Lindsay E. Hansen Drew E. Eppehimer Maria C. Dzul Bridget R. Deemer Charles B. Yackulic 20260323 tabular digital data https://doi.org/10.5066/P13WENJO Lindsay E. Hansen Drew E. Eppehimer Maria C. Dzul Bridget R. Deemer Charles B. Yackulic 20250521 publication These are the data used for growth modeling in the paper ‘Growth of a threatened desert fish becomes resource dependent when released from temperature limitation in a regulated river’. Growth of ectotherms is strongly tied to temperature but can vary with other factors, especially food acquisition rates. River regulation is widespread globally and often significantly alters both environmental conditions (e.g., flow, turbidity, and temperature) and aquatic food webs, modifying the quality and quantity of resources available to consumers. To understand how food availability, water temperature, and other environmental factors are associated with fish growth (defined here as a change in length) in a large, regulated desert river, we fit Bayesian state-space growth models to data collected for federally listed humpback chub (Gila cypha; 'HBC') at two different reaches located ~240 river kilometers apart in the Colorado River within the Grand Canyon, Arizona, USA. Hypolimnetic water releases from Glen Canyon Dam, upriver of both reaches, results in colder summertime water temperatures than existed in the river pre-dam. Glen Canyon Dam also traps >95% of the sediment that previously moved through the Grand Canyon, as well as much of the allochthonous carbon. Data were collected as part of an ongoing native fish monitoring effort, involving mark-recapture of juvenile humpback chubs. Appropriate use of these data is in the associated state-space growth models, coded in the programming language R. 20120401 20221031 ground condition Complete None planned Grand Canyon National Park -113.9502 -111.6200 36.8100 35.5859 ISO 19115 Topic Category biota None humpback chub desert river fish gross primary productivity stream metabolism turbidity dam regulated river drought Grand Canyon Colorado River Common geographic areas Fish USGS Thesaurus turbidity droughts USGS Metadata Identifier USGS:682cedd5d4be021a0d6b7ce7 None Grand Canyon Arizona United States Colorado River No access constraints. Please see 'Distribution Information' for details. These data are marked with a Creative Common CC0 1.0 Universal License. These data are in the public domain and do not have any use constraints. Users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations. Lindsay E. Hansen US Geological Survey Fish Biologist mailing and physical

2255 N. Gemini Dr.

Flagstaff Arizona 86001 United States 949-616-9205 lhansen@usgs.gov Data analyzed in this study was collected by the U.S. Geological Survey Grand Canyon Monitoring and Research Center (GCMRC). Data collection was funded by the Bureau of Reclamation through the Glen Canyon Adaptive Management Program. Data used in this study will be made available in the USGS ScienceBase Catalog. Reported values represent monthly means based on available hourly data from USGS stream gages. Actual data matches with described details. We have checked for data duplication/omission. Covariate and measured biometric values fall within expected and reasonable ranges. Data represent occurrences at two locations: the Colorado River in western Grand Canyon (near Diamond Creek Confluence), and the Colorado River in eastern Grand Canyon (at the Little Colorado River Confluence or Bright Angel Creek Confluence). Gaps in measured covariate and biometric data were filled in via linear regression interpolation. U.S. Geological Survey 20240501 tabular digital data https://waterdata.usgs.gov/nwis Digital and/or Hardcopy 20120401 20221031 observed USGS Stream Gage Data Covariate data from USGS Stream Gages Bridget R. Deemer Charles B. Yackulic Robert O. Hall Michael J. Dodrill Ted A. Kennedy Jeffrey D. Muehlbauer David J. Topping Nicholas Voichick Michael D. Yard 20220625 publication Washington, DC PNAS Nexus 1 pgac094 Digital and/or Hardcopy 20120401 20221031 publication date GPP Estimates Gross primary productivity estimates Mark-recapture humpback chub data were obtained in the upriver reach between April 2012 and October 2022, and in the downriver reach between April 2017 and October 2022. Sampling trips were conducted in April-May, June-July, and September-October, with four January trips that ran between 2013-2016 (upriver reach only). These data represent a total of 36 sampling trips in the upriver reach and 18 sampling trips in the downriver reach, with no sampling in spring 2020. Fish were sampled using nighttime boat electrofishing (pulsed DC current, 15-20 amps, 200-300 volts) and un-baited hoop nets (6-mm nylon mesh, 50 - 60-cm diameter, 1-m long, single 10-cm throat) across the full 6-km river reach in both the upriver and the downriver reaches. Reaches were sampled in three full electrofishing passes over ten