DOI: 10.5061/dryad.x3ffbg7wh
title: Canis lupus capture targets

description: Island populations are at heightened risk of inbreeding due to reduced
 mating opportunities with unrelated conspecifics. Extensive inbreeding can
 result in inbreeding depression (reduced fitness of individuals with
 related parents). Alexander Archipelago wolves (Canis lupus ligoni) are a
 geographically isolated subspecies that occur in the Southeast Alaskan
 panhandle, USA and coastal British Columbia, Canada. Wolves on the Prince
 of Wales Island complex (POW) in Southeast Alaska are expected to have
 lower levels of resiliency because they are a small, insular population
 that has experienced habitat fragmentation and cycles of moderate to heavy
 harvest. To understand the extent of population structure and inbreeding
 in Alexander Archipelago wolves, we designed a DNA hybridization capture
 for wolves and sequenced captured DNA from 58 individuals sampled from
 across Southeast Alaska during 2002–2016. Estimates of the proportion of
 the genome in runs of homozygosity (FROH) regardless of run length
 revealed that POW wolves were most inbred compared to wolves in other
 areas of Southeast Alaska. Wolves on POW also had more long (≥10 Mb) runs
 of homozygosity than the other populations we assessed, indicating more
 frequent mating between individuals with recent common ancestors (1–10
 generations ago). This pattern indicates a smaller population size for POW
 wolves in the recent past compared to other Southeast Alaskan populations.
 Wolves on POW exhibit an extent of inbreeding similar to that observed in
 Isle Royale National Park wolves, a population that has exhibited severe
 inbreeding depression. Our work demonstrates the utility of using genomic
 capture data to infer individual inbreeding so that proactive management
 (e.g. setting population targets and harvest quotas, curtailing habitat
 alteration, etc.) can be considered to ensure the long-term sustainability
 of small, isolated populations.
description: # Canis lupus capture targets
 [https://doi.org/10.5061/dryad.x3ffbg7wh](https://doi.org/10.5061/dryad.x3ffbg7wh) ## Description of the data and file structure This dataset contains the capture targets used in Zarn et al. (in review), to obtain sequence data from 58 individuals sampled from across Southeast Alaska during 2002–2016, and used to quantify the extent of population structure and inbreeding in Alexander Archipelago wolves. We used a custom hybridization-based capture to target tens of thousands of non-coding SNPs. We have submitted the study capture targets ("181102_CanFam31_ZARNwolfSNPsV2_EZ_HX1_capture_targets.bed"), primary capture targets ("181102_CanFam31_ZARNwolfSNPsV2_EZ_HX1_primary_targets.bed"), and the coverage summary ("181102_CanFam31_ZARNwolfSNPsV2_EZ_HX1_coverage_summary.txt"). The coverage summary details the reference genome used (CanFam3.1), the number of regions covered, the length of base pairs in the regions, and statistics of probe coverage and estimated coverage of target bases covered, the % of target bases covered. In addition the file provides information regarding the total capture targets and the total capture space in base pair units.  Usage notes - files may be viewed with Microsoft notepad, on the USCS Genome Browser (https://genome.ucsc.edu/goldenPath/help/customTrack.html), or using BEDtools v2.29 (Quinlan & Hall, 2010). ## Access information Other publicly accessible locations of the data: * Raw DNA sequence reads generated in this study were submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database under Accession Project no. PRJNA1194631. Data was derived from the following sources: * Genetics data were derived from wolf tissue samples collected from 2002 - 2016 by the authors.