Data for: Rapid evolution of recombination landscapes during the divergence of cichlid ecotypes in Lake Masoko

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 ..., 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. , , # 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 starti...