This content will become publicly available on August 30, 2023
Title: The generality of cryptic dietary niche differences in diverse large-herbivore assemblages
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. more »
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. « less
Potter, Arjun B.; Hutchinson, Matthew C.; Pansu, Johan; Wursten, Bart; Long, Ryan A.; Levine, Jonathan M.; Pringle, Robert M.(
, Journal of Ecology)
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 bemore »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.« less
Coverdale, Tyler C.; O’Connell, Ryan D.; Hutchinson, Matthew C.; Savagian, Amanda; Kartzinel, Tyler R.; Palmer, Todd M.; Goheen, Jacob R.; Augustine, David J.; Sankaran, Mahesh; Tarnita, Corina E.; et al(
, Proceedings of the National Academy of Sciences)
African savannas are the last stronghold of diverse large-mammal communities, and a major focus of savanna ecology is to understand how these animals affect the relative abundance of trees and grasses. However, savannas support diverse plant life-forms, and human-induced changes in large-herbivore assemblages—declining wildlife populations and their displacement by livestock—may cause unexpected shifts in plant community composition. We investigated how herbivory affects the prevalence of lianas (woody vines) and their impact on trees in an East African savanna. Although scarce (<2% of tree canopy area) and defended by toxic latex, the dominant liana,Cynanchum viminale(Apocynaceae), was eaten by 15 wild large-herbivore species and was consumed in bulk by native browsers during experimental cafeteria trials. In contrast, domesticated ungulates rarely ate lianas. When we experimentally excluded all large herbivores for periods of 8 to 17 y (simulating extirpation), liana abundance increased dramatically, with up to 75% of trees infested. Piecewise exclusion of different-sized herbivores revealed functional complementarity among size classes in suppressing lianas. Liana infestation reduced tree growth and reproduction, but herbivores quickly cleared lianas from trees after the removal of 18-y-old exclosure fences (simulating rewilding). A simple model of liana contagion showed that, without herbivores, the long-term equilibrium could be eithermore »endemic (liana–tree coexistence) or an all-liana alternative stable state. We conclude that ongoing declines of wild large-herbivore populations will disrupt the structure and functioning of many African savannas in ways that have received little attention and that may not be mitigated by replacing wildlife with livestock.
Rojas, Connie A.; Ramírez-Barahona, Santiago; Holekamp, Kay E.; Theis, Kevin R.(
, Animal Microbiome)
Abstract
The gut microbiota is critical for host function. Among mammals, host phylogenetic relatedness and diet are strong drivers of gut microbiota structure, but one factor may be more influential than the other. Here, we used 16S rRNA gene sequencing to determine the relative contributions of host phylogeny and host diet in structuring the gut microbiotas of 11 herbivore species from 5 families living sympatrically in southwest Kenya. Herbivore species were classified as grazers, browsers, or mixed-feeders and dietary data (% C4 grasses in diet) were compiled from previously published sources. We found that herbivore gut microbiotas were highly species-specific, and that host taxonomy accounted for more variation in the gut microbiota (30%) than did host dietary guild (10%) or sample month (8%). Overall, similarity in the gut microbiota increased with host phylogenetic relatedness (r = 0.74) across the 11 species of herbivores, but among 7 closely related Bovid species, dietary %C4 grass values more strongly predicted gut microbiota structure (r = 0.64). Additionally, within bovids, host dietary guild explained more of the variation in the gut microbiota (17%) than did host species (12%). Lastly, while we found that the gut microbiotas of herbivores residing in southwest Kenya converge with those of distinct populations of conspecificsmore »from central Kenya, fine-scale differences in the abundances of bacterial amplicon sequence variants (ASVs) between individuals from the two regions were also observed. Overall, our findings suggest that host phylogeny and taxonomy strongly structure the gut microbiota across broad host taxonomic scales, but these gut microbiotas can be further modified by host ecology (i.e., diet, geography), especially among closely related host species.
