DOI: 10.5061/dryad.jdfn2z3pj
title: Data from: Experimentally induced low flows indicate climate change may shrink trophic niches of mountain-stream predators

description: Climate change is projected to decrease snowpack and advance snowmelt in
 mountain ranges globally—including in California’s Sierra Nevada, where
 streamflow in snow-dominated rivers is expected to peak up to 2 mo earlier
 and remain in baseflow conditions for extended periods of time. Predators
 may be particularly sensitive to low flows, owing to their larger body
 sizes, higher metabolic demands, and longer lifespans. Experimental
 manipulations can improve understanding of how these predators, and the
 food webs they are embedded in, are likely to respond to future snow
 droughts. We experimentally examined how the trophic ecology of predatory
 macroinvertebrates responds to the extended low flows expected under
 climate change. We manipulated flow regimes in outdoor, large-scale
 artificial streams in the Sierra Nevada to produce a current flow regime
 and 2 future regimes that advanced low-flow conditions by 3 and 6 wk,
 respectively. We performed stable isotope analysis on the
 macroinvertebrate community, focusing on 3 predatory taxa (Perlidae
 stoneflies [Plecoptera], Rhyacophila caddisflies [Trichoptera], and
 Turbellaria flatworms), as well as nonpredatory invertebrates (n = 310
 samples across 8 taxa). We examined the isotopic signals (δ15N and δ13C)
 of the predators and quantified how their isotopic niche areas, trophic
 positions, and energy sources varied seasonally and following low-flow
 treatments. We also performed gut content analysis of Perlidae, and we
 compared the predator assemblage response to that of other feeding groups.
 We found that low flows compressed the trophic niches of predatory taxa,
 with variable responses across taxa and treatments. Perlidae stoneflies
 had fewer prey items in their guts under extended low flows. Lastly, only
 the predator feeding group was severely affected by the most extreme
 low-flow treatment (62% niche compression). Our experiment suggests that
 climate-driven low flows will likely shift invertebrate predators’ diets,
 and thus foodweb structure, in Sierra Nevada streams. However, response
 diversity among taxa illustrates the need to preserve diverse alpine
 stream assemblages in the face of future hydroclimates.
description: --- title: "Cowell et al. 2025 ReadMe" date:
 "2024-11-11" ------------------ This README contains
 descriptions of all datasets used in the following paper: Cowell, A., K.
 Leathers, G. de Mendoza, G. Dwyer, D. Herbst, and A. Ruhi. 2025.
 Experimentally induced low flows indicate climate change may shrink
 trophic niches of mountain-stream predators. *Freshwater Science* 44.
 [https://doi.org/10.1086/737386](https://doi.org/10.1086/737386). The code
 used to perform the analysis can be found in the R Markdwon file named
 Cowell_et_al_2025_clean_code.Rmd. # Input data ### Isotopic_values.csv
 Dataset description: This dataset included sample identification and
 stable isotope analysis results. * Code: Numerical identifier of each
 sample. The first value identifies the visit number, the second digit
 identifies the channel, the third digit identifies the taxa, and the
 fourth digit identifies the replicate, generally 1-3. * Visit_number:
 Numerical identifier of the visit of 1-3 (see manuscript for associated
 dates and corresponding treatments). Extracted from the Code variable. *
 Visit_name: Month of visit. Derived from the Visit_number variable. *
 Channel: Numerical identifier of the experimental channel at SNARL where
 the sample was collected (channels #1-9). See the manuscript (Fig. 2A) for
 a diagram of which treatments each channel experienced. Dervied from the
 Code variable. * Treatment_name: Name of the treatment applied to the
 channel where the sample was collected. Derived from the Treatment_number
 variable. * Treatment_number: Numerical identifier for the treatment
 applied to the channel. Extracted from the Channel variable. See the
 manuscript for a detailed explanation of which treatments were applied to
 which channels * Taxa_number: Numerical identifier of each taxon sampled
 For the focal species: 3 - Perlidae, 8 - Turbellaria, 12 -
 Rhyacophilidae/Rhyacophila. Extracted from the Code variable. * Taxa_name:
 Name of the taxa sampled. Identified from the Taxa_number variable.
