Climatic warming and the future of bison as grazers

DNA data (genome skims and metabarcodes) paired with chemical data demonstrate utility for retrospective analysis of forage linked to fatal poisoning of cattle

Prepared and stored feeds, fodder, silage, and hay may be contaminated by toxic plants resulting in the loss of livestock. Several poisonous plants have played significant roles in livestock deaths from forage consumption in recent years in the Western United States including Salvia reflexa. Metagenomic data, genome skims and metabarcodes, have been used for identification and characterization of plants in complex botanical matrices including diet composition of animals, mixed forages, and herbal products. Here, chemistry, genome skims, and metabarcoding were used to retrospectively describe the composition of contaminated alfalfa hay from a case of Salvia reflexa (lanceleaf sage) poisoning that killed 165 cattle. Genome skims and metabarcoding provided similar estimates of the relative abundance of the Salvia in the hay samples when compared to chemical methods. Additionally, genome skims and metabarcoding provided similar estimates of species composition in the contaminated hay and rumen contents of poisoned animals. The data demonstrate that genome skims and DNA metabarcoding may provide useful tools for plant poisoning investigations.

Morphological patterns of the European bison (Bison bonasus) skull

This study aimed to investigate the effects of environmental factors, sexual selection, and genetic variation on skull morphology by examining the skull structure of the European bison, a species at risk of extinction, and comparing it to other bovid species. The skull of the European bison was significantly bigger than that of other species of the tribe Bovini, and the results revealed considerable morphological differences in skull shape compared to other Bovini samples. The bison skull exhibited a broader shape in the frontal region and a more laterally oriented cornual process. The frontal bone also significantly influenced skull shape variation within the European bison subspecies. Also, the findings indicated that cornual processes size significantly affected skull shape. Male Bison had larger skulls and more developed cornual ridges, and these morphological changes in the frontal region are thought to have also influenced the nuchal region, maxillary region, and facial bones. Furthermore, the differences in skull size observed between the Lowland-Pszczyna and Lowland-Białowieża lines, which share a closer origin than the Lowland-Carpathian lines, may reflect environmental and genetic adaptations over time. This research provides a reference point for future studies on the ecological and evolutionary factors influencing bison skull variations, with significant implications for the conservation of this species.

Japanese Yew (Taxus) poisoning of wild ungulates in Utah during the winter of 2022-2023

Taxus is a genus of coniferous shrubs and trees, commonly known as the yews, in the family Taxaceae. All species of yew contain taxine alkaloids, which are ascribed as the toxic principles. Anecdotally, free ranging ruminants such as antelope, deer, elk, and moose have been regarded as tolerant to yew. Herein several cases of intoxication of deer, elk, and moose by yew from the state of Utah in the winter of 2022-2023 are documented. Ingestion of yew was documented by three means among the poisoned cervids; plant fragments consistent with yew were visually observed in the rumen contents, chemical analysis, and subsequent detection of the taxines from rumen and liver contents, and identification of exact sequence variants identified as Taxus species from DNA metabarcoding. Undoubtedly, the record snowfall in Utah during the winter of 2022-2023 contributed to these poisonings.

Seasonal shifts in pronghorn antelope (Antilocapra americana) diets under a new lens: Examining diet composition using a molecular technique

Foraging is one of the most fundamental activities contributing to the maximization of an animal's fitness, and thus herbivores must optimize their diet selection and intake to meet their nutrient demands for survival, growth, and reproduction. Using plant DNA barcoding, we determined diet composition of five subpopulations of adult female pronghorn antelope (Antilocapra americana) grazing rangelands in southern and southeastern Idaho, USA. Fecal samples were collected for two years (2018-2019), and across metabolically-important adult female life history stages (late gestation, early lactation, breeding season). Plant DNA barcoding yielded 137 detected species within pronghorn diets across subpopulations and sampling periods with forbs being the most abundant. Pronghorn dietary functional group composition ranged from 52.2-60.3% from forbs followed by shrubs (22.6-28.2%), graminoids (8.7-15.7%), and legumes (5.5-9.6%). Dietary protein intake was also highest from forbs and ranged from 32.4-62.4% followed by graminoids (1.2-43.1%), shrubs (18.7-21.3%), and legumes (2.6-7.4%). We found significant intra- and interannual differences in the mean number of genera-based plant detections in pronghorn diets. Dietary protein intake of cultivated legumes (e.g., alfalfa [Medicago sativa] and sainfoin [Onobrychis viciifolia]) was lower than expected, ranging from <1.0-30.8%, suggesting that even within an agricultural-dominated landscape, factors other than plant nutritional composition contributed to pronghorn diets. Although the plant DNA barcoding technique exhibits limitations, it demonstrated potential for elucidating pronghorn dietary species richness, particularly for plants consumed in small proportions, as well as for observing temporal fluctuations in functional group composition and dietary protein intake explained through the interplay between environmental factors, plant chemical composition, and the animals' physiological needs.

An experimental design for obtaining DNA of a target species and its diet from a single non-invasive genetic protocol

Next-generation sequencing technology has enabled accurate insights into the diet of wildlife species. The protocols for faecal sample collection and DNA extraction for diet analysis have differed from those focusing on target species, even in most studies combining questions on both aspects. We designed an experiment to evaluate two protocols using 11 parameters and select a single one that will generate both target species (Asiatic wild ass, Equus hemionus, in Israel) and diet DNA, as an effective strategy to minimise time, effort, and cost without hampering efficiency. In Protocol A, we swabbed the outer surface of faecal boluses and extracted DNA using a Stool Kit, while for Protocol B, we homogenised faecal matter from inside the bolus followed by extraction using a Powersoil Kit. Protocol A performed significantly better for four parameters, which included, for the target species, microsatellite amplification success and the quantity of the GAPDH gene; and for its diet, the number of exact sequence variants (ESVs) obtained at genus level and plant genus richness. However, there was no significant difference in the amplification success of sex-linked and plant markers, total reads at genus level, number of genera obtained and plant genus composition. Although we chose Protocol A, both protocols yielded results for the target species and its diet, demonstrating that one single protocol can be used for both purposes, although a pilot study is recommended to optimise the protocol for specific systems. This strategy may also be useful for studies combining target species and their gut microbiome and parasitic load.

