Data from: Genomic tests of the species-pump hypothesis: recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands

Papadopoulou A, Knowles LL

Date Published: April 20, 2015

DOI: http://dx.doi.org/10.5061/dryad.23hs1

 

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Title Amphiacusta_5558SNPs_StructureFile.txt
Downloaded 7 times
Description A structure format file containing 5,558 single bi-allelic SNPs that were used for assessing population structure and genetic differentiation (for STRUCTURE, PCA and procrustes analyses, IBD and estimation of genetic diversity statistics).
Download Amphiacusta10pops5558SNPsStructure.txt (3.063 Mb)
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Title Amphiacusta_82443SNPs_ForQuartets.txt
Downloaded 10 times
Description A phylip file containing 82,443 single bi-allelic SNPs that were used for the quartet analysis (in SVDquartets).
Download Amphiacusta82443SNPsForQuartets.txt (12.20 Mb)
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Title sampleDownMSFS.py
Downloaded 21 times
Description Python script that downsamples the population sizes and calculates the joint folded Site Frequency Spectrum (for the minor allele frequency) of two populations based on a vcf file. Includes an example vcf input file and population map.
Download sampleDownMSFSWithExampleInputFiles.zip (6.087 Mb)
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Title InputFilesForFastsimcoal.zip
Downloaded 16 times
Description A set of folders containing the input files for analyses with fastsimcoal2, including the calculated joint Site Frequency Spectrum for each of the focal population pairs. Folder and file names follow the population codes used consistently throughout the manuscript.
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When using this data, please cite the original publication:

Papadopoulou A, Knowles LL (2015) Genomic tests of the species-pump hypothesis: recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands. Evolution 69(6): 1501–1517. http://dx.doi.org/10.1111/evo.12667

Additionally, please cite the Dryad data package:

Papadopoulou A, Knowles LL (2015) Data from: Genomic tests of the species-pump hypothesis: recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.23hs1
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