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

description: 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
 population sizes are generally small (&lt;500), suggesting a limited
 ability to maintain adaptive variability if genetic exchange with nearby
 populations became eliminated. We identify genomic regions potentially
 shaped by selection; SNPs exhibiting population divergence exceeding
 expectations under drift and a putative selective sweep acting within one
 lake to which the competitive brown trout was introduced during the
 sampling period. Identified genes appear involved in immunity and salinity
 tolerance. Present results suggest that genetically vulnerable populations
 of Arctic charr have maintained neutral and putatively adaptive genetic
 diversity despite small effective sizes, attesting the importance of
 continued protection and assurance of gene flow among populations.
description: Please find in the published article
description: \## 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. Year of sample collection is also provided after
 '_' sign. This excel file is named as "Sample
 desciption.xls". -The snps from nuclear genome are found in the
 following vcf
 "Arctic_charr_variants_only.filtered_adjQD2_fullfilterd_28-11-2021.setid.vcf.recode.vcf" -Treemix allele frequency file based on the 77 snps from mito-genome is available as "Arctic_charr_mtDNA.filtered_adjQD2.p.treemix" \## Access to raw data Illumina raw sequences from this study (from which these filtered data are extracted) have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under project accession number PRJEB62707