DOI: 10.5061/dryad.brv15dvh6
title: Data for: Harvest and decimation affect genetic drift and the effective population size in wild reindeer

description: Harvesting and culling are methods used to monitor and manage wildlife
 diseases. An important consequence of these practices is a change in the
 genetic dynamics of affected populations that may threaten their long-term
 viability. The effective population size (Ne) is a fundamental parameter
 for describing such changes as it determines the amount of genetic drift
 in a population. Here, we estimate Ne of a harvested wild reindeer
 population in Norway. Then we use simulations to investigate the genetic
 consequences of management efforts for handling a recent spread of chronic
 wasting disease, including increased adult male harvest and population
 decimation. The Ne/N ratio in this population was found to be 0.124 at the
 end of the study period, compared to 0.239 in the preceding 14-year
 period. The difference was caused by increased harvest rates with a high
 proportion of adult males (older than 2.5 years) being shot (15.2 % in
 2005-2018 and 44.8 % in 2021). Increased harvest rates decreased Ne in the
 simulations, but less sex-biased harvest strategies had a lower negative
 impact. For harvest strategies that yield stable population dynamics,
 shifting the harvest from calves to adult males and females increased Ne.
 Population decimation always resulted in decreased genetic variation in
 the population, with higher loss of heterozygosity and rare alleles with
 more severe decimation or longer periods of low population size. A very
 high proportion of males in the harvest had the most severe consequences
 for the loss of genetic variation. This study clearly shows how the
 effects of harvest strategies and changes in population size interact to
 determine the genetic drift of a managed population. The long-term genetic
 viability of wildlife populations subject to disease will also depend on
 the population impacts of the disease and how these interact with
 management actions.
description: <strong>Data collection</strong><br>The data
 was collected from the wild reindeer population at Hardangervidda in
 Southern Norway (60°09’55’’ N, 07°27’58’’ E). The Hardangervidda
 population is subject to annual harvest before the rut in late summer or
 the beginning of autumn (August-September). Generally, hunters do not
 differentiate between female and male calves, and it is also difficult to
 determine the sex of yearlings (1.5 years old) during hunting. Thus,
 harvest quotas generally separate between calves (0.5 years old), females
 (2.5 years and older), yearlings (females and males 1.5 years old), and
 free licenses (animals of any age and sex). The latter category is
 typically used to shoot adult males (2.5 years and older), as their size
 and status as trophy is considered attractive by hunters. Data on the
 number of harvested animals in each of the six categories (calves,
 yearlings, and adults of both sexes) were collected as reported by
 hunters. Four different annual surveys are performed
 throughout the year to monitor the population size and structure. First, a
 minimum estimate for the population size is made using flight transects
 during mid-winter (January-March), where all observed groups of reindeer
 are photographed and counted. Second, the annual calf production is
 estimated using flight transects during summer (late June to mid-July),
 where a subset of groups with females, calves, and yearling males are
 photographed and the ratio of calves to adult females and yearlings of
 both sexes are calculated. Adult males generally aggregate in separate
 groups in other areas at this time of the year. Third, data is recorded on
 the number of calves, yearlings, and adults of both sexes that are shot
 during the harvest (August-September). Finally, the population age and sex
 structure are estimated using ground surveys just after the harvest
 (September-October). At this time of the year the reindeer aggregate in
 groups with both sexes and can be classified into age and sex classes
 (calves, females, yearling males, and adult males). Data on population
 sizes in the years 2005-2021 were collected from an established Bayesian
 integrated population model which uses data from these four surveys for
 this population (Viljugrein et al. 2023).
 <strong>Additional data</strong><br>Additional
 data on fertility for females, average summer survival for calves, and
 survival for adult animals in the Hardangervidda population were collected
 from Mysterud et al. (2020), data on mating skew for male reindeer were
 collected from Røed et al. (2005), data on primary sex ratio was collected
 from Loison and Strand (2005) and data on the distribution of age-specific
 fertilities were collected from Skogland (1985, 1989). These additional
 data are provided in the main text of the publication.
 <strong>References</strong> 
 Loison, A., Strand, O. 2005. Allometry and variability of
 resource allocation to reproduction in a wild reindeer population.
 Behavioural Ecology, 16: 624-633. Mysterud, A., Hopp,
 P., Alvseike, K.R., Benestad, S.L., Nilsen, E.B., Rolandsen, C.M., Strand,
 O., Våge, J., Viljugrein, H. 2020. Hunting strategies to increase
 detection of chronic wasting disease in cervids. Nature Communications,
 11: 4392. Røed, K.H., Holand, Ø., Gjøstein, H.,
 Hansen, H. 2005. Variation in male reproductive success in a wild
 population of reindeer. Journal of Wildlife Management, 69:
 1163-1170. Skogstad, T. 1985. The effects of
 density-dependent resource limitations on the demography of wild reindeer.
