Western burrowing owl genomics

Migration is driven by a combination of environmental and genetic factors, but many questions remain about those drivers. Potential interactions between genetic and environmental variants associated with different migratory phenotypes are rarely the focus of study. We pair low coverage whole genome resequencing with a de novo genome assembly to examine population structure, inbreeding, and the environmental factors associated with genetic differentiation between migratory and resident breeding phenotypes in a species of conservation concern, the western burrowing owl (Athene cunicularia hypugaea). Our analyses reveal a dichotomy in gene flow depending on whether the population is resident or migratory, with the former being genetically structured and the latter exhibiting no signs of structure. Among resident populations, we observed significantly higher genetic differentiation, significant isolation‐by‐distance, and significantly elevated inbreeding. Among migratory breeding groups, on..., Details regarding sample collection, genome sequencing, and sequence processing may be found in Methods S1; but notably, we sequenced a reference genome to high coverage and 202 burrowing owl samples collected across their migratory and resident breeding range to low coverage. Because our resequencing dataset was low coverage, we used variant detection and analytical methods that largely did not require called genotypes. This included both genotype likelihoods as estimated in the program ANGSD (Korneliussen et al., 2014) and a single‐read‐sampling (SRS) method that randomly selects one read per variant to temper the bias of high variation in locus‐to‐locus depths. Using these methods, files were prepared for analyses as described below using the following four filtering and genotyping frameworks and conditions: (1) Using ANGSD to produce genotype likelihood files for all individuals in the BEAGLE format (‐doGlf 3) and a minor allele frequency file (‐domaf 1) with restrictive filtering t..., ANGSD, The data files are 4 treatments of whole genome sequences at low coverage collected for \~120 Burrowing Owls sampled throughout western North America.

Treatment 1: 1) Using ANGSD to produce genotype likelihood files for all individuals in the BEAGLE format (-doGlf 3) and a minor allele frequency file (-domaf 1) with restrictive filtering that uses a conservative minimum minor allele frequency (-minmaf 0.05), a low maximum likelihood of being polymorphic (-SNP\_pval 1e-6), and verifying variants by removing sites with excessive mismatches from the reference genome (-C 50), and confirming variants using a base alignment quality estimation (-baq 1). These have the suffix '.glf.gz' and there are versions for all migrants and each individual resident breeding population.

Treatment 2: Using the HaplotypeCaller module in GATK (McKenna et al., 2010) to call genotypes for all individuals sequenced, filtered by removing insert/deletion variants, and kept only biallelic variants found in 50% of ...