Browsers or Grazers? New Insights into Feral Burro Diet Using a Non-Invasive Sampling and Plant DNA Metabarcoding Approach

Ungulates play a large role in shaping ecosystems and communities by influencing plant composition, structure, and productivity. We investigated the summer diets of feral burros in two ecosystems in which they are found in the United States: a subtropical desert in Arizona and a temperate juniper shrubland in Utah. Between 24 June and 16 July of 2019, we gathered 50 burro fecal samples from each location and used plant DNA metabarcoding to determine the burros' diets. We found that during our sampling period the burros in the Sonoran Desert consumed a higher proportion of woody browse and had a narrower dietary niche breadth and lower degree of diet diversity compared to the burros in the juniper shrubland ecosystem, where the burros consumed higher proportions of graminoids and forbs and had a higher diet diversity index and broader dietary niche breadth. The burros in the Sonoran Desert relied primarily on Prosopis spp. (mesquite) and Poaceae grasses, whereas the burros in the juniper shrubland relied on a wider variety of forb and grass species, likely due to the greater variability in the forage species temporally and spatially available in that temperate ecosystem. We found that feral burros are highly adaptable with respect to diet and appear to be employing a mixed feeding strategy, similar to their ancestor, the African wild ass, to meet their nutritional needs in whichever ecosystem they are found.

Foraging history of individual elephants using DNA metabarcoding

Individual animals should adjust diets according to food availability. We used DNA metabarcoding to construct individual-level dietary timeseries for elephants from two family groups in Kenya varying in habitat use, social position and reproductive status. We detected at least 367 dietary plant taxa, with up to 137 unique plant sequences in one fecal sample. Results matched well-established trends: elephants tended to eat more grass when it rained and other plants when dry. Nested within these switches from 'grazing' to 'browsing' strategies, dietary DNA revealed seasonal shifts in food richness, composition and overlap between individuals. Elephants of both families converged on relatively cohesive diets in dry seasons but varied in their maintenance of cohesion during wet seasons. Dietary cohesion throughout the timeseries of the subdominant 'Artists' family was stronger and more consistently positive compared to the dominant 'Royals' family. The greater degree of individuality within the dominant family's timeseries could reflect more divergent nutritional requirements associated with calf dependency and/or priority access to preferred habitats. Whereas theory predicts that individuals should specialize on different foods under resource scarcity, our data suggest family bonds may promote cohesion and foster the emergence of diverse feeding cultures reflecting links between social behaviour and nutrition.

Impacts of large herbivores on terrestrial ecosystems

Large herbivores play unique ecological roles and are disproportionately imperiled by human activity. As many wild populations dwindle towards extinction, and as interest grows in restoring lost biodiversity, research on large herbivores and their ecological impacts has intensified. Yet, results are often conflicting or contingent on local conditions, and new findings have challenged conventional wisdom, making it hard to discern general principles. Here, we review what is known about the ecosystem impacts of large herbivores globally, identify key uncertainties, and suggest priorities to guide research. Many findings are generalizable across ecosystems: large herbivores consistently exert top-down control of plant demography, species composition, and biomass, thereby suppressing fires and the abundance of smaller animals. Other general patterns do not have clearly defined impacts: large herbivores respond to predation risk but the strength of trophic cascades is variable; large herbivores move vast quantities of seeds and nutrients but with poorly understood effects on vegetation and biogeochemistry. Questions of the greatest relevance for conservation and management are among the least certain, including effects on carbon storage and other ecosystem functions and the ability to predict outcomes of extinctions and reintroductions. A unifying theme is the role of body size in regulating ecological impact. Small herbivores cannot fully substitute for large ones, and large-herbivore species are not functionally redundant - losing any, especially the largest, will alter net impact, helping to explain why livestock are poor surrogates for wild species. We advocate leveraging a broad spectrum of techniques to mechanistically explain how large-herbivore traits and environmental context interactively govern the ecological impacts of these animals.

Domestic Cattle in a National Park Restricting the Sika Deer Due to Diet Overlap

Managers need to know the extent of the conflict between livestock and wild animals. Although many studies have reported the conflict between livestock and wild animals, few have checked the extent of the conflict. Cattle raising in the Northeast Tiger and Leopard National Park is considered one of the main driving forces behind the restricted distribution of sika deer. To understand whether foraging competition is contributing to avoidance patterns between sika deer and cattle, we investigated their feeding habits using DNA barcoding and high-throughput sequencing. Our study shows that although cattle are grazers in the traditional division of herbivores, their diet shifted to a predominance of dicotyledonous woody plants, and this diet shift resulted in a high degree of dietary overlap between sika deer and cattle. Moreover, compared to sika deer, cattle diets are more diverse at the species level with a wider ecological niche. Our results confirm that overlapping dietary niches and the superior competitive abilities of cattle contribute to the restricted distribution of the sika deer, which has critical implications for the conservation of their predators. Our study suggests that cattle grazing should be prohibited in the Park and effective measures should be taken for the benefit of sika deer.