Negash, Enquye W.; Alemseged, Zeresenay; Bobe, René; Grine, Frederick; Sponheimer, Matt; Wynn, Jonathan G.(
, Proceedings of the National Academy of Sciences)
Diet provides critical information about the ecology and environment of herbivores. Hence, understanding the dietary strategies of fossil herbivores and the associated temporal changes is one aspect of inferring paleoenvironmental conditions. Here, we present carbon isotope data from more than 1,050 fossil teeth that record the dietary patterns of nine herbivore families in the late Pliocene and early Pleistocene (3.6 to 1.05 Ma) from the Shungura Formation, a hominin-bearing site in southwestern Ethiopia. An increasing trend toward C4herbivory has been observed with attendant reductions in the proportions of browsers and mixed feeders through time. A high proportion of mixed feeders has been observed prior to 2.9 Ma followed by a decrease in the proportion of mixed feeders and an increase in grazers between 2.7 and 1.9 Ma, and a further increase in the proportion of grazers after 1.9 Ma. The collective herbivore fauna shows two major change points in carbon isotope values at ∼2.7 and ∼2.0 Ma. While hominin fossils from the sequence older than 2.7 Ma are attributed toAustralopithecus, the shift at ∼2.7 Ma indicating the expansion of C4grasses on the landscape was concurrent with the first appearance ofParanthropus. The link between the increased C4herbivory and more open landscapesmore »suggests thatAustralopithecuslived in more wooded landscapes compared to later hominins such asParanthropusandHomo, and has implications for key morphological and behavioral adaptations in our lineage.
Dietary DNA metabarcoding enables researchers to identify and characterize trophic interactions with a high degree of taxonomic precision. It is also sensitive to sources of bias and contamination in the field and lab. One of the earliest and most common strategies for dealing with such sensitivities has been to filter resulting sequence data to remove low-abundance sequences before conducting ecological analyses based on the presence or absence of food taxa. Although this step is now often perceived to be both necessary and sufficient for cleaning up datasets, evidence to support this perception is lacking and more attention needs to be paid to the related risk of introducing other undesirable errors. Using computer simulations, we demonstrate that common strategies to remove low-abundance sequences can erroneously eliminate true dietary sequences in ways that impact downstream dietary inferences. Using real data from well-studied wildlife populations in Yellowstone National Park, we further show how these strategies can markedly alter the composition of individual dietary profiles in ways that scale-up to obscure ecological interpretations about dietary generalism, specialism, and niche partitioning. Although the practice of removing low-abundance sequences may continue to be a useful strategy to address a subset of research questions that focus
on a subset of relatively abundant food resources, its continued widespread use risks generating misleading perceptions about the structure of trophic networks. Researchers working with dietary DNA metabarcoding data—or similar data such as environmental DNA, microbiomes, or pathobiomes—should be aware of potential drawbacks and consider alternative bioinformatic, experimental, and statistical solutions.
Methods
We used fecal DNA metabarcoding to characterize the diets of bison and bighorn sheep in winter and summer. Our analyses are based on 35 samples (median per species per season = 10) analyzed using the P6 loop of the chloroplast trnL(UAA) intron together with publicly available plant reference data (Illumina sequence read data are available at NCBI (BioProject: PRJNA780500)). Obicut was used to trim reads with a minimum quality threshold of 30, and primers were removed from forward and reverse reads using cutadapt. All further sequence identifications were performed using obitools; forward and reverse sequences were aligned using the illuminapairedend command using a minimum alignment score of 40, and only joined sequences retained. We used the obiuniq command to group identical sequences and tally them within samples, enabling us to quantify the relative read abundance (RRA) of each sequence. Sequences that occurred ≤2 times overall or that were ≤8 bp were discarded. Sequences were considered to be likely PCR artifacts if they were highly similar to another sequence (1 bp difference) and had a much lower abundance (0.05%) in the majority of samples in which they occurred; we discarded these sequences using the obiclean command. Overall, we characterized 357 plant sequences and a subset of 355 sequences were retained in the dataset after rarefying samples to equal sequencing depth. We then applied relative read abundance thresholds from 0% to 5% to the fecal samples. We compared differences in the inferred dietary richness within and between species based on individual samples, based on average richness across samples, and based on the total richness of each population after accounting for differences in sample size.
