README

Metabolizable energy and biomass of plants consumed by caribou (Rangifer tarandus) in tundra communities of northern Alaska and deer (Odocoileus spp.) in forests and grasslands of Washington, United State of America

knitr::opts_chunk$set(echo = TRUE)

Abstract

A ubiquitous interaction operates at the base of food webs in many terrestrial ecosystems of the world, creating the foundation for bottom-up regulation of consumers. This interaction plays out as follows. Populations of herbivores deplete plant biomass by foraging. Increasing herbivore population size intensifies this depletion, which in turn, creates a negative feedback regulating herbivore population growth. Large herbivores and the plants they consume offer a useful system for studying this interaction because populations of large herbivores are often regulated by density dependence, defined as the reduction in the per-capita growth rate that occurs as populations grow. Diminished body mass of individuals has been repeatedly observed in high density populations, implicating plant-mediated, diminished nutrition as the primary cause of density dependence. However, there is no general explanation for why these nutritional deficiencies occur. The data deposited here were used to demonstrate a new model of the feedbacks from plant biomass to herbivores The model shows how reduced nutrition of herbivores can result from increased dilution of metabolizable energy in the plant tissue they consume as populations grow even when a large fraction of the consumable plant biomass remains uneaten. This result provides a tidy, mechanistic explanation for bottom-up control of population dynamics of primary consumers in a green world.

Description of the data

The data are found in the file me_biomass_for_repository.csv. The file contains 37597 records. Some of these records were used to produce the data summaries (means, standard errors, etc) reported in Wagoner et al. (2013); Ulappa et al. (2020); and Hull et al. (2020). The file also contains records from Spalinger and Welker unpublished. None of the data in me_biomass_for_repository.csv have been published previously. They were obtained directly from the authors.

Usage notes

Each record contains the following fields:

1. Veg_type specifies the plant community, management treatment (if these were imposed), and season.
2. Species is a code for the plant type, a combination of taxonomic information and plant part.
3. Site is a code for a spatial replicate within Veg_type. Sites also contain plot level replicates in the Splainger and Welker data.
4. KgDM_Ha is the biomass of the Species at a site in kilograms of dry matter per hectare. The value for this field is zero if the species was not present.
5. ME is the site or plot mean metabolizable energy content of the Species field in kJ per gram dry matter. It is estimated as 18.392 kJ gross energy per gram dry matter \times the coefficient of dry matter digestibility \times estimated proportion of digested energy that is metabolized (0.82, Robbins (1983)). Dry matter digestibility was estimated using the summative equations of Robbins (1983) and Robbins et al. (1995).
6. ME.SD is the standard deviation of the distribution of the sample mean ME.
7. presence is an indicator variable with value one if a Species is present at a site and zero otherwise.
8. consumer_species is the common name of the large herbivore in the study providing the data on metabolizable energy concentration.
9. Veg_type_consumer_species is a concatenation of Veg_type and consumer_species.
10. Source is code for the three formats of data that were assembled into the common format of me_biomass_for_repository.csv.
11. cite is the citation that contains summaries of the data. The data have never been previously published
12. body_mass is the estimated mean body mass of consumer_species

Missing data

Missing data are indicated by NA. NA appears in all fields except presence when a Species was absent from a site.

Location

United States of America, Alaska, Northern Alaska

United States of America, Washington

Sharing/Access information

Links to other publicly accessible locations of the data: None

Code/Software

All of the results reported in the paper can be reproduced by running the R script, A_WorkFlow.R. Scripts in this workflow are found in this repository.
Required packages are:
[1] "cowplot" "latex2exp" "LaplacesDemon"
[4] "doParallel" "iterators" "foreach"[7] "dclone" "Matrix" "parallel"[10] "MCMCvis" "rjags" "coda"[13] "readxl" "forcats" "stringr"[16] "dplyr" "purrr" "readr"[19] "tidyr" "tibble" "ggplot2"[22] "tidyverse" "stats" "graphics"[25] "grDevices" "utils" "datasets"[28] "methods" "base"

Literature cited

S. J. Wagoner, L. A. Shipley, R. C. Cook, and L. Hardesty. Spring cattle grazing and mule deer nutrition in a bluebunch wheatgrass community. Journal of Wildlife Management, 77(5):897907, 2013.
I. T. Hull, L. A. Shipley, S. L. Berry, C. Loggers, and T. R. Johnson. Effects of fuel reduction timber harvests on forage resources for deer in northeastern Washington. Forest Ecology and Management, 458, 2020.
C. T. Robbins, Wildlife feeding and nutrition. Academic Press, New York. 336pp., 1983.
C. T. Robbins, D. E. Spalinger, and W. Van Hoven. Adaptation of ruminants to browse and grass diets: Are anatomical-based browser-grazer interpretations valid? Oecologia, 103(2):208213, 1995.
A. C. Ulappa, L. A. Shipley, R. C. Cook, J. G. Cook, and M. E. Swanson. Silvicultural herbicides and forest succession influence understory vegetation and nutritional ecology of black-tailed deer in managed forests. Forest Ecology and Management, 470, 2020.