nights (before 2017) or six nights (2017 and after), each comprised of twenty-four 250-m sites on the left and right sides of the river, with a goal electrofishing time of 20 minutes per site. Each reach was divided into two sub-reaches separated into upstream sites and downstream sites (each representing half of the 6 km reach), which we sampled on alternate nights. We used six passes of 120 hoop nets set throughout the entire 6 km reach, set and checked diurnally at 24-hour intervals. During each trip, all captured humpback chub were measured for total length (length of a fish measured from the tip of the snout to the tip of the longer lobe of the caudal fin), scanned for a 134.2 kHz passive integrated transponder (PIT) tag, and all individuals larger than 80-mm (total length) were administered a unique PIT tag if they were previously unmarked, according to Grand Canyon fisheries research protocol. We fit our growth models to the period between initial mark and subsequent recapture for each individual fish to avoid over-representation of individuals. We used linear regression to populate total length measurements for individuals that were only measured to their fork length, then removed individuals that were missing both lengths, leaving a total of 5,464 and 1,836 individuals in the upriver and downriver reaches, respectively, available for use in our modeling. Compared to other native fishes in the system, humpback chub exhibit site fidelity and generally do not exhibit large migrations within the mainstem, although humpback chub frequently move between the upriver reach and the Little Colorado River tributary, and some individuals may exhibit transience and move longer distances. 20240501 We included the following environmental covariates in our humpback chub growth models: water temperature, turbidity exceedance threshold, gross primary productivity (hereafter GPP), mean monthly flow (i.e., discharge), and two indicators for specific flow regime experiments: a large volume ‘high flow’ experiment and a low, steady release ‘bug flow’ experiment. We obtained temperature, turbidity, and flow data from 6000 series Yellow Springs Instruments water quality sondes deployed at USGS stream gages deployed in the Colorado River. We used the gages in the mainstem river that were downriver of our two reaches: the gage upriver from the Bright Angel Creek confluence (54.9 river kilometers downstream from Lee’s Ferry (hereafter rkm), USGS Gage 09402500, U.S. Geological Survey 2024) was used for the upriver reach, and the gage upriver from the Diamond Creek confluence (rkm 140.2, USGS Gage 09404200, U.S. Geological Survey 2024) was used for the downriver reach data. Downriver gages were used to reflect the influence of major tributaries on the river habitat. Because primary productivity cannot be measured directly, and because oversaturation of dissolved oxygen in Grand Canyon precludes accurate calculation of net ecosystem production/ecosystem respiration, we model GPP estimates from a single station GPP model in the R package streamMetabolizer (Appling et al. 2018, model name b_np_oipp_tr_plrckm.stan) using canyon-shading estimates together with daily oxygen, flow, and temperature data to create daily GPP estimates (Deemer et al. 2022). We use estimates of GPP at the Little Colorado River confluence (rkm 38.3, USGS Gage 09383100, U.S. Geological Survey 2024) for the upriver reach and at the Diamond Creek confluence (USGS Gage 09404200) for the downriver reach. We include two covariates to represent flow conditions in the Grand Canyon: mean monthly flow (or “discharge”) and high flow experiments. Typically, mean outflows have fluctuated between 225 and 450 m3/s, based on season, water year inflows, and month-to-month changes in dam operations. We summarize the baseline flow information into a mean monthly flow covariate. We also include a high flow experiment covariate, with four events conducted during our study (maximum flows were 1262 m3/s in 2012, 1053 m3/s in 2013, 1085 m3/s in 2014, and 1042 m3/s in 2016). We assumed the effect of a high flow experiment persisted for three months following a similar assumption in other studies of fish in the system.We created indicator variables for the high flow experiment and bug flow experiment. In this approach, months during which these experimental flows occurred (and, in the case of the high flow experiment, for the subsequent two months) were assigned a ‘1’, and months without these effects were assigned a ‘0’. During our study, there were 12 months with a high flow experiment (plus three-month lag time) indicator and16 months with a bug flow experiment indicator. USGS Stream Gage Data GPP Estimates 20240501 Bright_Angel_Gage_enviro_covariates.csv Comma Separated Value (CSV) file containing data. Producer Defined Date This attribute (Date) represents the year and month for each corresponding monthly mean covariate column. Producer