DOI: 10.5061/dryad.871db
title: Data from: Temporal genetic analysis of the endangered tidewater goby: metapopulation dynamics or drift in isolation?

description: 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.
description: 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
 (&gt;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