10.5061/DRYAD.Q9T27N9
Doellman, Meredith M.
Notre Dame University
Ragland, Gregory J.
Hood, Glen R.
Meyers, Peter J.
Egan, Scott P.
Powell, Thomas H.Q.
Lazorchak, Peter
Johns Hopkins University
Glover, Mary M.
Notre Dame University
Tait, Cheyenne
Notre Dame University
University of Notre Dame
Schuler, Hannes
Notre Dame University
University of Notre Dame
Hahn, Daniel A.
Berlocher, Stewart H.
Smith, James J.
Michigan State University
Nosil, Patrik
University of Sheffield
Feder, Jeffrey L.
Hahn, Daniel
University of Florida
Berlocher, Stewart
University of Illinois at Urbana Champaign
Meyers, Peter
Notre Dame University
University of Notre Dame
Egan, Scott
Notre Dame University
University of Notre Dame
Feder, Jeffrey
Notre Dame University
University of Notre Dame
Hood, Glen
Rice University
Powell, Thomas
Queens College, CUNY
State University of New York
Ragland, Gregory
University of Colorado Boulder
Data from: Genomic differentiation during speciation-with-gene-flow:
comparing geographic and host-related variation in divergent life history
adaptation in Rhagoletis pomonella
Dryad
dataset
2019
eclosion time
initial diapause depth
latitudinal clines
apple maggot fly
Holocene
Rhagoletis pomonella
National Science Foundation
https://ror.org/021nxhr62
DEB-1638997
2019-05-15T00:00:00Z
2019-05-15T00:00:00Z
en
https://doi.org/10.3390/genes9050262
12194084223 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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.
United States
Midwestern