Effects of hunting on mating, relatedness, and genetic diversity in a puma population

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 fa..., , , # 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 analyse...