Fig. 4

Patterns of genomic variation in 11 Iberian and one Eurasian lynx. a Average heterozygosity in non-overlapping syntenic 100-kb windows in one Iberian lynx from Doñana, one from Andújar (Sierra Morena) and one Eurasian lynx; chromosome A1 is shown as an illustrative example. Long runs of homozygosity are evident in the Iberian individuals. b Length of the genome covered by runs of homozygosity of different sizes in each Iberian lynx individual. Both large and medium size ROH are more abundant in Doñana, indicating higher inbreeding and a longer recent history of low effective size. c Linkage disequilibrium (LD) decay in Iberian lynx populations. Doñana has remained small (50–80 lynxes) and isolated at least since the 1950s, whereas Andújar was part of a large and well connected population until the 1960s; then it became progressively contracted and isolated and reached its lowest size at around 60 animals by 2002. d Heterozygous SNP rates in genome-sequenced mammals. Modified from Cho et al. [43] and updated with the addition of data for Altai Neanderthal [114], cheetah and feral domestic cat [115], Yangtze river dolphin [116], gibbon [117], minke whale [118], Eastern mountain gorilla [46], dromedary and Bactrian camel [119], Wrangle Is. mammoth [120], and blind mole rat [121]. The Iberian lynx genome- and species-wide SNP rate and heterozygosity are the lowest reported to date