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Data from: Demography predicts genetic effective size in a desert stream fish community


Pilger, Tyler (2022), Data from: Demography predicts genetic effective size in a desert stream fish community, Dryad, Dataset,


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 Sample collection methods for short-term ecological studies are available in Microsatellite genotype available at were used to estimate contemporary migration rates using the program BIMr, see uploaded supplementary material for details.

Usage Notes

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.