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 >99% (plains zebra) to <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.
Representation of trnL-P6 metabarcode sequences across samples
A 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.txt
Representation of ITSpoa metabarcode sequences across samples
A 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.txt
Representation of ITSast metabarcode sequences across samples
A 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.txt
Representation of ITScyp metabarcode sequences across samples
A 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.txt
Dietary DNA metabarcode sequences in fasta format
All 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.fasta
Local plant DNA reference library information
This 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