DOI: 10.5061/dryad.bvq83bkp1
title: Data from: How accurate is genomic prediction across wild populations?

description: 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 prediction accuracy, and sought to provide a
 mechanistic understanding of the across-population accuracy by relating it
 to several population-differentiation measures. Predictions across
 populations were generally less accurate and more variable than within
 populations, and across-population accuracy covaried with some
 population-differentiation metrics. Our results underline the necessity of
 understanding the mechanisms governing genomic prediction accuracy, and of
 developing methods that exploit genomic data in novel ways.
description: 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 (&gt; 0.35) was not repeatable when samples
 were re-genotyped. 73 samples had heterozygosity &gt; 0.35, and IIDs are
 appended \__HIGHHET so they can be easily excluded if needed. --- The
 adult morphology data file is a semicolon-delimited text-file with name:
 "sparrow_pheno.csv". Adult morphology data is included for
 genotyped adult individuals that were captured at least once as adult in
 any of our study populations during years 1992-2023. There are in total
 13428 records for 5888 adult individuals in the phenotype data file. ---
 Description of variables: ringnr: anonymized version of unique individual
 ID (number on the metal ring) adult_sex: the sex of the bird (1=male;
 2=female), based solely on phenotypic information year: year of
 measurement month: month of measurement day: day of measurement locality:
 the number of the locality (island) where the bird was captured when it
 was measured hatch_year: the bird's known or assumed hatch year
 max_year: the last year the bird was recorded alive first_locality: the
 first locality where the bird was recorded (this is the bird's known
 or assumed hatching locality) last_locality: the last locality where the
 bird was recorded (this is generally the locality where the bird was
 (potentially) breeding) body_mass: body mass of the bird at measurement
 (in g) thr_bill_depth: the bird's bill depth (=height) at
 measurement, adjusted to Thor Harald Ringsby-measurement (in mm)
 thr_bill_length: the bird's bill length at measurement, adjusted to
 Thor Harald Ringsby-measurement (in mm) thr_tarsus: the length of the
 bird's right tarsus at measurement, adjusted to Thor Harald
 Ringsby-measurement (in mm) thr_wing: the length of the bird's right
 wing at measurement, adjusted to Thor Harald Ringsby-measurement (in mm)
 --- The names and study systems of the most important localities are: A)
 The Helgeland metapopulation study system 20: Nesøy (farm island) 22:
 Myken (non-farm island) 23: Træna (non-farm island) 24: Selvær (non-farm
 island) 26: Gjerøy (farm island) 27: Hestmannøy (farm island) 28: Indre
 Kvarøy (farm island) 34: Lovund (non-farm island) 35: Sleneset (non-farm
 island) 38: Aldra (farm island) 331: Lurøy (farm island) 332: Onøy (farm
 island) B) The "southern system" (these localities are
 islands/archipelagos with farms) 60: Leka 61: Vega 63: Vikna 67: Lauvøya,
 Selnes and Flenstad 68: Rånes --- For information on names and locations
 of the other localities please contact Henrik Jensen.