Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis
Authors/Creators
- 1. University of Sheffield
- 2. University of Copenhagen
- 3. Institute of Science and Technology Austria
- 4. Florida State University
- 5. University of Gothenburg
Description
Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome.
Notes
SNPs.gz
SNPs used for generating linkage map (for QTL analysis) and estimating genomic relationship matrices
Pedigree.txt
Pedigree data for generating linkage map, required input for Lep-Map3
First line is the family name, second individual name, third and fourth are the father and mother. Line 5 is the sex of each individual (1 male, 2 female, 0 unknown). Last line is 0, not used
QTL.map.txt
Linkage map used for QTL analysis
Row names correspond to markerIDs in "Geno.QTL.csv"
1. column: contig; 2. column: position; 3. column: Marker name; 4. column: Linkage group of the newly generated map; 5. column: Linkage group in previous map (based on crossing Crab ecotype individuals); 6. column: Map position in the new map
Pheno.QTL.csv
Phenotypes for QTL analysis in the format for the Rpackage "qtl"
The first column ("ind") gives the individual ID, the last column ("id") matches the phenotypic data to the genetic data in "Geno.QTL.csv".
Geno.QTL.csv
Genotypic data used for QTL analysis in the format required for the Rpackage "qtl"
First column: Individual id to match genotypic data with phenotypic data in a separate file (Pheno.QTL.csv); remaining columns: genotypes (phased data obtained from Lep-Map3); first row: marker IDs; second row gives the linkage group; third row: cM positions of markers
QTL_analysis.R
Rscript for QTL analysis and adjusting linkage group numbering and marker order to be consistent with the previous Littorina linkage map.
Pheno.txt
Phenotypic data used for variance partitioning. First column gives the individual ID
GRM_LG.zip
Inverse of genomic relationship matrices in ASReml format based on marker of a focal linkage group X (Ginv_LGX.txt) or excluding markers of a focal linkage group (Ginv_LGXNOT.txt).
GRM.txt: Genomic relationship matrix between individuals based on genetic markers of all linkage groups. Individual IDs are the same as in Pheno.txt
GRM.inv.txt: Inverse of GRM.txt in ASReml format.
Variance_partitioning.R
Rscript for variance partitioning across linkage groups.
Files
Geno.QTL.csv
Files
(142.4 MB)
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