Dating the genetic bottleneck of the america cheetah
We assessed the extent and pattern of genomic diversity using seven different measures, each of which affirmed the remarkable reduction in the cheetah’s genic and genomic variability. Second, genomes were parsed into 50-kbp windows, which were used to estimate SNV density; in total, 46,787 windows comprised 2.337 Gb or 99.12 % of the total length of the genome.
First, cheetahs display the lowest overall genome-wide SNV incidence among 11 species including the human, domestic cat, gorilla, lion and Tasmanian devil, and 90 % less than a feral domestic cat (Boris from St. The majority of windows showed 8–15-fold less variation in cheetahs than in the human, domestic cat or wildcat (Fig. The only sampled species or population with comparable or lower genomic variation than the cheetah was the Gir Forest lions from Asia, a population known to have undergone extreme genetic homogenization in its recent history [ Estimates of genome diversity in the cheetah genome relative to other mammal genomes. SNV rate for each individual was estimated using all variant positions, with repetitive regions not filtered.
As a species, cheetahs show a dramatic reduction in overall genetic variation revealed by multiple genomic markers, including an ability to accept reciprocal skin grafts from unrelated cheetahs .
Their genetic depletion correlates with elevated juvenile mortality, extreme abnormalities in sperm development, difficulties until recently in achieving sustainable captive breeding, and increased vulnerability to infectious disease outbreaks .
Compared to other Felidae species, cheetahs show constitutive impairments in reproduction, including low fecundity in captivity, an average of 80 % malformed spermatozoa per ejaculate and an elevated incidence of acrosomal defects, as has been observed in other inbred natural populations .The extreme reduction in coding gene variants would explain the initial discovery of the cheetah’s depauperate genetic variation three decades ago with studies using allozymes, cellular protein electrophoretic variants and gene-based restriction fragment length polymorphism (RFLP) [: Table S26).When we compared the structural organization and gene order of the MHC with other species, the cheetah and domestic cat were highly similar, but different from the dog and human.The MHC-SNV reductions in the inbred cat and cheetah involve both synonymous and non-synonymous amino acid-altering substitutions.These numerous function-altering variants reflect a history of pathogen-based frequency-dependent selection driving MHC diversity higher across mammals (Additional file Patterns of whole-genome sequence variation were used to model and infer the population history of cheetahs from eastern and southern Africa (from Tanzania and Namibia, respectively) using the diffusion approximation to the allele frequency spectrum (AFS) implemented in the Da Di software tool .