Fig. 4

Comparison of genetic evolutionary potential between the two snow leopard lineages. A–D The northern lineage exhibited lower genome-wide heterozygosity and population-level genomic diversity, along with higher levels of linkage disequilibrium (LD) and inbreeding coefficients (Froh) compared to the southern lineage. E Statistics information for five types of ROH (50 ~ 100 kb; 100 ~ 500 kb; 500 kb ~ 1 Mb; 1 ~ 3 Mb; 3 ~ 5 Mb). Overall, the northern lineage displayed a greater number of ROHs across all categories compared to the southern lineage. F The northern lineage showed a higher level of historical inbreeding (ROH length < 1 Mb), while recent inbreeding (ROH length ≥ 1 Mb) levels were comparable between the two lineages. G A negative correlation was observed between Froh and genome-wide heterozygosity in snow leopards. H–K The northern lineage harbored a higher genetic load compared to the southern lineage. This was demonstrated by a higher ratio of loss-of-function (LOF) to synonymous variants (H), a higher ratio of deleterious to synonymous variants (I), a higher ratio of the absolute counts of four homozygous-derived genotypes (LOF, deleterious, tolerated, and synonymous variants) (J), and a lower ratio of absolute counts of four heterozygous-derived genotypes (K)