Regional ecosystem responses to environmental drivers in cold-water lakes evaluated using stable isotopes of salmonid fishes - Data files and R Code

This repository contains the data files and R script necessary to reproduce analyses, figures, and tables in Cobain et al. (2026). The use of these data and scripts should cite and reference the accompanying paper:Cobain, M. R. D., Amundsen, P.-A., Brabrand, Å., Byström, P., Davidsen, J. G., Gjelland, K. Ø., Hansen, J. E., Helland, I. P., Hesthagen, T., Johnsen, S. I., Jones, R. I., Kahilainen, K. K., Kangosjärvi, H., Kjærstad, G., Knudsen, R., Lakka, H.-K., Museth, J., Power, M., Rognerud, S. , Sánchez-Hernández, J., Sandlund, O. T., & Eloranta, A. P. (2026) Regional ecosystem responses to environmental drivers in cold-water lakes evaluated using stable isotopes of salmonid fishes. Limnology & Oceanography, 71(2), e70333. https://aslopubs.onlinelibrary.wiley.com/doi/10.1002/lno.70333 For full details on data compilations, see:Eloranta, A. P., Jones, R I., Amundsen, P.-A., Knudsen, R., Finstad, A. G., Byström, P., Karlsson, J., Helland, I. P., Gjelland, K. Ø., Johnsen, S. I., Museth, J., Hesthagen, T., Davidsen, J. G., Rognerud, S., & Brabrand, Å. (2022). Stable isotope data from Fennoscandian lakes collated in COLDWEBS project. V. 23.9.2022. https://doi.org/10.17011/jyx/dataset/83320Stable isotope data are compiled from a variety of projects conducted across Fennoscandia (see manuscript and supplementary information) and covers brown trout (Salmo trutta), Arctic charr (Salvelinus alpinus), and European whitefish (Coregonus lavaretus), and associated baseline sampling provided in two separate csv files. All necessary data files and model objects are provided in .RData format and an accompanying R script (R version 4.5.2) for reproducibility of analyses:CobainEtAl_MetaData.txt: README text file detailing contents of other filesCobainEtAl_Code.R - R script file for reproducing all analyses, figures and table valuesCobainEtAl_Fish_SI_Dataset.csv - Fish stable isotope data and associated environmental variablesCobainEtAl_Lake_Dataset.csv - Descriptive data of lakesCobainEtAl_Baselines_SI_Dataset.csv - Baseline stable isotope dataFennoscandian_Data.RData - Data file containing all datasets for reproductionCharr_GLMM.RData - MCMCglmm model object for Arctic charrTrout_GLMM.RData - MCMCglmm model object for brown troutManuscript Abstract:Diverse environmental drivers influence food web production flows, a key ecosystem function, yet their relative importance remains poorly known. We compiled thousands of bulk stable isotope measurements (carbon and nitrogen) of brown trout (Salmo trutta, n = 2854) and Arctic charr (Salvelinus alpinus, n = 3062) from 120 cold-water lakes across northern Europe, spanning 0.02 to 1090 km2 in size, to quantify the relative importance of nine potential drivers of energy and nutrient flows. Fish community type and individual body size matched the well-described ecologies of the two species: charr shifted from littoral to pelagic sources with interspecific competition, and trout opportunistically increased their trophic position with piscivorous prey availability. The anthropogenic impacts of water-level regulation and catchment modification were mirrored in the two species, resulting in decreased δ13C values, implying increased relative pelagic production in regulated lakes, and increased δ15N values, possibly due to increasing cross-boundary nutrient flows, respectively. Lake size and climatic drivers (summer precipitation and winter temperature) elicited strong species-specific changes in isotope signatures, suggesting that top-down ecological responses can dominate over ecosystem-wide changes in production flows within lake food webs. No isotopic trends were observed with catchment productivity or lake shape complexity at the regional scale, contrasting with insights from local scale studies. This spatial mismatch suggests that environmental drivers of ecosystem processes playing out at the regional scale cannot necessarily be extrapolated from localised studies. Substantial correlated random lake effects suggest that unexplained local baseline shifts are isotopically captured by these generalist fishes.Papers associated with contributing data: Eloranta, A. P., Kahilainen, K. K., Amundsen, P. A., Knudsen, R., Harrod, C., & Jones, R. I. (2015). Lake size and fish diversity determine resource use and trophic position of a top predator in high‐latitude lakes. Ecology and Evolution, 5(8), 1664-1675. https://doi.org/10.1002/ece3.1464 [data: https://doi.org/10.5061/dryad.sc59f]Lakka, H. K., Kangosjärvi, H., Savikko, A., Arnekleiv, J. V., & Qvenild, T. (2024). Arktisia lohikaloja loisivan sukasjuotikkaan (Acanthobdella peledina) esiintymisestä ja ekologiasta Suomen tunturijärvissä. Luonnon tutkija, 127(1). https://journal.fi/luonnontutkija/article/view/144888Qvenild, T., Fjeld, E., Fjellheim, A., Hammar, J., Hesthagen, T., & Lakka, H. K. (2021). Upper thermal threshold of Lepidurus arcticus (Branchiopoda, Notostraca) in lakes on the southern outreach of its distribution range. Fauna norvegica, 41. https://doi.org/10.5324/fn.v41i0.3832Thomas, S.M., Harrod, C., Hayden, B., Malinen, T. & Kahilainen, K.K. (2017). Ecological speciation in a generalist consumer expands the trophic niche of a dominant predator. Scientific Reports, 7, 8765. Https://doi.org/10.1038/s41598-017-08263-9Tore Qvenild, Jo Vegar Arnekleiv og Hanna-Kaisa Lakka. (2023). Børsteigla Acanthobdella peledina i Fennoskandia. Fauna, 76 (3–4), 106 -121