DOI: 10.5061/dryad.bnzs7h4hm
title: Effects of hunting on mating, relatedness, and genetic diversity in a puma population

description: Hunting mortality can affect population abundance, demography, patterns of
 dispersal and philopatry, breeding, and genetic diversity.  We
 investigated the effects of hunting on the reproduction and genetic
 diversity in a puma population in western Colorado, USA. We genotyped over
 11,000 single nucleotide polymorphisms (SNPs), using double-digest,
 restriction site-associated DNA sequencing (ddRADseq) in 291 tissue
 samples collected as part of a study on the effects of hunting on puma
 population abundance and demography in Colorado from 2004−2014. The study
 was designed with a reference period (years 1−5), during which hunting was
 suspended, followed by a treatment period (years 6−10), in which hunting
 was reinstated. Our objectives were to examine the effects of hunting on:
 (1) paternity and male reproductive success; (2) the relatedness between
 pumas within the population, and (3) genetic diversity.  We found
 that hunting reduced the average age of male breeders. The number of
 unique fathers siring litters increased each year without hunting and
 decreased each year during the hunting period. Mated pairs were generally
 unrelated during both time periods, and females were more closely related
 than males. Hunting was also associated with increased relatedness among
 males and decreased relatedness among females in the population. Finally,
 genetic diversity increased during the period without hunting and
 decreased each year when hunting was present. This study demonstrates the
 utility of merging demographic data with large-scale genomic datasets in
 order to better understand the consequences of management actions.
 Specifically, we believe that this study highlights the need for long-term
 experimental research in which hunting mortality is manipulated, including
 at least one non-harvested control population, as part of a broader
 adaptive, zone management scheme.
description: # Effects of hunting on mating, relatedness, and genetic diversity in a
 puma population
 [https://doi.org/10.5061/dryad.bnzs7h4hm](https://doi.org/10.5061/dryad.bnzs7h4hm) Included is: the raw sequencing data, VCF files and Plink outputs for both the paternity analyses dataset and the overall dataset, and an excel spreadsheet with necessary sample information. ## Description of the data and file structure As described in the paper, this is ddRAD-seq data. There is raw sequencing data from four separate libraries. Samples are divided into 6 different folders to reduce file sizes. The first library was sequenced on a HiSeq4000 machine using 100 bp single-end sequencing. The remaining 3 libraries were sequenced on a HiSeq4000 machine using 150 bp paired-end sequencing. The raw sequence data has been demultiplexed and trimmed to the standard 95 bps. Two separate datasets were used in the study and the VCF files for each dataset are included here. For the full dataset used in all analyses other than the paternity analyses, we removed loci that were sequenced in less than 75% of individuals (-- geno 0.25).  Then we removed samples that had more than 50% missing data (-- mind 0.5).  Finally, we filtered out all loci with a minor allele frequency less than 0.01 (-- maf 0.01). For the paternity analyses dataset, we removed loci that were sequenced in less than 90% of individuals (-- geno 0.1), samples that had more than 70% of missing data (-- mind 0.7), and loci with a minor allele frequency less than 0.3  (-- maf 0.3).  Additionally, we removed loci that were not in Hardy-Weinberg proportions (--hwe 0.005 using the p midpoint adjustment).  Finally, we used Plink to create a blacklist and subsequently remove loci that were found to be in statistical linkage disequilibrium (r &gt; 0.2) using a proxy filter (--indep-pairwise 50 5 0.2). The Excel spreadsheet has all relevant metadata on sequence ID, sample number, sex, birth year, and death year. ## Sharing/Access information Some samples, denoted as "\*\_CSU\_lib\_trim95" in the spreadsheet, were downloaded from: Trumbo, Daryl R et al. (2019). Urbanization impacts apex predator gene flow but not genetic diversity across an urban-rural divide [Dataset]. Dryad. [https://doi.org/10.5061/dryad.12jm63xsr](https://doi.org/10.5061/dryad.12jm63xsr). ## Code/Software No special code was utilized.