Defined The date column uses a yy-mmm format, where the numeric portion represents the last two digits of the year and the three-letter abbreviation represents the month. For example, 12-APR corresponds to April 2012, 13-JUN to June 2013. The numeric value is not a day of the month. Month This attribute (Month) represents the month interval for each covariate mean value. Producer Defined 1 127 Month Temp This attribute represents mean monthly temperature estimated from 15-minute data collected at a USGS mainstem stream gage at the Bright Angel Creek confluence. Producer Defined 8.077633543 21.83825448 degrees celsius TempQ This attribute represents mean monthly temperature estimated from 15-minute data collected at a USGS mainstem stream gage at the Bright Angel Creek confluence, raised to the power of 2 (quadratic). Producer Defined 65.3132681 476.9950683 degrees celsius Turb This attribute represents the proportion of days per month that mainstem turbidity was higher than 50 FNU at the USGS stream gage at Bright Angel Creek. Producer Defined 0.0 1.0 Proportion of days in a month with daily mean turbidity over 50 formazin nephelometric units GPP_BAC This attribute represents mean monthly gross primary productivity estimates generated based on dissolved oxygen data from the Bright Angel Creek USGS stream gage, plus local barometric pressure data and estimated light measurements. Producer Defined 0.470979969 5.309570191 g O2 m-2 d-1 mean_flow Mean monthly flow rate estimated from 15-minute data at the Bright Angel Creek USGS stream gage. Producer Defined 8172.379032 18037.60081 cubic feet per second sd_flow Mean monthly standard deviation in flow rate estimated from 15-minute data at the Bright Angel Creek USGS stream gage. Producer Defined 49.30631052 2370.89445 cubic feet per second HFE This attribute is an indicator for if an experimental high flow event occurred during the month, or if it is within 3 months of a high flow experiment (1 = occurrence, 0 = no occurrence). Producer Defined 0 1 Bug This attribute is an indicator for if a 'bug flow' (experimental steady, low volume flow) occurred during the month (1 = occurrence, 0 = no occurrence). Producer Defined 0 1 Biomass Estimates of humpback chub biomass based on abundance data. These data were used in preliminary model runs but not in final versions of our model. Producer Defined << empty cell >> No Data Producer defined 84427.92 956701 grams GPP_60 This attribute represents gross primary productivity estimates generated based on dissolved oxygen data from the 60 mile USGS stream gage, plus barometric pressure data from Page, Arizona and local light measurements. Producer Defined 0.288187906 9.128957545 g O2 m-2 d-1 Diamond_Gage_enviro_covariates.csv Comma Separated Value (CSV) file containing data. Producer Defined Date This attribute (Date) represents the year and month for each corresponding monthly mean covariate column. Producer Defined The date column uses a yy-mmm format, where the numeric portion represents the last two digits of the year and the three-letter abbreviation represents the month. For example, 12-APR corresponds to April 2012, 13-JUN to June 2013. The numeric value is not a day of the month. Month This attribute (Month) represents the month interval for each covariate mean value. Producer Defined 1 127 month Temp This attribute represents mean monthly temperature estimated from 15-minute data collected at a USGS mainstem stream gage at the Diamond Creek confluence. Producer Defined 8.360196393 24.05316866 degrees celsius TempQ This attribute represents mean monthly temperature estimated from 15-minute data collected at a USGS mainstem stream gage at the Diamond Creek confluence, raised to the power of 2 (quadratic). Producer Defined 70.38301662 578.6414803 degrees celsius Turb This attribute represents the proportion of days per month that mainstem turbidity was higher than 50 FNU at the USGS stream gage at Diamond Creek. Producer Defined 0.0 1.0 Proportion of days in a month with daily mean turbidity over 50 formazin nephelometric units GPP This attribute represents mean monthly gross primary productivity estimates generated based on dissolved oxygen data from the Diamond Creek USGS stream gage, plus local barometric pressure data and estimated light measurements. Producer Defined 0.264451552 3.117834603 g O2 m-2 d-1 mean_flow Mean monthly flow rate estimated from 15-minute data at the Diamond Creek USGS stream gage. Producer Defined 8841.624859 18491.05126 cubic feet per second sd_flow Mean monthly standard deviation in flow rate estimated from 15-minute data at the Bright Angel Creek USGS stream gage. Producer Defined << empty cell >> No Data Producer defined nan nan HFE This attribute is an indicator for if an experimental high flow event occurred during the month, or if it is within 3 months of a high flow experiment (1 = occurrence, 0 = no occurrence). Producer Defined 0 1 Bug This