Data from: Consistent scaling of inbreeding depression in space and time in a house sparrow metapopulation
Data files
Jul 15, 2020 version files 4.10 MB
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AR_INLA.R
12.38 KB
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Dryad_readme.txt
4.14 KB
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Estimating_FROH.R
1.44 KB
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Estimating_inbreeding_coefficients.txt
1.52 KB
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Estimating_pedigree_F.R
2.03 KB
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Genotypes_sequoia.raw
3.84 MB
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lethal_equivalents_LRS_AR.R
13.34 KB
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lethal_equivalents_survival.R
6.95 KB
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LRS_INLA.R
10.96 KB
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morphology_INLA.R
17.53 KB
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Multivariate_MCMCglmm.R
16.07 KB
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Pedigree_Sequoia.R
1.14 KB
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pedigree.txt
51.94 KB
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Permutations_F_variance.R
9.34 KB
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Permutations_F-interactions_fitness_spatiotemporal.R
13.87 KB
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Permutations_F-interactions_spatiotemporal.R
19.99 KB
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Pop_size_1997_2012.csv
1.23 KB
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Pop_size_1998_2013.csv
1.27 KB
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Sequoia_lifehistory.txt
37.41 KB
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Survival_JAGS.R
19.03 KB
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variance_explained_survival.R
7.81 KB
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Variance_partitioning_F.R
6.21 KB
Jan 19, 2023 version files 608.49 MB
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AR_INLA.R
12.38 KB
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ch.csv
95.44 KB
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Data.txt
501.31 KB
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density.csv
146.25 KB
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Dryad_readme.txt
4.14 KB
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Estimating_FROH.R
1.44 KB
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Estimating_inbreeding_coefficients.txt
1.52 KB
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Estimating_pedigree_F.R
2.03 KB
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fgrm.csv
53.56 KB
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FROH_original.txt
37.96 KB
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froh.csv
53.65 KB
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gen_sex.csv
8.18 KB
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Genotypes_pruned.map
2.83 MB
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Genotypes_pruned.zip
235.56 MB
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Genotypes_sequoia.raw
3.84 MB
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Genotypes.map
4.37 MB
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Genotypes.zip
360.72 MB
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island_status.csv
8.18 KB
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island.csv
8.18 KB
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lethal_equivalents_LRS_AR.R
13.34 KB
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lethal_equivalents_survival.R
6.95 KB
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LRS_INLA.R
10.96 KB
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morphology_INLA.R
17.53 KB
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Multivariate_MCMCglmm.R
16.07 KB
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Pedigree_Sequoia.R
1.14 KB
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pedigree.txt
51.94 KB
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Permutations_F_variance.R
9.34 KB
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Permutations_F-interactions_fitness_spatiotemporal.R
13.87 KB
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Permutations_F-interactions_spatiotemporal.R
19.99 KB
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Pop_size_1997_2012.csv
1.23 KB
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Pop_size_1998_2013.csv
1.27 KB
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README.md
4.46 KB
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Sequoia_lifehistory.txt
37.41 KB
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Survival_JAGS.R
19.03 KB
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variance_explained_survival.R
7.81 KB
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Variance_partitioning_F.R
6.21 KB
Abstract
Inbreeding may increase the extinction risk of small populations. Yet, studies using modern genomic tools to investigate inbreeding depression in nature have been limited to single populations, and little is known about the dynamics of inbreeding depression in subdivided populations over time. Natural populations often experience different environmental conditions and differ in demographic history and genetic composition; characteristics that can affect the severity of inbreeding depression. We utilised extensive long-term data on more than 3100 individuals from eight islands in an insular house sparrow metapopulation to examine the generality of inbreeding effects. Using genomic estimates of realised inbreeding, we discovered that inbred individuals had lower survival probabilities and produced fewer recruiting offspring than non-inbred individuals. Inbreeding depression, measured as the decline in fitness related traits per unit inbreeding, did not vary appreciably among populations or with time. As a consequence, populations with more resident inbreeding (due to their demographic history) paid a higher total fitness cost, evidenced by a larger variance in fitness explained by inbreeding within these populations. Our results are in contrast to the idea that effects of inbreeding generally depend on ecological factors and genetic differences among populations, and expand the understanding of inbreeding depression in natural subdivided populations.
Methods
Data has been collected from house sparrows on eight islands in the Helgeland archipelago in Norway. Datasets include SNP-genotypes for pedigree construction, pedigree, SNP-genotypes, fitness estimates and morphological data. Scripts include estimation of genomic and pedigree inbreeding coefficients and conducting analyses on the effects of inbreeding on fitness and morphological traits.
Usage notes
Description of the data and scripts are given in the Dryad_readme file.