10.5061/DRYAD.SXKSN0332
Pilger, Tyler
0000-0003-3956-0323
University of New Mexico
Data from: Demography predicts genetic effective size in a desert stream
fish community
Dryad
dataset
2021
FOS: Biological sciences
Agosia chrysogaster
Catostomus insignis
Gila nigra
Meda fulgida
Micropterus dolomieu
Pantosteus clarkii
Rhinichthys osculus
Tiaroga cobitis
recurring extirpations
Metapopulation models
effective number of breeders
contemporary effective population size
Ameiurus natalis
2022-02-23T00:00:00Z
2022-02-23T00:00:00Z
en
https://doi.org/10.1111/mec.14079
https://doi.org/10.5061/dryad.d5j4m
https://doi.org/10.1890/07-1489.1
https://doi.org/10.1139/cjfas-2014-0153
https://doi.org/10.5281/zenodo.5475436
3394316 bytes
5
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Demographic data collected during long-term diversity monitoring and
short-term ecological surveys were used to calculate summary statistics to
compare with estimates of genetic effective size for nine species
occurring in the Gila River, New Mexico, USA. Diversity survey data
collected by New Mexico Department of Game and Fish from 1988 to 2010 were
converted to presence/absence data to create detection histories for each
of the nine focal species. Simple occupancy models of detection histories
implemented using program PRESENCE were used to estimate the annual
probability of sites becoming extirpated. A second data source from
affiliated short-term ecological studies provided numbers of individuals
captured and area sampled and was used to estimate mean density of adult
individuals across sample sites. These data were also used to calculated
an index of commonness that incorporates both relative abundance and study
wide occupancy. Microsatellite genotypes from a previous study and Dryad
submission were used to estimate effective number of breeders and genetic
effective size (estimates included in this submission) for each species
and contemporary migration rates. Migration rates were estimated using the
Bayesian assignment model implemented in program BIMr. Outputs from all
independent model runs and code to process output files are included with
this data submission.
Sample collection methods for standardized long-term survey data are
available in https://doi.org/10.1890/07-1489.1. Sample collection methods
for short-term ecological studies are available in
https://doi.org/10.1139/cjfas-2014-0153. Microsatellite genotype available
at https://doi.org/10.5061/dryad.d5j4m were used to estimate contemporary
migration rates using the program BIMr, see uploaded supplementary
material for details.
Occupancy modeling using detection histories were performed in program
PRESENCE (Hines 2006). Resulting epsilon estimates are included in text
file of metapopulation statistics. All other computations were performed
using the R environment (R Core Team 2021) and associated code is
included. Output files from Bayesian inference to estimate migration
rates from microsatellite genotypes using BIMr (Faubet and Gaggiotti 2008)
are included with R code to process and summarize across 10 independent
model runs. See README file for file details.