DOI: 10.5061/dryad.1vhhmgqrs
title: Investigating the morphological and genetic divergence of arctic char (Salvelinus alpinus) populations in lakes of arctic Alaska

description: 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 model-based clustering of morphometric traits
 corrected for allometry, we did not detect morphological differences
 within and across char populations. Genomic analyses using 15,934 SNPs
 obtained from genotyping-by-sequencing demonstrated differences among lake
 groups related to historical biogeography, but within lake groups and
 within individual lakes, genetic differentiation was not related to total
 body length. We used PERMANOVA to identify environmental and biological
 factors related to observed char size structure. Significant predictors
 included water transparency (i.e., a primary productivity proxy), char
 density (fish·ha-1), and lake group. Larger char occurred in lakes with
 greater primary production and lower char densities, suggesting less
 intraspecific competition and resource limitation. Thus, char populations
 in more productive and connected lakes may prove more stable to
 environmental changes, relative to food-limited and closed lakes, if lake
 productivity increases concomitantly. Our findings provide some of the
 first descriptions of genomic characteristics of char populations in
 arctic Alaska, and offer important consideration for the persistence of
 these populations for subsistence and conservation.
description: 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, <em>Ecology
 & Evolution</em>. 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 &lt;
 50% missing data, minor allele frequency &gt; 0.01, and only one site
 per locus using vcftools, resulting in the
 file <strong>variants_nolowcov10k_miss0.5_maf0.01.vcf.gz</strong>. The R script for analyzing this VCF is <strong>char_PCA_from_covariance.R</strong>. 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, resulting in the files <strong>variants_LTER_nolowcov10k_miss0.5_maf0.01_noSex.vcf.gz </strong>and <strong>variants_FOG_nolowcov10k_miss0.5_maf0.01_noSex.vcf.gz</strong>. These two files were analyzed in R using the scripts <strong>char_PCA_from_covariance_LTER_clean.R</strong> and <strong>char_PCA_from_covariance_FOG_clean.R</strong>, respectively.
description: The metadata corresponding to the individuals in these VCFs can
 be found in
 <strong>AC_GBSdata_Master_Clean.csv</strong>.