DOI: 10.5061/dryad.mkkwh70vv
title: Multiple dimensions of dietary diversity in large mammalian herbivores

description: Theory predicts that trophic specialization (i.e., low dietary diversity)
 should make consumer populations sensitive to environmental disturbances,
 yet diagnosing specialists is complicated both by the difficulty of
 precisely quantifying diet composition and by definitional ambiguity—what
 makes a diet ‘diverse’? We sought to characterize the relationship between
 taxonomic dietary diversity (TDD) and phylogenetic dietary diversity (PDD)
 in a species-rich community of large mammalian herbivores in semi-arid
 East African savanna. We hypothesized that TDD and PDD would be positively
 correlated within and among species, because taxonomically diverse diets
 are likely to include plants from many lineages. By using DNA
 metabarcoding to analyze 1,281 fecal samples collected across multiple
 seasons, we compiled high-resolution diet profiles for 25 sympatric
 large-herbivore species. For each of these populations, we calculated TDD
 and PDD with reference to a DNA reference library for local plants.
 Contrary to our hypothesis, measures of TDD and PDD were either
 uncorrelated or negatively correlated with each other. Thus, these metrics
 reflect distinct dimensions of dietary specialization both within and
 among species. In general, grazers and ruminants exhibited greater TDD,
 but lower PDD, than did browsers and non-ruminants. We found significant
 seasonal variation in TDD and/or PDD for all but four species (Grevy’s
 zebra, buffalo, elephant, Grant’s gazelle), but the relationship between
 TDD and PDD was consistent across seasons for all but one of the 12
 best-sampled species (plains zebra). In this large-herbivore assemblage,
 taxonomic generalists can be phylogenetic specialists, and vice
 versa. These two dimensions of dietary diversity suggest contrasting
 implications for efforts to predict how species will respond to climate
 change and other environmental perturbations. For example, network models
 predict that populations with high TDD but low PDD should be insensitive
 to phylogenetically ‘random’ losses of food species, yet highly sensitive
 to environmental changes that locally disadvantage entire plant
 lineages—such as changing rainfall patterns, altered fire regimes, and
 woody encroachment, all of which influence the relative abundance of the
 grass lineage (Poaceae) relative to trees and shrubs in ecosystems
 worldwide.
description: The data and scripts contained within the zip file are organized
 into three subdirectories.    The
 subdirectory titled 'MammalInfoAndDietProfiles' contains 5 input
 data used for diet analyses:  1. The file
 SpListForTree.csv contains information on mammalian species identifiers,
 the names used in the megaphylogeny cited in the main text, the body mass
 (g) extracted from the sources listed (Bmsource), digestive
 morphophysiology (ruminant or non-ruminant) and the domestication status
 (domesticated or wild). 
 2. otutable_compositeprofile.csv contains composite diet profiles
 generated from data within the file otutable_rarefiedsamples.csv in
 order to enable species-level analyses in this paper.
   The subdirectory titled
 'Phylogeny' contains 5 input files used to construct and analyze
 the dietary plant phylogeny: 1. RaxmlScript.txt is the
 code used to run RAXML with all input files described below.
 2. metabarcodeP6alignment.phy represents the alignment of the
 trnL-P6 sequences. 3. metabarcodeP6alignment_INDEL.phy
 is a modification of the trnL-P6 alignment that codes for INDELs as a 5th
 state for analysis in RAXML. 4. constraint_tree_bladj
 represents the constraint tree used to define family-level relationships
 among taxa in the phylogenetic analysis.
 5. 20190918_RAxMLbladj is the output of the RAXML analysis, with
 branchlengths adjusted to represent time before present using BladJ and
 fossil calibration dates as described in the main text.
   The subdirectory titled
 'VegetationAvailability' contains 1 input file used to analyze
 vegetation availability:
 1. VertVeg_Master_Vv326_20171009.csv represents