DOI: 10.5061/dryad.9cf75
title: Data from: Localizing FST outliers on a QTL map reveals evidence for large genomic regions of reduced gene exchange during speciation-with-gene-flow

description: Populations that maintain phenotypic divergence in sympatry typically show
 a mosaic pattern of genomic divergence, requiring a corresponding mosaic
 of genomic isolation (reduced gene flow). However, mechanisms that could
 produce the genomic isolation required for divergence-with-gene-flow have
 barely been explored, apart from the traditional localized effects of
 selection and reduced recombination near centromeres or inversions. By
 localizing FST outliers from a genome scan of wild pea aphid host races on
 a Quantitative Trait Locus (QTL) map of key traits, we test the hypothesis
 that between-population recombination and gene exchange are reduced over
 large ‘divergence hitchhiking’ (DH) regions. As expected under divergence
 hitchhiking, our map confirms that QTL and divergent markers cluster
 together in multiple large genomic regions. Under divergence hitchhiking,
 the nonoutlier markers within these regions should show signs of reduced
 gene exchange relative to nonoutlier markers in genomic regions where
 ongoing gene flow is expected. We use this predicted difference among
 nonoutliers to perform a critical test of divergence hitchhiking. Results
 show that nonoutlier markers within clusters of FST outliers and QTL
 resolve the genetic population structure of the two host races nearly as
 well as the outliers themselves, while nonoutliers outside DH regions
 reveal no population structure, as expected if they experience more gene
 flow. These results provide clear evidence for divergence hitchhiking, a
 mechanism that may dramatically facilitate the process of
 speciation-with-gene-flow. They also show the power of integrating genome
 scans with genetic analyses of the phenotypic traits involved in local
 adaptation and population divergence.
description: JoinmapInputGenotypeFileJoinMapGenotypeInputFile: Contains the microsatellite genotypes for each of the 198 F2 in the mapping cross. The genotypes are coded according to the JoinMap segregation types. Rows at the top are wrapped around in this tab-delimited text file, but will load into Excel properly. These 5 rows are: Markername, segregationType, Phase, Markertype, marker# The left-most column contains the F2 ID numbers. These data were classified as "CP" for Joinmap, since they came from an outcrossed population.DryadJoinmapInputGenotypeFile.txtTraitsFileF2Phenotypic values for each of the 198 F2 used in the QTL map. Values are BLUPs from a mixed model ANOVA. File is tab delimited.DryadTraitsFileF2.txtMarkerIDcodesMarkerIDcodes.txt: This file matches the marker id codes used on the map in Fig1 to the markerNames used in the Joinmap datafiles. Columns are markerName, code used in Fig. 1, LinkageGroup,location on LG in cM.DryadVia_MarkerIDcodes.txtFDIST_Summary195markers_msat&AFLP&codomContains the output of Fdist2 for all markers-- microsatellites, AFLPs and sequence-tagged codoms. Columns are: markerName, outlier?(0 = non-outlier, 1= marginal outlier, 2 = significant outlier),Fst,(1-p) at Round1,(1-p) at Round2, (1-p) at Round3, heterozygosityDryadFDIST_Summary195msat&AFLP&codom.txtSTRUCTURE data Class1Rep1STRUCTURE input file for the 196 pea aphids from the wild populations from Tompkins County, New York, USA. Clones beginning with ABR and AFR were collected from alfalfa fields.Clones beginning with CBR and CFR were collected from clover fields. Columns in each dataset are: CloneID, Marker1, Marker2, Marker3, Marker4, Marker5. All markers are unlinked. To findthe markers on the map, use the ID codes in the file called "MarkerIDcodes.txt"C1_1.txtSTRUCTURE data Class1Rep2STRUCTURE input file for the 196 pea aphids from the wild populations from Tompkins County, New York, USA. Clones beginning with ABR and AFR were collected from alfalfa fields.Clones beginning with CBR and CFR were collected from clover fields. Columns in each dataset are: CloneID, Marker1, Marker2, Marker3, Marker4, Marker5. All markers are unlinked. To findthe markers on the map, use the ID codes in the file called "MarkerIDcodes.txt"C1_2.txtSTRUCTURE data Class1Rep3STRUCTURE input file for the 196 pea aphids from the wild populations from Tompkins County, New York, USA. Clones beginning with ABR and AFR were collected from alfalfa fields.Clones beginning with CBR and CFR were