Ecological niche differences are necessary for stable species coexistence but are often difficult to discern. Models of dietary niche differentiation in large mammalian herbivores invoke the quality, quantity, and spatiotemporal distribution of plant tissues and growth forms but are agnostic toward food plant species identity. Empirical support for these models is variable, suggesting that additional mechanisms of resource partitioning may be important in sustaining large-herbivore diversity in African savannas. We used DNA metabarcoding to conduct a taxonomically explicit analysis of large-herbivore diets across southeastern Africa, analyzing ∼4,000 fecal samples of 30 species from 10 sites in seven countries over 6 y. We detected 893 food plant taxa from 124 families, but just two families—grasses and legumes—accounted for the majority of herbivore diets. Nonetheless, herbivore species almost invariably partitioned food plant taxa; diet composition differed significantly in 97% of pairwise comparisons between sympatric species, and dissimilarity was pronounced even between the strictest grazers (grass eaters), strictest browsers (nongrass eaters), and closest relatives at each site. Niche differentiation was weakest in an ecosystem recovering from catastrophic defaunation, indicating that food plant partitioning is driven by species interactions, and was stronger at low rainfall, as expected if interspecific competition is a predominant driver. Diets differed more between browsers than grazers, which predictably shaped community organization: Grazer-dominated trophic networks had higher nestedness and lower modularity. That dietary differentiation is structured along taxonomic lines complements prior work on how herbivores partition plant parts and patches and suggests that common mechanisms govern herbivore coexistence and community assembly in savannas.
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DNA metabarcoding reveals broadly overlapping diets in three sympatric North American hummingbirds
Hummingbirds, a highly diverse avian family, are specialized vertebrate pollinators that feed upon carbohydrate-rich nectar to fuel their fast metabolism while consuming invertebrates to obtain protein. Previous work has found that morphologically diverse hummingbird communities exhibit higher diet specialization on floral resources than morphologically similar hummingbird communities. Due to the difficulties of studying avian diets, we have little understanding whether hummingbirds show similar patterns with their invertebrate prey. Here, we use DNA metabarcoding to analyze floral and invertebrate diets of 3 species of sympatric North American hummingbirds. We collected fecal samples from 89 Anna’s (Calypte anna), 39 Black-chinned (Archilochus alexandri), and 29 Calliope (Selasphorus calliope) hummingbirds in urban and rural localities as well as across an elevational gradient from sea level to 2,500 meters above sea level in California, USA. We found hummingbirds showed high dietary overlap in both invertebrate and plant resources, with few invertebrate and plant families common to most individuals and many families found in only a few individuals. Chironomidae was the most common invertebrate family across all species, and Rosaceae and Orobanchaceae were the most common plant families. Anna’s Hummingbirds had significantly higher invertebrate diet diversity than Black-chinned Hummingbirds when found at the same sites, but we found no difference in plant diet diversity among any of the 3 species. Hummingbirds in urban sites had higher plant diet diversity than in rural sites, but we found no effect of elevation on dietary richness. Our study shows how DNA metabarcoding can be used to non-invasively investigate previously unknown life-histories of well-studied birds, lending insight to community structure, function, and evolution.
more » « less- NSF-PAR ID:
- 10360902
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Ornithology
- Volume:
- 139
- Issue:
- 1
- ISSN:
- 0004-8038
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Theory predicts that trophic specialization (i.e. low dietary diversity) should make consumer populations sensitive to environmental disturbances. Yet diagnosing specialization 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 a 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 analyse 1,281 faecal 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); however, the relationship between TDD and PDD was consistent across seasons for all but one of the 12 best‐sampled species (plains zebra).
Our results show that taxonomic generalists can be phylogenetic specialists, and vice versa. These two dimensions of dietary diversity suggest contrasting implications for efforts to predict how consumers will respond to climate change and other environmental perturbations. For example, populations with low TDD may be sensitive to phylogenetically ‘random’ losses of food species, whereas populations with low PDD may be comparatively more sensitive to environmental changes that disadvantage entire plant lineages—and populations with low dietary diversity in both taxonomic and phylogenetic dimensions may be most vulnerable of all.
