Data from: Experimentally induced low flows indicate climate change may shrink trophic niches of mountain-stream predators
Data files
Jul 23, 2025 version files 10.27 MB
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Channels_community_abundance.csv
102.44 KB
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Channels_discharge.csv
1.60 MB
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Channels_dissolved_oxygen.csv
1.09 MB
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Channels_temperature.csv
48.58 KB
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Convict_Creek_discharge.txt
164.88 KB
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Cowell_et_al_2025_clean_code.Rmd
130.07 KB
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Individual_Perlidae_Info.csv
1.99 KB
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Isotopic_niche_areas_modes.csv
458 B
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Isotopic_niche_areas_posteriors.csv
1.98 MB
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Isotopic_values.csv
36.11 KB
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Perlidae_gut_NMDS.csv
1.59 KB
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Prey_Info_per_Individual.csv
11.39 KB
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README.md
15.06 KB
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Responses_by_feeding_group_modes.csv
1.31 KB
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Responses_by_feeding_group_posteriors.csv
2.60 MB
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Trophic_pathways_modes.csv
1.44 KB
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Trophic_pathways_posteriors.csv
2.49 MB
Abstract
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.
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.
The code used to perform the analysis can be found in the R Markdwon file named Cowell_et_al_2025_clean_code.Rmd.
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 > 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.