collected from clover fields. Columns in each dataset are: CloneID, Marker1, Marker2, Marker3, Marker4, Marker5. All markers are unlinked. To findthe markers on the map, use the ID codes in the file called "MarkerIDcodes.txt"C1_3.txtSTRUCTURE data Class1Rep4STRUCTURE input file for the 196 pea aphids from the wild populations from Tompkins County, New York, USA. Clones beginning with ABR and AFR were collected from alfalfa fields.Clones beginning with CBR and CFR were collected from clover fields. Columns in each dataset are: CloneID, Marker1, Marker2, Marker3, Marker4, Marker5. All markers are unlinked. To findthe markers on the map, use the ID codes in the file called "MarkerIDcodes.txt"C1_4.txtSTRUCTURE data Class2Rep1STRUCTURE input file for the 196 pea aphids from the wild populations from Tompkins County, New York, USA. Clones beginning with ABR and AFR were collected from alfalfa fields.Clones beginning with CBR and CFR were collected from clover fields. Columns in each dataset are: CloneID, Marker1, Marker2, Marker3, Marker4, Marker5. All markers are unlinked. To findthe markers on the map, use the ID codes in the file called "MarkerIDcodes.txt"C2_1.txtSTRUCTURE data Class2Rep2STRUCTURE input file for the 196 pea aphids from the wild populations from Tompkins County, New York, USA. Clones beginning with ABR and AFR were collected from alfalfa fields.Clones beginning with CBR and CFR were collected from clover fields. Columns in each dataset are: CloneID, Marker1, Marker2, Marker3, Marker4, Marker5. All markers are unlinked. To findthe markers on the map, use the ID codes in the file called "MarkerIDcodes.txt"C2_2.txtSTRUCTURE data Class2Rep3STRUCTURE input file for the 196 pea aphids from the wild populations from Tompkins County, New York, USA. Clones beginning with ABR and AFR were collected from alfalfa fields.Clones beginning with CBR and CFR were collected from clover fields. Columns in each dataset are: CloneID, Marker1, Marker2, Marker3, Marker4, Marker5. All markers are unlinked. To findthe markers on the map, use the ID codes in the file called "MarkerIDcodes.txt"C2_3.txtSTRUCTURE data Class2Rep4STRUCTURE input file for the 196 pea aphids from the wild populations from Tompkins County, New York, USA. Clones beginning with ABR and AFR were collected from alfalfa fields.Clones beginning with CBR and CFR were collected from clover fields. Columns in each dataset are: CloneID, Marker1, Marker2, Marker3, Marker4, Marker5. All markers are unlinked. To findthe markers on the map, use the ID codes in the file called "MarkerIDcodes.txt"C2_4.txtSTRUCTURE data Class3Rep1STRUCTURE input file for the 196 pea aphids from the wild populations from Tompkins County, New York, USA. Clones beginning with ABR and AFR were collected from alfalfa fields.Clones beginning with CBR and CFR were collected from clover fields. Columns in each dataset are: CloneID, Marker1, Marker2, Marker3, Marker4, Marker5. All markers are unlinked. To findthe markers on the map, use the ID codes in the file called "MarkerIDcodes.txt"C3_1.txtSTRUCTURE data Class3Rep2STRUCTURE input file for the 196 pea aphids from the wild populations from Tompkins County, New York, USA. Clones beginning with ABR and AFR were collected from alfalfa fields.Clones beginning with CBR and CFR were collected from clover fields. Columns in each dataset are: CloneID, Marker1, Marker2, Marker3, Marker4, Marker5. All markers are unlinked. To findthe markers on the map, use the ID codes in the file called "MarkerIDcodes.txt"C3_2.txtSTRUCTURE data Class3Rep3STRUCTURE input file for the 196 pea aphids from the wild populations from Tompkins County, New York, USA. Clones beginning with ABR and AFR were collected from alfalfa fields.Clones beginning with CBR and CFR were collected from clover fields. Columns in each dataset are: CloneID, Marker1, Marker2, Marker3, Marker4, Marker5. All markers are unlinked. To findthe markers on the map, use the ID codes in the file called "MarkerIDcodes.txt"C3_3.txtSTRUCTURE data Class3Rep4STRUCTURE input file for the 196 pea aphids from the wild populations from Tompkins County, New York, USA. Clones beginning with ABR and AFR were collected from alfalfa fields.Clones beginning with CBR and CFR were collected from clover fields. Columns in each dataset are: CloneID, Marker1, Marker2, Marker3, Marker4, Marker5. All markers are unlinked. To findthe markers on the map, use the ID codes in the file called "MarkerIDcodes.txt"C3_4.txt