DOI: 10.5061/dryad.j9kd51cc1
title: Data from: Divergent diapause life history timing drives both allochronic speciation and reticulate hybridization in an adaptive radiation of Rhagoletis flies

description: Divergent adaptation to new ecological opportunities can be an important
 factor initiating speciation. However, as niches are filled during
 adaptive radiations, trait divergence driving reproductive isolation
 between sister taxa may also result in trait convergence with more
 distantly related taxa, increasing the potential for reticulated gene flow
 across the radiation. Here, we demonstrate such a scenario in a recent
 adaptive radiation of Rhagoletis fruit flies, specialized on different
 host plants. Throughout this radiation, shifts to novel hosts are
 associated with changes in diapause life history timing, which act as
 “magic traits” generating allochronic reproductive isolation and
 facilitating speciation-with-gene-flow. Evidence from laboratory rearing
 experiments measuring adult emergence timing and genome-wide
 DNA-sequencing surveys supported allochronic speciation between
 summer-fruiting Vaccinium spp.-infesting Rhagoletis mendax and its
 hypothesized and undescribed sister taxon infesting fall-fruiting
 sparkleberries. The sparkleberry fly and R. mendax were shown to be
 genetically discrete sister taxa, exhibiting no detectable gene flow and
 allochronically isolated by a two-month average difference in emergence
 time corresponding with host availability. At sympatric sites across the
 southern USA, the later fruiting phenology of sparkleberries overlaps with
 that of flowering dogwood, the host of another more distantly related and
 undescribed Rhagoletis taxon. Laboratory emergence data confirmed broadly
 overlapping life history timing and genomic evidence supported on-going
 gene flow between sparkleberry and flowering dogwood flies. Thus,
 divergent phenological adaptation can drive the initiation of reproductive
 isolation, while also enhancing genetic exchange across broader adaptive
 radiations, potentially serving as a source of novel genotypic variation
 and accentuating further diversification.
description: Eclosion data
 <em>sbdbbbcf.eclosions.csv</em> A
 comma delimited table of all eclosion data used in the paper, including
 site, host, and year eclosed, as well as the number of days
 (post-"overwinter" chilling) to adult eclosion and number of
 flies eclosed.  Filtered vcf files with genotype
 probabilities These are vcf files 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.
 <em>sbdbbb.vcf.gz</em> The final
 filtered vcf file used for population genomic analyses including only
 flies collected from sparkleberry, deerberry, and blueberry
 hosts. 
 <em>sbdbbbcfpom.vcf.gz</em> The
 final filtered vcf file used for expanded population genomic analyses
 including flies collected from sparkleberry, deerberry, blueberry,
 flowering dogwood, and southern hawthorn hosts.
 <em>pomgroup.vcf.gz</em> The final
 filtered vcf file used for the population-based <em>R.
 pomonella</em> species group neighbor-joining network. 
 <em>pomgroup.phylo.subset.txt</em>
 The subset of 230 individuals (the five individuals, from each
 population, with the lowest proportion of missing data) used for the
 individual-based phylogenetic analyses, including a maximum likelihood
 phylogeny, phylogenetic network, and ASTRAL species tree.
 Files mapping barcodes to individual IDs Tab
 delimited files; column 1 = inline barcode (5' end of the forward
 read), column 2 = sample id (sample id in the vcf file). Note that these
 files should not be combined for processing, as barcodes are unique only
 within each file.
 <em>barcodes.cf.1.txt</em>
 Flowering dogwood-infesting flies collected from Steven F. Austin
 Experimental Forest, TX.
 <em>barcodes.cf.2.txt</em>
 Flowering dogwood-infesting flies collected from O’leno State
 Park, FL (cf14.ole.*) and Land between the Lakes
 National Recreation Area, KY (cf1[56].lbl.*).
 <em>barcodes.cf.zeph.txt</em>
 Flowering dogwood-infesting flies collected from Santee, SC
 (cf14.sc.*) and <em>R. zephyria</em> collected from Union Gap,
 WA (S14.UG.*), Medora, ND (S14.ND.*), and Buffalo River State Park, MN
 (S14.BP.*).
