The genome of Boris, an outbred feral domestic cat living in St. The first seven chromosome homologues of the genomes of Boris, Cinnamon and Chewbacca are displayed for direct comparison.
The Da Di approximation compares the expected allele frequency and the observed AFS over the parameter value space by computing a composite-likelihood score for the best of distinctive but plausible evolutionary scenarios.
The scenarios were simulated with the AFS data and the results were used to calculate the likelihoods of best fit for each model (see Fig. a Demographic history of two cheetah populations (southern in Namibia and eastern in Tanzania) based on Da Di analyses.
Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs.
Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.08 % homozygous), Virunga Mountain Gorilla (78.12 %), inbred Abyssinian cat (62.63 %), Tasmanian devil, domestic dog and other mammalian species.
A parallel analysis using the pairwise sequentially Markovian coalescent (PSMC) algorithm for estimating demographic history lent support to the inference of decreasing cheetah population size in the last 100,000 years (Additional file Modern cheetahs display multiple physiological correlates of inbreeding depression in both captive and free-ranging populations.
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 .
b SNV density in cheetahs, four other felids and human based upon estimates in 50-kbp sliding windows.
Of these, 38,661 fragments had lengths less than the specified window size and thus were excluded from further analysis; most of those fragments are contigs with length less than 500 bp, and thus 46,787 windows of total length 2.337 Gb were built and analyzed.
c Number of SNVs in protein-coding genes in felid genomes.