Data from: Hybrid speciation by sorting of parental incompatibilities in Italian sparrows

Hermansen JS, Haas F, Bailey RI, Nederbragt AJ, Trier CN, Marzal A, Sætre G

Date Published: September 11, 2014

DOI: http://dx.doi.org/10.5061/dryad.v6f4d

 

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Title structure_input_file
Downloaded 16 times
Description 'structure_input.txt': input file used when running structure. numbers in second column refer to: 1: house sparrows from Oslo, Norway 2: house sparrows from Hradec Králové, Czech Republic 3: house sparrows from sympatric population near Badajoz, Spain 4: Spanish sparrows from sympatric population near Badajoz, Spain 5: Spanish sparrows from the Gargano Peninsula 6: Spanish sparrows from Sardinia 7: F1-hybrids from aviary
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Title Genotypes for house sparrow reference population
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Description Genotypes for the individuals in the house sparrow reference population for the 77 SNP markers.
Download genotypes_house.xlsx (67.86 Kb)
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Title Genotypes for Spanish sparrow reference population
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Description Genotypes for the individuals in the spanish sparrow reference population for the 77 SNP markers
Download genotypes_spanish.xlsx (63.62 Kb)
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Title Genotypes for parental sympatry test population
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Description Genotypes for the individuals in the admixed test population. 'BGC column' refers to the number given to indivudlas by the bgc output.
Download genotypes_spain.xlsx (90.25 Kb)
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Title Genotypes for the hybrid-parents test population
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Description Genotypes for the individuals in the hybrid-parents test population. 'BGC column' refers to the number given to individuals by the bgc output.
Download genotypes_italy.xlsx (188.9 Kb)
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Title File to link locus names with bgc output
Downloaded 17 times
Description File showing which loci refers to which 'bgc output number' for all 77 markers, only autosomal markers and only Z-linked markers
Download loci.xlsx (49.18 Kb)
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Title File with the code used when running bgc
Downloaded 25 times
Description File with the code used when running bgc
Download bgc_code.txt (103 bytes)
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Title bgc input file for house sparrow parental population (reference population), all 77 markers
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Description bgc input file for house sparrow parental population (reference population)
Download house.txt (1.187 Kb)
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Title bgc input file for Spanish sparrow parental population (reference population), all 77 markers
Downloaded 8 times
Description bgc input file for Spanish sparrow parental population (reference population)
Download spanish.txt (1.123 Kb)
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Title bgc input file for hybrid-parent test population, all 77 markers
Downloaded 14 times
Description bgc input file for hybrid-parent test population, all 77 markers
Download admixed_spain.txt (51.50 Kb)
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Title a.out_parental sympatry
Downloaded 13 times
Description Output from BGC run on parental sympatry test population: estimates of cline parameter alpha for the 77 loci.
Download a.out_spain.txt (4.432 Kb)
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Title b.out_parental sympatry
Downloaded 9 times
Description Output from BGC run on parental sympatry test population: estimates of cline parameter beta for the 77 loci.
Download b.out_spain.txt (4.332 Kb)
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Title hi.out_parental sympatry
Downloaded 10 times
Description Output from BGC run on parental sympatry test population: estimates of hybrid index.
Download hi.out_spain.txt (7.919 Kb)
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Title qa.out_parental sympatry
Downloaded 9 times
Description Output from BGC run on parental sympatry test population: estimates of alpha parameter quantiles for the 77 loci.
Download qa.out_spain.txt (4.652 Kb)
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Title qb.out_parental sympatry
Downloaded 6 times
Description output from BGC run on parental sympatry test population: estimates of beta parameter quantiles for the 77 loci
Download qb.out_spain.txt (4.575 Kb)
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Title bgc input file for house sparrow parental population (reference population) when analysing autosomal loci separately
