Monitoring genome-wide diversity over contemporary time with new indicators applied to Arctic charr populations

Genetic diversity is fundamental to the adaptive potential and survival of species. Although its importance has long been recognized in science, it has a history of neglect within policy – until now. The new Global Biodiversity Framework recently adopted by the Convention on Biological Diversity, states that genetic diversity must be maintained at levels assuring adaptive potential of populations, and includes metrics for systematic monitoring of genetic diversity in so called indicators. Similarly, indicators for genetic diversity are being developed at national levels. Here, we apply new indicators for Swedish national use to one of the northernmost salmonid fishes, the Arctic charr (Salvelinus alpinus). We sequence whole genomes to monitor genetic diversity over four decades in three landlocked populations inhabiting protected alpine lakes in central Sweden. We find levels of genetic diversity, inbreeding and load to differ among lakes but remain stable over time. Effective populatio..., Please find in the published article, , \## Title of dataset

Monitoring genome-wide diversity over contemporary time with new indicators applied to Arctic charr populations. DOI: https://doi.org/10.5061/dryad.w6m905qw0

The current dataset contain the final vcf extracted from whole-genome sequencing of Arctic charr individuals. Origin of fishes (i.e. sample/population composition) can be extracted from \"Sample description.xls\" file. After quality filtering, we retained 3,421,773 and 77 bi-allelic SNPs from the nuclear and mitochondrial genomes, respectively.

The treemix file extracted from mt-genome data (77SNPs) that was used for constructing of the phyllogenetic tree is titled as \"Arctic_charr_mtDNA.filtered_adjQD2.p.treemix\".

The vcf (3,421,773 SNPs) was used for most of the analyses described in the article. For details please read the 'materials and method' and 'results' section of the published article.

\## Description of the data and file structure

-Sample id and their collection Lakes are given in the excel file...