DOI: 10.5061/dryad.0j4m5
title: Data from: Detection of genetic incompatibilities in non-model systems using simple genetic markers: hybrid breakdown in the haplodiploid spider mite Tetranychus evansi

description: When two related species interbreed, their hybrid offspring frequently
 suffer from reduced fitness. The genetics of hybrid incompatibility are
 described by the Bateson–Dobzhansky–Muller (BDM) model, where fitness is
 reduced by epistatic interactions between alleles of heterospecific
 origin. Unfortunately, most empirical evidence for the BDM model comes
 from a few well-studied model organisms, restricting our genetic
 understanding of hybrid incompatibilities to limited taxa. These systems
 are predominantly diploid and incompatibility is often complete, which
 complicates the detection of recessive allelic interactions and excludes
 the possibility to study viable or intermediate stages. Here, we advocate
 research into non-model organisms with haploid or haplodiploid
 reproductive systems and incomplete hybrid incompatibility because (1)
 dominance is absent in haploids and (2) incomplete incompatibility allows
 comparing affected with unaffected individuals. We describe a novel
 two-locus statistic specifying the frequency of individuals for which two
 alleles co-occur. This approach to studying BDM incompatibilities requires
 genotypic characterization of hybrid individuals, but not genetic mapping
 or genome sequencing. To illustrate our approach, we investigated genetic
 causes for hybrid incompatibility between differentiated lineages of the
 haplodiploid spider mite Tetranychus evansi, and show that strong, but
 incomplete, hybrid breakdown occurs. In addition, by comparing the
 genotypes of viable hybrid males and inviable hybrid male eggs for eight
 microsatellite loci, we show that nuclear and cytonuclear BDM interactions
 constitute the basis of hybrid incompatibility in this species. Our
 approach opens up possibilities to study BDM interactions in non-model
 taxa, and may give further insight into the genetic mechanisms behind
 hybrid incompatibility.
description: Adjusted residual
 haplotype count R scriptThis R script shows how
 the regression of adjusted residual haplotype count on allele indicator
 was performedKnegt_etal_Adjusted_residuals.RDataset for regression of adjusted residual haplotype count against allele indicator - comparison viable I versus inviable IThis dataset was used for the regression of adjusted residual haplotype count against allele indicator, in the comparison of viable hybrids cytotype I versus inviable hybrids cytotype I. See the R script for details of the analysis.Knegt_etal_Adjusted_residuals1.csvDataset for regression of adjusted residual haplotype count against allele indicator - comparison viable II versus inviable IIThis dataset was used for the regression of adjusted residual haplotype count against allele indicator, in the comparison of viable hybrids cytotype II versus inviable hybrids cytotype II. See the R script for details of the analysis.Knegt_etal_Adjusted_residuals2.csvR script for the comparison of allele frequencies between hybrid groupsKnegt_etal_Allele_frequencies.RAllele frequencies - FisherDataset used for comparison of allele frequencies between hybrid groups: Fisher exact tests of independence. See R script for details.Knegt_etal_Allele_frequencies1.csvAllele frequencies - CMHDataset used for comparison of allele frequencies between hybrid groups: Cochran-Mantel-Haenszel tests. See R script for details.Knegt_etal_Allele_frequencies2.csvR script for analysis of F1 hatch rateKnegt_etal_F1_hatch_rate.RF1 hatch ratesKnegt_etal_F1_hatch_rate.csvR script for analysis of F1 ovipositionKnegt_etal_F1_oviposition.RF1 ovipositionKnegt_etal_F1_oviposition.csvR script for analysis of F1 sex ratioKnegt_etal_F1_sex_ratio.RF1 sex ratioKnegt_etal_F1_sex_ratio.csvR script for analysis of F2 hatch ratesKnegt_etal_F2_hatch_rate.RF2 hatch rateKnegt_etal_F2_hatch_rate.csvR script for analysis of parental ovipositionKnegt_etal_Parental_oviposition.RParental ovipositionKnegt_etal_Parental_oviposition.csvR script for CMH tests among hybrid groups using their haplotype counts as inputKnegt_etal_Haplotype_counts.RHaplotype countsKnegt_etal_Haplotype_counts1.csv