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Data from: Genetic and evolutionary correlates of fine-scale recombination rate variation in Drosophila persimilis

When using this data, please cite the original article:

Stevison LS, Noor MAF (2010) Genetic and evolutionary correlates of fine-scale recombination rate variation in Drosophila persimilis. Journal of Molecular Evolution 71(5-6): 332-345. doi:10.1007/s00239-010-9388-1

Additionally, please cite the Dryad data package:

Stevison LS, Noor MAF (2010) Data from: Genetic and evolutionary correlates of fine-scale recombination rate variation in Drosophila persimilis. Dryad Digital Repository. doi:10.5061/dryad.1877
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Dryad Package Identifier doi:10.5061/dryad.1877    226 views  
Abstract 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.
Keywords genome evolution, molecular evolution,
Date Deposited 2010-08-20T14:58:27Z
Scientific Names Drosophila persimilis
Drosophila pseudoobscura
Drosophila miranda
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SNPMarkers.csv    70 views   21 downloads View File Details
A 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.
Download: SNPMarkers.csv ( 83.60Kb )
To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data.  


Recombinationintervals.csv    78 views   34 downloads View File Details
A 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.
Download: Recombinationintervals.csv ( 77.95Kb )
To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data.  


chromosome2alignmentannotated.gz    85 views   26 downloads View File Details
Zipped 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.
Download: chromosome2alignmentannotated.gz ( 124.5Mb )
To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data.  


Perl scripts for analysis    65 views   25 downloads View File Details
Zipped 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.
Download: LSSScriptsFINAL.zip ( 164.7Kb )
To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data.  


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