Conservation Genomic Analyses of African and Asiatic Cheetahs (Acinonyx jubatus) Across Their Current and Historical Species Range

Abstract

words)Cheetahs (Acinonyx jubatus) are majestic carnivores and the fastest land animals; yet, they are quickly heading towards an uncertain future. Threatened by habitat loss, human-interactions and illegal trafficking, there are only approximately 7,100 individuals remaining in the wild. Cheetahs used to roam large parts of Africa, and Western and Southern Asia. Today they are confined to about 9% of their original distribution. To investigate their genetic diversity and conservation status, we generated genome-wide data from historical and modern samples of all four currently recognized subspecies, along with mitochondrial DNA (mtDNA) and major histocompatibility complex (MHC) data. We found clear genetic differentiation between the subspecies, thus refuting earlier assumptions that cheetahs show only little population differentiation. Our analyses further showed that cheetahs from East Africa are more closely related to A. j. soemmeringii than they are to A . j. juabtus. This raises the need for a reclassification of the cheetah subspecies, as East African cheetahs are currently included into A . j. juabtus. We detected stronger inbreeding in the Critically Endangered A. j. venaticus (Iran) and A. j. hecki (Northwest Africa), and show that overall genome-wide heterozygosity in cheetah is lower than that reported for other threatened and endangered felids, such as tigers and lions. Furthermore, we show that MHC class II diversity in cheetahs is generally higher than previously reported, but still lower than in other felids. Our results provide new and important information for efficient genetic monitoring, subspecies assignments and evidence-based conservation policy decisions.

Comparative Genomics of the Major Histocompatibility Complex (MHC) of Felids

“…The most information has been collected on the MHC class II ( DRB ) genes and their diversity in selected populations using either SNP or microsatellites markers. Such studies were performed for the leopard cat ( Prionailurus bengalensis ) ( Saka et al, 2018 ), the Lynx genus ( Lynx lynx , Lynx pardinus , Lynx canadensis and Lynx rufus ) ( Marmesat et al, 2017 ), the cheetah ( Acinonyx jubatus ) ( Drake et al, 2004 ; Prost et al, 2020 ) and others (e.g., Wang et al, 2008 ; Wei et al, 2010 ). Since these data were produced mainly for characterizing the genetic diversity of selected free-ranging species, they are presented and discussed in the section dedicated to genetic diversity of wild felids.…”

Chromosomal-level reference genome assembly of the North American wolverine (Gulo gulo luscus): a resource for conservation genomics

“…Our wolverine genome has a heterozygosity SNV level of 0.065%, which is nearly identical to the 0.063% value calculated for the Eurasian river otter, marginally below the 0.070% (East Asian) to 0.095% (African) values calculated for the five major human ethnic populations, and is markedly higher than the 0.023% value for the Tasmanian devil, where reduced genetic diversity is believed to be a major contributing factor to devil facial tumor disease, a transmissible cancer ( Epstein et al 2016 ; Storfer et al 2017 ). Deleterious traits have been attributed to the reduced genetic diversity in the cheetah (O’Brien et al 1985 , 2017 ), although a recent report has shown clear genetic differentiations between different cheetah subspecies, refuting earlier assumptions that cheetahs showed little population differentiation ( Prost et al 2020 ). Quite possibly, genetic diversity in cheetah populations might be higher than previously thought.…”

Unlocking the potential of a validated single nucleotide polymorphism array for genomic monitoring of trade in cheetahs (Acinonyx jubatus)

“…The cheetah (A. jubatus) samples were distinct and clustered separately whereas African wildcat and domestic cat grouped together and lion and leopard were in a single cluster. For the subspecies distinction, the in silico analysis using the full 240 SNPs extracted from the data of Prost et al [30] 9 showed a clear distinction between the five classically recognized subspecies (A. j. jubatus, A. j. raineyi, A. j. soemmeringii, A. j. hecki and A. j. venaticus; Supplementary Figure 7). Overall, the clustering was highly similar to that obtained with 3,743 SNPs in Prost et al 2020.…”

“…For the subspecies distinction, the in silico analysis using the full 240 SNPs extracted from the data of Prost et al [30] 9 showed a clear distinction between the five classically recognized subspecies (A. j. jubatus, A. j. raineyi, A. j. soemmeringii, A. j. hecki and A. j. venaticus; Supplementary Figure 7). Overall, the clustering was highly similar to that obtained with 3,743 SNPs in Prost et al 2020. The in vivo test applying the array using available samples of A. j. jubatus and A. j. soemmeringii also showed a strong discrimination between the two cheetah subspecies (Figure 4b).…”

“…We further investigated the marker set's ability to accurately assign samples to their respective species/sub-species applying Principal Component Analysis (PCA). To do so, we first carried out an in silico PCA by extracting the 240 SNPs from the data set of Prost et al [30] and running ANGSD and PCangsd [31]. This data set includes individuals of all five classically described subspecies (A. j. jubatus, A. j. raineyi, A. j. soemmeringii, A. j. hecki and A. j. venaticus).…”