DOI: 10.5061/dryad.1877
title: Data from: Genetic and evolutionary correlates of fine-scale recombination rate variation in Drosophila persimilis

description: Recombination is fundamental to meiosis in many species and generates
 variation on which natural selection can act, yet fine-scale linkage maps
 are cumbersome to construct. We generated a fine-scale map of
 recombination rates across two major chromosomes in Drosophila persimilis
 using 181 SNP markers spanning two of five major chromosome arms. Using
 this map, we report significant fine-scale heterogeneity of local
 recombination rates. However, we also observed “recombinational
 neighborhoods,” where adjacent intervals had similar recombination rates
 after excluding regions near the centromere and telomere. We further found
 significant positive associations of fine-scale recombination rate with
 repetitive element abundance and a 13-bp sequence motif known to associate
 with human recombination rates. We noted strong crossover interference
 extending 5–7 Mb from the initial crossover event. Further, we observed
 that fine-scale recombination rates in D. persimilis are strongly
 correlated with those obtained from a comparable study of its sister
 species, D. pseudoobscura. We documented a significant relationship
 between recombination rates and intron nucleotide sequence diversity
 within species, but no relationship between recombination rate and intron
 divergence between species. These results are consistent with selection
 models (hitchhiking and background selection) rather than mutagenic
 recombination models for explaining the relationship of recombination with
 nucleotide diversity within species. Finally, we found significant
 correlations between recombination rate and GC content, supporting both
 GC-biased gene conversion (BGC) models and selection-driven codon bias
 models. Overall, this genome-enabled map of fine-scale recombination rates
 allowed us to confirm findings of broader-scale studies and identify
 multiple novel features that merit further investigation.
description: SNPMarkers.csvA list of all the markers used in the publication and their genomic position as well as respective locations in both the D. pseudoobscura and D. persimilis genome. This also includes the sequence of each SNP and the base position in the two strains of D. persimilis used for genotyping.Recombinationintervals.csvA list of all intervals with the number of inferred crossovers, the physical distance in both D. pseudoobscura and D. persimilis and the name of the two markers at the endpoints of the interval (found in 'SNP markers.csv'). Also included are the 95% confidence intervals of the recombination rate as well as various genomic features, such as GC counts, GC3 counts, diversity and divergence.chromosome2alignmentannotated.gzZipped archive of chromosome 2 sequence alignment including Drosophila persimilis sequence (2 strains), D. pseudoobscura, D. miranda, and others. This file also includes the annotation information.Perl scripts for analysisZipped set of scripts, sample input and sample output files of programs used to design SNPs to distinguish 2 lines of D. persimilis, and further to extract GC content, diversity, divergence, and motif abundance of a published genomic sequence for correlation to recombination rate variation.LSSScriptsFINAL.zip