Quantification of loss of haplotype diversity in the highly inbred Scandinavian wolf population. Quantification of loss of haplotype diversity in the highly inbred Scandinavian wolf population

The concepts of genetic drift and inbreeding have been studied nearly for a century and genetic drift is thought to be a dominating force behind the change of allele frequency in small populations. However, empirical studies in wild mammalian populations are rare and direct estimation of population-level genetic diversity at the whole-genome scale have become affordable just recently. In this study we analysed phased whole-genome re-sequencing data of 76 Scandinavian wolves to obtain a direct empirical measure of the extent of haplotype diversity loss across time. Our empirical results revealed that 30 years of inbreeding resulted in a considerable loss of already limited haplotype diversity of the three founder individuals of the re-established population that has lost 24% of the female founders diploid genome, as well as 15% and 10% of the inferred first and second male founders’ genomes. We show that large segments from founder chromosomes are lost in the first generations of inbreeding and highlight the genomic regions of low haplotype diversity. This study presents a novel view of using population-level whole-genome re-sequencing data to visualize and directly quantify the consequences of genetic drift in a small inbred population.