Mechanisms of individual variation in large herbivore diets: Roles of spatial heterogeneity and state-dependent foraging

Many populations of consumers consist of relatively specialized individuals that eat only a subset of the foods consumed by the population at large. Although the ecological significance of individual-level diet variation is recognized, such variation is difficult to document, and its underlying mechanisms are poorly understood. Optimal foraging theory provides a useful framework for predicting how individuals might select different diets, positing that animals balance the "opportunity cost" of stopping to eat an available food item against the cost of searching for something more nutritious; diet composition should be contingent on the distribution of food, and individual foragers should be more selective when they have greater energy reserves to invest in searching for high-quality foods. We tested these predicted mechanisms of individual niche differentiation by quantifying environmental (resource heterogeneity) and organismal (nutritional condition) determinants of diet in a widespread browsing antelope (bushbuck, Tragelaphus sylvaticus) in an African floodplain-savanna ecosystem. We quantified individuals' realized dietary niches (taxonomic richness and composition) using DNA metabarcoding of fecal samples collected repeatedly from 15 GPS-collared animals (range 6-14 samples per individual, median 12). Bushbuck diets were structured by spatial heterogeneity and constrained by individual condition. We observed significant individual-level partitioning of food plants by bushbuck both within and between two adjacent habitat types (floodplain and woodland). Individuals with home ranges that were closer together and/or had similar vegetation structure (measured using LiDAR) ate more similar diets, supporting the prediction that heterogeneous resource distribution promotes individual differentiation. Individuals in good nutritional condition had significantly narrower diets (fewer plant taxa), searched their home ranges more intensively (intensity-of-use index), and had higher-quality diets (percent digestible protein) than those in poor condition, supporting the prediction that animals with greater endogenous reserves have narrower realized niches because they can invest more time in searching for nutritious foods. Our results support predictions from optimal foraging theory about the energetic basis of individual-level dietary variation and provide a potentially generalizable framework for understanding how individuals' realized niche width is governed by animal behavior and physiology in heterogeneous landscapes.

Bison movements change with weather: Implications for their continued conservation in the Anthropocene

Animal movement patterns are affected by complex interactions between biotic and abiotic landscape conditions, and these patterns are being altered by weather variability associated with a changing climate. Some animals, like the American plains bison (Bison bison L.; hereafter, plains bison), are considered keystone species, thus their response to weather variability may alter ecosystem structure and biodiversity patterns. Many movement studies of plains bison and other ungulates have focused on point-pattern analyses (e.g., resource-selection) that have provided information about where these animals move, but information about when or why these animals move is limited. For example, information surrounding the influence of weather on plains bison movement in response to weather is limited but has important implications for their conservation in a changing climate. To explore how movement distance is affected by weather patterns and drought, we utilized 12-min GPS data from two of the largest plains bison herds in North America to model their response to weather and drought parameters using generalized additive mixed models. Distance moved was best predicted by air temperature, wind speed, and rainfall. However, air temperature best explained the variation in distance moved compared to any other single parameter we measured, predicting a 48% decrease in movement rates above 28°C. Moreover, severe drought (as indicated by 25-cm depth soil moisture) better predicted movement distance than moderate drought. The strong influence of weather and drought on plains bison movements observed in our study suggest that shifting climate and weather will likely affect plains bison movement patterns, further complicating conservation efforts for this wide-ranging keystone species. Moreover, changes in plains bison movement patterns may have cascading effects for grassland ecosystem structure, function, and biodiversity. Plains bison and grassland conservation efforts need to be proactive and adaptive when considering the implications of a changing climate on bison movement patterns.

Reintroducing bison results in long-running and resilient increases in grassland diversity

The widespread extirpation of megafauna may have destabilized ecosystems and altered biodiversity globally. Most megafauna extinctions occurred before the modern record, leaving it unclear how their loss impacts current biodiversity. We report the long-term effects of reintroducing plains bison (Bison bison) in a tallgrass prairie versus two land uses that commonly occur in many North American grasslands: 1) no grazing and 2) intensive growing-season grazing by domesticated cattle (Bos taurus). Compared to ungrazed areas, reintroducing bison increased native plant species richness by 103% at local scales (10 m²) and 86% at the catchment scale. Gains in richness continued for 29 y and were resilient to the most extreme drought in four decades. These gains are now among the largest recorded increases in species richness due to grazing in grasslands globally. Grazing by domestic cattle also increased native plant species richness, but by less than half as much as bison. This study indicates that some ecosystems maintain a latent potential for increased native plant species richness following the reintroduction of native herbivores, which was unmatched by domesticated grazers. Native-grazer gains in richness were resilient to an extreme drought, a pressure likely to become more common under future global environmental change.

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. 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.

Evidence, causes, and consequences of declining nitrogen availability in terrestrial ecosystems

The productivity of ecosystems and their capacity to support life depends on access to reactive nitrogen (N). Over the past century, humans have more than doubled the global supply of reactive N through industrial and agricultural activities. However, long-term records demonstrate that N availability is declining in many regions of the world. Reactive N inputs are not evenly distributed, and global changes-including elevated atmospheric carbon dioxide (CO₂) levels and rising temperatures-are affecting ecosystem N supply relative to demand. Declining N availability is constraining primary productivity, contributing to lower leaf N concentrations, and reducing the quality of herbivore diets in many ecosystems. We outline the current state of knowledge about declining N availability and propose actions aimed at characterizing and responding to this emerging challenge.

The precautionary principle and dietary DNA metabarcoding: Commonly used abundance thresholds change ecological interpretation

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 laboratory. One of the earliest and most common strategies for dealing with such sensitivities has been to remove all low-abundance sequences and conduct ecological analyses based on the presence or absence of food taxa. Although this step is now often perceived to be necessary, evidence of its sufficiency is lacking and more attention to the risk of introducing other errors is needed. Using computer simulations, we demonstrate that common strategies to remove low-abundance sequences can erroneously eliminate true dietary sequences in ways that impact downstream 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 dietary profiles in ways that scale-up to obscure ecological interpretations about dietary generalism, specialism, and composition. Although the practice of removing low-abundance sequences may continue to be a useful strategy to address research questions that focus on a subset of relatively abundant foods, 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 drawbacks and consider alternative bioinformatic, experimental, and statistical solutions.

