Data from: Some like it cold: A general habitat association model for smallmouth bass in stratified lakes
Data files
Nov 24, 2025 version files 146.10 KB
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Bass_Temp_FLEN.csv
14.29 KB
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comparison_lake_data.csv
49.87 KB
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Occu_depths.csv
300 B
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Ope_data.csv
41.58 KB
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README.md
6.52 KB
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Temp_DO_data.csv
33.54 KB
Abstract
Associations between fish distribution and environmental or spatial gradients at the population level represent habitat use models with potential to be transferable if model parameters are stationary among populations and over years. Further, population-level habitat use models represent the scale of effect – habitat relevant to within population distribution and processes. Here we show that for a widely recognized warm water fish species (smallmouth bass; Micropterus dolomieu), habitat use based on occupancy models extends their distribution in lakes deeper into the metalimnion and hypolimnion – some bass like it cold. Lake depth at net sites was the gradient used to model habitat use in a comparative lake set (n=11 lakes) and for a large lake with three surveys over a decade. Bayesian quantile regression, with lakes as random effects, revealed all sizes of bass were present in shallow, warm areas of lakes as expected based on thermal preferences. Large adult bass, and not smaller fish, were found at deeper, colder depths producing a significant pattern of large fish found at deeper sites, thus confirming earlier tracking studies. The depth covariate was similar across lakes (no significant difference among lakes with one exception) in the comparative lake set. Over years, the depth covariate was also similar (no significant difference among years) and comparable to the comparative lake set. This consistency points to a general stationary habitat model for smallmouth bass during the summer season. We provide guidance for habitat managers based on this stationarity.
Descriptions of .R Files:
Comparison_bass_occupancy.R - Code to recreate the occupancy analysis of the multi-lake dataset and Figure 4. Uses "Comparison_Lake_data.csv" file so make sure working directory is set where that file is located. 'ubms' package version used in analysis is listed in script and manuscript, newer versions may give slightly different results from tweaks to default priors.
Opeongo_bass_occupancy.R - Code to recreate the occupancy analysis specific to lake Opeongo and Figure 6. Uses "Ope_data.csv" file so make sure working directory is set where that file is located. 'ubms' package version used in analysis is listed in script and manuscript, newer versions may give slightly different results from tweaks to default priors
histograms_and_Quantile_regresion.R - Code to create Figures 2, 3, and 5 in manuscript. Also contains code to reproduce Quantile regression in a previous version of the manuscript (left in for those who may be interested). Uses "Bass_Temp_Flen.csv" and "Occu_depths.csv" files so make sure working directory is set where those files are located.
Data Definitions for CSV files
comparison_lake_data.csv: Called by Comparison_bass_occupancy.R; this file contains pass-level count and presence absence data for smallmouth bass in the multi-lake comparison, with site-level depth and temperature as well as ID columns for each lake.
- PRJ_CD - Project code of each netting survey
- Site - Code for each site in each netting survey
- P1_SB_Count -Pass 1, Panel 1 count of Smallmouth Bass
- P2_SB_Count -Pass 1, Panel 2 count of Smallmouth Bass
- P3_SB_Count -Pass 2, Panel 1 count of Smallmouth Bass
- P4_SB_Count -Pass 2, Panel 2 count of Smallmouth Bass
- P5_SB_Count -Pass 3, Panel 1 count of Smallmouth Bass
- P6_SB_Count -Pass 3, Panel 2 count of Smallmouth Bass
- P1_SB_PA - Pass 1, Panel 1 presence/absence of Smallmouth Bass
- P2_SB_PA - Pass 1, Panel 2 presence/absence of Smallmouth Bass
- P3_SB_PA - Pass 2, Panel 1 presence/absence of Smallmouth Bass
- P4_SB_PA - Pass 2, Panel 2 presence / absence of Smallmouth Bass
- P5_SB_PA - Pass 3, Panel 1 presence/absence of Smallmouth Bass
- P6_SB_PA - Pass 3, Panel 2 presence/absence of Smallmouth Bass
- X - Easting coordinate of net site in meters; UTM zone 17N
- Y - Northing coordinate of net site in meters; UTM zone 17N
- AVG_Depth - average depth of site in meters
- AVG_Temp - average temperature of site in degrees Celsius
- lk2 - ID for identifying Lauder lake survey sites
- lk3 - ID for identifying Cache lake survey sites
- lk4 - ID for identifying Canoe lake survey sites
- lk5 - ID for identifying Rock lake survey sites
- lk6 - ID for identifying Tea lake survey sites
- lk7 - ID for identifying Whitefish lake survey sites
- lk8 - ID for identifying Happy Isle lake survey sites
- lk9 - ID for identifying Ragged lake survey sites
- lk10 - ID for identifying Cedar lake survey sites
- lk11 - ID for identifying lake of Two Rivers survey sites
Ope_data.csv: Called by Opeongo_bass_occupancy.R; this file contains pass-level count and presence-absence data for smallmouth bass in lake Opeongo across multiple years, with site-level depth and temperature as well as a Year column that describes survey year.
