Data and code from: Parasite-mediated inbreeding depression in wild red deer
Data files
Oct 31, 2025 version files 1.51 MB
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adult_ecg_df.csv
116.73 KB
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adult_fluke_df.csv
124.19 KB
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adult_strong_df.csv
150.65 KB
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AdultEcgMesh.rds
116.37 KB
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AdultFlukeMesh.rds
115.61 KB
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AdultStrongMesh.rds
117.93 KB
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ecg_df.csv
42.94 KB
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EcgMesh.rds
176.48 KB
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fluke_df.csv
67.31 KB
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FlukeMesh.rds
174.56 KB
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inbreeding_code.R
32.08 KB
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README.md
2.80 KB
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strong_df.csv
109.43 KB
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StrongMesh.rds
162.07 KB
Abstract
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.
Associated data files for:
Adam Z. Hasik1 (ORCiD ID 0000-0002-4069-7186), Anna M. Hewett1,2 (ORCiD 0000-0002-9335-5649),
Katie Maris1, Sean J. Morris1, Ali Morris1, Gregory F. Albery3 (ORCiD ID 0000-0001-6260-2662),
Josephine M. Pemberton1 (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
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.