The Potential of Bison Restoration as an Ecological Approach to Future Tribal Food Sovereignty on the Northern Great Plains

Future climate projections of warming, drying, and increased weather variability indicate that conventional agricultural and production practices within the Northern Great Plains (NGP) will become less sustainable, both ecologically and economically. As a result, the livelihoods of people that rely on these lands will be adversely impacted. This is especially true for Native American communities, who were relegated to reservations where the land is often vast but marginal and non-tribal operators have an outsized role in food production. In addition, NGP lands are expected to warm and dry disproportionately relative to the rest of the United States. It is therefore critical to identify models of sustainable land management that can improve ecological function and socio-economic outcomes for NGP communities, all while increasing resilience to a rapidly changing climate. Efforts led by Native American Nations to restore North American Plains bison (Bison bison bison) to tribal lands can bring desired socio-ecological benefits to underserved communities while improving their capacity to influence the health of their lands, their people, and their livelihoods. Ecological sustainability will depend on the restoration of bison herds and bison’s ability to serve as ecosystem engineers of North America’s Plains. The historically broad distribution of bison suggests they can adapt to a variety of conditions, making them resilient to a wide range of management systems and climates. Here we review bison’s ecological, cultural, and economic value using four case studies from tribal communities within the NGP. We discuss the potential contributions of bison to food sovereignty, sustainable economies, and conservation of a working landscape with limited protections and significant risk of conversion. The ecological role of bison within this setting has potential due to cultural acceptance and the vast availability of suitable lands; however, it is critical to address tribal needs for funding support, enhanced community capacity, and solving complex landownership for these goals to be achieved.

Ecology: A revolution in resource partitioning

Resource partitioning stabilizes species coexistence but has long been difficult to measure. DNA metabarcoding reveals previously hidden dimensions of this problem and insights relevant for understanding and fostering coexistence - not just among wild carnivores, but also between carnivores and people.

Assessing the nutritional consequences of switching foraging behavior in wood bison

Diet is one of the most common traits used to organize species of animals into niches. For ruminant herbivores, the breadth and uniqueness of their dietary niche are placed on a spectrum from browsers that consume woody (i.e., browse) and herbaceous (i.e., forbs) plants, to grazers with graminoid-rich diets. However, seasonal changes in plant availability and quality can lead to switching of their dietary niche, even within species. In this study, we examined whether a population of wood bison (Bison bison athabascae) in northeast Alberta, Canada, seasonally switched their foraging behavior, and if so, whether this was associated with changes in nutrient acquisition. We hypothesized that bison should switch foraging behaviors from grazing in the winter when standing, dead graminoids are the only foliar plants readily available to browsing during spring and summer as nutritious and digestible foliar parts of browse and forbs become available. If bison are switching foraging strategy to maximize protein consumption, then there should be a corresponding shift in the nutritional niche. Alternatively, if bison are eating different plants, but consuming similar amounts of nutrients, then bison are switching their dietary niche to maintain a particular nutrient composition. We found wood bison were grazers in the winter and spring, but switch to a browsing during summer. However, only winter nutrient consumption of consumed plants differed significantly among seasons. Between spring and summer, bison maintained a specific nutritional composition in their diet despite compositional differences in the consumed plants. Our evidence suggests that bison are selecting plants to maintain a target macronutrient composition. We posit that herbivore's can and will switch their dietary niche to maintain a target nutrient composition.

Determining the influence of snow and temperature on the movement rates of wood bison (Bison bison athabascae)

Snow is understood to limit wildlife movements, often being the most important determinant of winter movement for animals in the boreal forest. However, the combined effect of snow and temperature on the movement ecology of animals at high latitudes is less understood. Here, we used GPS-collar data from a small population of wood bison (Bison bison athabascae Rhoads, 1898) in northeastern Alberta, Canada, to develop a series of generalized additive mixed models characterizing the effect of cumulative snow depth, daily change in snow depth, and temperature on movement rates. Our most supported model included cumulative snow depth, temperature, and day of winter. Bison movements decreased in the first 75 days of winter during snow accumulation and dramatically increased in the final 14 days of winter during snow melt. Cumulative snow depth, not daily change in snow depth, reduced wood bison movement rates, and movement rates increased more rapidly in warmer temperatures than in temperatures below −6.4 °C. By quantifying both the direction and the magnitude of snow and temperature’s effects on bison movement, our study fills critical knowledge gaps relating to the winter movement ecology of wood bison and contributes to a growing body of knowledge informing their conservation in the Anthropocene.

Seasonal dynamics of diet-gut microbiota interaction in adaptation of yaks to life at high altitude

Dietary selection and intake affect the survival and health of mammals under extreme environmental conditions. It has been suggested that dietary composition is a key driver of gut microbiota variation; however, how gut microbiota respond to seasonal dietary changes under extreme natural conditions remains poorly understood. Sequencing plant trnL (UAA) region and 16S rRNA gene analysis were employed to determine dietary composition and gut microbiota in freely grazing yaks on the Tibetan plateau. Dietary composition was more diverse in winter than in summer, while Gramineae and Rosaceae were consumed frequently all year. Turnover of seasonal diet and gut microbiota composition occurred consistently. Yaks shifted enterotypes in response to dietary change between warm and cold seasons to best utilize nitrogen and energy, in particular in the harsh cold season. Our findings provide insights into understanding seasonal changes of diet–microbiota linkages in the adaptation of mammals to high altitudes.

