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.

Eclosion data

sbdbbbcf.eclosions.csv

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.

sbdbbb.vcf.gz

The final filtered vcf file used for population genomic analyses including only flies collected from sparkleberry, deerberry, and blueberry hosts. 

sbdbbbcfpom.vcf.gz

The final filtered vcf file used for expanded population genomic analyses including flies collected from sparkleberry, deerberry, blueberry, flowering dogwood, and southern hawthorn hosts.

pomgroup.vcf.gz

The final filtered vcf file used for the population-based R. pomonella species group neighbor-joining network. 

pomgroup.phylo.subset.txt

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.

barcodes.cf.1.txt

Flowering dogwood-infesting flies collected from Steven F. Austin Experimental Forest, TX.

barcodes.cf.2.txt

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.*).

barcodes.cf.zeph.txt

Flowering dogwood-infesting flies collected from Santee, SC (cf14.sc.*) and R. zephyria collected from Union Gap, WA (S14.UG.*), Medora, ND (S14.ND.*), and Buffalo River State Park, MN (S14.BP.*).

barcodes.pom.1.txt

R. pomonella 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.

barcodes.pom.2.txt

R. pomonella 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.*).

barcodes.pom.mex.txt

Mexican R. pomonella 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).

barcodes.sb.bb.txt

R. mendax 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.*).

barcodes.sb.cf.txt

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.*). 

barcodes.sb.db.bb.txt

Sparkleberry-infesting flies colleced from O’leno State Park, FL (v14.osb.*), R. mendax 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.*).

barcodes.sb.db.cf.txt

Sparkleberry-infesting flies colleced from Tuskegee National Forest, AL (SB.AL.*), Ouachita National Forest, AR (SB.AR.*), and Clemson Experimenal Forest, SC (SB.SC.*); R. mendax 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

sbdbbb.sexlinked.txt

Sex-associated SNPs removed prior to population genomic analyses including only flies collected from sparkleberry, deerberry, and blueberry hosts. 

sbdbbbcfpom.sexlinked.txt

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

rhagoletis_pomonella_23Aug2018_tkMps.fasta.gz

The draft R. pomonella 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

R. pomonella collected from apple and downy hawthorn at Grant, MI, Fennville, MI, Dowagiac, MI, and Urbana, IL: https://doi.org/10.5061/dryad.k42t7g2

R. mendax collected from blueberry at Fennville, MI: https://doi.org/10.5061/dryad.nk98sf7pr

R. zephyria collected at St. Cloud, WA: https://doi.org/10.5061/dryad.x0k6djhfj