Individual–resource networks reveal distinct fruit preferences of selective individuals from a generalist population of the Helmeted Manakin

Ecological studies traditionally assume that generalist populations are homogeneous in the use of food resources, but empirical evidence supports that intraspecific differences in morphology, physiology and behaviour affect foraging decisions and promote diet variation among individuals. Furthermore, the temporal availability of resources may shape the dynamics of population trophic niche, which ultimately depends on individual niches. In this study, we investigated the seasonal changes in individual-based networks between the Helmeted Manakin Antilophia galeata, a generalist frugivorous bird, and fruiting plants, following theoretical models of interindividual diet variation based on the Optimal Diet Theory. Selective individuals were the majority of the generalist population of the Helmeted Manakin. Our results suggest that the structure of the individual-resource networks varied seasonally. We found that modularity was higher than expected by chance in the wet season, when fruit availability was also higher. In the dry season, modules disappeared and the network became more nested. These findings are consistent with the Distinct Preference Model of diet variation. We suggest that downscaling ecological networks to the individual level may reveal emergent properties that, albeit existent, are not evident in species–resources networks.     

Network analyses support the role of prey preferences in shaping resource use patterns within five animal populations

Individual variation is an inherent aspect of animal populations and understanding the mechanisms shaping resource use patterns within populations is crucial to comprehend how individuals partition resources. Theory predicts that differences in prey preferences among consumers and/or differences in the likelihood of adding new resources to their diets are key mechanisms underlying intrapopulation variation in resource use. We developed network models based on optimal diet theory that simulate how individuals consume resources under varying scenarios of individual variation in prey preferences and in the willingness of consuming alternate resources. We then investigated how the structure of individual–resource networks generated under each model compared to the structure of observed networks representing five classical examples of individual diet variation. Our results support the notion that, for the studied populations, individual variation in prey preferences is the major factor explaining patterns in individual–resource networks. In contrast, variation in the willingness of adding prey does not seem to play an important role in shaping patterns of resource use. Individual differences in prey preferences in the studied populations may be generated by complex behavioral rules related to cognitive constraints and experience. Our approach provides a pathway for mapping foraging models into network patterns, which may allow determining the possible mechanisms leading to variation in resource use within populations.     

Interindividual patterns of resource use in three subtropical Atlantic Forest frogs

Studies with disparate taxa suggest that generalist populations are composed of relatively specialist individuals that use a narrow part of a population's resource pool. Models based on optimum diet theory (ODT) can be used to predict different patterns of variation in resource use among individuals. In this work, we investigated the diet and measured the degree of individual specialization of three anuran species, Hypsiboas leptolineatus, Pseudis cardosoi and Scinax granulatus, from the Atlantic Forest of southern Brazil. The study is based on gut content obtained using a stomach‐flushing technique. Additionally, we tested for a correlation between the individuals’ diet and morphological variation. Furthermore, we applied methods based on network theory to investigate patterns of resource use among individuals of each species. All three study species showed generalized diets and significant values of individual specialization. However, we did not find any correlation between diet and morphology, indicating that diet variation is not a consequence of morphological trade‐offs. The individual‐resource networks of H. leptolineatus and S. granulatus showed a nested pattern. This result indicates the presence of individuals with more diverse diets than others, and the diets of the more specialist individuals are a predictable subset of the diets of the more generalist ones. The individual‐resource network of P. cardosoi did not show a distinct pattern, diverging from what was predicted by optimal diet theory‐based models. Although nested or modular patterns are commonly found in individual‐resource networks, our results indicate that they are not ubiquitous and that random patterns can also be found.     