Integrating omics to characterize eco-physiological adaptations: How moose diet and metabolism differ across biogeographic zones

With accelerated land conversion and global heating at northern latitudes, it becomes crucial to understand, how life histories of animals in extreme environments adapt to these changes. Animals may either adapt by adjusting foraging behavior or through physiological responses, including adjusting their energy metabolism or both. Until now, it has been difficult to study such adaptations in free-ranging animals due to methodological constraints that prevent extensive spatiotemporal coverage of ecological and physiological data.Through a novel approach of combining DNA-metabarcoding and nuclear magnetic resonance (NMR)-based metabolomics, we aim to elucidate the links between diets and metabolism in Scandinavian moose Alces alces over three biogeographic zones using a unique dataset of 265 marked individuals.Based on 17 diet items, we identified four different classes of diet types that match browse species availability in respective ecoregions in northern Sweden. Individuals in the boreal zone consumed predominantly pine and had the least diverse diets, while individuals with highest diet diversity occurred in the coastal areas. Males exhibited lower average diet diversity than females.We identified several molecular markers indicating metabolic constraints linked to diet constraints in terms of food availability during winter. While animals consuming pine had higher lipid, phospocholine, and glycerophosphocholine concentrations in their serum than other diet types, birch- and willow/aspen-rich diets exhibit elevated concentrations of several amino acids. The individuals with highest diet diversity had increased levels of ketone bodies, indicating extensive periods of starvation for these individuals.Our results show how the adaptive capacity of moose at the eco-physiological level varies over a large eco-geographic scale and how it responds to land use pressures. In light of extensive ongoing climate and land use changes, these findings pave the way for future scenario building for animal adaptive capacity.

Seasonal patterns of bison diet across climate gradients in North America

North American plains bison (Bison bison) have been reintroduced across their former range, yet we know too little about their current diet to understand what drove their past migrations as well as observed continental-scale variation in weight gain and reproduction. In order to better understand the seasonal diets of bison at the continental scale, bison fecal material was collected monthly from April to September in 2019 across 45 sites throughout the conterminous United States. Fecal material was analyzed for dietary quality using near infrared spectroscopy and dietary composition with DNA metabarcoding. As observed in previous research, dietary quality peaked in June and was on average greatest for sites with cold, wet climates. Yet, in April, dietary quality was highest in warmer regions, likely reflecting earlier phenology of plants in southern than northern regions. Independent of climate and season, bison that consumed more warm-season grasses had lower dietary protein concentrations. Interpreting the relative abundance of sequences from different plant species as the relative intake of protein from those species, only 38% of bison protein intake came from grasses. An equal amount of dietary protein came from legumes (38%) and 22% from non-leguminous forbs. Seasonal shifts in bison diet were also clear, in part, following the phenology of functional groups. For example, cool-season grass protein intake was highest in May, while legume protein intake was highest in August. Comparing data taken in June and September 2018 in a previous study with corresponding data in 2019, on average, June [CP] was 20% higher in 2019 than 2018, while September [CP] did not differ between years. Dietary functional group composition was generally similar in amounts and relationships with climate between years, yet in September 2019, legumes contributed 20% more protein and warm-season grasses 14% less than in September 2018. In all, this research demonstrates that bison consistently rely on eudicots for protein with the functional group composition of their diet in some ways consistent across space and time, but also spatially and temporally variable. The early-season inversion of plant quality gradients would have been a strong driver of migratory behavior for large numbers of bison optimizing protein intake. As most bison currently experience protein deficiency, optimizing protein intake under current non-migratory conditions will require increasing the relative abundance of high-protein species such as N₂-fixing species.

Limits to host colonization and speciation in a radiation of parasitic finches

Parasite lineages vary widely in species richness. In some clades, speciation is linked to the colonization of new hosts. This is the case in the indigobirds and whydahs (Vidua), brood-parasitic finches whose nestlings mimic the phenotypes of their specific hosts. To understand the factors limiting host colonization and, therefore, speciation, we simulated the colonization of a host using cross-fostering experiments in the field. Despite DNA barcoding suggesting that host species feed their chicks similar diets, nestling Vidua had low survival in their new host environment. Nestling Vidua did not alter their begging calls plastically to match those of the new hosts and were fed less compared to both host chicks and to Vidua chicks in their natural host nests. This suggests that a key hurdle in colonizing new hosts is obtaining the right amount rather than the right type of food from host parents. This highlights the importance of mimetic nestling phenotypes in soliciting feeding from foster parents and may explain why successful colonizations tend to be of hosts closely related to the ancestral one. That nonmimetic chicks are fed less but not actively rejected by host parents suggests how selection from hosts can be sufficiently intense to cause parasite adaptation, yet sufficiently relaxed that parasitic chicks can sometimes survive in and colonize new host environments even if they lack accurate mimetic phenotypes. The difficulties of soliciting sufficient food from novel foster parents, together with habitat filters, likely limit the colonization of new hosts and, therefore, speciation in this parasite radiation.

Functional traits of the world's late Quaternary large-bodied avian and mammalian herbivores

Prehistoric and recent extinctions of large-bodied terrestrial herbivores had significant and lasting impacts on Earth's ecosystems due to the loss of their distinct trait combinations. The world's surviving large-bodied avian and mammalian herbivores remain among the most threatened taxa. As such, a greater understanding of the ecological impacts of large herbivore losses is increasingly important. However, comprehensive and ecologically-relevant trait datasets for extinct and extant herbivores are lacking. Here, we present HerbiTraits, a comprehensive functional trait dataset for all late Quaternary terrestrial avian and mammalian herbivores ≥10 kg (545 species). HerbiTraits includes key traits that influence how herbivores interact with ecosystems, namely body mass, diet, fermentation type, habitat use, and limb morphology. Trait data were compiled from 557 sources and comprise the best available knowledge on late Quaternary large-bodied herbivores. HerbiTraits provides a tool for the analysis of herbivore functional diversity both past and present and its effects on Earth's ecosystems.

