DOI: 10.5061/dryad.1rn8pk0qm
title: Data from: Population genomic diversity and structure at the discontinuous southern range of the Great Gray Owl in North America

description: Species' distributions are often discontinuous near the edge of the
 range where the environment may be more variable than the core of the
 range. Range discontinuity can reduce or cut off gene flow to small
 peripheral populations and lead to genetic drift and subsequent loss of
 genetic diversity. The southern extent of the Great Gray Owl (
 Strixnebulosa) range in North America is discontinuous, unlike their
 northern core range across the boreal forests. We sampled owls from five
 different locations on the periphery of the range across the western US
 (Wyoming, Idaho, California, northern Oregon, and southern Oregon) to
 investigate genetic population structure and genetic diversity. Using a
 reduced-representation genomic sequencing approach to genotype 123
 individuals at 4,817 single nucleotide polymorphic loci, we identified
 four genetically differentiated populations: California, southern Oregon,
 northern Oregon, and Wyoming and Idaho grouped together as a single Rocky
 Mountain population. The four genetically differentiated populations of
 Great Gray Owls identified in this study display high differentiation and
 low genetic variation, which is suggestive of long-term isolation and lack
 of connectivity, potentially caused by range discontinuity. The
 populations that lack habitat connectivity to the rest of the breeding
 range (i.e. those in California and Oregon) had lower genetic diversity
 than the Rocky Mountain population that is connected to the core of the
 range. These factors and other risks (such as disease and human-caused
 mortality) heighten susceptibility of these range-edge populations to
 future habitat and climate changes, genetic diversity erosion, and
 potential extinction vortex. For these reasons, protecting and monitoring
 this species on the southern edge of their range is vital.
description: See: Mendelsohn B, Bedrosian B, Love Stowell SM, Gagne RB, LaCava
 MEF, Godwin BL, Hull JM, and Ernest HB. (2020) Population genomic
 diversity and structure at the discontinuous southern range of the Great
 Gray Owl in North America. Conservation Genetics.
description: File Descriptions:
 <strong>individual_IDs.xlsx:</strong> assigned ID
 codes for each individual and the state the sample was collected
 <strong>sample_information.xlsx:</strong> location
 data (approximate) where each sample was collected, date collected, USGS
 band number (if banded), age, sex, collector, and identification
 codes
 <strong>variants_4817snps_123inds.vcf: </strong>Reads
 from each individual was mapped to the de novo reference.We filtered for
 sites with minimum base and mapping quality scores (Q-score) of 20, kept a
 max-depth of 100 reads per site per individual, and omitted insertions and
 deletions. We called biallelic SNPs with a Q-score of 20 or higher 25
 resulting in 222,753 sites. These sites were thinned to one SNP per 136 bp
 sequence read. In addition, we removed SNPs with a minor allele frequency
 less than 0.05, missing data in more than 25% of individuals, or a minimum
 read depth per site per individual less than 3.
 <strong>assembly_GG_rep_comb_0.95.fa:
 </strong>synthetic reference from our data created with the
 cd-hit-est package in CD-HIT to cluster sequences. We used the sequences
 from all 123 individuals and a 0.95 sequence identity threshold, resulting
 in 1,099,773 unique contigs
 <strong>FST_function.R:</strong> function in R to
 calculate Hudson's F<sub>ST</sub> from allele frequencies
 for population differentiation
 <strong>PCA_function.R</strong>: function in R to
 generate Principal Component Analysis from genotype point
 estimates <strong>parse_barcodes.pl:
 </strong>Script in perl to demultiplex pooled libraries into
 individual samples by unique barcodes. This script allows and corrects for
 one mismatch in the barcode and removes the adapter sequences from the
 reads, leaving only genomic DNA sequences.
 <strong>splitfastq.pl</strong>: Script in perl to
 create a separate fastq file for each individual's reads
 <strong>vcf2mpgl.pl: </strong>Script in perl to
 convert a vcf file to 'multiple population genotype
 likelihoods', outputting the probabilty that the individual at that
 site is a heterozygote and each of the homozygotes (3
 likelihoods)
 <strong>gl2genest.pl: </strong>Script in perl to
 convert genotype likelihoods to genotype point estimates, on a scale of
 0-2. If all genotypes are equally likely, NA is returned