Data from: Localizing FST outliers on a QTL map reveals evidence for large genomic regions of reduced gene exchange during speciation-with-gene-flow

 

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Title JoinmapInputGenotypeFile
Downloaded 16 times
Description JoinMapGenotypeInputFile: 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.
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Title TraitsFileF2
Downloaded 8 times
Description Phenotypic values for each of the 198 F2 used in the QTL map. Values are BLUPs from a mixed model ANOVA. File is tab delimited.
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Title MarkerIDcodes
Downloaded 10 times
Description MarkerIDcodes.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.
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Title FDIST_Summary195markers_msat&AFLP&codom
Downloaded 7 times
Description Contains 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, heterozygosity
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Title STRUCTURE data Class1Rep1
Downloaded 7 times
Description STRUCTURE 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"
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Title STRUCTURE data Class1Rep2
Downloaded 6 times
Description STRUCTURE 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"
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Title STRUCTURE data Class1Rep3
Downloaded 2 times
Description STRUCTURE 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"
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Title STRUCTURE data Class1Rep4
Downloaded 6 times
Description STRUCTURE 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"
Download C1_4.txt (6.38 Kb)
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Title STRUCTURE data Class2Rep1
Downloaded 3 times
Description STRUCTURE 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"
Download C2_1.txt (6.138 Kb)
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Title STRUCTURE data Class2Rep2
Downloaded 5 times
Description STRUCTURE 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"
Download C2_2.txt (6.09 Kb)
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Title STRUCTURE data Class2Rep3
Downloaded 9 times
Description STRUCTURE 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"
Download C2_3.txt (6.458 Kb)
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Title STRUCTURE data Class2Rep4
Downloaded 7 times
Description STRUCTURE 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"
Download C2_4.txt (6.506 Kb)
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Title STRUCTURE data Class3Rep1
Downloaded 4 times
Description STRUCTURE 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"
Download C3_1.txt (6.609 Kb)
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Title STRUCTURE data Class3Rep2
Downloaded 3 times
Description STRUCTURE 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"
Download C3_2.txt (6.38 Kb)
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Title STRUCTURE data Class3Rep3
Downloaded 11 times
Description STRUCTURE 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"
Download C3_3.txt (6.436 Kb)
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Title STRUCTURE data Class3Rep4
Downloaded 5 times
Description STRUCTURE 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"
Download C3_4.txt (6.051 Kb)
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When using this data, please cite the original publication:

Via S, Conte G, Mason-Foley C, Mills K (2012) Localizing FST outliers on a QTL map reveals evidence for large genomic regions of reduced gene exchange during speciation-with-gene-flow. Molecular Ecology 21(22): 5546–5560. http://dx.doi.org/10.1111/mec.12021

Additionally, please cite the Dryad data package:

Via S, Conte G, Mason-Foley C, Mills K (2012) Data from: Localizing FST outliers on a QTL map reveals evidence for large genomic regions of reduced gene exchange during speciation-with-gene-flow. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.9cf75
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