Resolving Food-Web Structure

Food webs are a major focus and organizing theme of ecology, but the data used to assemble them are deficient. Early debates over food-web data focused on taxonomic resolution and completeness, lack of which had produced spurious inferences. Recent data are widely believed to be much better and are used extensively in theoretical and meta-analytic research on network ecology. Confidence in these data rests on the assumptions ( a) that empiricists correctly identified consumers and their foods and ( b) that sampling methods were adequate to detect a near-comprehensive fraction of the trophic interactions between species. Abundant evidence indicates that these assumptions are often invalid, suggesting that most topological food-web data may remain unreliable for inferences about network structure and underlying ecological and evolutionary processes. Morphologically cryptic species are ubiquitous across taxa and regions, and many trophic interactions routinely evade detection by conventional methods. Molecular methods have diagnosed the severity of these problems and are a necessary part of the cure.

Feeding preferences and nutritional niche of wild water buffalo (Bubalus arnee) in Koshi Tappu Wildlife Reserve, Nepal

The nutritional characteristics of food resources play an important role in the foraging behavior of animals and can provide information valuable to their conservation and management. We examined the nutritional ecology of wild water buffalo (Bubalus arnee; hereafter "buffalo") in the Koshi Tappu Wildlife Reserve of Nepal during autumn using a multidimensional nutritional niche framework. We identified 54 plant species as being foraged by buffalo. We found that buffalo consumed graminoids and forbs 2-3 times more frequently than browse items. Proximate analyses of the 16 most frequently foraged plants indicated that buffalo diets were highest in carbohydrate (40.41% ± 1.82%) followed by crude protein (10.52% ± 0.93%) and crude fat (1.68% ± 0.23%). The estimated macronutrient balance (i.e., realized nutrient niche) of the buffalo diet (20.5% protein: 72.8% carbohydrate: 6.7% lipid) was not significantly different than the average balance of all analyzed food items based on 95% confidence regions. Our study suggests that buffalo are likely macronutrient specialists, yet may be generalists in the sense that they feed on a wide range of food items to achieve a nutrient balance similar to that available in forage items. However, the four most frequently consumed items tended to be higher in protein energy than less frequently consumed foods, suggesting some preference for higher protein forage relative to relatively abundant carbohydrates. Although limited in scope, our study provides important information on the nutritional ecology of buffalo, which may be useful for the conservation and management of this endangered species.

Dual-locus DNA metabarcoding reveals southern hairy-nosed wombats (Lasiorhinus latifrons Owen) have a summer diet dominated by toxic invasive plants

Habitat degradation and summer droughts severely restrict feeding options for the endangered southern hairy-nosed wombat (SHNW; Lasiorhinus latifrons). We reconstructed SHNW summer diets by DNA metabarcoding from feces. We initially validated rbcL and ndhJ diet reconstructions using autopsied and captive animals. Subsequent diet reconstructions of wild wombats broadly reflected vegetative ground cover, implying local rather than long-range foraging. Diets were all dominated by alien invasives. Chemical analysis of alien food revealed Carrichtera annua contains high levels of glucosinolates. Clinical examination (7 animals) and autopsy (12 animals) revealed that the most degraded site also contained most individuals showing signs of glucosinolate poisoning. We infer that dietary poisoning through the ingestion of alien invasives may have contributed to the recent population crashes in the region. In floristically diverse sites, individuals appear to be able to manage glucosinolate intake by avoidance or episodic feeding but this strategy is less tractable in the most degraded sites. We conclude that recovery of the most affected populations may require effective Carrichtera management and interim supplementary feeding. More generally, we argue that protection against population decline by poisoning in territorial herbivores requires knowledge of their diet and of those food plants containing toxic principles.

Trophic rewilding revives biotic resistance to shrub invasion

Trophic rewilding seeks to rehabilitate degraded ecosystems by repopulating them with large animals, thereby re-establishing strong top-down interactions. Yet there are very few tests of whether such initiatives can restore ecosystem structure and functions, and on what timescales. Here we show that war-induced collapse of large-mammal populations in Mozambique's Gorongosa National Park exacerbated woody encroachment by the invasive shrub Mimosa pigra-considered one of the world's 100 worst invasive species-and that one decade of concerted trophic rewilding restored this invasion to pre-war baseline levels. Mimosa occurrence increased between 1972 and 2015, a period encompassing the near extirpation of large herbivores during the Mozambican Civil War. From 2015 to 2019, mimosa abundance declined as ungulate biomass recovered. DNA metabarcoding revealed that ruminant herbivores fed heavily on mimosa, and experimental exclosures confirmed the causal role of mammalian herbivory in containing shrub encroachment. Our results provide mechanistic evidence that trophic rewilding has rapidly revived a key ecosystem function (biotic resistance to a notorious woody invader), underscoring the potential for restoring ecological health in degraded protected areas.

Covariation of diet and gut microbiome in African megafauna

Diet and gut microbiome composition are important for health and nutrition in mammals, but how they covary in response to environmental change remains poorly understood—both because diet composition is rarely quantified precisely, and because studies of diet−microbiome linkages in captive animals may not accurately reflect the dynamics of natural communities. By analyzing diet−microbiome linkages in an assemblage of large mammalian herbivores in Kenya, we found that seasonal changes in diet and microbiome composition were strongly correlated within some populations, whereas other populations exhibited little temporal turnover in either diet or microbiome. Identifying mechanisms that generate species-specific variation in the sensitivity of the diet−microbiome nexus to environmental changes could help to explain differential population performance and food-web structure within ecological communities.

