Declining and isolated populations lose genetic diversity due to genetic drift, what could cause a reduction of fitness and adaptive potential. Balancing selection, recombination and mutation opposes the action of genetic drift by generating or maintaining diversity in functional areas of the genome. The concurrent action between these forces and genetic drift may vary in different demographic scenarios and result in distinct diversity patterns across the genome. We aim to study these coexisting processes in Lynx lynx and Lynx pardinus populations with different demographic histories. In addition to contemporary patterns, we will assess diachronic changes in Iberian lynx genome using ancient and historical samples. To do so, we will use high throughput sequencing data. We will also take advantage of the newly annotated Iberian lynx genome and recently developed analysis methods, such as genomic scans.