DOI: 10.5061/dryad.76hdr7t5z
title: Estimating drivers and identifying uncertainties in smallmouth bass population dynamics in an invaded river network

description: Smallmouth bass (Micropterus dolomieu) is an important recreational
 sportfish and destructive non-native species when introduced into
 freshwater habitats. There is therefore a need to understand the drivers
 of, and uncertainties in, smallmouth bass population dynamics for various
 management objectives. We combined long-term smallmouth bass catch-effort
 and early life history data from a non-native population in the Green
 River sub-basin of the upper Colorado River to develop a demographic model
 that links interannual variability in environmental conditions to
 recruitment in three river reaches. We used the model to quantify how
 hydrology, river temperature, and exploitation drive smallmouth bass
 population dynamics. Early life stages were influenced by timing of
 hatching and discharge. Dispersal of age-0 fish and density-dependent
 dynamics were identified as primary sources of uncertainty. Determining
 the true nature of density-dependent dynamics is important, as the impact
 of exploitation-based management actions is dependent on the strengths of
 any density-dependent feedbacks. Our model provides a framework to predict
 smallmouth bass population responses to future climate conditions,
 reservoir operations, and exploitation levels.
description: We compiled smallmouth bass catch-effort data collected by boat
 electrofishing during non-native removal efforts in the Yampa and Green
 rivers in 2005 through 2022 . We used catch data from the Lily Park, Yampa
 Canyon, and Middle Green River reaches.  Each spring and summer, multiple
 sampling trips were conducted in each reach. We defined a trip as a full
 sampling occasion comprised of multiple electrofishing passes from the top
 of the reach to the bottom. Sampling trips typically lasted 2 – 4 days. On
 most trips, counts of removed fish were summarized by three size classes
 (&lt;100 mm, 100-200 mm, and &gt;200 mm). Catch-effort data for
 each study reach were extracted from annual reports which have sampling
 details (Lily Park: Project # 125/98c, Yampa Canyon: Project # 110, Middle
 Green: Project # 123a) and are publicly available on the Upper Colorado
 River Endangered Fish Recovery Program website
 (https://coloradoriverrecovery.org/uc/documents/work-plan-documents/annual-reports/). In addition to catch data for each removal reach, we also used observations of recaptured tagged smallmouth bass to estimate movement rates among our reaches of interest. Smallmouth bass were sometimes tagged with individual Floy tags during early removal trips to estimate abundance each year. The Recovery Program compiled encounter locations for marked and recaptured Floy-tagged fish across the reaches of interested using the Species, Tagging, Research and Monitoring System database (https://streamsystem.org/index.php). We calculated hydrologic metrics based on conditions in the Green River at the U.S. Geological Survey (hereafter USGS) gage at Jensen (#09261000; USGS 2023a) and in the Yampa River from the USGS gage at Deerlodge Park (#09260050; USGS 2023b; Figure 1). Temperature metrics for the Green River were also obtained from the Jensen gage, while temperature data from the Yampa River were collected at Echo Park by USFWS (Figure 1). The temperature logger at Echo Park was periodically out of service, in those cases we used daily mean temperature from Deerlodge Park to fill in any data gaps. Mean daily discharge and temperature for each river was summarized as metrics used to predict smallmouth bass hatch dates based on equations from Bestgen and Hill (2016) or as other predictors included in the model. Calculation of each flow metric is described below in description of the model. The data included here as been simplified and formatted to fit the smallmouth bass population dynamics model presented in the associated paper with this data and code release. 