A major challenge in biology is to understand how phylogeny, diet, and environment shape the mammalian gut microbiome. Yet most studies of nonhuman microbiomes have relied on relatively coarse dietary categorizations and have focused either on individual wild populations or on captive animals that are sheltered from environmental pressures, which may obscure the effects of dietary and environmental variation on microbiome composition in diverse natural communities. We analyzed plant and bacterial DNA in fecal samples from an assemblage of 33 sympatric large-herbivore species (27 native, 6 domesticated) in a semiarid East African savanna, which enabled high-resolution assessment of seasonal variation in both diet and microbiome composition. Phylogenetic relatedness strongly predicted microbiome composition (r = 0.91) and was weakly but significantly correlated with diet composition (r = 0.20). Dietary diversity did not significantly predict microbiome diversity across species or within any species except kudu; however, diet composition was significantly correlated with microbiome composition both across and within most species. We found a spectrum of seasonal sensitivity at the diet−microbiome nexus: Seasonal changes in diet composition explained 25% of seasonal variation in microbiome composition across species. Species’ positions on (and deviations from) this spectrum were not obviously driven by phylogeny, body size, digestive strategy, or diet composition; however, domesticated species tended to exhibit greater diet−microbiome turnover than wildlife. Our results reveal marked differences in the influence of environment on the degree of diet−microbiome covariation in free-ranging African megafauna, and this variation is not well explained by canonical predictors of nutritional ecology.

Using DNA Metabarcoding To Evaluate the Plant Component of Human Diets: a Proof of Concept

Current methods for capturing human dietary patterns typically rely on individual recall and as such are subject to the limitations of human memory. DNA sequencing-based approaches, frequently used for profiling nonhuman diets, do not suffer from the same limitations. Here, we used metabarcoding to broadly characterize the plant portion of human diets for the first time. The majority of sequences corresponded to known human foods, including all but one foodstuff included in an experimental plant-rich diet. Metabarcoding could distinguish between experimental diets and matched individual diet records from controlled settings with high accuracy. Because this method is independent of survey language and timing, it could also be applied to geographically and culturally disparate human populations, as well as in retrospective studies involving banked human stool.

Dietary intake is difficult to measure reliably in humans because approaches typically rely on self-reporting, which can be incomplete and biased. In field studies of animals, DNA sequencing-based approaches such as metabarcoding have been developed to characterize diets, but such approaches have not previously been widely applied to humans. Here, we present data derived from sequencing of a chloroplast DNA marker (the P6 loop of the trnL [UAA] intron) in stool samples collected from 11 individuals consuming both controlled and freely selected diets. The DNA metabarcoding strategy resulted in successful PCR amplification in about 50% of samples, which increased to a 70% success rate in samples from individuals eating a controlled plant-rich diet. Detection of plant taxa among sequenced samples yielded a recall of 0.86 and a precision of 0.55 compared to a written diet record during controlled feeding of plant-based foods. The majority of sequenced plant DNA matched common human food plants, including grains, vegetables, fruits, and herbs prepared both cooked and uncooked. Moreover, DNA metabarcoding data were sufficient to distinguish between baseline and treatment diet arms of the study. Still, the relatively high PCR failure rate and an inability to distinguish some dietary plants at the sequence level using the trnL-P6 marker suggest that future methodological refinements are necessary. Overall, our results suggest that DNA metabarcoding provides a promising new method for tracking human plant intake and that similar approaches could be used to characterize the animal and fungal components of our omnivorous diets.

IMPORTANCE Current methods for capturing human dietary patterns typically rely on individual recall and as such are subject to the limitations of human memory. DNA sequencing-based approaches, frequently used for profiling nonhuman diets, do not suffer from the same limitations. Here, we used metabarcoding to broadly characterize the plant portion of human diets for the first time. The majority of sequences corresponded to known human foods, including all but one foodstuff included in an experimental plant-rich diet. Metabarcoding could distinguish between experimental diets and matched individual diet records from controlled settings with high accuracy. Because this method is independent of survey language and timing, it could also be applied to geographically and culturally disparate human populations, as well as in retrospective studies involving banked human stool.

A Case for Eustress in Grazing Animals

Herbivores grazing in extensive systems are exposed to a series of challenges, rooted in the inherent spatial and temporal variability of their environment that potentially constrain their health, nutrition, and welfare. Nevertheless, in this review, we argue that challenges induced by some biotic (e.g., vegetation) and abiotic (e.g., terrain) factors may also be viewed as "positive" sources of stress or eustress, since they present complex problems, that when solved successfully elicit a greater degree of behavioral plasticity and adaptability in grazing animals. Chemically and structurally diverse landscapes require animals to display complex behaviors and exhibit adaptive capabilities, like building a balanced and safe diet or finding shelter, which ultimately lead to positive emotional states. Thus, maintaining or enhancing the diversity occurring in natural systems represent a management approach that can be used to improve welfare and prepare the animal for an efficient adaptation to future, and potentially unknown, environmental challenges.

Cascading impacts of large-carnivore extirpation in an African ecosystem

Populations of the world's largest carnivores are declining and now occupy mere fractions of their historical ranges. Theory predicts that when apex predators disappear, large herbivores become less fearful, occupy new habitats, and modify those habitats by eating new food plants. Yet experimental support for this prediction has been difficult to obtain in large-mammal systems. After the extirpation of leopards and African wild dogs from Mozambique's Gorongosa National Park, forest-dwelling antelopes [bushbuck (Tragelaphus sylvaticus)] expanded into treeless floodplains, where they consumed novel diets and suppressed a common food plant [waterwort (Bergia mossambicensis)]. By experimentally simulating predation risk, we demonstrate that this behavior was reversible. Thus, whereas anthropogenic predator extinction disrupted a trophic cascade by enabling rapid differentiation of prey behavior, carnivore restoration may just as rapidly reestablish that cascade.

