How accurate is genomic prediction across wild populations?

Evolutionary ecology seeks to understand causes and consequences of evolutionary changes across time and space, and genomic data present novel opportunities to investigate these processes. Genomic prediction - predicting individual genetic values from high-density marker data - has revolutionized breeding programs and medical genetics. In wild populations, however, genomic prediction has been used in comparatively few studies, and largely within populations. Applications that instead operate across populations could answer questions related to spatially varying evolutionary processes, such as local adaptation. A severe challenge for across-population genomic prediction, however, is the decrease in accuracy when training models on data from one population and predicting genetic values in another. Here, we applied genomic prediction across wild house sparrow populations and compared the accuracy to within-population models. We also highlighted limitations of the current theory for genomic..., , The genotype data is located in the files \"sparrow_snp.fam\", \"sparrow_snp.bim\" and \"sparrow_snp.bed\".

This dataset is the combined 70K and 200K SNPs data from both Helgeland and the southern systems (Åfjord, Vega, Vikna, Leka) plus some Faroe islands samples. The dataset contains all successfully genotyped samples (14015).

In the .fam file, the FID column (column 1) corresponds to an anonymized version of the ring number of the bird.
The IID column (column 2) is identical, except in the following cases:

1. Birds that were genotyped multiple times have a been marked with \"_i\" for the i'th genotyping (e.g., ANON00008 was genotyped twice, and these two samples are differentiated ANON00008_1 and ANON00008_2 in the IID column).
2. Samples that have mismatching genetic and phenotypic sex have had their IIDs flagged with a “MISSEX”, with degrees 1 to 3 identifying the severity of the mismatch.
3. High heterozygosity was a sign of poor genotyping quality because high heterozygosity (> 0.35) ...,