Dobrynin et al., Genome Biology, 2015

 The African cheetah  Fastest land animal  Ancestors were distributed in the Americas, Europe and Asia until ~10,000 – 12,000 years ago  Massive extinction reduced their range to eastern and southern Africa  Likely evolved from common ancestor with the American puma

 Dramatic reduction in genetic variability due to bottleneck(s)  Conservation icon symbol  A model for the impacts of increased inbreeding  Fastest land animal

 Actually seven genome sequences  Main subject – Chewbaaka, a male from Namibia  Seven mate-paired libraries of varying insert sizes (170 bp, 500 bp, 800 bp, 2000 bp, 5000 bp, 10,000 bp, and 20,000 bp)  Sequenced to ~75x coverage and assembled using SOAPdenovo2  Used the existing domestic cat genome to help with the assembly and map to chromosomes  Other six genomes were sequenced at 5-6X coverage using 500 bp insert libraries

 Genome size = Gb  N50 contigs = 28.2 kb  N50 scaffolds = 3.1 Mb  20,343 coding genes  39.5% repetitive content

 ‘Remarkable reduction in the cheetah’s genic and genomic variability  Lowest Single Nucleotide Variants among 11 other sequenced mammals  90% lower than the domestic cat SNV rate in mammals.

 ‘Remarkable reduction in the cheeta’s genic and genomic variability  Lowest Single Nucleotide Variants among 11 other sequenced mammals  90% lower than the domestic cat  Very few variants in coding gene complement Number of SNVs in protein-coding genes in felid genomes.

 ‘Remarkable reduction in the cheeta’s genic and genomic variability  Lowest Single Nucleotide Variants among 11 other sequenced mammals  90% lower than the domestic cat  Very few variants in coding gene complement  fold longer stretches of homozygous DNA when compared to domestic cat  93% of the genome is homozygous The genome of Boris, an outbred feral domestic cat living in St. Petersburg (top) is compared to Cinnamon, a highly inbred Abyssinian cat (Fca-6.2 reference for domestic cat genome sequence [19, 20], middle) and a cheetah (Chewbacca, bottom) as described here. Approximately 15,000 regions of 100 Mb across the genome for each species were assessed for SNVs. Regions of high variability ( >40 SNVs/100 kbp) are colored red; highly homozygous regions (≤40 SNVs/100 kbp) are colored green. The first seven chromosome homologues of the genomes of Boris, Cinnamon and Chewbacca are displayed for direct comparison.

 Population genomic analysis supports “an expanding population that subdivides into two bottlenecked derivative populations”

 Cheetahs have reproductive problems characteristic of inbreeding depression  92 genes with high rates of non- synonymous mutations.  18 were associated with reproduction  946 genes with signatures of selection  Several associated with cardiac and muscle function  Others associated with energy production

 Are the changes to genes that are apparently adaptive for high-speed pursuit the same as the genes associated with adaptations to high-altitude living?  Do you find the same genes under selection in non-mammal speed demons?  How could you test the hypothesis that the ‘energetic’ genes are actually associated with high-speed pursuit evolution?