 Includes both focal predators and other taxa within the community. Dervied
 from the Taxa_number variable. * d15N: Isotopic ratio of nitrogen in
 permil (‰), provided by analysis done at Center for Stable Isotope
 Biogeochemistry at the University of California, Berkeley. See manuscript
 for more detail. * d13C: Stable isotopic ratio of carbon in permil (‰),
 provided by analysis done at Center for Stable Isotope Biogeochemistry at
 the University of California, Berkeley. See manuscript for more detail. *
 Treatment_easy: Derived from the Treatment_name and Visit_number. All
 samples collected in May/June (i.e., before any treatment) are grouped
 together as 'peak runoff'. These are the treatments under which
 the samples are analyzed, as described in the manuscript. ###
 Convict_Creek_discharge.txt Dataset description: This dataset includes the
 historical flow regime of Convict Creek, which was used to establish the
 flow regime of the 'current' treatment in the experiment. *
 agency_cd: Organization that collected the data- in this case, the U.S.
 Geological Survey (USGS). * site_no: Unique site identifier. All values
 are 10265200, corresponding to the USGS gauge on Convict Creek. *
 datetime: Date when the discharge measurement was taken, formatted as
 year-month-day. Discharge was recorded daily from 1960 to 1974. *
 7385_00060_00003: Mean daily discharge, measured in cubic feet per second
 (cfs). The variable name follows the format TS_parameter_statistic, where
 the parameter is discharge, the unit is cfs, and the statistic is the
 mean. * 7385_00060_00003_cd: Data-value qualification code from the USGS.
 All entries are 'A', which means "Approved for publication
 - processing and review completed." ### Channels_discharge.csv
 Dataset description: This dataset includes the discharge of each channel,
 averaged for each day by treatment. Discharge was calculated from raw
 water level and velocity measurements transformed using a rating curve for
 each channel. Water level was measured every 5 min throughout the
 experiment with Hobo loggers and water velocity was measured with a
 current meter 17 to 26 times throughout the experiment. * date: Date of
 measurement, in the format month/day/year. * Treatment: The treatment
 applied to the channel; T1 = 6-week-early, T2 = three-week early, and CC =
 current treatment, as described in Methods. * meanQ: Mean daily discharge,
 measured in L/s, averaged over all channels in a given treatment,
 calculated with Discharge_Av_Chan. * sd: Standard deviation of the daily
 discharge, measured in L/s. * lower: Low range of discharge, calculated as
 meanQ - sd, measured in L/s. * upper: High range of discharge, calculated
 as meanQ + sd, measured in L/s. ### Channels_temperature.csv Dataset
 description: This dataset includes daily maximum water temperatures of the
 nine channels at SNARL. Water temperature was measured every 5 min
 throughout the experiment with Hobo loggers. * day: Date of measurement,
 in the format month/day/year. * Channel: Channel number at SNARL where the
 sample was collected. * Temp_Max_Chan: Maximum daily water temperature in
 a channel in degrees Celsius (C). NA indicate temperatures were not able
 to be measured at that time. * Treatment: The treatment of the channels;
 T1 = 6-week-early, T2 = three-week early, and CC = current treatment, as
 described in Methods. * mean: Average daily water temperature, averaged
 over all channels in a given treatment, calculated from Temp_Max_Chen, in
 degrees C. * sd: Standard deviation of average daily water temperature,
 averaged over all channels in a given treatment, in degrees C. ###
 Channels_dissolved_oxygen.csv Dataset description: This dataset includes
 the dissolved oxygen of each channel, averaged for each day by treatment.
