DOI: 10.5061/dryad.80c3q54
title: Data from: Fine‐scale geographic patterns of gene flow and reproductive character displacement in drosophila subquinaria and d. recens

description: When two species are incompletely isolated, strengthening premating
 isolation barriers in response to the production of low fitness hybrids
 may complete the speciation process. Here we use the sister species
 Drosophila subquinaria and D. recens to study the conditions under which
 this reinforcement of species boundaries occurs in natural populations. We
 first extend the region of known sympatry between these species, and then
 we conduct a fine-scale geographic survey of mate discrimination coupled
 with estimates of gene flow within and admixture between species. Within
 D. subquinaria reinforcement is extremely effective: we find variation in
 mate discrimination both against D. recens males as well as against
 conspecific allopatric males on the scale of a few kilometers and in the
 face of gene flow both from conspecific populations and introgression from
 D. recens. In D. recens we do not find evidence for increased mate
 discrimination in sympatry, even where D. recens is rare, consistent with
 substantial gene flow throughout the species’ range. Finally, we find that
 introgression between species is asymmetric, with more from D. recens into
 D. subquinaria than vice versa. Within each species admixture is highest
 in the geographic region where it is rare relative to the other species,
 suggesting that when hybrids are produced they are of low fitness. In sum,
 reinforcement within D. subquinaria is effective at maintaining species
 boundaries, but even when reinforcing selection is strong it may not
 always result in a pattern of strong reproductive character displacement
 due to variation in the frequency of hybridization and gene flow from
 neighboring populations.
description: Recens raw mating
 dataRaw mating data in .csv
 format of mate trials for D. recens females. Column 1 has the block (i.e.
 day), Column 2 has the individual female replicate number, Column 3 has
 the female line (see Table 1 of the paper for the population
 abbreviations), Column 4 has the male type, and Column 5 is whether mating
 took place with 1=yes and 0=no.recens_mating_data.csvSubquinaria raw mating dataRaw mating data in .csv format of mate trials for D. subquinaria females. Column 1 has the block (i.e. day), Column 2 has the individual female replicate number, Column 3 has the female line (see Table 1 of the paper for the population abbreviations), Column 4 has the male type, and Column 5 is whether mating took place with 1=yes and 0=no.subquinaria_mating_data.csvMicrosatellite data for D. recens and D. subquinariaAll microsatellite data with annotations, in structure format. Column 1 contains the unique label, Column 2 contains the unique fly ID (Species_Population_number), Column 3 indicates the sex of the fly (Female or Male), Column 4 indicates the population (see table 1 of the paper for abbreviations), Column 5 indicates the species (subquinaria or recens), Column 6 indicates the unique population number, and the remaining columns have the microsatellite genotypes. Loci with an X at the end of the name are on the X-chromosome. Missing data are indicated by a -9.microsat_all_data_struct.csvStructure analysesThis folder contains the data, program files, and scripts to run the structure analyses. Sub-folders are by genome location (all loci, X-linked, autosomal) and by subset of samples (only recens, only subquinaria, both species (i.e., all)). Within the structure data file, each individual is coded by Species_population_individual in the first column and the population number in the second column.structure_analyses.zipDAPC analysesThis folder contains the files to run the DAPC analyses, including the R code and input files. Analyses were completed by genome location (all loci, X-linked, autosomal) and by subset of samples (only recens, only subquinaria, both species (i.e., all)).DAPC.zipHzar clines R code and dataThis folder contains the data and R code to determine 1) the distance of each population from the crest of the Rockies and 2) the D. subquinaria clines in mating rate, admixture, and species composition.hzar_clines.zip