DOI: 10.5061/dryad.7q0nq
title: Data from: Effects of inversions on within- and between-species recombination and divergence

description: Chromosomal inversions disrupt recombination in heterozygotes by both
 reducing crossing over within inverted regions and increasing it elsewhere
 in the genome. The reduction of recombination in inverted regions
 facilitates the maintenance of hybridizing species, as outlined by various
 models of chromosomal speciation. We present a comprehensive comparison of
 the effects of inversions on recombination rates and on nucleotide
 divergence. Within an inversion differentiating Drosophila pseudoobscura
 and D. persimilis, we detected one double-recombinant among 9739 progeny
 from F1 hybrids screened, consistent with published double crossover
 frequencies observed within species. Despite similar rates of exchange
 within and between species, we found no sequence-based evidence of ongoing
 gene exchange between species within this inversion, but significant
 exchange was inferred within species. We also observed greater
 differentiation at regions near inversion breakpoints between species vs.
 within species. Moreover, we observed strong ‘interchromosomal effect’
 (higher recombination in inversion heterozygotes between species) with up
 to 9-fold higher recombination rates along collinear segments of
 chromosome two in hybrids. Further, we observed that regions most
 susceptible to changes in recombination rates corresponded to regions with
 lower recombination rates in homokaryotypes. Finally, we showed that
 interspecies nucleotide divergence is lower in regions with greater
 increases in recombination rate, potentially resulting from greater
 interspecies exchange. Overall, we have identified several similarities
 and differences between inversions segregating within vs. between species
 in their effects on recombination and divergence. We conclude that these
 differences are most likely due to lower frequency of heterokaryotypes and
 to fitness consequences from the accumulation of various incompatibilities
 between species. Additionally, we have identified possible effects of
 inversions on interspecies gene exchange that had not been considered
 previously.
description: ScriptsScripts used to calculate average pairwise differences between all 6 pairwise combinations along the XR chromosome between Drosophila pseudoobscura, Drosophila persimilis, Sex-Ratio Drosophila persimilis, and Drosophila miranda. These output file can then be used to calculate RND between D pseudoobscura, D persimilis, and SR D persimilis in another program such as Microsoft Excel. All scripts are written in Perl. Author: Kenneth Hoehn. Date: May-5-2011. Sections: 1. Constructing the combined, raw input file from PILEUP outputs (skip if combined input file is provided); 2. Necessary input files for final analysis; 3. Editing combined input file and calculating average pairwise differences; 4. Calculating RND; 5. Double checking output; 6. Simple window writing script. See README.txt for more details.Multiple genome alignment of XRThis document contains the multiple genome alignment file associated with this publication. A total of four XR chromosome sequences were used for this study – one D. miranda, one D. pseudoobscura, and two D. persimilis.XR_PsPerMir_combined_g1g2_MSH39.txt