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Abstract Dietary metabarcoding—the process of taxonomic identification of food species from DNA in consumer guts or faeces—has been rapidly adopted by ecologists to gain insights into biocontrol, invasive species and the structure of food webs. However, an outstanding issue with metabarcoding is the semi‐quantitative nature of the data it provides: because metabarcoding is likely to produce false negatives for some prey more often than for other prey, we cannot infer relative frequencies of prey in the diet. To correct for this, we can adjust detected prey frequencies using DNA detectability half‐lives unique to each predator–prey combination. Because the feeding experiments required to deduce these half‐lives are time‐ and resource‐intensive, our ability to weight the frequency of observations using their detectability has thus far been limited to systems with just a few prey. Here, we present a meta‐analysis of 24 spider prey DNA half‐lives and show that these half‐lives are predictable given predator and prey mass, predator family, digestion temperature and DNA amplicon length. We further provide a new technique for weighting observations with half‐lives, which allows not just for the ranking of prey in the diet, but reveals the proportion of the diet each prey comprises. Lastly, we apply this method to published dietary metabarcoding data to calculate half‐lives and proportion of the predator's diet for 35 prey families, demonstrating that this technique can generate improved understanding of diets in real, diverse systems.
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Abstract Megafauna assemblages have declined or disappeared throughout much of the world, and many efforts are underway to restore them. Understanding the trophic ecology of such reassembling systems is necessary for predicting recovery dynamics, guiding management, and testing general theory. Yet, there are few studies of recovering large‐mammal communities, and fewer still that have characterized food‐web structure with high taxonomic resolution.
In Gorongosa National Park, large herbivores have rebounded from near‐extirpation following the Mozambican Civil War (1977–1992). However, contemporary community structure differs radically from the prewar baseline: medium‐sized ungulates now outnumber larger bodied species, and several apex carnivores remain locally extinct.
We used DNA metabarcoding to quantify diet composition of Gorongosa’s 14 most abundant large‐mammal populations. We tested five hypotheses: (i) the most abundant populations exhibit greatest individual‐level dietary variability; (ii) these populations also have the greatest total niche width (dietary diversity); (iii) interspecific niche overlap is high, with the diets of less‐abundant species nested within those of more‐abundant species; (iv) partitioning of forage species is stronger in more structurally heterogeneous habitats; and (v) selectivity for plant taxa converges within guilds and digestive types, but diverges across them.
Abundant (and narrow‐mouthed) populations exhibited higher among‐individual dietary variation, but not necessarily the greatest dietary diversity. Interspecific dietary overlap was high, especially among grazers and in structurally homogenous habitat, whereas niche separation was more pronounced among browsers and in heterogeneous habitat. Patterns of selectivity were similar for ruminants—grazers and browsers alike—but differed between ruminants and non‐ruminants.
Synthesis . The structure of this recovering food web was consistent with several hypotheses predicated on competition, habitat complexity, and herbivore traits, but it differed from patterns observed in more intact assemblages. We propose that intraspecific competition in the fastest‐recovering populations has promoted individual variation and a more nested food web, wherein rare species use subsets of foods eaten by abundant species, and that this scenario is reinforced by weak predation pressure. Future work should test these conjectures and analyse how the taxonomic dietary niche axis studied here interacts with other mechanisms of diet partitioning to affect community reassembly following wildlife declines. -
Austin, A (Ed.)Sympatric large mammalian herbivore species differ in diet composition, both by eating different parts of the same plant and by eating different plant species. Various theories proposed to explain these differences are not mutually exclusive, but are difficult to reconcile and confront with data. Moreover, whereas several of these ideas were originally developed with reference to within-plant partitioning (i.e., consumption of different tissues), they may analogously apply to partitioning of plant species; this possibility has received little attention. Plant functional traits provide a novel window into herbivore diets and a means of testing multiple hypotheses in a unified framework. We used DNA metabarcoding to characterize the diets of 14 sympatric large-herbivore species in an African savanna and analyzed diet composition in light of 27 functional traits that we measured locally for 204 plant species. Plant traits associated with the deep phylogenetic split between grasses and eudicots formed the primary axis of resource partitioning, affirming the generality and importance of the grazer-browser spectrum. A secondary axis comprised plant traits relevant to herbivore body size. Plant taxa in the diets of large-bodied species were lower on average in digestible energy and protein, taller on average (especially among grazers), and tended to be higher in tensile strength, zinc, stem-specific density, and potassium (and lower in sodium, stem dry matter content, and copper). These results are consistent with longstanding hypotheses linking body size with forage quality and height, yet they also suggest the existence of undiscovered links between herbivore body size and a set of rarely considered food-plant traits. We also tested the novel hypothesis that the leaf economic spectrum (LES), a major focus in plant ecology, is an axis of resource partitioning in large-herbivore assemblages; we found that the LES was a minor axis of individual variation within a few species, but had little effect on interspecific dietary differentiation. Synthesis. These results identify key plant traits that underpin the partitioning of food-plant species in large-herbivore communities and suggest that accounting for multiple plant traits (and tradeoffs among them) will enable a deeper understanding of herbivore-plant interaction networks.more » « less
