Data from: Temporal genetic analysis of the endangered tidewater goby: metapopulation dynamics or drift in isolation?
| Main Authors: | Kinziger, Andrew P., Hellmair, Michael, McCraney, William Tyler, Jacobs, David K., Goldsmith, Greg |
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| Format: | info dataset Journal |
| Terbitan: |
, 2015
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/5000597 |
Daftar Isi:
- Extinction and colonization dynamics are critical to understanding the evolution and conservation of metapopulations. However, traditional field studies of extinction–colonization are potentially fraught with detection bias and have rarely been validated. Here, we provide a comparison of molecular and field-based approaches for assessment of the extinction–colonization dynamics of tidewater goby (Eucyclogobius newberryi) in northern California. Our analysis of temporal genetic variation across 14 northern California tidewater goby populations failed to recover genetic change expected with extinction–colonization cycles. Similarly, analysis of site occupancy data from field studies (94 sites) indicated that extinction and colonization are very infrequent for our study populations. Comparison of the approaches indicated field data were subject to imperfect detection, and falsely implied extinction–colonization cycles in several instances. For northern California populations of tidewater goby, we interpret the strong genetic differentiation between populations and high degree of within-site temporal stability as consistent with a model of drift in the absence of migration, at least over the past 20–30 years. Our findings show that tidewater goby exhibit different population structures across their geographic range (extinction–colonization dynamics in the south vs. drift in isolation in the north). For northern populations, natural dispersal is too infrequent to be considered a viable approach for recolonizing extirpated populations, suggesting that species recovery will likely depend on artificial translocation in this region. More broadly, this work illustrates that temporal genetic analysis can be used in combination with field data to strengthen inference of extinction–colonization dynamics or as a stand-alone tool when field data are lacking.
- Microsatellite genotypes for northern California tidewater goby populationsMicrosatellite 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.Goby Combined.genepop.txtTidewater Goby Occupancy History Northcoast Haul DataTidewater 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.Genetic and geographic distance data for isolation by distance analysisGenetic 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).Distance data KM above FST below.xlsxInput file used to construct neighbor joining tree using PHYLIP.Input file used to construct neighbor joining tree using PHYLIP. Population IDs, 1-36, defined in companion file uploaded with this data package.infile.txtBootstrap consensus tree from neighbor joining analysis using PHYLIP.Bootstrap consensus tree from neighbor joining analysis using PHYLIP. Population IDs, 1-36, defined in companion file uploaded with this data package.outtree.consense.txtProject/parameter input file for Bayesian cluster analysis using STRUCTURE.Project input file containing parameters for Bayesian cluster analysis using STRUCTURE. Site IDs, 1-47, are defined in companion file with this data package.GobyFull.spjGenotypic data (input file) for Bayesian cluster analysis using STRUCTURE.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.project_dataSite location information file, including site IDs, date of collection, and geographic coordinates.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).Site IDs References STRUCTURE.xlsx