description: # Estimating drivers and identifying uncertainties in smallmouth bass
 population dynamics in an invaded river network
 [https://doi.org/10.5061/dryad.76hdr7t5z](https://doi.org/10.5061/dryad.76hdr7t5z) ## Description of the data and file structure This data and code describe the population dynamics of smallmouth bass in the Green River sub-basin of the Colorado River. Data included in the model include catch-effort data for electrofishing passes fit to an age structured model. Data included observed catch of adults (greater than 200 mm TL), sub-adults (100-200 mm), and age-0 (&lt;100 mm) smallmouth bass in each reach, summarized and standardized predicted end of summer lengths of age-0 fish, discharge conditions during the hatch, the number of electrofishing passes during each sampling trip (effort), and index information for organizing catch by electrofishing pass, year, and reach in the population model.  ### Files and variables #### File: data\_revision.zip **Description:** Contains data files necessary to fit smallmouth bass population model and run removal scenarios, including catch and effort data, indexing information, and standardized covariates. Note data are organized as matrices without column or row labels to be directly used in models (code provided). Data files include: * dpg.csv: matrix where each column represents a year (2004-2022) and each row represents an electrofishing trip, with the total number or rows determined by the max number of electrofishing trips conducted across all years. Values in the cells are the number of cohorts (1-31) vulnerable to capture on each electrofishing trip in the Middle Green River. For example, a value of 31 indicates fish hatched from day 1 of hatch to the 31st day of hatch are all vulnerable to electrofishing exploitation, while a value of 5 indicates only fish hatched during the first five days of the hatching period are vulnerable to capture.  999 indicates no electrofishing pass was conducted. Used in fitted model.  * dpg.max.effort.csv: matrix where each column is a combinations of each year (2004-2022) and reach (Lily, Yampa Canyon, and Middle Green) and each row represents an electrofishing trip, with the total number or rows determined by the max number of electrofishing trips conducted across all years and reaches. Values in the cells are the number of cohorts (1-31) vulnerable to capture on each electrofishing trip , used in the max effort simulation scenario.  999 indicates no electrofishing pass was conducted. * flow.csv: matrix of discharge on each day of the 31 day hatch period in each reach in each year. Rows indicate each of the 31 days of hatch and columns represent each year by reach combination. For example, the first three columns contain standardized discharge for the Lily, Yampa Canyon, and Middle Green reaches, respectively, in 2004. Data were standardized and centered based on means and standard deviations of discharge in each reach.  * length.csv: matrix of predicted end of summer lengths of age-0 fish hatched on each day of the 31 day hatch period in each reach in each year. Rows indicate each of the 31 days of hatch and columns represent each year by reach combination. For example, the first three columns contain standardized end of summer lengths for the Lily, Yampa Canyon, and Middle Green reaches, respectively, in 2004. Lengths were standardized using a mean of 59mm and a standard deviation of 19mm.  * np.csv: observed number of electrofishing trips in each year (columns; 2004-2022) in each reach (rows; Lily, Yampa Canyon, and Middle Green). * np0.csv: observed number of electrofishing trips occurring after predicted smallmouth bass hatch in each year (columns; 2004-2022) in each reach (rows; Lily, Yampa Canyon, and Middle Green). * np0.max.effort.csv: simulated number of electrofishing trips occurring after predicted smallmouth bass hatch in each year (columns) in each reach (rows; Lily, Yampa Canyon, and Middle Green) assuming the maximum number of electrofishing trips can occur each year. Used in simulation model.  * pC0_obs.csv: observed number of age-0 smallmouth bass captured on each pass in each year in the Middle Green river reach.  * pCA_obs.csv: observed number of adult smallmouth bass captured on each pass in each year across all reaches.  * pCA_obs_lily.csv: observed number of adult smallmouth bass captured on each pass in each year in the Lily Park river reach. * pCA_obs_yc.csv: observed number of adult smallmouth bass captured on each pass in each year in the Yampa Canyon river reach. * pCA_obs_mg.csv: observed number of adult smallmouth bass captured on each pass in each year in the Middle Green river reach. * pCSA_obs.csv: observed number of sub-adult smallmouth bass captured on each pass in each year across all reaches.  * pCSA_obs_lily.csv: observed number of sub-adult smallmouth bass captured on each pass in each year in the Lily Park river reach. * pCSA_obs_yc.csv: observed number of sub-adult smallmouth bass captured on each pass in each year in the Yampa Canyon river reach. * pCSA_obs_mg.csv: observed number of sub-adult smallmouth bass captured on each pass in each year in the Middle Green river reach. #### File: code\_revision.zip **Description:**  R scripts containing code to fit smallmouth bass population model, run the simulation model for removal scenarios, and plot results for fitted model and simulation model and Stan file containing statistical population model.  * fit_model.R: code to prepare data, fit population model to observed catch, and summarize and plot results * Shepard_model_final.stan: model code * run_sim.R: code to prepare data, run simulations for exploitation scenarios, and export results * sim_code.R: model simulation functions * sim_plots.R: code to plot results of simulations for exploitation scenarios ## Code/software All data files can be viewed and edited using any programs that can open comma separated text files. Program R is required to run all code files and Stan is required to fit the population model. Any packages used to organize data or plot results are included at the top of the scripts.  ## Access information Other publicly accessible locations of the data: * NA Data was derived from the following sources: * [https://coloradoriverrecovery.org/uc/documents/work-plan-documents/annual-reports/](https://coloradoriverrecovery.org/uc/documents/work-plan-documents/annual-reports/) * [https://waterdata.usgs.gov/monitoring-location/09261000/#dataTypeId=continuous-00065-0&period=P7D&showMedian=false](https://waterdata.usgs.gov/monitoring-location/09261000/#dataTypeId=continuous-00065-0&period=P7D&showMedian=false) * [https://waterdata.usgs.gov/monitoring-location/09260050/#dataTypeId=continuous-00065-0&period=P7D&showMedian=false](https://waterdata.usgs.gov/monitoring-location/09260050/#dataTypeId=continuous-00065-0&period=P7D&showMedian=false)