Investigating the morphological and genetic divergence of arctic char (Salvelinus alpinus) populations in lakes of arctic Alaska ...

• Main Authors: Klobucar, Stephen L., Rick, Jessica, Mandeville, Elizabeth, Wagner, Catherine, Budy, Phaedra
• Format: Dataset
• Language: English
• Published: Dryad 2020
• Subjects: FOS Biological sciences; Arctic; Atlantic salmon; Salvelinus alpinus; Alaska
• Online Access: https://dx.doi.org/10.5061/dryad.1vhhmgqrs; https://datadryad.org/stash/dataset/doi:10.5061/dryad.1vhhmgqrs

Polymorphism facilitates coexistence of divergent morphs (e.g., phenotypes) of the same species by minimizing intraspecific competition, especially when resources are limiting. Arctic char (Salvelinus sp.) are a Holarctic fish often forming morphologically, and sometimes genetically, divergent morphs. In this study, we assessed the morphological and genetic diversity and divergence of 263 individuals from seven populations of arctic char with varying length-frequency distributions across two distinct groups of lakes in northern Alaska. Despite close geographic proximity, each lake group occurs on landscapes with different glacial ages and surface water connectivity, and thus were likely colonized by fishes at different times. Across lakes, a continuum of physical (e.g., lake area, maximum depth) and biological characteristics (e.g., primary productivity, fish density) exists, likely contributing to characteristics of present-day char populations. Although some lakes exhibit bimodal size distributions, using ... : Arctic char were collected from lakes in northern Alaska, DNA was extracted, genotyping-by-sequencing libraries were prepared, and libraries were sequenced as explained in Klobucar et al. 2021, Ecology & Evolution. Raw fastq reads (archived in NCBI BioProject PRJNA687211, https://www.ncbi.nlm.nih.gov/bioproject/?term=prjna687211) were aligned to the Atlantic salmon genome (NCBI BioProject PRJNA287919; Lien et al., 2016) using bwa, and variants were called using samtools and bcftools. These variants were then filtered to retain sites with < 50% missing data, minor allele frequency > 0.01, and only one site per locus using vcftools, resulting in the file variants_nolowcov10k_miss0.5_maf0.01.vcf.gz. The R script for analyzing this VCF is char_PCA_from_covariance.R. Additionally, variants were called on (1) only individuals from the LTER lakes, and (2) only individuals from the FOG lakes, and filtered as described. In addition, scaffolds containing significant sex-associated loci were removed, ...