Waste not, want not: microsatellites remain an economical and informative technology for conservation genetics
Data files
Sep 07, 2023 version files 71.38 MB
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BCVI_Micro_Genotypes.csv
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BCVI_Micro_LandscapeGeneticData.csv
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BCVI_SNP_Genotypes_90GenotypeRate.vcf
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BCVI_SNP_Genotypes.vcf
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BCVI_SNP_LandscapeGeneticData.csv
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README.md
Abstract
Comparisons of microsatellite and single-nucleotide polymorphisms (SNPs) have found that SNPs outperform microsatellites in population genetic analyses, calling into question the continued utility of microsatellites in population and landscape genetics. Yet highly polymorphic markers may be of value in species that have reduced genetic variation. This study repeated analyses previously done using microsatellites with SNPs developed from ddRAD sequencing in the black-capped vireo source-sink system. SNPs provided greater resolution of genetic diversity, population differentiation, and migrant detection but could not reconstruct parentage relationships due to insufficient heterozygosities. The biological inferences made by both sets of markers were similar: asymmetrical gene flow from source sites to the remaining sink sites. With the landscape genetic analyses, we found different results between the two molecular markers, but associations of the top environmental features (riparian, open habitat, agriculture, and human development) with dispersal estimates were shared between marker types. Despite the higher precision of SNPs, we find that microsatellites effectively uncover population processes and patterns and are superior for parentage analyses in this species with reduced genetic diversity. This study illustrates the continued applicability and relevance of microsatellites in population genetic research.
README: Waste not, want not: microsatellites remain an economical and informative technology for conservation genetics
https://doi.org/10.5061/dryad.n5tb2rbwk
Description of the data and file structure
The same 185 black-capped vireo samples are represented in both the microsatellite (micro) and SNP genotype datasets below.
- BCVI_Micro_Genotypes.csv: genepop file format
- BCVI_SNP_Genotypes_90GenotypeRate.vcf
- BCVI_SNP_Genotypes.vcf
Landscape data includes
- a) At-site predictor variables: elevation, Euclidean distance, water, development, forest, scrub, open, agriculture, riparian, the proportion of scrub habitat, and brown-headed cowbird (BHCO) management
- b) Between-site variables: elevation, Euclidean distance, water, development, forest, scrub, open, agri-culture, and riparian
BCVI_Micro_LandscapeGeneticData.csv
BCVI_SNP_LandscapeGeneticData.csv
Code files included:
- BCVI_ANOVA.R
- LG_HybridApproach.R
- LG_UnivarModel_opt.R
Sharing/Access information
Microsatellite data is also featured in related articles:
https://doi.org/10.1007/s10592-020-01314-1
https://doi.org/10.1002/ece3.4764
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