Data from: The genetic architecture of recombination rates is polygenic and differs between the sexes in wild house sparrows (Passer domesticus)
Data files
Mar 10, 2025 version files 296.04 MB
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2024_Sparrow_Recomb_GWAS_DRYAD.zip
296.04 MB
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README.md
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Abstract
Meiotic recombination through chromosomal crossing-over is a fundamental feature of sex and an important driver of genomic diversity. It ensures proper disjunction, allows increased selection responses, and prevents mutation accumulation; however, it is also mutagenic and can break up favourable haplotypes. This cost/benefit dynamic is likely to vary depending on mechanistic and evolutionary contexts, and indeed, recombination rates show huge variation in nature. Identifying the genetic architecture of this variation is key to understanding its causes and consequences. Here, we investigate individual recombination rate variation in wild house sparrows (Passer domesticus). We integrate genomic and pedigree data to identify autosomal crossover counts (ACC) and intra-chromosomal allelic shuffling () in 13,056 gametes transmitted from 2,653 individuals to their offspring. Females had 1.37 times higher ACC, and 1.55 times higher
than males. ACC and
were heritable in females and males (ACC h2 = 0.23 and 0.11;
h2 = 0.12 and 0.14), but cross-sex additive genetic correlations were low (rA = 0.29 and 0.32 for ACC and
). Conditional bivariate analyses showed that all measures remained heritable after accounting for genetic values in the opposite sex, indicating that sex-specific ACC and
can evolve somewhat independently. Genome-wide models showed that ACC and
are polygenic and driven by many small-effect loci, many of which are likely to act in trans as global recombination modifiers. Our findings show that recombination rates of females and males can have different evolutionary potential in wild birds, providing a compelling mechanism for the evolution of sexual dimorphism in recombination.
The genetic architecture of recombination rates is polygenic and differs between the sexes in wild house sparrows (Passer domesticus)
This is a data repository for the article: The genetic architecture of recombination rates is polygenic and differs between the sexes in wild house sparrows (Passer domesticus).
Authors: John B. McAuley, Bertrand Servin, Hamish A. Burnett, Cathrine Brekke, Lucy Peters, Ingerid J. Hagen, Alina K. Niskanen, Thor Harald Ringsby, Arild Husby, Henrik Jensen, Susan E. Johnston.
The associated scripts are archived on Github at https://github.com/susjoh/2024_Sparrow_Recomb_GWAS alongside information on how to run them. The curating of code and data in this repository is the responsibility of Susan Johnston. Any questions or queries should be directed to her.
Please note: these data are provided for reproducibility of the above analyses. People have spent a substantial part of their careers collecting it and many studies are ongoing, particularly by early career researchers. If you wish to use these data, please consider contacting the project manager Prof. Henrik Jensen (henrik.jensen@ntnu.no) and including those who collected and curated the data as collaborators.
Data file information:
70K_data/70K_200K_maf_gen_mind.RData
GenABEL formatted dataset with SNP genotypes at 65,840 autosomal loci before quality control described in the main manuscript.
70K_data/70K_200K_maf_gen_mind_v5.bed/.bim/.fam
PLINK formatted dataset with SNP genotypes at 56,767 autosomal loci after quality control described in the main manuscript.
70K_data/70K_200K_maf_gen_mind_v5.fam.orig
This is the original .fam file that was used relative to the 70K_200K_maf_gen_mind_v5 data for the first iteration of YAPP.
70K_data/Helgeland_pedigree_2023-03-17.txt
Pedigree data for the Helgeland population.
70K_data/0_SNP_Summary_Autosomal.txt
SNP summary data from GenABEL. Chromosome = chromosome ID; Position = base pair position on passer_domesticus_v1.0; Strand = strand information; A1 = reference allele; A2 - alternate allele; NoMeasured = number of genotypes available; CallRate = call rate; Q.2 = minor allele frequency; P.11, P.12, P.22 = genotype frequencies at A1A1, A1A2, A2A2, respectively; Pexact = P value for Hardy Weinberg Equilibrium Exact Test (HWE, chi-sq); Fmax = deviation from HWE; Plrt = P value for Hardy Weinberg Equilibrium Likelihood Ratio Test; SNP = SNP identifier.
70K_data/0_ID_Summary_Autosomal.txt
Individual Genotype Summary data from GenABEL. NoMeasured = Number of SNP genotypes; NoPoly - Number of Polymorphic SNP Genotypes; Hom = Proportion of homozygous genotypes; E(Hom) = Expectation of homozygous genotypes; F = Inbreeding Coefficient; CallPP = individual call rate' Het = Proportion of heterozygous genotypes; id = individual identity.
gwas_results/6_GWAS_Results_EB.txt
GWAS and Empirical Bayes false discovery results for all loci with non-zero effects on autosomal crossover count (ACC) and intra-chromosomal shuffling ({\bar{r}}_{intra}). Chromosome = chromosome; Position = base pair position on passer_domesticus_v1.0; Strand = DNA strand information; A1 = reference allele; A2 - alternate allele; effB = slope of allelic effects; se_effB = standard error of the slope; chi2.1df = chi-squared association statistic; P1df = uncorrected P-value; Pc1df = corrected P-value after genomic control; SNP.Name = SNP identifier; ExpP = expected P-value under a null distribution for PP-plots in Supplementary Figure S5 of the associated paper; Sex = sex in which the GWAS was conducted. Model = response variable; Q.2 = minor allele frequency; Cumu = cumulative base pair position for plotting Manhattan plots; betahat = slope estimated from Empirical Bayes analysis; sebetahat = standard error of betahat; NegativeProb = probability of negative sign of the slope; PositiveProb = probability of negative sign of the slope; lfsr = local false sign rate; lfdr = local false discovery rate; qvalue = significance of the effect; PosteriorMean = posterior mean value; PosteriorSD = posterior standard deviation.
linkage_map/passer_domesticus_linkage_map_v6.txt
Autosomal linkage maps. chr = Chromosomes, snpid = SNP identifier, Mb = base pair position, male_cM = male centiMorgan position, female_cM = female centiMorgan position.
All data were collected from the meta-population of house sparrows inhabiting an 18-island archipelago covering 1600 km2 off the Helgeland coast in Northern Norway (midpoint of 66°32’N, 12°32’E), which has been subject to an individual-based long-term study since 1993. Birds are routinely captured and individually marked from the beginning of May to the middle of August and for approximately one month in the autumn using mist nets (adults and fledged juveniles), or as fledglings in accessible nests during the breeding season. A small (25 µl) blood sample is collected from the brachial vein for DNA from every captured bird. All SNPs used in our analysis were taken from two custom house sparrow Axiom SNP arrays (200K and 70K) based on the resequencing of 33 individual house sparrows, resulting in the dataset here of 65,840 SNPs in 12,965 individuals.. All SNP positions are given relative to the house sparrow genome assembly Passer_domesticus-1.0 (GenBank Assembly GCA_001700915.1).