DOI: 10.5061/dryad.k42t7g2
title: Data from: Standing geographic variation in eclosion time and the genomics of host race formation in Rhagoletis pomonella fruit flies

description: Taxa harboring high levels of standing variation may be more likely to
 adapt to rapid environmental shifts and experience ecological speciation.
 Here, we characterize geographic and host-related differentiation for
 10,241 single nucleotide polymorphisms in Rhagoletis pomonella fruit flies
 to infer if standing genetic variation in adult eclosion time in the
 ancestral hawthorn (Crataegus spp.)-infesting host race, as opposed to new
 mutations, contributed substantially to its recent shift to earlier
 fruiting apple (Malus domestica). Allele frequency differences associated
 with early versus late eclosion time within each host race were
 significantly related to geographic genetic variation and host race
 differentiation across four sites, arrayed from north to south along a 430
 km transect, where the host races co-occur in sympatry in the Midwest USA.
 Host fruiting phenology is clinal, with both apple and hawthorn trees
 fruiting earlier in the North and later in the South. Thus, we expected
 alleles associated with earlier eclosion to be at higher frequencies in
 northern populations. This pattern was observed in the hawthorn race
 across all four populations; however, allele frequency patterns in the
 apple race were more complex. Despite the generally earlier eclosion
 timing of apple flies and corresponding apple fruiting phenology, alleles
 on chromosomes 2 and 3 associated with earlier emergence were
 paradoxically at lower frequency in the apple than hawthorn host race
 across all four sympatric sites. However, loci on chromosome 1 did show
 higher frequencies of early eclosion associated alleles in the apple than
 hawthorn host race at the two southern sites, potentially accounting for
 their earlier eclosion phenotype. Thus, although extensive clinal genetic
 variation in the ancestral hawthorn race exists and contributed to the
 host shift to apple, further study is needed to resolve details of how
 this standing variation was selected to generate earlier eclosing apple
 fly populations in the North.
description: Population assignment
 for each individual from geographic surveyColumn 1 contains the
 individual ID for each sample from the geographic survey. Column 2
 contains the site and host for each population.DoellmanRpomonella2018.ids.txtDowagiacHawthorn.fq.gzFastq file containing demultiplexed sequences for samples from hawthorn fruits at Dowagiac, MI.DowagiacApple.fq.gzFastq file containing demultiplexed sequences for samples from apple fruits at Dowagiac, MI.FennvilleHawthorn.fq.gzFastq file containing demultiplexed sequences for samples from hawthorn fruits at Fennville, MI.FennvilleApple.fq.gzFastq file containing demultiplexed sequences for samples from apple fruits at Fennville, MI.GrantHawthorn.fq.gzFastq file containing demultiplexed sequences for samples from hawthorn fruits at Grant, MI.GrantApple.fq.gzFastq file containing demultiplexed sequences for samples from apple fruits at Grant, MI.UrbanaHawthorn.fq.gzFastq file containing demultiplexed sequences for samples from hawthorn fruits at Urbana, IL.UrbanaApple.fq.gzFastq file containing demultiplexed sequences for samples from apple fruits at Urbana, IL.