DOI: 10.5061/dryad.r7sqv9sh0
title: Data and R scripts for: Effects of hunting on genetic diversity, inbreeding and dispersal in Finnish black grouse (Lyrurus tetrix)

description: While intensive hunting activities, such as commercial fishing and trophy
 hunting, can have profound influences on natural populations, less
 intensive recreational hunting can also have more subtle effects on animal
 behaviour, habitat use and movement, with implications for population
 persistence. Lekking species such as the black grouse (Lyrurus tetrix) may
 be especially prone to hunting as leks are temporally and spatially
 predictable, making them easy targets. Furthermore, inbreeding in black
 grouse is mainly avoided through female-biased dispersal, so any
 disruptions to dispersal caused by hunting could lead to changes in gene
 flow, leading to an increasing risk of inbreeding. We therefore
 investigated the impact of hunting on genetic diversity, inbreeding and
 dispersal on a metapopulation of black grouse in Central Finland. We
 genotyped 1,065 adult males and 813 adult females from twelve lekking
 sites (six hunted, six unhunted) and 200 unrelated chicks from seven sites
 (two hunted, five unhunted) at up to thirteen microsatellite loci. Our
 initial confirmatory analysis of sex-specific fine-scale population
 structure revealed little genetic structure in the metapopulation. Levels
 of inbreeding did not differ significantly between hunted and unhunted
 sites in both adults and chicks. However, immigration rates into hunted
 sites were significantly higher among adults compared to immigration into
 unhunted sites. We conclude that the influx of migrants into hunted sites
 may compensate for the loss of harvested individuals, thereby increasing
 gene flow and mitigating inbreeding. Given the absence of any obvious
 potential barriers to gene flow in Central Finland, a spatially
 heterogeneous matrix of hunted and unhunted regions may be crucial to
 ensure sustainable harvests into the future.
description: We extracted genomic DNA from
 whole blood using a BioSprint 15 DNA Blood Kit (Qiagen, Ref. 940017) and a
 Kingfisher magnetic particle processor. Individual male black grouse were
 genotyped at 12 autosomal microsatellite loci (BG6, BG15, BG16, BG18,
 BG19, BG20 (Piertney
 & Höglund, 2001);
 TTT1, TTD2, TTD3 (Caizergues et al., 2001); TUD6, TUT3, TUT4, (Segelbacher et al., 2000). The adults were additionally genotyped at
 TTT2 (Caizergues et al.,
 2001) bringing the total number of microsatellites
 genotyped in adults and chicks to 13 and 12 respectively. Microsatellite
 genotyping was performed following the protocol described
 in (Lebigre et al.,
 2007).
description: This repository contains the raw data and R scripts executed to
 produce the manuscript results and its figures. The full workflow
 including other softwares as well as intermediate data files can be found
 at https://github.com/rshuhuachen/blackgrouse-hunting. To execute the workflow, execute the R scripts in order from 1 - 7 in R or RStudio. Raw genotypes are uploaded as .stru files, formatted to be analysed with STRUCTURE software, as well as .csv files where one row represents one individual. To open the raw data files, any text editor will suffice, and to execute the workflow, R is required with the necessary packages installed. Please refer to the README file for full details on the scripts and raw data files.