Other
The readme file contains an explanation of each of the variables in the dataset. Information on the methodology can be found in the associated manuscript referenced above. More>>
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This content will become publicly available on August 30, 2023
Pansu, Johan, Hutchinson, Matthew C., Anderson, T. Michael, te Beest, Mariska, Begg, Colleen M., Begg, Keith S., Bonin, Aurelie, Chama, Lackson, Chamaillé-Jammes, Simon, Coissac, Eric, Cromsigt, Joris P., Demmel, Margaret Y., Donaldson, Jason E., Guyton, Jennifer A., Hansen, Christina B., Imakando, Christopher I., Iqbal, Azwad, Kalima, Davis F., Kerley, Graham I., Kurukura, Samson, Landman, Marietjie, Long, Ryan A., Munuo, Isaack Norbert, Nutter, Ciara M., Parr, Catherine L., Potter, Arjun B., Siachoono, Stanford, Taberlet, Pierre, Waiti, Eusebio, Kartzinel, Tyler R., and Pringle, Robert M.. The generality of cryptic dietary niche differences in diverse large-herbivore assemblages. Retrieved from https://par.nsf.gov/biblio/10362738. Proceedings of the National Academy of Sciences 119.35 Web. doi:10.1073/pnas.2204400119.
Pansu, Johan, Hutchinson, Matthew C., Anderson, T. Michael, te Beest, Mariska, Begg, Colleen M., Begg, Keith S., Bonin, Aurelie, Chama, Lackson, Chamaillé-Jammes, Simon, Coissac, Eric, Cromsigt, Joris P., Demmel, Margaret Y., Donaldson, Jason E., Guyton, Jennifer A., Hansen, Christina B., Imakando, Christopher I., Iqbal, Azwad, Kalima, Davis F., Kerley, Graham I., Kurukura, Samson, Landman, Marietjie, Long, Ryan A., Munuo, Isaack Norbert, Nutter, Ciara M., Parr, Catherine L., Potter, Arjun B., Siachoono, Stanford, Taberlet, Pierre, Waiti, Eusebio, Kartzinel, Tyler R., & Pringle, Robert M.. The generality of cryptic dietary niche differences in diverse large-herbivore assemblages. Proceedings of the National Academy of Sciences, 119 (35). Retrieved from https://par.nsf.gov/biblio/10362738. https://doi.org/10.1073/pnas.2204400119
Pansu, Johan, Hutchinson, Matthew C., Anderson, T. Michael, te Beest, Mariska, Begg, Colleen M., Begg, Keith S., Bonin, Aurelie, Chama, Lackson, Chamaillé-Jammes, Simon, Coissac, Eric, Cromsigt, Joris P., Demmel, Margaret Y., Donaldson, Jason E., Guyton, Jennifer A., Hansen, Christina B., Imakando, Christopher I., Iqbal, Azwad, Kalima, Davis F., Kerley, Graham I., Kurukura, Samson, Landman, Marietjie, Long, Ryan A., Munuo, Isaack Norbert, Nutter, Ciara M., Parr, Catherine L., Potter, Arjun B., Siachoono, Stanford, Taberlet, Pierre, Waiti, Eusebio, Kartzinel, Tyler R., and Pringle, Robert M..
"The generality of cryptic dietary niche differences in diverse large-herbivore assemblages". Proceedings of the National Academy of Sciences 119 (35). Country unknown/Code not available. https://doi.org/10.1073/pnas.2204400119.https://par.nsf.gov/biblio/10362738.
@article{osti_10362738,
place = {Country unknown/Code not available},
title = {The generality of cryptic dietary niche differences in diverse large-herbivore assemblages},
url = {https://par.nsf.gov/biblio/10362738},
DOI = {10.1073/pnas.2204400119},
abstractNote = {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.},
journal = {Proceedings of the National Academy of Sciences},
volume = {119},
number = {35},
author = {Pansu, Johan and Hutchinson, Matthew C. and Anderson, T. Michael and te Beest, Mariska and Begg, Colleen M. and Begg, Keith S. and Bonin, Aurelie and Chama, Lackson and Chamaillé-Jammes, Simon and Coissac, Eric and Cromsigt, Joris P. and Demmel, Margaret Y. and Donaldson, Jason E. and Guyton, Jennifer A. and Hansen, Christina B. and Imakando, Christopher I. and Iqbal, Azwad and Kalima, Davis F. and Kerley, Graham I. and Kurukura, Samson and Landman, Marietjie and Long, Ryan A. and Munuo, Isaack Norbert and Nutter, Ciara M. and Parr, Catherine L. and Potter, Arjun B. and Siachoono, Stanford and Taberlet, Pierre and Waiti, Eusebio and Kartzinel, Tyler R. and Pringle, Robert M.},
}
