DOI: 10.5061/dryad.q9t27n9
title: Data from: Genomic differentiation during speciation-with-gene-flow: comparing geographic and host-related variation in divergent life history adaptation in Rhagoletis pomonella

description: A major goal of evolutionary biology is to understand how variation within
 populations gets partitioned into differences between reproductively
 isolated species. Here, we examine the degree to which diapause life
 history timing, a critical adaptation promoting population divergence,
 explains geographic and host-related genetic variation in ancestral
 hawthorn and recently derived apple-infesting races of Rhagoletis
 pomonella. Our strategy involved combining experiments on two different
 aspects of diapause (initial diapause intensity and adult eclosion time)
 with a geographic survey of genomic variation across four sites where
 apple and hawthorn flies co-occur from north to south in the Midwestern
 USA. The results demonstrated that the majority of the genome showing
 significant geographic and host-related variation can be accounted for by
 initial diapause intensity and eclosion time. Local genomic differences
 between sympatric apple and hawthorn flies were subsumed within broader
 geographic clines; allele frequency differences within the races across
 the Midwest were 2 to 3-fold greater than those between the races in
 sympatry. As a result, sympatric apple and hawthorn populations displayed
 more limited genomic clustering compared to geographic populations within
 the races. The findings suggest that with reduced gene flow and increased
 selection on diapause equivalent to that seen between geographic sites,
 the host races may be recognized as different genotypic entities in
 sympatry, and perhaps species, a hypothesis requiring future genomic
 analysis of related sibling species to R. pomonella to test. Our findings
 concerning the way selection and geography interplay could be of broad
 significance for many cases of earlier stages of divergence-with-gene
 flow, including (1) where only modest increases in geographic isolation
 and the strength of selection may greatly impact genetic coupling and (2)
 the dynamics of how spatial and temporal standing variation is extracted
 by selection to generate differences between new and discrete units of
 biodiversity.
description: VCF file for all
 individuals and SNPs included in the study.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.DoellmanGenes2018.vcfNatural or experimental population for each individual in the studyColumn 1 contains the individual ID for each sample in the study. Column 2 contains the site and host for each of the geographic populations or the treatment group for each experiment (Haw/Apple_E or Haw/Apple_L for early and late eclosing flies, respectively; GrantHaw/Apple32d or GrantHaw/Apple7d for prewinter selected or control samples, respectively).DoellmanGenes2018.ids.txtGrantApple.fq.gzFastq file containing demultiplexed sequences for the control (7 day) samples from the apple selection experiment.GrantApple32d.fq.gzFastq file containing demultiplexed sequences for the long pre-winter treatment (32 day) samples from the apple selection experiment.GrantHawthorn.fq.gzFastq file containing demultiplexed sequences for the control (7 day) samples from the hawthorn selection experiment.GrantHawthorn32d.fq.gzFastq file containing demultiplexed sequences for the long pre-winter treatment (32 day) samples from the hawthorn selection experiment.