 Dissolved oxygen was measured every 5 min throughout the experiment with
 Hobo loggers. * day: Date of measurement, in the format month/day/year. *
 Treatment: The treatment of the channels; T1 = 6-week-early, T2 =
 three-week early, and CC = current treatment, as described in Methods. *
 DO_av_trt_d: The minimum dissolved oxygen across channels for that
 treatment and day, measured in mg/L. * DO_min_trt_d: The minimum dissolved
 oxygen across channels for that treatment and day, measured in mg/L. *
 Date: Date of measurement, in the format month/day/year hour:minute:second
 AM/PM. ### Channels_community_abundance.csv Dataset description: This
 dataset contains the abundance and size of all taxa in the community
 throughout the experiment. Macroinvertebrates were sampled using a Surber
 sampler. Only samples from channels assigned to the current or
 six-week-early treatments were reported. * Sample: The visit when the
 sample was collected, # 1-6 (see manuscript for associated dates and
 corresponding treatments). * Treatment: The treatment of the channels;
 Advance = 6-week-early, Current = current treatment, as described in
 Methods. * Lowest: The lowest taxonomic identification possible for the
 individual, typically genus. * Channel: Channel number at SNARL where the
 sample was collected. * Replicate: The number of the replicate of samples
 taken for that Treatment, Channel, and Date. * Av_size_mm: The average
 size, in millimeters (mm), of individuals of a given taxa in a sample. If
 n &gt; 0, NA means we were unable to measure the full length of the
 individual, usually because it was not complete. If n = 0, NA means there
 were no individuals in the sample to measure. * n: The number of
 individuals of a given taxa in a sample. NA means there were no
 indiviudals in that sample. * Date: Date of sample, in the format
 month/day/year. * Abundance: The number of individuals of a given taxa in
 the community for that sampling date/period. ###
 Individual_Perlidae_Info.csv Dataset description: This dataset contains
 description of each individual Perlidae in the gut content analysis, as
 well as summary details of its gut contents. * Code_Lowest: Numerical
 identifier of each sample. The first value identifies the sample or visit
 number, the second digit identifies the channel, the third digit
 identifies the Perlidae genus, and the fourth digit identifies the
 replicate, generally 1-3. * Lowest_ID: The genus of the Perlidae
 individual, either Doroneuria or Calineuria. * Body_Length_mm: The size,
 in millimeters (mm), of the individual. NA/na signify the body was not
 complete, i.e., missing some part of it, but complete enough for
 identification with a complete gut. * Magnification: The magnification of
 the lenses on the microscope when measuring the individual. * Gut_Empty:
 Yes or no whether the gut of an individual contained any organic matter. *
 Presence_Animal: Yes or no whether the gut of an individual contained any
 portion of a macroinvertebrate or other organism. * Presence_Plant_Fungi:
 Yes or no whether the gut of an individual contained any plant or fungal
 matter. ### Prey_Info_per_Individual.csv Dataset description: This dataset
 contains information each prey item found within the gut contents of each
 individual Perlidae. * Code_Lowest: Numerical identifier of the individual
 that the prey item was found inside of. The first value identifies the
 sample or visit number, the second digit identifies the channel, the third
 digit identifies the Perlidae genus, and the fourth digit identifies the
 replicate, generally 1-3. * Prey_Item: Taxon grouping of prey items,
 typically either the order or family of macroinvertebrate prey items. Also
 includes groups for plants and unknown organisms. * Lowest_ID: The lowest
 taxonomic identification possible for the prey item. * Length_mm: The
 size, in millimeters (mm), of the prey item. NA/na signify the body was
 not complete, i.e., missing some part of it, but complete enough for
 identification. * Notes: Miscellaneous notes of sample processing for
 record-keeping purposes. Empty cells indicate no notes were necessary. *
 Notes2: Additional miscellaneous notes. Empty cells indicate no notes were
 necessary. ### Perlidae_gut_NMDS.csv Dataset description: This dataset
 contains the mean gut contents (as abundance) of different taxamoic groups
 (generally genus) for Perlidae individuals. In all columns named after a
 taxon, an empty cell indicates no abundance of that taxa within the gut of
 that Perlidae individual. * Code_Lowest: Numerical identifier of each
 individual Perlidae. The first value identifies the sample or visit