Between‐individual variation drives the seasonal dynamics in the trophic niche of a Neotropical marsupial

The dynamics of population niches result from the variation in resource use within individuals and also from the variation between individuals. The prevalence of one mechanism or the other leads to competing hypotheses about the major mechanisms underlying the empirical observations of the contraction/expansion dynamics of the trophic niche in natural populations. In this study, we investigated how within‐ and between‐individual variation in resource use shapes the food niche dynamics of the woolly mouse opossum, Marmosa paraguayana (Didelphimorphia: Didelphidae), in a remnant of the highly seasonal Cerrado in south‐eastern Brazil. To do so, we analysed the faecal samples of live‐trapped individuals to determine their diets within the wet and dry seasons. In addition to a seasonal shift in the composition of the diet, the population trophic niche was significantly wider during the dry season than the wet season. This expansion resulted from larger between‐individual variation in the dry season that was not related to sex preferences, whereas the individual niche widths did not significantly increase from the wet to the dry seasons. Our findings add to the growing list of animal populations that show individual‐level variation in resource use. Furthermore, these results represent a pattern of individual‐level response to seasonal changes that is different from patterns reported for other organisms. We suggest that a pathway to build more realistic foraging models and produce more accurate predictions on population and community dynamics is to consider between‐individual variation and short‐term niche dynamics.     

Structure and mechanism of diet specialisation: testing models of individual variation in resource use with sea otters

Studies of consumer-resource interactions suggest that individual diet specialisation is empirically widespread and theoretically important to the organisation and dynamics of populations and communities. We used weighted networks to analyze the resource use by sea otters, testing three alternative models for how individual diet specialisation may arise. As expected, individual specialisation was absent when otter density was low, but increased at high-otter density. A high-density emergence of nested resource-use networks was consistent with the model assuming individuals share preference ranks. However, a density-dependent emergence of a non-nested modular network for 'core' resources was more consistent with the 'competitive refuge' model. Individuals from different diet modules showed predictable variation in rank-order prey preferences and handling times of core resources, further supporting the competitive refuge model. Our findings support a hierarchical organisation of diet specialisation and suggest individual use of core and marginal resources may be driven by different selective pressures.     

Intraspecific variation in species interactions promotes the feasibility of mutualistic assemblages

Patterns of resource use observed at the species level emerge from the way individuals exploit the range of available resources. Hence, accounting for interindividual differences in resource use, such as pollinator use by plants, is essential to advance our understanding of community assembly and persistence. By using finely resolved data on plant–pollinator interactions, we evaluated how interindividual plant variation in pollinator use scales up to affect community structure and dynamics. All co-occurring plant species comprised specialists interacting with proper subsets of pollinators that visited generalists, and differences in interaction patterns were driven by among-individual trait variation. Furthermore, the nested structure and feasibility of plant–pollinator communities were maximised at higher levels of interindividual plant variation in traits and pollinator use. Our study sheds light on how pervasive properties of community structure arise from individual-level processes and contributes to elucidate the importance of preserving intraspecific variation in traits and resource use within populations.     

The marine side of a terrestrial carnivore: intra-population variation in use of allochthonous resources by arctic foxes

Inter-individual variation in diet within generalist animal populations is thought to be a widespread phenomenon but its potential causes are poorly known. Inter-individual variation can be amplified by the availability and use of allochthonous resources, i.e., resources coming from spatially distinct ecosystems. Using a wild population of arctic fox as a study model, we tested hypotheses that could explain variation in both population and individual isotopic niches, used here as proxy for the trophic niche. The arctic fox is an opportunistic forager, dwelling in terrestrial and marine environments characterized by strong spatial (arctic-nesting birds) and temporal (cyclic lemmings) fluctuations in resource abundance. First, we tested the hypothesis that generalist foraging habits, in association with temporal variation in prey accessibility, should induce temporal changes in isotopic niche width and diet. Second, we investigated whether within-population variation in the isotopic niche could be explained by individual characteristics (sex and breeding status) and environmental factors (spatiotemporal variation in prey availability). We addressed these questions using isotopic analysis and Bayesian mixing models in conjunction with linear mixed-effects models. We found that: i) arctic fox populations can simultaneously undergo short-term (i.e., within a few months) reduction in both isotopic niche width and inter-individual variability in isotopic ratios, ii) individual isotopic ratios were higher and more representative of a marine-based diet for non-breeding than breeding foxes early in spring, and iii) lemming population cycles did not appear to directly influence the diet of individual foxes after taking their breeding status into account. However, lemming abundance was correlated to proportion of breeding foxes, and could thus indirectly affect the diet at the population scale.     

