Data from: A test of genomic modularity among life-history adaptations promoting speciation with gene flow
Ragland, Gregory, University of Notre Dame
Doellman, Meredith M., Notre Dame University, University of Notre Dame
Meyers, Peter J., Notre Dame University, University of Notre Dame
Hood, Glen R., Notre Dame University, University of Notre Dame, Rice University
Egan, Scott P., Notre Dame University, University of Notre Dame, Rice University
Powell, Thomas H. Q., Binghamton University, Notre Dame University, University of Notre Dame, University of Florida
Hahn, Daniel A., University of Florida
Nosil, Patrik, University of Sheffield
Feder, Jeffrey L., Notre Dame University, University of Notre Dame
Ragland, Gregory J., Notre Dame University, University of Notre Dame
Published Jul 28, 2017 on Dryad.
Cite this dataset
Ragland, Gregory et al. (2017). Data from: A test of genomic modularity among life-history adaptations promoting speciation with gene flow [Dataset]. Dryad. https://doi.org/10.5061/dryad.kn568
Speciation with gene flow may require adaptive divergence of multiple traits to generate strong ecologically based reproductive isolation. Extensive negative pleiotropy or physical linkage of genes in the wrong phase affecting these diverging traits may therefore hinder speciation, while genetic independence or “modularity” among phenotypic traits may reduce constraints and facilitate divergence. Here, we test whether the genetics underlying two components of diapause life history, initial diapause intensity and diapause termination timing, constrain differentiation between sympatric hawthorn and apple-infesting host races of the fly Rhagoletis pomonella through analysis of 10,256 SNPs measured via genotyping-by-sequencing (GBS). Loci genetically associated with diapause termination timing were mainly observed for SNPs mapping to chromosomes 1–3 in the genome, most notably for SNPs displaying higher levels of linkage disequilibrium (LD), likely due to inversions. In contrast, selection on initial diapause intensity affected loci on all five major chromosomes of the genome, specifically those showing low levels of LD. This lack of overlap in genetically associated loci suggests that the two diapause phenotypes are largely modular. On chromosome 2, however, intermediate level LD loci and a subgroup of high LD loci displayed significant negative relationships between initial diapause intensity and diapause termination time. These gene regions on chromosome 2 therefore affected both traits, while most regions were largely independent. Moreover, loci associated with both measured traits also tended to exhibit highly divergent allele frequencies between the host races. Thus, the presence of nonoverlapping genetic modules likely facilitates simultaneous, adaptive divergence for the measured life-history components.
Filtered vcf file with genotype probabilities
This is a vcf file generated using the GATK unified genotyper, then filtered as describe in the paper. The PL field provides the phred-scaled and normalized genotype probabilities produced using the GATK model.
File mapping barcodes and ids to population/phenotype
column 1 = inline barcode (5' end of the forward read), column 2 = sample id (sample id in the vcf file), column 3 = population_phenotype: Haw_L = Hawthorn late, Haw_E = Hawthorn early, Apple_L = Apple late, Apple_E = Apple early