 number, the second digit identifies the channel, the third digit
 identifies the Perlidae genus, and the fourth digit identifies the
 replicate, generally 1-3. * Each column in the range 'Ameletus'
 to 'Wormaldia' reflects the abundance of the taxa named by the
 column. The taxa represent mostly genera, and range from orders to
 subgenera. Some columns contain the abundance for mulitple genera,
 indicated by a dash between the taxa names. The 'unknown animal'
 column The abundance of prey items that we were confident were organisms,
 and not plant material or sediment, but were unable to identify to any
 taxonimc group. Empty cells indicate there were no individuals of that
 taxa in the gut contents. --- # Output files Files were outputs of all
 Bayesian analyses are saved, named after the Methods subheading. The
 Bayesian model can produce slightly different results due to the
 stochastic nature of the MCMC sampling process. For reproducibility, we
 have saved the specific model outputs used in the manuscript. If these are
 loaded into the R Markdown file and the code is run as provided, the
 results should match those reported in the manuscript. If you rerun the
 models independently, you may observe minor variation in the outputs,
 particularly in the decimal places of summary statistics such as the mode
 and credible intervals. ### Isotopic_niche_areas_modes.csv Dataset
 description: This dataset contains the summary statistics of the SIBER
 model used to calculate the isotopic niche area, or SEAb, of each predator
 in each treatment. * mode: The mode of the posterior distributions of
 isotopic niche area, or SEAb, for a given predator in a given treatment,
 measured in permil squared (‰^2). * Treatment: The treatment of the
 sample. * Taxa: The focal predatory taxa. * lower: The lower 95% credible
 interval of the SEAb, measured in ‰^2. * upper: The upper 95% credible
 interval of the SEAb, measured in ‰^2. ###
 Isotopic_niche_areas_posteriors.csv Dataset description: This dataset
 contains the full posterior distributions of the SIBER model used to
 calculate the isotopic niche area, or SEAb, of each predator in each
 treatment. * Treatment: The treatment of the samples. * Taxa: The focal
 predatory taxa. * area: The isotopic niche area, or SEAb, measured in
 permil squared (‰^2). ### Trophic_pathways_modes.csv Dataset description:
 This dataset contains the summary statistics of the simmr model used to
 calculate the dietary proportion of algal-derived energy of each predator
 in each treatment. * Predator: The focal predatory taxa. * Treatment: The
 treatment of the samples. * Source: The taxa used to represent algal- or
 detrital-derived energy, filtered only to Heptageniidae for algal-derived
 energy. * Proportion: The mode of the posterior distribution for the
 dietary proportion, between 0 and 1. * SD: The standard deviation of the
 posterior distribution for the dietary proportion. * LowerCI: The lower
 95% credible interval of the dietary proportion, between 0 and 1. *
 UpperCI: The upper 95% credible interval of the dietary proportion,
 between 0 and 1. ### Trophic_pathways_posteriors.csv Dataset description:
 This dataset contains the full posterior distributions of the simmr model
 used to calculate the dietary proportion of algal-derived energy of each
 predator in each treatment. * Proportion: The dietary proportion, between
 0 and 1, of algal-derived energy for a given predator in a given
 treatment. * Treatment: The treatment of the samples. * Source: The taxa
 used to represent algal- or detrital-derived energy, here only
 Heptageniidae. * Predator: The focal predatory taxa. ###
 Responses_by_feeding_group_modes.csv Dataset description: This dataset
 contains the summary statistics of the SIBER model used to calculate the
 isotopic niche area, or SEAb, of each feeding group in each treatment. *
 mode: The mode of the posterior distributions of isotopic niche area, or
 SEAb, for a given group in a given treatment, measured in permil squared
 (‰^2). * Treatment: The treatment of the samples. * Group: The feeding
 groupas described in Methods. * lower: The lower 95% credible interval of
 the SEAb, measured in ‰^2. * upper: The upper 95% credible interval of the
 SEAb, measured in ‰^2. ### Responses_by_feeding_group_posteriors.csv
 Dataset description: This dataset contains the full posterior distribution
 of the SIBER model used to calculate the isotopic niche area, or SEAb, of
 each feeding group in each treatment. * Treatment: The treatment of the
 sample. * Group: The feeding group as described in Methods. * area: The
 isotopic niche area, or SEAb, measured in ‰^2.