice president of the formal Saudi Wildlife Authority Dr. Hani Tatwany for their support and encouragement since the beginning of the project. We are also grateful to all personnel involved in the Arabian Leopard programme at the Royal Commission for AlUla and their partners in the Arabian Leopard project for support, with the Approval of Saudi Wildlife Authority under permit SWA/6386. GM-R was funded by an FPI grant from the Ministerio de Ciencia, Innovación y Universidades, Spain (PRE2019-088729), AT is supported by “la Caixa”” doctoral fellowship program (LCF/BQ/DR20/11790007), BB-C was funded by FPU grant from Ministerio de Ciencia, Innovación y Universidades, Spain (FPU18/04742) and HT-C was supported by a "Juan de la Cierva - Formación" postdoctoral fellowship (FJC2021-046832-I) funded by MCIN/AEI/10.13039/501100011033 and by the European Union NextGenerationEU/PRTR