Data from: Temporal genetic analysis of the endangered tidewater goby: metapopulation dynamics or drift in isolation?

Kinziger AP, Hellmair M, McCraney WT, Jacobs DK, Goldsmith G

Date Published: October 15, 2015

DOI: http://dx.doi.org/10.5061/dryad.871db

 

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Title Microsatellite genotypes for northern California tidewater goby populations
Downloaded 15 times
Description Microsatellite genotypes in GENEPOP format for northern California tidewater goby populations. Definitions for site abbreviations and geographic coordinates of sampling locations can be found in the accompanying publication.
Download Goby Combined.genepop.txt (122.5 Kb)
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Title Tidewater Goby Occupancy History Northcoast Haul Data
Downloaded 40 times
Description Tidewater goby occupancy data for northern California tidewater goby populations. Data includes presence (1) absence(0) from 94 sites between 1897 and 2014. Primary sampling periods are years and secondary sampling sessions are repeat seine hauls within years. For additional descriptions of the data please see accompanying publication.
Download Tidewater Goby Occupancy History Northcoas....xlsx (499.0 Kb)
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Title Genetic and geographic distance data for isolation by distance analysis
Downloaded 14 times
Description Genetic and geographic distance data for analysis of conformance to an isolation by model of gene flow. Values above the diagonal are geographic distances (km) and values below diagonal are genetic distances (Fst). Data are for the 19 spatially isolated locations with large sample sizes. Only those collections with large sample sizes were included in the analysis (>19).
Download Distance data KM above FST below.xlsx (51.01 Kb)
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Title Input file used to construct neighbor joining tree using PHYLIP.
Downloaded 6 times
Description Input file used to construct neighbor joining tree using PHYLIP. Population IDs, 1-36, defined in companion file uploaded with this data package.
Download infile.txt (13.72 Kb)
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Title Bootstrap consensus tree from neighbor joining analysis using PHYLIP.
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Description Bootstrap consensus tree from neighbor joining analysis using PHYLIP. Population IDs, 1-36, defined in companion file uploaded with this data package.
Download outtree.consense.txt (788 bytes)
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Title Project/parameter input file for Bayesian cluster analysis using STRUCTURE.
Downloaded 5 times
Description Project input file containing parameters for Bayesian cluster analysis using STRUCTURE. Site IDs, 1-47, are defined in companion file with this data package.
Download GobyFull.spj (228 bytes)
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Title Genotypic data (input file) for Bayesian cluster analysis using STRUCTURE.
Downloaded 6 times
Description Project input file containing genotypic data for Bayesian cluster analysis using STRUCTURE. Site IDs, 1-47, are defined in companion file with this data package.
Download project_data (156.6 Kb)
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Title Site location information file, including site IDs, date of collection, and geographic coordinates.
Downloaded 21 times
Description Site, collection year, sample ID, and within population microsatellite DNA genetic diversity [sample size (N), observed heterozygosity (Ho), Hardy-Weinberg expected heterozygosity (He), allelic richness (A), rarified allelic richness (Ar), rarified number of private alleles (Ap), inbreeding effective size (Nei) and 95% confidence interval (CI)] for northern California tidewater goby populations (listed from north to south). Also included are site reference numbers for analysis using PHYLIP (1-36) and STRUCTURE (1-47).
Download Site IDs References STRUCTURE.xlsx (47.97 Kb)
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When using this data, please cite the original publication:

Kinziger AP, Hellmair M, McCraney WT, Jacobs DK, Goldsmith G (2015) Temporal genetic analysis of the endangered tidewater goby: metapopulation dynamics or drift in isolation? Molecular Ecology 24(22): 5544-5560. http://dx.doi.org/10.1111/mec.13424

Additionally, please cite the Dryad data package:

Kinziger AP, Hellmair M, McCraney WT, Jacobs DK, Goldsmith G (2015) Data from: Temporal genetic analysis of the endangered tidewater goby: metapopulation dynamics or drift in isolation? Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.871db
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