A flux-based model incorporating molecular diet data reveals the importance of feeding selectivity in shaping food web dynamics.
Supplementary dataset to: DNA metabarcoding highlights cyanobacteria as the main source of primary production in a pelagic food web model.
Andreas Novotny, Baptiste Serandour, Susanne Kortsch, Benoit Gauzens, Kinlan Mehdi Goulwen Jan, and Monika Winder 2023
Contact: Andreas Novotny, mail@andreasnovotny.se
Models that estimate rates of energy flow in complex food webs often fail to account for species-specific prey selectivity of diverse consumer guilds. While DNA metabarcoding is increasingly used for dietary studies, its application for food web modeling has been limited due to methodological biases. Here we used data from dietary metabarcoding studies of zooplankton to calculate prey selectivity indices and assess energy fluxes in a pelagic resource-consumer network. We show that food web dynamics are influenced by species prey selectivity and temporal match-mismatch in growth cycles and that cyanobacteria are the main source of primary production in the investigated coastal pelagic food web. The latter challenges the common assumption that cyanobacteria are not supporting food web productivity, a result that is increasingly relevant as global warming promotes cyanobacteria dominance. While this is the first time that DNA metabarcoding is used to quantify energy fluxes in a food web model, the approach presented here can easily be extended to other ecosystems.
This directory contains the code and the data sets needed to set up the model, and reproduce the results and figures of the manuscript. Vignette_and_Analysis.Rmd guide the data filtration, model setup, and the creation of figures.
All data needed for the analysis is found under /Data. Figures and tables will be saved in /Outputs and named after their manuscript counterparts.
The following data sets are found in the /Data directory:
Contains annotated DNA sequences of zooplankton and water samples. The dataframe data frameollowing columns:
OTU DNA sequence identified by Illumina sequencing and DADA2 inference.
Sample Unique zooplankton or water sample ID
SORTED_genus Microscopically identified genus of pooled zooplankton individuals. Alternatively Water for water samples.
SAMPLE_date Date of environmental sampling.
Domain Assigned clade of OTU sequence in the SILVA database.
Supergroup Assigned clade of OTU sequence in the SILVA database.
Phylum Assigned clade of OTU sequence in the SILVA database.
Class Assigned clade of OTU sequence in the SILVA database.
Order Assigned clade of OTU sequence in the SILVA database.
Family Assigned clade of OTU sequence in the SILVA database.
Genus Assigned clade of OTU sequence in the SILVA database.
Species Assigned clade of OTU sequence in the SILVA database.
STATION_ID Id of sampling location
Abundance Relative read abundance of OTU, relative to all OTUs per Sample
Phytoplankton observations downloaded from https://sharkweb.smhi.se/hamta-data/. See the database for metadata description.
Zooplankton observations downloaded from https://sharkweb.smhi.se/hamta-data/. See the database for metadata description.
Temperature observations downloaded from https://sharkweb.smhi.se/hamta-data/. See the database for metadata description.
Contains the major model output, and can be recreated in the Vignette.
The model has been tested with the following dependencies:
R version 4.2.1 (2022-06-23 Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.6.1
attached base packages: stats graphics grDevices utils datasets methods base
other attached packages: lubridate_1.8.0 circlize_0.4.15 svglite_2.1.0 igraph_1.3.5 xts_0.12.2 zoo_1.8-11 forcats_0.5.2 stringr_1.4.1 dplyr_1.0.10 purrr_0.3.5 readr_2.1.3 tidyr_1.2.1 tibble_3.1.8 ggplot2_3.3.6 tidyverse_1.3.2
loaded via a namespace (and not attached): lattice_0.20-45 assertthat_0.2.1 digest_0.6.29 utf8_1.2.2 R6_2.5.1 cellranger_1.1.0 backports_1.4.1 reprex_2.0.2 evaluate_0.17 httr_1.4.4 pillar_1.8.1 GlobalOptions_0.1.2 rlang_1.0.6 googlesheets4_1.0.1readxl_1.4.1 rstudioapi_0.14 jquerylib_0.1.4 car_3.1-0 rmarkdown_2.17 googledrive_2.0.0 munsell_0.5.0 broom_1.0.1 compiler_4.2.1 modelr_0.1.9 xfun_0.33 systemfonts_1.0.4 pkgconfig_2.0.3 shape_1.4.6 htmltools_0.5.3 tidyselect_1.2.0 fansi_1.0.3 crayon_1.5.2 tzdb_0.3.0 dbplyr_2.2.1 withr_2.5.0 ggpubr_0.4.0 grid_4.2.1 jsonlite_1.8.2 gtable_0.3.1 lifecycle_1.0.3 DBI_1.1.3 magrittr_2.0.3 scales_1.2.1 cachem_1.0.6 cli_3.4.1 stringi_1.7.8 carData_3.0-5 ggsignif_0.6.4 fs_1.5.2 bslib_0.4.0 xml2_1.3.3 ellipsis_0.3.2 generics_0.1.3 vctrs_0.4.2 tools_4.2.1 glue_1.6.2 hms_1.1.2 abind_1.4-5 fastmap_1.1.0 yaml_2.3.5 colorspace_2.0-3 gargle_1.2.1 rstatix_0.7.0 rvest_1.0.3 knitr_1.40 haven_2.5.1 sass_0.4.2