10.5061/DRYAD.871DB
Kinziger, Andrew P.
Humboldt State University
Hellmair, Michael
University of California Los Angeles
McCraney, William Tyler
University of California Los Angeles
Jacobs, David K.
University of California Los Angeles
Goldsmith, Greg
Arcata Fish and Wildlife Office; 1655 Heindon Road Arcata CA 95521 USA
Data from: Temporal genetic analysis of the endangered tidewater goby:
metapopulation dynamics or drift in isolation?
Dryad
dataset
2015
metapopulation
tidewater goby
Holocene
Eucyclogobius newberryi
2015-10-15T15:36:29Z
2015-10-15T15:36:29Z
en
https://doi.org/10.1111/mec.13424
891971 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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
California