 Journal of Animal Ecology, 54: 359-374. Skogstad, T.
 1989. Natural selection of wild reindeer life history traits by food
 limitation and predation. Oikos, 55: 101-110.
 Viljugrein, H. 2023. Data and Figure-Scripts for the Paper ‘An
 Infectious Disease Outbreak and Increased Mortality in Wild Alpine
 Reindeer’. Zenodo. doi: 10.5281/zenodo.7624490
description: # Data for: Harvest and decimation affect genetic drift and the effective
 population size in wild reindeer
 [https://doi.org/10.5061/dryad.brv15dvh6](https://doi.org/10.5061/dryad.brv15dvh6) These data were used in analyses of the effective population size (Ne) of the wild reindeer population and to investigate the impact of management procedures implemented in the population on Ne using simulation. The management procedures included changes in harvest strategies, such as increases in the proportion of adult males harvested, and population decimations. The harvest strategies and population decimations considered are based on the management's need to handle the recent spread of chronic wasting disease in wild populations of cervids in Norway. ## Description of the data and file structure Two data files are provided, 1) Counts of harvested animals in the age classes calves, yearlings, and adults of both sexes (filename: harvest_counts_hardangervidda_05-21.csv) and 2) Estimated population sizes before harvest from 2005 to 2021 (filename: population_size_hardangervidda_05-21.csv). Both data sets are provided as semi-colon (;) delimited CSV files, with informative variable names. ### File 1: Counts of harvested animals Filename: **harvest_counts_hardangervidda_05-21.csv** The following variables are found in the data set. Note that names on the variables with the number of harvested animals are in Norwegian. "Bukk" translates to male reindeer and "simle" translates to female reindeer. Animals are shot for meat by licensed hunters during an annual harvest in August-September each year. Annual quotas for the harvest are set by the authorities. Hunters are required to report the number, age, and sex of harvested animals within their quota. * year: The year in which animals were harvested * felte_kalv_bukk: Counts of the number of male calves (age 0.5 years old) shot * felte_kalv_simle: Counts of the number of female calves (age 0.5 years old) shot * felte_bukk_1: Counts of the number of male yearlings (age 1.5 years old) shot * felte_simle_1: Counts of the number of female yearlings (age 1.5 years old) shot * felte_bukk_2plus: Counts of the number of male adults (age 2.5 years old or older) shot * felte_simle_2plus: Counts of the number of female adults (age 2.5 years old or older) shot ### File 2: Estimated population sizes before harvest Filename: **population_size_hardangervidda_05-21.csv** The following variables are found in the data set. Population sizes are estimates based on survey data using a Bayesian integrated population model (see above, Viljugrein et al. 2023). Population size estimates are provided for the years 2005-2022, but estimates from the year 2022 should not be used for analyses as they may be subject to changes when data from later years is available and can inform the model to allow more precise estimates. * category: The variable is a composite variable with information on sex, age, and year. Years are coded with numbers 1-18, starting with 2005 (1) and ending with 2022 (18). Age is classified as "0" (calves), "1" (yearlings), and "ad" (adults aged 2.5 years or older). Sex is coded with "f" for females and "m" for males. In addition, estimates for the total population size are provided and are coded with "tot". Hence, "Ntot[1]" is the total population size in 2005, and "N0m[5]" is the population size of male calves in 2009. * mean: This is the estimated mean population size from the posterior distribution in the Bayesian integrated population model * sd: This is the estimated standard deviation of population size from the posterior distribution in the Bayesian integrated population model * 2.5 %: This is the estimated lower 95 % credible interval (2.5 % percentile) of population size from the posterior distribution in the Bayesian integrated population model * 50 %: This is the estimated 50 % percentile of population size from the posterior distribution in the Bayesian integrated population model * 97.5 %: This is the estimated upper 95 % credible interval (97.5 % percentile) in population size from the posterior distribution in the Bayesian integrated population model ## Sharing/Access information Data on population sizes were derived from the following sources: * Viljugrein, H. 2023. Data and Figure-Scripts for the Paper ‘An Infectious Disease Outbreak and Increased Mortality in Wild Alpine Reindeer’. Zenodo. doi: 10.5281/zenodo.7624490 ## Code/Software In addition to the data files, the R-script for performing all analyses and data management in the publication "Harvest and decimation affect genetic drift and the effective population size in wild reindeer" is provided (filename: reindeer_ne_analyses_2024-03-14.R). ### File: R-script for the analyses and data management Filename: **reindeer_ne_analyses_2024-03-14.R** The script for running analyses in the software R is annotated with detailed comments explaining each of the steps in the analyses and data management. The script was executed in R software version 4.3.3 and all R-packages which is required is loaded at the beginning of the script, make sure that all these are available for running the R script.