DOI: 10.5061/dryad.v15dv425w
title: Data for: Rapid evolution of recombination landscapes during the divergence of cichlid ecotypes in Lake Masoko

description: Variation of recombination rate along the genome is of crucial importance
 to rapid adaptation and organismal diversification. Many unknowns remain
 regarding how and why recombination landscapes evolve in nature. Here, we
 reconstruct recombination maps based on linkage disequilibrium and use
 subsampling and simulations to derive a new measure of recombination
 landscape evolution: the Population Recombination Divergence Index (PRDI).
 Using PRDI, we show that fine-scale recombination landscapes differ
 substantially between two cichlid fish ecotypes of Astatotilapia
 calliptera that diverged only ~2,500 generations ago. Perhaps
 surprisingly, recombination landscape differences are not driven by
 divergence in terms of allele frequency (FST) and nucleotide diversity
 (Δπ): although there is some association, we observe positive PRDI in
 regions where FST and Δπ are zero. We found a stronger association between
 evolution of recombination and 47 large haplotype blocks that are
 polymorphic in Lake Masoko, cover 21% of the genome, and appear to include
 multiple inversions. Among haplotype blocks, there is a strong and clear
 association between the degree of recombination divergence and differences
 between ecotypes in heterozygosity, consistent with recombination
 suppression in heterozygotes. Overall, our work provides a holistic view
 of changes in population recombination landscapes during early stages of
 speciation with gene flow.
description: We used population genetic data to infer recombination landscapes
 for the two ecotypes of cichlids from lake Masoko using pyrho. Here, we
 are uploading the population genetic data in a VCF file and the
 recombination maps. 
description: # Data for: Rapid evolution of recombination landscapes during the
 divergence of cichlid ecotypes in Lake Masoko We have submitted the raw
 data that we used in our analysis. This repository contains the following
 files: 1- All_genome_benthic_a_bp15_pyrho_chr.optimize.zip 2-
 All_genome_benthic_b_bp15_pyrho_chr.optimize.zip 3-
 All_genome_littoral_a_bp15_pyrho_chr.optimize.zip 4-
 All_genome_littoral_b_bp15_pyrho_chr.optimize.zip 5-
 All_genome_replicate_pyrho_2kb.optimize.zip
 6-Astac_SelectedVariantsFiltered_indels_biallonly.vcf.gz ## Description of
 the data and file structure ###
 All\_genome\_benthic\_a\_bp15\_pyrho\_chr.optimize.zip;
 All\_genome\_benthic\_b\_bp15\_pyrho\_chr.optimize.zip;
 All\_genome\_littoral\_a\_bp15\_pyrho\_chr.optimize.zip;
 All\_genome\_littoral\_b\_bp15\_pyrho\_chr.optimize.zip These files (1 to
 4) contain the raw inferred maps for subsamples a and b for both ecotypes.
 * The first column represents the chromosome name * The second column
 represents the starting position of the interval * The third column
 represents the ending position of the interval * The last column
 represents the population recombination rate inferred for this interval
 ### All\_genome\_replicate\_pyrho\_2kb.optimize.zip This file (5) contains
 the mean recombination rate calculated in 2 kb windows along the genome
 for the 9 maps obtained by permutation. * The first column represents the
 chromosome name * The second column represents the starting position of
 the interval * The third column represents the ending position of the
 interval * The next 36 columns provide the mean population recombination
 rate for each replicate (1 to 9) for the benthic a, benthic b, littoral an
 and littoral b subsamples. ###
 Astac\_SelectedVariantsFiltered\_indels\_biallonly.vcf.gz This file (6)
 contains the VCF file used to infer recombination maps. ## Code/Software
 The code used to run these datasets are available on Github
 ([https://github.com/MarionTalbi/MasokoPaper](https://github.com/MarionTalbi/MasokoPaper))