Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates

Abstract

The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya using an average mammalian microsatellite mutation rate and at 4700–44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70–110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity.

Library Construction for Ancient Genomics: Single Strand or Double Strand?

“…Bovine, mammoth, and the 1400 year-old human samples were extracted and purified in a separate, contained, dedicated ancient DNA laboratory where protective clothing and decontamination of reagents, surfaces and equipment was employed (17, 18). After removing surfaces of the teeth and bones, the underlying areas were ground into powder either by low-speed drilling with a heat-sterilized drill bit using a Dremel Fortiflex (Dremel Europe, Breda, The Netherlands), or cut into fragments with a Dremel 4000 (Dremel Europe) equipped with a diamond saw blade and then powdered using a freezer mill (SPEX CertiPrep 6750, Metuchen, NJ).…”

Range-Wide Snow Leopard Phylogeography Supports Three Subspecies

“…The low microsatellite diversity and lack of mtDNA variation within snow leopards is typical of felids or subspecies that have either been historically isolated, or have undergone recent population bottlenecks, such as the Far Eastern leopard (Panthera pardus orientalis, Uphyrkina et al 2001), Sumatran tiger (Panthera tigris sumatrae, Luo et al 2004), North American puma (Puma concolor cougar, Culver et al 2000), North American ocelot (Leopardus pardalis albescens, Janecka et al 2011b), and the Asiatic cheetah (Acinonyx jubatus venaticus, Charruau et al 2011). Although we sequenced a limited amount of mtDNA, Luo et al (2004) detected 4-6 haplotypes for the same segments in tigers despite analyzing fewer individuals.…”

Continued decline in genetic diversity among wild cheetahs (Acinonyx jubatus) without further loss of semen quality

“…This finding was subsequently confirmed by six additional measures of genomic variation (O'Brien, 1994), a lack of diversity in MHC class II-DRB alleles (Castro-Prieto et al, 2011), and the whole-genome sequencing of Namibian and Tanzanian cheetahs (Dobrynin et al, 2015). The cheetah's lack of genetic diversity is attributed to a severe population bottleneck that occurred~12,000 years ago (Driscoll et al, 2002;O'Brien et al, 1985), from which the entire extant species is derived (Charruau et al, 2011). Intriguingly, recent genome sequencing suggests that a second ancient bottleneck occurred N 100,000 years ago, coincident with the migration of cheetahs into Africa (Dobrynin et al, 2015).…”