Data for: Rapid evolution of recombination landscapes during the divergence of cichlid ecotypes in Lake Masoko
Data files
Dec 05, 2024 version files 9.81 GB
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All_genome_benthic_a_bp15_pyrho_chr.optimize.zip
13.31 MB
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All_genome_benthic_b_bp15_pyrho_chr.optimize.zip
13.34 MB
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All_genome_littoral_a_bp15_pyrho_chr.optimize.zip
17.24 MB
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All_genome_littoral_b_bp15_pyrho_chr.optimize.zip
17.12 MB
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All_genome_replicate_pyrho_2kb.optimize.zip
33.73 MB
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Astac_SelectedVariantsFiltered_indels_biallonly.vcf.gz
9.71 GB
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README.md
2.03 KB
Abstract
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.
README: 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)
Methods
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.