Diet niche relationships among North American grassland and shrubsteppe birds

Summary We consider the dietary relationships of the numerically dominant breeding bird species in four North American grassland/shrubsteppe habitats, sampled over 2–3 consecutive years. Overall, the diets of these species contained primarily insects: orthopterans comprised 29% of the diet biomass, coleopterans 24%, and lepidopteran larvae 23%, while seeds contributed 15% of the average diet. These diets varied substantially, however, and we evaluated several aspects of this variation. Intersexual differences in diets within a species were few, despite the occurrence of significant sexual size dimorphism in several species. For many species, however, there were substantial shifts in dietary composition between years at a given location; overall, the average between-year similarity of species' dietary composition was 70%. Different species exhibited rather different diet patterns. Horned Larks were relatively omnivorous, had broad diet composition niches, and varied considerably in diets between different locations. Meadowlarks were also broad-niched and geographically variable in their diets, but were the most highly carnivorous of the species we considered. Dietary niche breadths of Grasshopper Sparrows were intermediate, but diet composition was rather stable, both between years and between locations. Chestnut-collared Longspurs exhibited narrow diet niches, but substantial annual variation: each year this species apparently exploited a different but limited set of prey types rather heavily. Larger avian predators generally consumed a broader array of functional groups of prey, but did not differ in the taxonomic variety of their diets from small birds. Variation in diet composition between individuals within local populations was considerable; in most species, an individual contained on the average 30–40% of the prey taxa represented in entire population smaples.Patterns of dietary overlap among species were quite inconsistent from year to year at most locations, although at the shrubsteppe site overlap among all species present was consistently quite high. Relatively few cooccurring species pairs exhibited low diet overlap. The degree of diet niche overlap was unrelated to body size differences of the birds, despite as much as six-fold differences in weight among some coexisting species. Relationships of the bird species on another dimension of the trophic niche, prey size, also differed substantially between sites and years. The ranking of co-occurring species by the mean sizes of the prey they consumed generally did not parallel their rankings by body sizes, and in some cases the smallest and the largest species present ate prey of similar sizes. At the shrubsteppe site, all the breeding species exhibited quite similar frequency distributions of prey sizes in their diets.As species number and diversity increased in the breeding avifaunas, diet niche breadths generally decreased, species packing by prey size decreased, and diet composition niche overlap remained relatively unchanged. These trends are in at least partial agreement with predictions of diffuse competition theory, but the patterns were derived from broad inter-site comparisons of overall site averages, and the relationships generally did not hold within local assemblages of species. In general, our attempts to match values of dietary niche features with site characteristics failed to demonstrate close agreement with the predictions of prevailing ecological theory based upon assumptions of resource limitation and competition. Instead, our findings seem generally most consistent with the suggestion that food is not normally limiting to bird populations in these systems, and individuals and populations are exploiting the food resources in an opportunistic fashion, which leads to considerable individual, between-year, and between-location variation in diet compositions and interspecific overlaps.Our attempts to discern clear relationships that accord with theoretical expectations in these avian assemblages are thwarted by our lack of detailed information on the resource base and by the lack of clear tests that will separate alternative hypotheses of community organization and structuring. We suggest that these complications may compromise the findings of many community studies.     

Nested diets: a novel pattern of individual-level resource use

Many generalist populations may actually be composed of relatively specialist individuals. This 'individual specialization' may have important ecological and evolutionary implications. Although this phenomenon has been documented in more than one hundred taxa, it is still unclear how individuals within a population actually partition resources. Here we applied several methods based on network theory to investigate the intrapopulation patterns of resource use in the gracile mouse opossum Gracilinanus microtarsus . We found evidence of significant individual specialization in this species and that the diets of specialists are nested within the diets of generalists. This novel pattern is consistent with a recently proposed model of optimal foraging and implies strong asymmetry in the interactions among individuals of a population.     

