DOI: 10.5061/dryad.2fg10
title: Data from: DNA metabarcoding illuminates dietary niche partitioning by African large herbivores

description: Niche partitioning facilitates species coexistence in a world of limited
 resources, thereby enriching biodiversity. For decades, biologists have
 sought to understand how diverse assemblages of large mammalian herbivores
 (LMH) partition food resources. Several complementary mechanisms have been
 identified, including differential consumption of grasses versus
 nongrasses and spatiotemporal stratification in use of different parts of
 the same plant. However, the extent to which LMH partition food-plant
 species is largely unknown because comprehensive species-level
 identification is prohibitively difficult with traditional methods. We
 used DNA metabarcoding to quantify diet breadth, composition, and overlap
 for seven abundant LMH species (six wild, one domestic) in semiarid
 African savanna. These species ranged from almost-exclusive grazers to
 almost-exclusive browsers: Grass consumption inferred from mean sequence
 relative read abundance (RRA) ranged from &gt;99% (plains zebra) to
 &lt;1% (dik-dik). Grass RRA was highly correlated with isotopic
 estimates of % grass consumption, indicating that RRA conveys reliable
 quantitative information about consumption. Dietary overlap was greatest
 between species that were similar in body size and proportional grass
 consumption. Nonetheless, diet composition differed between all
 species—even pairs of grazers matched in size, digestive physiology, and
 location—and dietary similarity was sometimes greater across grazing and
 browsing guilds than within them. Such taxonomically fine-grained diet
 partitioning suggests that coarse trophic categorizations may generate
 misleading conclusions about competition and coexistence in LMH
 assemblages, and that LMH diversity may be more tightly linked to plant
 diversity than is currently recognized.
description: Representation of
 trnL-P6 metabarcode sequences across samplesA matrix of samples by
 sequences reporting the count of sequence reads for each trnL-P6 sequence
 in each sample Column names refer to the sequence identities in the
 Supporting Information Appendix Table S3, where taxonomic information
 about each sequence is reported.P6_readcountclean.txtRepresentation of ITSpoa metabarcode sequences across samplesA matrix of samples by sequences reporting the count of sequence reads for each ITSpoa sequence (i.e., Poaceae-specific ITS marker) in each sample. Column names refer to the sequence identities in the Supporting Information Appendix Table S7, where taxonomic information about each sequence is reported.ITSpoa_readcountclean.txtRepresentation of ITSast metabarcode sequences across samplesA matrix of samples by sequences reporting the count of sequence reads for each ITSast sequence (i.e., Asteraceae-specific ITS marker) in each sample. Column names refer to the sequence identities in the Supporting Information Appendix Table S7, where taxonomic information about each sequence is reported.ITSast_readcountclean.txtRepresentation of ITScyp metabarcode sequences across samplesA matrix of samples by sequences reporting the count of sequence reads for each ITScyp sequence (i.e., Cyperaceae-specific ITS marker) in each sample. Column names refer to the sequence identities in the Supporting Information Appendix Table S7, where taxonomic information about each sequence is reported.ITScyp_readcountclean.txtDietary DNA metabarcode sequences in fasta formatAll DNA metabarcode sequences in the final dataset are given in fasta format. Each sequence identifier corresponds to a sequence ID listed in the Supporting Information Appendix Table S3 (for trnL-P6 sequences) or Table S7 (for family-specific ITS markers; poa=Poaceae, ast=Asteraceae, and cyp=Cyperaceae)metabarcode_sequences.fastaLocal plant DNA reference library informationThis file contains taxonomic information on the 1369 plant vouchers collected from Mpala Research Centre in Kenya that were used to produce the local plant DNA reference library for taxonomic assignation of dietary plant DNA sequences. The file includes (a) the project name and sample identifier required to access continuously updated data from the barcode of life datasystems (i.e., "BOLD") at boldsystems.org; (b) voucher locations and identifiers; and (c) the finest-level taxonomic identifications obtained to date. The DNA sequences associated with these specimens have been submitted to GenBank under the following accessions: KR737583 - KR738717 (trnL), KR733684 - KR734339 (ITS), KR736355 - KR737573 (rbcL), KR734343 - KR735185 (matK), and KR735186 - KR736041 (trnH-psbA). Sequence data associated with specific specimens may be obtained from GenBank by searching for the relevant BOLD Process Identifier.BOLDLibrary_2015PNAS_DRYAD.txt