DOI: 10.5061/dryad.vx0k6dk2z
title: Data and code from: Parasite-mediated inbreeding depression in wild red deer

description: Inbreeding depression is the reduction in fitness of inbred individuals
 relative to their more outbred counterparts. Parasitism also reduces
 fitness and is a route by which inbreeding depression may operate, yet the
 complete pathway from inbreeding to parasitism to fitness has almost never
 been documented in the wild. Using high-quality, individual-level data on
 fitness in juveniles and adult females, longitudinal infection data for
 three gastrointestinal helminth parasites, and genomic inbreeding
 coefficients, we test for parasite-mediated inbreeding depression in a
 wild ungulate population (red deer, Cervus elaphus). We found evidence for
 parasite-mediated inbreeding depression via strongyle nematodes in
 juvenile survival, independent of direct adverse effects of inbreeding on
 survival and indirect effects of inbreeding on survival via birth weight.
 Inbreeding also reduced fitness in reproductive adults by reducing
 overwinter survival. Our study reveals three independent pathways by which
 inbreeding depresses fitness and highlights the rarely-studied route of
 parasitism.
description: Associated data files for: # Parasite-mediated inbreeding depression in
 wild red deer Adam Z. Hasik^1^ (ORCiD ID 0000-0002-4069-7186), Anna M.
 Hewett^1,2^ (ORCiD 0000-0002-9335-5649), Katie Maris^1^, Sean J.
 Morris^1^, Ali Morris^1^, Gregory F. Albery^3^ (ORCiD ID
 0000-0001-6260-2662), Josephine M. Pemberton^1^ (ORCiD ID
 0000-0002-0075-1504) ^1^ Institute of Ecology and Evolution, University of
 Edinburgh, Edinburgh, UK ^2^ Department of Ecology and Evolution,
 University of Lausanne, Lausanne, Switzerland ^3^ Department of Zoology,
 Trinity College Dublin, Dublin, Ireland *Author for correspondence: Adam
 Z. Hasik, Institute of Evolutionary Biology, University of Edinburgh,
 Edinburgh, UK; email: [adamzhasik@gmail.com](mailto:adamzhasik@gmail.com)
 This file contains: Descriptions of the data set associated with the
 analyses presented in the paper. inbreeding_code.r – R file containing all
 code necessary to analyze the data strong_df.csv, fluke_df.csv, and
 ecg_df.csv – these are the data files containing infection and inbreeding
 data for all of the juvenile deer. The following are explanations of the
 variables: ``` E - Easting N - Northing FROH - Inbreeding coefficient
 MumCode - Maternal ID of the deer BirthWt - Birth weight of the deer
 BirthDay - Birthd day (Julian day) of the deer AgeCat - Age category of
 the deer (C = Calf, Y= Yearling) Survived.mod - Overwinter survival (1 =
 survived, 0 = did not survive) Season - Season of sample collection
 (Summer, Autumn, Spring) Sex - Sex of the deer (F = female, M = male) Name
 - ID of individual deer Year - Deer year in which a given sample was
 collected lEPG - log(number of parasites per gram of feces + 1) ```
 adult_strong_df.csv, adult_fluke_df.csv, and adult_ecg_df.csv – these are
 the data files containing infection and inbreeding data for all of the
 adult deer. The following are explanations of the variables: ``` E -
 Easting N - Northing FROH - Inbreeding coefficient Age - Age of the deer
 in years Survived.mod - Overwinter survival (1 = survived, 0 = did not
 survive) Fecundity - Reproductive success of the deer in the next year (1
 = had a calf, 0 = did not have a calf) Reprod.t1 - Reproductive status of
 the deer in the current year (None = no offspring, Summer = calf died in
 the summer, Winter = raised calf up to/through winter) Season - Season of
 sample collection Name - ID of individual deer Year - Deer year in which a
 given sample was collected lEPG - log(number of parasites per gram of
 feces + 1) ``` StrongMesh.rds, FlukeMesh.rds, EcgMesh.rds,
 AdultStrongMesh.rds, AdultFlukeMesh.rds, AdultEcgMesh.rds - these are the
 data files for the spatial mesh fields for each dataset. Data files are
 for use in INLA models and can be opened in R with the readRDS() function.