Testing the niche variation hypothesis with a measure of body condition

Individual variation and fitness are cornerstones of evolution by natural selection. The niche variation hypothesis (NVH) posits that when interspecific competition is relaxed, intraspecific competition should drive niche expansion by selection favoring use of novel resources and that among‐individual variation should confer a selective advantage. Population‐level niche expansion could be achieved by all individuals using all available resources, or by each individual using a unique combination of resources, thereby increasing among‐individual dietary niche variation. Although individual variation can lead to species‐level evolutionary and ecological change, observed variation does not ensure a beneficial outcome. We used carbon and nitrogen stable isotope analysis of claw keratin and a Bayesian stable isotope mixing model to estimate the summer (July–September) assimilated diet of individual female black Ursus americanus and brown U. arctos bears. We quantified variation in dietary niche in both populations, and assessed diet relative to percentage body fat. We hypothesized that if the NVH held, percentage body fat would be similar for individuals of the same species across much of the dietary range of observed proportional salmon contributions to individual bear diets. Although we found greater differences in dietary niches between than within species, we observed greater among‐individual dietary variation in the brown bear population. Moreover, we found that within each species individual female bears achieved similar ranges of percentage body fat at various levels of salmon in the diet. Our results provide support for the NVH. Linking individual dietary niches to measures of physiological condition related to fitness can offer new insights into eco‐evolutionary processes related to food resource use.     

Among‐individual diet variation within a lake trout ecotype: Lack of stability of niche use

In a polyphenic species, differences in resource use are expected among ecotypes, and homogeneity in resource use is expected within an ecotype. Yet, using a broad resource spectrum has been identified as a strategy for fishes living in unproductive northern environments, where food is patchily distributed and ephemeral. We investigated whether specialization of trophic resources by individuals occurred within the generalist piscivore ecotype of lake trout from Great Bear Lake, Canada, reflective of a form of diversity. Four distinct dietary patterns of resource use within this lake trout ecotype were detected from fatty acid composition, with some variation linked to spatial patterns within Great Bear Lake. Feeding habits of different groups within the ecotype were not associated with detectable morphological or genetic differentiation, suggesting that behavioral plasticity caused the trophic differences. A low level of genetic differentiation was detected between exceptionally large‐sized individuals and other piscivore individuals. We demonstrated that individual trophic specialization can occur within an ecotype inhabiting a geologically young system (8,000–10,000 yr BP), a lake that sustains high levels of phenotypic diversity of lake trout overall. The characterization of niche use among individuals, as done in this study, is necessary to understand the role that individual variation can play at the beginning of differentiation processes.     

Metabarcoding reveals selective dietary responses to environmental availability in the diet of a nocturnal,aerial insectivore,the European Nightjar (Caprimulgus europaeus)

Many bird species are vulnerable to environmental change, so knowledge of their diet and its variation can help understand population status and flexibility to respond to change. Insectivorous species are predicted to have a flexible diet within and between individuals, which can respond to naturally fluctuating prey abundance, thus allowing opportunistic exploitation of available resources. We analysed the diet of a nocturnal, aerial insectivore, the European Nightjar Caprimulgus europaeus, using high-throughput metabarcoding. We quantified diet diversity and composition of 130 faecal samples from nests and roosts on a northern breeding site in the UK from 2015 to 2018, and compared differences among individuals and years. Although dominated by moths, diet varied significantly between individual faecal samples and between years and months. Prey species composition varied between years, and was more variable between samples in 2017 than in other years. Faecal samples were significantly more likely to contain moth species with a wingspan of > 60 mm and less likely to contain moth species of < 25 mm wingspan. This indicated size-selective foraging, which also varied between months and years. Diet was driven by interindividual variation, indicating population-level flexibility in prey choice. Metabarcoding provided a valuable tool in the exploration of insectivorous diets, but efforts are needed to build comprehensive reference libraries in order to compile full prey species lists.     