Downloaded 4 times
Description input file for house sparrow parental population (reference population) when analysing autosomal loci separately in parental sympatry
Download house_autosomal.txt (851 bytes)
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Title bgc input file for Spanish sparrow parental population (reference population) when analysing autosomal loci separately in parental sympatry
Downloaded 4 times
Description bgc input file for Spanish sparrow parental population (reference population) when analysing autosomal loci separately in parental sympatry
Download spanish_autosomal.txt (801 bytes)
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Title bgc input file for parental sympatry test population when analysing autosomal loci separately
Downloaded 16 times
Description bgc input file for parental sympatry test population when analysing autosomal loci separately
Download admixed_spain_autosomal.txt (36.76 Kb)
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Title b.out_autosomal_parental sympatry
Downloaded 2 times
Description output from BGC run on parental sympatry test population: estimates of cline parameter beta for the 55 autosomal loci analyzed separately
Download b.out_spain_autosomal.txt (3.105 Kb)
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Title bgc input file for house sparrow parental population (reference population) when analysing Z-linked loci separately in parental sympatry
Downloaded 2 times
Description bgc input file for house sparrow parental population (reference population) when analysing Z-linked loci separately in parental sympatry
Download house_Z.txt (311 bytes)
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Title bgc input file for Spanish sparrow parental population (reference population) when analysing Z-linked loci separately in parental sympatry
Downloaded 4 times
Description bgc input file for Spanish sparrow parental population (reference population) when analysing Z-linked loci separately i parental sympatry
Download spanish_Z.txt (297 bytes)
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Title bgc input file for test population when analysing Z-linked loci separately in parental sympatry
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Description bgc input file for test population when analysing Z-linked loci separately in parental sympatry
Download admixed_spain_Z.txt (14.05 Kb)
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Title b.out_Z_parental sympatry
Downloaded 11 times
Description output from BGC: estimates of cline parameter beta for the 21 Z-linked loci analyzed separately in parental sympatry
Download b.out_spain_Z.txt (1.2 Kb)
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Title bgc input file for hybrid-parents test population (all 77 loci)
Downloaded 5 times
Description bgc input file for hybrid-parents test population (all 77 loci)
Download admixed_italy.txt (135.4 Kb)
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Title a.out_hybrid-parents analysis
Downloaded 8 times
Description output from BGC: estimates of cline parameter alpha for 77 the loci used in the hybrid-parents analysis
Download a.out_italy.txt (4.407 Kb)
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Title b.out_hybrid-parents analysis
Downloaded 5 times
Description output from BGC: estimates of cline parameter beta for 77 the loci used in the hybrid-parents analysis
Download b.out_italy.txt (4.368 Kb)
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Title hi.out_hybrid-parents analysis
Downloaded 11 times
Description output from BGC: estimates of hybrid index for the individuals in the hybrid-parents test population
Download hi.out_italy.txt (21.14 Kb)
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Title qa.out_hybrid-parents analysis
Downloaded 7 times
Description bgc output from hybrid-parents analysis: estimates of alpha parameter quantiles for the 77 loci
Download qa.out_italy.txt (4.652 Kb)
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Title qb.out_hybrid-parents analysis
Downloaded 10 times
Description bgc output from hybrid-parents analysis: estimates of beta parameter quantiles for the 77 loci
Download qb.out_italy.txt (4.575 Kb)
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When using this data, please cite the original publication:

Hermansen JS, Haas F, Trier CN, Bailey RI, Nederbragt AJ, Marzal A, Sætre G (2014) Hybrid speciation by sorting of parental incompatibilities in Italian sparrows. Molecular Ecology 23(23): 5831-5842. http://dx.doi.org/10.1111/mec.12910

Additionally, please cite the Dryad data package:

Hermansen JS, Haas F, Bailey RI, Nederbragt AJ, Trier CN, Marzal A, Sætre G (2014) Data from: Hybrid speciation by sorting of parental incompatibilities in Italian sparrows. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.v6f4d
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