DOI: 10.5061/dryad.t4b8gtj61
title: 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 States of America

description: 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 fit 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: Methods and sampling design are described in:
 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):897–907, 2013.
 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.
 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. N. T. Hobbs, in press. A general, resource-based
 explanation for density dependence in populations of large herbivores.
 Ecological Monographs.
description: R code is included in the repository.
description: *** 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 --- ```{r setup, include=FALSE} 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.