 <em>barcodes.pom.1.txt</em>
 <em>R. pomonella</em> collected from southern red
 hawthorn at Brazos Bend State Park, TX (R09.BB.*), eastern mayhaw at Byron
 USDA ARS, GA (M08.B.*), western mayhaw at Dewey Wills Wildlife Management
 Area, LA (M08.DW.*), and blueberry hawthorn (B07.A.* and BA.*) and western
 hawthorn (M06.A.*) at Steven F. Austin Experimental Forest, TX.
 <em>barcodes.pom.2.txt</em>
 <em>R. pomonella</em> collected from western mayhaw
 (M06.A.*) at Steven F. Austin Experimental Forest, TX, green hawthorn at
 Brazos Bend State Park, TX (G0[78].BB.*), and green hawthorn at Dewey
 Wills Wildlife Management Area, LA (G09.DW.*).
 <em>barcodes.pom.mex.txt</em>
 Mexican <em>R. pomonella</em> collected in San
 Joaquín, Querétaro, Mexico (SMO), Xoxoncaxtla, Puebla, Mexico
 (SMO), Piletas, Veracruz, Mexico (SMO), Tancítaro, Michoacán, Mexico
 (EVTM), Angangueo, Michoacán, Mexico (EVTM), and Coajomulco, Morelos,
 Mexico (EVTM).
 <em>barcodes.sb.bb.txt</em>
 <em>R. mendax </em>collected from blueberries at
 Kentville, NS (V.NS.*) and sparkleberry-infesting flies colleced from Land
 between the Lakes National Recreation Area, KY (V.LBL.*) and Byron, GA
 (V89.BGA.*).
 <em>barcodes.sb.cf.txt</em>
 Sparkleberry-infesting flies colleced from Land between the Lakes
 National Recreation Area, KY (va16.LBL.*) and Shawnee National Forest,
 IL (v15.GOG.*) and flowering dogwood-infesting flies collected at Tuskegee
 National Forest, AL (cf99.AL.*). 
 <em>barcodes.sb.db.bb.txt</em>
 Sparkleberry-infesting flies colleced from O’leno State Park, FL
 (v14.osb.*), <em>R. mendax</em> collected from deerberry
 at Aiken, SC (V.AKSC.*) and O’leno State Park, FL (v14.odb.*), and
 blueberry at Kentville, NS (V.NS.* ) and Jasper-Pulaski State Park,
 IN(v.jp.* and v14.jp.*).
 <em>barcodes.sb.db.cf.txt</em>
 Sparkleberry-infesting flies colleced from Tuskegee National
 Forest, AL (SB.AL.*), Ouachita National Forest, AR (SB.AR.*), and Clemson
 Experimenal Forest, SC (SB.SC.*); <em>R. mendax</em> collected
 from deerberry at Tuskegee National Forest, AL (DB.AL.*), Ouachita
 National Forest, AR (DB.AR.*), and Clemson Experimenal Forest, SC
 (DB.SC.*); and flowering dogwood-infesting flies collected from Ouachita
 National Forest, AR (cf17.ou.*) and O’leno State Park,
 FL (cf14.ole.*). Sex-associated loci removed from
 population genomic analyses
 <em>sbdbbb.sexlinked.txt</em>
 Sex-associated SNPs removed prior to population genomic analyses
 including only flies collected from sparkleberry, deerberry, and blueberry
 hosts. 
 <em>sbdbbbcfpom.sexlinked.txt</em>
 Sex-associated SNPs removed prior to expanded population genomic
 analyses including flies collected from sparkleberry, deerberry,
 blueberry, flowering dogwood, and southern hawthorn hosts.
 Draft genome assembly
 <em>rhagoletis_pomonella_23Aug2018_tkMps.fasta.gz</em> The draft <em>R. pomonella</em> assembly is now publically available as RefSeq accession: GCF_013731165.1. This fasta version includes the scaffold names that appear in the vcf files uploaded here. New sequence data All newly reported data can be found in the SRA (BioProject: PRJNA716653). Previously published sequence data <em>R. pomonella</em> collected from apple and downy hawthorn at Grant, MI, Fennville, MI, Dowagiac, MI, and Urbana, IL: https://doi.org/10.5061/dryad.k42t7g2 <em>R. mendax </em>collected from blueberry at Fennville, MI: https://doi.org/10.5061/dryad.nk98sf7pr <i>R. zephyria</i> collected at St. Cloud, WA: https://doi.org/10.5061/dryad.x0k6djhfj