Trophic niche, age structure and seasonality in Dolichopoda cave crickets

Shifts in feeding habits are expected to occur during adaptation to cave life Doltchopoda cave crickets inhabit both natural and artificial caves showing differences in population size, fecundity, phenology and age structure Compared to artificial caves, typically holding a seasonal age structure, populations from natural caves maintain a constantly heterogeneous age structure Faecal content analysis of 605 individuals from 24 natural and artificial cave populations, enabled us to characterize their trophic niche and to investigate its variation The results of multivariate analyses and measures of niche breadth and niche overlap outlined differences in trophic resource exploitation between natural and artificial cave populations Seasonal variation in diet occurred in both types of caves, and it was greater in artificial cave populations However, within any season, differences in feeding habits between individuals were much greater in natural caves resulting in a wider heterogeneity in trophic resources exploitation. Such heterogeneity appears to be mainly due to differences in diet between individuals of different developmental stages In fact, in a sample of 15 populations we found a positive, statistical significant correlation between niche breadth and heterogeneity in age structure These data are discussed in a broader evolutionary context in order to understand the role of limited resources availability in shaping and maintaining heterogeneity in age structure of Dolichopoda populations     

Genomic patterns of homozygosity in worldwide human populations

Genome-wide patterns of homozygosity runs and their variation across individuals provide a valuable and often untapped resource for studying human genetic diversity and evolutionary history. Using genotype data at 577,489 autosomal SNPs, we employed a likelihood-based approach to identify runs of homozygosity (ROH) in 1,839 individuals representing 64 worldwide populations, classifying them by length into three classes—short, intermediate, and long—with a model-based clustering algorithm. For each class, the number and total length of ROH per individual show considerable variation across individuals and populations. The total lengths of short and intermediate ROH per individual increase with the distance of a population from East Africa, in agreement with similar patterns previously observed for locus-wise homozygosity and linkage disequilibrium. By contrast, total lengths of long ROH show large interindividual variations that probably reflect recent inbreeding patterns, with higher values occurring more often in populations with known high frequencies of consanguineous unions. Across the genome, distributions of ROH are not uniform, and they have distinctive continental patterns. ROH frequencies across the genome are correlated with local genomic variables such as recombination rate, as well as with signals of recent positive selection. In addition, long ROH are more frequent in genomic regions harboring genes associated with autosomal-dominant diseases than in regions not implicated in Mendelian diseases. These results provide insight into the way in which homozygosity patterns are produced, and they generate baseline homozygosity patterns that can be used to aid homozygosity mapping of genes associated with recessive diseases.     

Fruit preferences by fishes in a Neotropical floodplain

The diets of frugivorous animals result from the interaction between feeding preference and ecological factors such as availability of alternative resources and interactions with other frugivores. A better understanding of frugivore diets will enable predictions about the vulnerability of plant populations to anthropogenic or natural environmental changes. In addition, frugivores with greater variation in diet (generalists) are potentially more resilient to habitat changes than specialists. Here, we combined data on diets of frugivorous fishes with visual censuses on fruit availability to evaluate if fishes are selective or opportunistic in their use of fruits in floodplain habitats. We found a high diversity of fruit species (74 species) frequently consumed by four common species of frugivorous fishes during the flooding season. The identity of preferred fruits, rather than their availability, had a stronger effect on the patterns of fruit consumed by fishes in this system. Fruit preferences by fish may influence the long-term persistence and the maintenance of plant diversity in floodplain habitats. Possible disturbances of fish populations with selective consumption and the plant populations on which they depend could increase the vulnerability of both populations involved. Thus, selectivity may affect ecological and evolutionary processes associated with frugivory by fish.     

Spatial and seasonal variability in the trophic role of aquatic insects: An assessment of functional feeding group applicability

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Sex and Season Affect Individual-Level Diet Variation in the Neotropical Marsupial Gracilinanus microtarsus (Didelphidae)

Individual-level diet variation was investigated in Gracilinanus microtarsus , an insectivorous marsupial whose diet is affected by sex and season in the highly seasonal Brazilian Cerrado. To measure individual-level diet variation, the diets of individual males and females were compared to that of their population in the warm-wet and cool-dry seasons using the proportional similarity index (PS _i ). This index varies from 1 (complete overlap between the individual i  's and population's diets) toward 0 (decreasing overlap). Mean PS _i values were computed as a measure of the degree of interindividual diet variation (the larger the mean PS _i value, the smaller the variation among individuals' diets). Interindividual diet variation among females was similar between seasons, whereas among males it decreased from the warm-wet to the cool-dry season. Diet variation among males is probably reduced in the cool-dry season because of constraints on food consumption generated by interactions between endogenous (physiological needs associated with high rates of body mass growth) and exogenous (food limitation) factors.     