attribute is an indicator for if a 'bug flow' (experimental steady, low volume flow) occurred during the month (1 = occurrence, 0 = no occurrence). Producer Defined 0 1 HumpbackChub_east_wide.csv Comma Separated Value (CSV) file containing data. Producer Defined PITTAG This attribute (PITTAG) in the data table represents the unique PIT (Passive Integrated Transponder) tag number given to individual fish Producer Defined The attribute values represent unique identification for each tagged humpback chub in our study. Trip_ID.1 This attribute (Trip_ID.1) represents the unique sampling trip that a humpback chub was caught on for the first time. Producer Defined The attribute values represent the agency and launch date for research trips conducted by different agencies during the study. river_code.1 This attribute (River_Code) represents the name of the river or creek where each fish was captured Producer Defined COR Colorado River Producer defined start_rkm.1 This attribute represents river kilometer. River kilometer begins at Lee's Ferry. Producer Defined NA No Data Producer defined 26.76 131.53 kilometers RM.1 This attribute represents river mile. River mile begins at Lee's Ferry. Producer Defined 60.36 65.89 miles species_code.1 This attribute represents the species that corresponds with each PITTAG. Only humpback chub are represented in these data. Producer Defined HBC Humpback chub Producer defined total_length.1 This attribute represents the total length (measurement from tip of nose to tip of tail) on the first capture date Producer Defined 69.0 440.0 millimeters fork_length.1 This attribute represents the fork length (measurement from tip of nose to fork in the tail) on the first capture date. Producer Defined 12 398 millimeters start_datetime.1 This attribute represents the date and time of the first capture for each fish. Producer Defined The attribute values represent date of capture in the format mm/dd/yyyy h:mm. date.1 This attribute represents the date of the first capture for each fish. Producer Defined The attribute values represent date of capture in the format mm/dd/yyyy. converted_date.1 This attribute represents the first day of the month during which the first capture of a fish occurred. Producer Defined The attribute values represent date of capture in the format mm/dd/yyyy. month.1 This attribute (Month.1) represents the month interval of the first capture of a fish. Producer Defined 1 127 Trip_ID.2 This attribute (Trip_ID.2) represents the unique sampling trip that a humpback chub was caught on for the second time. Producer Defined The attribute values represent the agency and launch date for research trips conducted by different agencies during the study river_code.2 This attribute (River_Code) represents the name of the river or creek where each fish was captured during its second capture. Producer Defined COR Colorado River Producer defined start_rkm.2 This attribute represents river kilometer a fish was captured at during its second capture. River kilometer begins at Lee's Ferry. Producer Defined NA No Data Producer defined 26.599 131.84 kilometers RM.2 This attribute represents river mile a fish was captured at during its second capture. River mile begins at Lee's Ferry. Producer Defined 60.36 66.08 miles species_code.2 This attribute represents the species that corresponds with each PITTAG. Only humpback chub are represented in these data. Producer Defined HBC Humpback chub Producer defined total_length.2 This attribute represents the total length (measurement from tip of nose to tip of tail) on the second capture date Producer Defined 69.0 433.0 millimeters fork_length.2 This attribute represents the fork length (measurement from tip of nose to fork in the tail) on the second capture date. Producer Defined 49 482 millimeters start_datetime.2 This attribute represents the date and time of the second capture for each fish. Producer Defined The attribute values represent date of capture in the format mm/dd/yyyy h:mm. date.2 This attribute represents the date of the second capture for each fish. Producer Defined The attribute values represent date of capture in the format mm/dd/yyyy. converted_date.2 This attribute represents the first day of the month during which the second capture of a fish occurred. Producer Defined The attribute values represent date of capture in the format mm/dd/yyyy. month.2 This attribute represents the month interval of the second capture of a fish. Producer Defined 1 127 Delta_T This attribute represents that number of months in between the first and second capture of an individual fish. Producer Defined 0 118 Delta_T_Squared Number of months between the first and second capture raised to the second power. Producer Defined 0 13924 HumpbackChub_west_wide.csv Comma Separated Value (CSV) file containing data. Producer Defined PITTAG This attribute (PITTAG) in the data table represents the unique PIT (Passive Integrated