Data from: The genetic basis of dispersal in a vertebrate metapopulation
Data files
Feb 13, 2024 version files 362.95 MB
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GGAM_data_GeneticArchitecture.txt
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GWAS_data_genotype_GeneticArchitecture.raw
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GWAS_data_phenotype_GeneticArchitecture.dat
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README.md
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SNPpedigree_GeneticArchitecture.txt
Abstract
Dispersal affects evolutionary processes by changing population size and genetic composition, influencing the viability and persistence of populations. Investigating which mechanisms underlie variation in dispersal phenotypes and whether populations harbor adaptive potential for dispersal is crucial to understanding the eco-evolutionary dynamics of this important trait. Here, we investigate the genetic architecture of dispersal among successfully recruited individuals in an insular metapopulation of house sparrows. We use an extensive long-term individual-based ecological data set and high-density single nucleotide polymorphism (SNP) genotypes for over 2500 individuals. We conducted a genome-wide association study (GWAS), finding a relationship between dispersal probability and an SNP located near genes known to regulate circadian rhythmic, glycogenesis and exercise performance, among other functions. However, this SNP only explained 3.8% of variance, suggesting that dispersal is a polygenic trait. We then used an animal model to estimate heritable genetic variation (σA2 ), which composes 10% of the total variation in dispersal probability. Finally, we investigated differences in σA2 across populations occupying ecologically relevant habitat types (farm vs. non-farm) using a genetic-groups animal model. We found different adaptive potentials across habitats, with higher mean breeding value, σA2 , and heritability for the habitat presenting lower dispersal rates, suggesting also different roles of environmental variation. Our results suggest a complex genetic architecture of dispersal, and demonstrate that adaptive potential may be environment-dependent in key eco-evolutionary traits. The eco-evolutionary implications of such environment-dependence and consequent spatial variation are likely to become ever more important with the increased fragmentation and loss of suitable habitats for many natural populations.
README: Data from: The genetic basis of dispersal in a vertebrate metapopulation
https://doi.org/10.5061/dryad.80gb5mkxh
Readme file for data in: "The genetic basis of dispersal in a vertebrate metapopulation", Dilan Saatoglu, Sarah L. Lundregan, Evelyn Fetterplace, Debora Goedert, Arild Husby, Alina K. Niskanen, Stefanie Muff and Henrik Jensen
Dilan Saatoglu
dilansaatoglu@gmail.com
January 29th 2024
Description of the data and file structure
The following datasets are included:
SNPpedigree_GeneticArchitecture.txt: A metapopulation-level pedigree that was constructed based on parentage analyses using individual high-density SNP-genotype data in the R-package sequoia (Huisman, 2007; Niskanen et al., 2020). Individual, dam and sire IDs can be found in this file. Any missing parents (i.e. sire and dam) are encoded as “NA” in the pedigree. The "Real.Individual" column indicates whether the individual is a real individual ("1") or a dummy individual ("0").
GGAM_data_GeneticArchitecture.txt: Data used in the genetic group animal models. It includes ID (ID), natal island code (natal.island; further explanation provided below), dispersal status (Dispersal.status; 1 = dispersers; 0 = residents), hatch year (hatch.year), sex (sex; 1 = female; 0 = male), scaled sex values used in the model (sex_scaled), scaled habiat values used in the model (NonfarmIsland_scaled), the farm (q_i1; FarmGG_proportion) and non-farm (q_i2; NonfarmGG_proportion) genetic group proportion origins.
GWAS_data_phenotype_GeneticArchitecture.dat: Phenotype data used in GWA analysis. Extracted by using GENABEL R package function 'save.gwaa.data'. For more information see https://rdrr.io/cran/GenABEL/ .
GWAS_data_genotype_GeneticArchitecture.raw: Genotype data used in GWA analysis. Extracted by using GENABEL R package function 'save.gwaa.data'. For more information see https://rdrr.io/cran/GenABEL/ .
Island codes and names, and each island's habitat type (in parenthesis) are as follows:
20=Nesøy (farm)\
22=Myken (non-farm)\
23=Træna (non-farm)\
24=Selvær (non-farm)\
26=Gjerøy (farm)\
27=Hestmannøly (farm)\
28=Indre Kvarøy (farm)\
34=Lovund (non-farm)\
35=Sleneset (non-farm)\
38=Aldra (farm)\
331=Lurøy (farm)\
332=Onøy (farm)
References
Huisman, J. (2017). Pedigree reconstruction from SNP data: parentage assignment, sibship clustering and beyond. Molecular Ecology Resources, 17(5), 1009-1024. https://doi.org/10.1111/1755-0998.12665
Niskanen, A. K., Billing, A. M., Holand, H., Hagen, I. J., Araya-Ajoy, Y. G., Husby, A., … Jensen, H. (2020). Consistent scaling of inbreeding depression in space and time in a house sparrow metapopulation. Proceedings of the National Academy of Sciences of the United States of America, 117(25), 14584–14592. https://doi.org/10.1073/pnas.1909599117