Beyond ecological opportunity: Prey diversity rather than abundance shapes predator niche variation

1. Ecological opportunity (i.e. the diversity of available resources) has a pivotal role in shaping niche variation and trophic specialisation of animals. However, ecological opportunity can be described with regard to both diversity and abundance of resources. The degree to which these two components contribute to niche variation remains unexplored.
2. To address this, we used an extensive dataset on fish diet and benthic invertebrate diversity and density from 73 sampling events in three Norwegian rivers in order to explore realised trophic niches and the response of dietary niche variation along gradients of resource diversity (potential trophic niches), resource density (as a proxy of resource abundance) and fish density (as a proxy of inter‐ and intra‐specific competition) in a freshwater top predator (the brown trout, Salmo trutta L.).
3. Linear models indicated that individual and population niche variation increased with increasing ecological opportunity in terms of prey diversity. However, no simple cause‐and‐effect associations between niche indices and prey abundance were found. Our multiple regression analyses indicated that the abundance of certain resources (e.g. Chironomidae) can interact with prey diversity to determine individual and population realised trophic niches. Niche variation (within‐individual component and inter‐individual diet variation) decreased with increasing inter‐ and intra‐specific competition.
4. This study extends prevailing trophic ecology theory by identifying diversity, rather than density, of available prey resources as a primary driver of niche variation in fish of temperate riverine systems with no extensive resource limitation. The study also shows that ecological opportunity may mask the direction of the effect (compression or expansion) of competition on niche variation when food resources are diverse.
5. Our study provides novel empirical insight to the driving forces behind niche variation and reveals that diversity, rather than density, of available prey resources may be a primary driver of niche variation in freshwater fish. Our study supports the view that a broader potential trophic niche promotes broader realised trophic niche variation by individuals, which leads to individual niche diversification by opening access to alternatives resources, resulting in a concomitant rise in the realised trophic niche width of the population.

     

Availability of food resources and habitat structure shape the individual‐resource network of a Neotropical marsupial

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Spatiotemporal food web dynamics along a desert riparian–upland transition

Increased awareness of spatiotemporal variation in species interactions has motivated the study of temporally-resolved food web dynamics at the landscape level. Empiricists have focused attention on cross-habitat flows of materials, nutrients, and prey, largely ignoring the movement of predators between habitats that differ in productivity (and how predators integrate pulses in resource availability over time). We set out to study seasonal variation in food web interactions between mammalian carnivores and their rodent prey along a riparian–upland gradient in semi-arid southeastern Arizona which features both spatial and temporal heterogeneity in resource availability. Specifically, we tested whether mammalian carnivores spill over from productive, near-river habitats into adjacent, desert-scrub habitats; and if they do, to document the effects of this spillover on rodent communities. Furthermore, we examined seasonal variation in top-down effects by measuring changes in carnivore diet and distribution patterns and rodent populations over time. The results indicate that carnivores track seasonally-abundant resources across the landscape, varying both their diet and movement patterns. In turn, desert-scrub rodent population dynamics track seasonal shifts in carnivore habitat use but not resource availability, suggesting that predation plays a role in structuring rodent communities along the San Pedro River. Further evidence comes from data on rodent community composition, which differs between desert-scrub habitats near and far from the river, despite similarities in resource availability. Our data also suggest that seasonal omnivory helps predators survive lean times, increasing their effects on prey populations. Taken together, these results underscore the importance of spatiotemporal variation in species interactions, highlighting the complexity of natural systems and the need for further detailed studies of food web dynamics.