The potential of aerosol eDNA sampling for the characterisation of commercial seed lots

Seed shipments, silos and storage houses often contain weed seeds or seeds of restricted crops such as undeclared genetically modified (GM) varieties. Random sub-sampling is the favoured approach to detect unwanted biological materials in seed lots but is prohibitively expensive or else ineffective for the huge volumes of seeds moved in commercial operations. This study uses maize and cowpea seed admixtures as an exemplar to evaluate the feasibility of using aerosol sampling of "seed dust" as an alternative to seed sub-sampling. In an initial calibration phase, qPCR of the rbcL barcode followed by high-resolution melting (HRM) of a DNA titration series revealed a strong linear relationship between mix composition and HRM profiles. However, the relationship became skewed when flour mixes were used to build the titration, implying a DNA extraction bias favouring cowpea. Aerosol samples of seed dust above a titration of mixed seed samples were then collected along vertical and lateral axes. Aerosols were characterised by light microscopy, qPCR-HRM and next-generation DNA sequencing (Illumina MiSeq). Both molecular approaches again showed bias but this time in a reverse direction to flour samples. Microscopic examination of the aerosol sample suggested this divergence could be attributed to differences in abundance of airborne starch particles. Despite the bias, it was nevertheless possible to estimate relative abundance of each species using the abundance of minibarcodes. In light of these results we explore the feasibility of aerosol sampling for commercial seed lot characterisation.

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

Advances in DNA sequencing technology have revolutionized the field of molecular analysis of trophic interactions, and it is now possible to recover counts of food DNA sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer's diet should we work strictly with data sets summarizing frequency of occurrence of different food taxa, or is it possible to use relative number of sequences? Both approaches are applied to obtain semi-quantitative diet summaries, but occurrence data are often promoted as a more conservative and reliable option due to taxa-specific biases in recovery of sequences. We explore representative dietary metabarcoding data sets and point out that diet summaries based on occurrence data often overestimate the importance of food consumed in small quantities (potentially including low-level contaminants) and are sensitive to the count threshold used to define an occurrence. Our simulations indicate that using relative read abundance (RRA) information often provides a more accurate view of population-level diet even with moderate recovery biases incorporated; however, RRA summaries are sensitive to recovery biases impacting common diet taxa. Both approaches are more accurate when the mean number of food taxa in samples is small. The ideas presented here highlight the need to consider all sources of bias and to justify the methods used to interpret count data in dietary metabarcoding studies. We encourage researchers to continue addressing methodological challenges and acknowledge unanswered questions to help spur future investigations in this rapidly developing area of research.

DNA metabarcoding of orchid-derived products reveals widespread illegal orchid trade

In eastern Mediterranean countries orchids continue to be collected from the wild for the production of salep, a beverage made of dried orchid tubers. In this study we used nrITS1 and nrITS2 DNA metabarcoding to identify orchid and other plant species present in 55 commercial salep products purchased in Iran, Turkey, Greece and Germany. Thirty samples yielded a total of 161 plant taxa, and 13 products (43%) contained orchid species and these belonged to 10 terrestrial species with tuberous roots. Another 70% contained the substitute ingredient Cyamopsis tetraganoloba (Guar). DNA metabarcoding using the barcoding markers nrITS1 and nrITS2 shows the potential of these markers and approach for identification of species used in salep products. The analysis of interspecific genetic distances between sequences of these markers for the most common salep orchid genera shows that species level identifications can be made with a high level of confidence. Understanding the species diversity and provenance of salep orchid tubers will enable the chain of commercialization of endangered species to be traced back to the harvesters and their natural habitats, and thus allow for targeted efforts to protect or sustainably use wild populations of these orchids.

Feeding Immunity: Physiological and Behavioral Responses to Infection and Resource Limitation

Resources are a core currency of species interactions and ecology in general (e.g., think of food webs or competition). Within parasite-infected hosts, resources are divided among the competing demands of host immunity and growth as well as parasite reproduction and growth. Effects of resources on immune responses are increasingly understood at the cellular level (e.g., metabolic predictors of effector function), but there has been limited consideration of how these effects scale up to affect individual energetic regimes (e.g., allocation trade-offs), susceptibility to infection, and feeding behavior (e.g., responses to local resource quality and quantity). We experimentally rewilded laboratory mice (strain C57BL/6) in semi-natural enclosures to investigate the effects of dietary protein and gastrointestinal nematode (Trichuris muris) infection on individual-level immunity, activity, and behavior. The scale and realism of this field experiment, as well as the multiple physiological assays developed for laboratory mice, enabled us to detect costs, trade-offs, and potential compensatory mechanisms that mice employ to battle infection under different resource conditions. We found that mice on a low-protein diet spent more time feeding, which led to higher body fat stores (i.e., concentration of a satiety hormone, leptin) and altered metabolite profiles, but which did not fully compensate for the effects of poor nutrition on albumin or immune defenses. Specifically, immune defenses measured as interleukin 13 (IL13) (a primary cytokine coordinating defense against T. muris) and as T. muris-specific IgG1 titers were lower in mice on the low-protein diet. However, these reduced defenses did not result in higher worm counts in mice with poorer diets. The lab mice, living outside for the first time in thousands of generations, also consumed at least 26 wild plant species occurring in the enclosures, and DNA metabarcoding revealed that the consumption of different wild foods may be associated with differences in leptin concentrations. When individual foraging behavior was accounted for, worm infection significantly reduced rates of host weight gain. Housing laboratory mice in outdoor enclosures provided new insights into the resource costs of immune defense to helminth infection and how hosts modify their behavior to compensate for those costs.

Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data

The taxonomic classification of DNA sequences has become a critical component of numerous ecological research applications; however, few studies have evaluated the strengths and weaknesses of commonly used sequence classification approaches. Further, the methods and software available for sequence classification are diverse, creating an environment in which it may be difficult to determine the best course of action and the trade-offs made using different classification approaches. Here, we provide an in silico evaluation of three DNA sequence classifiers, the rdp Naïve Bayesian Classifier, rtax and utax. Further, we discuss the results, merits and limitations of both the classifiers and our method of classifier evaluation. Our methods of comparison are simple, yet robust, and will provide researchers a methodological and conceptual foundation for making such evaluations in a variety of research situations. Generally, we found a considerable trade-off between accuracy and sensitivity for the classifiers tested, indicating a need for further improvement of sequence classification tools.