Transponder) tag number given to individual fish Producer Defined The attribute values represent unique identification for each tagged humpback chub in our study. Trip_ID.1 This attribute (Trip_ID.1) represents the unique sampling trip that a humpback chub was caught on for the first time. Producer Defined The attribute values represent the agency and launch date for research trips conducted by different agencies during the study. river_code.1 This attribute (River_Code) represents the name of the river or creek where each fish was captured Producer Defined COR Colorado River Producer defined start_rkm.1 This attribute represents river kilometer. River kilometer begins at Lee's Ferry. Producer Defined 64.209 369.71 kilometers RM.1 This attribute represents river mile. River mile begins at Lee's Ferry. Producer Defined 210.47 213.89 miles species_code.1 This attribute represents the species that corresponds with each PITTAG. Only humpback chub are represented in these data. Producer Defined HBC Humpback chub Producer defined total_length.1 This attribute represents the total length (measurement from tip of nose to tip of tail) on the first capture date Producer Defined 80.0 369.0 millimeters fork_length.1 This attribute represents the fork length (measurement from tip of nose to fork in the tail) on the first capture date. Producer Defined 67 329 millimeters start_datetime.1 This attribute represents the date and time of the first capture for each fish. Producer Defined The attribute values represent date of capture in the format mm/dd/yyyy h:mm. date.1 This attribute represents the date of the first capture for each fish. Producer Defined The attribute values represent date of capture in the format mm/dd/yyyy. converted_date.1 This attribute represents the first day of the month during which the first capture of a fish occurred. Producer Defined The attribute values represent date of capture in the format mm/dd/yyyy. month.1 This attribute (Month.1) represents the month interval of the first capture of a fish. Producer Defined 67 127 Trip_ID.2 This attribute (Trip_ID.2) represents the unique sampling trip that a humpback chub was caught on for the second time. Producer Defined The attribute values represent the agency and launch date for research trips conducted by different agencies during the study river_code.2 This attribute (River_Code) represents the name of the river or creek where each fish was captured during its second capture. Producer Defined COR Colorado River Producer defined start_rkm.2 This attribute represents river kilometer a fish was captured at during its second capture. River kilometer begins at Lee's Ferry. Producer Defined 64.29 369.66 kilometers RM.2 This attribute represents river mile a fish was captured at during its second capture. River mile begins at Lee's Ferry. Producer Defined 210.51 213.86 miles species_code.2 This attribute represents the species that corresponds with each PITTAG. Only humpback chub are represented in these data. Producer Defined HBC Humpback chub Producer defined total_length.2 This attribute represents the total length (measurement from tip of nose to tip of tail) on the second capture date Producer Defined 76.0 374.0 millimeters fork_length.2 This attribute represents the fork length (measurement from tip of nose to fork in the tail) on the second capture date. Producer Defined 69 337 millimeters start_datetime.2 This attribute represents the date and time of the second capture for each fish. Producer Defined The attribute values represent date of capture in the format mm/dd/yyyy h:mm. date.2 This attribute represents the date of the second capture for each fish. Producer Defined The attribute values represent date of capture in the format mm/dd/yyyy. converted_date.2 This attribute represents the first day of the month during which the second capture of a fish occurred. Producer Defined The attribute values represent date of capture in the format mm/dd/yyyy. month.2 This attribute represents the month interval of the second capture of a fish. Producer Defined 67 127 Delta_T This attribute represents that number of months in between the first and second capture of an individual fish. Producer Defined 0 55 Delta_T_Squared Number of months between the first and second capture raised to the second power. Producer Defined 0 3025 U.S. Geological Survey - ScienceBase mailing address

Denver Federal Center

Building 810

Mail Stop 302

Denver CO 80225 1-888-275-8747 sciencebase@usgs.gov Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data for other purposes, nor on all computer systems, nor shall the act of distribution constitute any such warranty. Digital Data https://doi.org/10.5066/P13WENJO None 20260323 Lindsay E. Hansen mailing and physical

2255 N. Gemini Dr.

Flagstaff Arizona 86001 United States 949-616-9205 lhansen@usgs.gov FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata FGDC-STD-001.1-1999