- PRJ_CD - Project code of each netting survey
- Site - Code for each site in each netting survey
- P1_SB_PA -Pass 1, Panel 1 count of Smallmouth Bass
- P2_SB_PA -Pass 1, Panel 2 count of Smallmouth Bass
- P3_SB_PA -Pass 2, Panel 1 count of Smallmouth Bass
- P4_SB_PA -Pass 2, Panel 2 count of Smallmouth Bass
- P1_SB_Count - Pass 1, Panel 1 presence / absence of Smallmouth Bass
- P2_SB_Count - Pass 1, Panel 2 presence / absence of Smallmouth Bass
- P3_SB_Count - Pass 2, Panel 1 presence / absence of Smallmouth Bass
- P4_SB_Count - Pass 2, Panel 2 presence / absence of Smallmouth Bass
- X - Easting coordinate of net site in meters; UTM zone 17N
- Y - Northing coordinate of net site in meters; UTM zone 17N
- P1_Average_Depth - average depth of first pass of site in meters
- P2_Average_Depth - average depth of second pass of site in meters
- AVG_Temp - average temperature of site in degrees Celsius
- Year - ID for identifying different years' survey sites (A = 2013 survey, B = 2019 survey, C = 2023 survey)
Bass_Temp_FLEN.csv: Called by histograms_and_Quantile_regresion.R; this data is the temperature at capture and fork length of individual bass caught in surveys from the multi-lake comparison dataset.
- PRJ_CD - Project code of each netting survey
- SPC - species code from database
- AVG_Temp - average temperature of capture in degrees Celsius
- AVG_tDepth - average depth of capture in meters
- FLENcm - fork length of Smallmouth bass in centimeters
Occu_depths.csv: Called by histograms_and_Quantile_regresion.R; this data is the depth at different modelled occupancy values as well as thermocline values for each lake.
- Lake - header column of lake name
- Cache - Depths of Occupancy and thermocline (in meters) for Cache Lake
- Canoe - Depths of Occupancy and thermocline (in meters) for Canoe Lake
- Cedar - Depths of Occupancy and thermocline (in meters) for Cedar Lake
- Happy Isle - Depths of Occupancy and thermocline (in meters) for Happy Isle Lake
- Lauder - Depths of Occupancy and thermocline (in meters) for Lauder Lake
- Ragged - Depths of Occupancy and thermocline (in meters) for Ragged Lake
- Rock - Depths of Occupancy and thermocline (in meters) for Rock Lake
- Smoke - Depths of Occupancy and thermocline (in meters) for Smoke Lake
- Tea - Depths of Occupancy and thermocline (in meters) for Tea Lake
- LOTR - Depths of Occupancy and thermocline (in meters) for Lake of Two Rivers
- Whitefish - Depths of Occupancy and thermocline (in meters) for Whitefish Lake
Temp_DO_data.csv: This data isn't called by the R codes but was included as it is the data used to predict site temperature, thermocline depth, and temperature at capture for individual fish.
- PRJ_CD - Project code of each temperature DO profile survey
- Location - Location ID of Temp/DO survey
- Lake - Lake Name
- Date - Date of Temp/DO survey (Blank values indicate no available date, but profiles were taken during time of survey).
- Depth - Depth of Temperature and DO measurement (in meters).
- Temp - Temperature of water (in degrees Celsius) at each depth
- DOConc - Dissolved oxygen concentration of water (in parts per million) at each depth
All lakes were surveyed using a depth stratified randomized netting survey with each depth stratum area based on the aerial coverage of a stratum.
The netting survey for each lake used a depth stratified random design with each lake partitioned into depth categories as follows: 1–3 m; 3-6 m; 6–12 m; 12–20 m; 20–x m; more. Net sites were allocated based on aerial percent of each stratum in each lake and therefore represents a fair sample of bottom habitat in the lake as reflected in depth. A net consisted of 8 panels of varying mesh size (38, 51, 64, 76, 89, 102, 114, and 127mm; totaling to 25m in length X 1.8 m in height). See article for availability of depth maps.
Each net set was comprised of two nets tied together in tandem (“strapped”) and separated by approximately 3 m. Netting locations were separated by a minimum of 250 m. Nets were set on bottom for one hour with each net location separated by a minimum of 250 m to reduce or eliminate gear competition. Employing 1-hour sets approached operational limits of field crews and was as close to an instantaneous point sample site estimate as could be achieved for habitat use analysis. Netting effort on all lakes occurred between 07:00 and 16:00. With each net lift, fish species were recorded, measured for length (FL, mm), and returned to the lake if alive. Each net set included covariates consisting of depth of set (m) and temperature at net depth (°C) derived from a spline model of a depth: temperature profile recorded in mid-survey for each lake. Our definition of metalimnion is the depth range of a temperature profile with the highest rate of change in temperature from warm surface waters to deep cold water. The thermocline is the single depth of greatest change in temperature with the smallest change in depth within the metalimnion (greatest Δ temp over smallest Δ depth; based on the minima of the first derivative of the spline function using function “deriv”). Dissolved oxygen (DO) was above 7 ppm in each lake at all depths so DO was not included as a habitat covariate in this study.