Data from: Chaotic genetic patchiness without sweepstakes reproduction in the shore crab Hemigrapsus oregonensis

Cornwell BH, Fisher JL, Morgan SG, Neigel JE

Date Published: May 5, 2016

DOI: http://dx.doi.org/10.5061/dryad.812mm

 

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Title haplotypeSequences
Downloaded 4 times
Description DNA sequences of partial cytochrome oxidase I sequences used for our analyses. These include both sequences from our study and those from Petersen (2007) doi:10.1007/s00227-006-0442-x
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Title totalSnpCounts
Downloaded 16 times
Description For each sample of individuals, number individuals with each of the four different nucleotides at sequence position 461 (SNP-461). The first section of the table is for SNP genotypes determined by TaqMan probes, the second sequence is for SNP genotypes determined by sequencing, and the third section combines numbers from both methods of genotyping.
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Title totalSnpFrequencies
Downloaded 13 times
Description SNP-461 allele frequencies for SNP genotypes determined from TaqMan probes, sequencing, and totals for both methods combined.
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Title combinedSequences
Downloaded 2 times
Description All partial COI sequences from this study and Petersen (2007), trimmed alignment.
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Title sequenceOrganizer
Downloaded 8 times
Description Perl script to organize sequences in combinedSequences.pl. Finds all unique haplotypes, names them h1, h2, h3... and writes fasta file of all unique haplotypes, writes file with number of occurrences of each haplotype, writes file of counts of each haplotype in each sample, writes input file for the software Arlequin, writes input file for the software IMa2
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Title combineSnps
Downloaded 7 times
Description Reads counts of SNPs alleles (A, T, C, or G) from one file with counts in samples for TaqMan genotyping and another file with counts in samples from sequence-based genotyping and combines them. Output SNP counts and SNP frequencies by location and an input file in Genepop format. Allows samples to be pooled into named aggregate collections
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Title sequencesToSnps
Downloaded 8 times
Description Reads sequences in fasta file, outputs SNP counts
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When using this data, please cite the original publication:

Cornwell BH, Fisher JL, Morgan SG, Neigel JE (2016) Chaotic genetic patchiness without sweepstakes reproduction in the shore crab Hemigrapsus oregonensis. Marine Ecology Progress Series 548: 139–152. http://dx.doi.org/10.3354/meps11628

Additionally, please cite the Dryad data package:

Cornwell BH, Fisher JL, Morgan SG, Neigel JE (2016) Data from: Chaotic genetic patchiness without sweepstakes reproduction in the shore crab Hemigrapsus oregonensis. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.812mm
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