Data from: Introgression between invasive and native blue mussels (genus Mytilus) in the central California hybrid zone.

Saarman NP, Pogson GH

Date Published: July 31, 2015

DOI: http://dx.doi.org/10.5061/dryad.53d34

 

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Title NewHybrids_v.1_input_file
Downloaded 9 times
Description This is the input file for NewHybrids v1 (Anderson & Thompson 2002; Anderson 2008) analyses, used to identify pure species and hybrids and to classify hybrids into categories (i.e., F1, F2, backcross with M. galloprovincialis, or backcross with M. trossulus). This file includes only diagnostic SNPs. We used Jeffreys-type priors and a burn in of 10,000 sweeps followed by 50,000 sweeps in five separate runs. Convergence of Q across runs were again checked.
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Title INTROGRESS_v.1.22_input_file_(locus_data)
Downloaded 12 times
Description This is file 1 (locus data) of 4 input files needed for running the R package INTROGRESS v1.22 (Gompert & Berkle 2010). These files together allow maximum-likelihood estimate of the ancestry (multilocus hybrid score) of each individual, and genomic cline analysis, which compares admixture at a single locus to average admixture across the rest of the genome. We used the parametric approach, first estimating a multilocus hybrid index and then fitting clines in genotype frequencies at individual SNPs as a function of the neutral expectation derived from the genome-wide hybrid index.
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Title INTROGRESS_v.1.22_input_file_(parent_1_data)
Downloaded 7 times
Description This is file 2 (parent 1 data) of 4 input files needed for running the R package INTROGRESS v1.22 (Gompert & Berkle 2010). These files together allow maximum-likelihood estimate of the ancestry (multilocus hybrid score) of each individual, and genomic cline analysis, which compares admixture at a single locus to average admixture across the rest of the genome. We used the parametric approach, first estimating a multilocus hybrid index and then fitting clines in genotype frequencies at individual SNPs as a function of the neutral expectation derived from the genome-wide hybrid index.
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Title INTROGRESS_v.1.22_input_file_(parent_2_data)
Downloaded 8 times
Description This is file 3 (parental 2 data) of 4 input files needed for running the R package INTROGRESS v1.22 (Gompert & Berkle 2010). These files together allow maximum-likelihood estimate of the ancestry (multilocus hybrid score) of each individual, and genomic cline analysis, which compares admixture at a single locus to average admixture across the rest of the genome. We used the parametric approach, first estimating a multilocus hybrid index and then fitting clines in genotype frequencies at individual SNPs as a function of the neutral expectation derived from the genome-wide hybrid index.
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Title INTROGRESS_v.1.22_input_file_(admix_data)
Downloaded 12 times
Description This is file 4 (admix data) of 4 input files needed for running the R package INTROGRESS v1.22 (Gompert & Berkle 2010). These files together allow maximum-likelihood estimate of the ancestry (multilocus hybrid score) of each individual, and genomic cline analysis, which compares admixture at a single locus to average admixture across the rest of the genome. We used the parametric approach, first estimating a multilocus hybrid index and then fitting clines in genotype frequencies at individual SNPs as a function of the neutral expectation derived from the genome-wide hybrid index.
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Title adegenet_package_v.1.4-2_input_file
Downloaded 11 times
Description This is the input file needed to performed a principle components analysis with the "adegenet" package version 1.4-2 (Jombart et al 2008) in the R version 3.1.0 environment (R Core Team, 2013). The results from this analysis were used to inform definitions of parental genotypes.
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Title STRUCTURE_v.2.3.4_input_file
Downloaded 4 times
Description This is the input file needed to run STRUCTURE v2.3.4 (Pritchard et al 2000; Falush et al 2003; Falush et al 2007), which we used to identify pure species and hybrids. STRUCTURE jointly assigns individuals probabilistically to the two parental classes without prior input. STRUCTURE analyses used all 1,337 SNPs that passed our primary filters. We used a burn in of 50,000 sweeps and then ran 100,000 sweeps in five separate runs checking for convergence of the estimated membership coefficient (Q) across runs.
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Title tags_from_STACKS_populations.pl_script
Downloaded 67 times
Description This was an output of the populations.pl script from the Stacks pipeline, used to filter SNPs scored in at least 75% of samples (parameter -r 0.75). This yielded a total of 1,337 SNPs. The original file name was "batch.8.catalog.tags.tsv". More information on the file format can be found at http://catchenlab.life.illinois.edu/stacks/comp/populations.php.
Download tags_from_STACKS_populations.pl_script.tsv.zip (33.13 Mb)
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Title SNPs_from_STACKS_populations.pl_script.tsv
Downloaded 67 times
Description This is the output of the populations.pl script from the Stacks pipeline, used to filter SNPs scored in at least 75% of samples (parameter -r 0.75). This yielded a total of 1,337 SNPs. The original file name was "batch.8.catalog.snps.tsv". More information on the file format can be found at http://catchenlab.life.illinois.edu/stacks/comp/populations.php. We compressed the file for convenience.
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When using this data, please cite the original publication:

Saarman NP, Pogson GH (2015) Introgression between invasive and native blue mussels (genus Mytilus) in the central California hybrid zone. Molecular Ecology 24(18): 4723–4738. http://dx.doi.org/10.1111/mec.13340

Additionally, please cite the Dryad data package:

Saarman NP, Pogson GH (2015) Data from: Introgression between invasive and native blue mussels (genus Mytilus) in the central California hybrid zone. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.53d34
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