Comparative support for the niche variation hypothesis that more generalized populations also are more heterogeneous

Damming of streams due to the construction of a highway in the Amazon rainforest favors individual trophic specialization in the fish (Bryconops giacopinii)

In Amazonian streams, damming caused by road construction changes the system's hydrological dynamics and biological communities. We tested whether the degree of specialization in fish (Bryconops giacopinii) individuals is higher in pristine stream environments with intact ecological conditions than in streams dammed due to the construction of a highway in the Amazon rainforest. To achieve this, stomach content data and stable isotopes (δ13C and δ15N) in tissues with varying isotopic incorporation rates (liver, muscle, and caudal fin) were used to assess the variation in consumption of different prey over time. The indices within-individual component (WIC)/total niche width (TNW) and individual specialization were employed to compare the degree of individual specialization between pristine and dammed streams. The condition factor and stomach repletion of sampled individuals were used to infer the intensity of intraspecific competition in the investigated streams. The species B. giacopinii, typically considered a trophic generalist, has been shown to be, in fact, a heterogeneous collection of specialist and generalist individuals. Contrary to our expectations, a higher degree of individual specialization was detected in streams dammed by the highway. In dammed streams, where intraspecific competition was more intense, individuals with narrower niches exhibited poorer body conditions than those with broader niches. This suggests that individuals adopting more restricted diets may have lower fitness, indicating that individual specialization may not necessarily be beneficial for individuals. Our results support the notion that intraspecific competition is an important mechanism underlying individual specialization in natural populations. Our results suggest that environmental characteristics (e.g., resource breadth and predictability) and competition for food resources interact in complex ways to determine the degree of individual specialization in natural populations.

Trophic niche partitioning and intraspecific variation in food resource use in the genus Pangasianodon in a reservoir revealed by stable isotope analysis of multiple tissues

Understanding the mechanism by which non-native fish species integrate into native communities is crucial for evaluating the possibility of their establishment success. The genus Pangasianodon, comprising Pangasianodon gigas and Pangasianodon hypophthalmus, has been introduced into reservoirs, which are non-native habitats, for fishery stock enhancement. P. gigas and P. hypophthalmus often successfully establish and co-occur in several Thai reservoirs, but there is little information on differences in food resource use between the two species. To investigate the trophic niche width of P. gigas and P. hypophthalmus in a Thai reservoir, we conducted stable carbon and nitrogen ratio (δ13C and δ15N) analyses. We examined the degree of individual specialization in both species using the δ13C and δ15N values of muscle and liver tissues, which provides long- and short-term diet information. The isotopic niches did not overlap between P. gigas and P. hypophthalmus. The δ15N value of P. gigas was significantly higher than that of P. hypophthalmus, whereas the δ13C value did not significantly differ between the two species. The isotopic niche sizes were larger in P. hypophthalmus than in P. gigas. Individual specialization was observed in P. hypophthalmus but not in P. gigas, indicating that intraspecific variation in food resource use was larger in P. hypophthalmus compared to P. gigas. These findings suggest that trophic niche partitioning was one of the factors facilitating the establishment success of P. gigas and P. hypophthalmus in a reservoir, but the establishment process may differ between the two species.

Genetic analysis of harvest samples reveals population structure in a highly mobile generalist carnivore

Delineating wildlife population boundaries is important for effective population monitoring and management. The bobcat (Lynx rufus) is a highly mobile generalist carnivore that is ecologically and economically important. We sampled 1225 bobcats harvested in South Dakota, USA (2014-2019), of which 878 were retained to assess genetic diversity and infer population genetic structure using 17 microsatellite loci. We assigned individuals to genetic clusters (K) using spatial and nonspatial Bayesian clustering algorithms and quantified differentiation (F ST and G ST ″ ) among clusters. We found support for population genetic structure at K = 2 and K = 4, with pairwise F ST and G ST ″ values indicating weak to moderate differentiation, respectively, among clusters. For K = 2, eastern and western clusters aligned closely with historical bobcat management units and were consistent with a longitudinal suture zone for bobcats previously identified in the Great Plains. We did not observe patterns of population genetic structure aligning with major rivers or highways. Genetic divergence observed at K = 4 aligned roughly with ecoregion breaks and may be associated with environmental gradients, but additional sampling with more precise locational data may be necessary to validate these patterns. Our findings reveal that cryptic population structure may occur in highly mobile and broadly distributed generalist carnivores, highlighting the importance of considering population structure when establishing population monitoring programs or harvest regulations. Our study further demonstrates that for elusive furbearers, harvest can provide an efficient, broad-scale sampling approach for genetic population assessments.

Niche partitioning and individual specialisation in resources and space use of sympatric fur seals at their range margin

Ecological theory predicts niche partitioning between high-level predators living in sympatry as a mechanism to minimise the selective pressure of competition. Accordingly, male Australian fur seals Arctocephalus pusillus doriferus and New Zealand fur seals A. forsteri that live in sympatry should exhibit partitioning in their broad niches (in habitat and trophic dimensions) in order to coexist. However, at the northern end of their distributions in Australia, both are recolonising their historic range after a long absence due to over-exploitation, and their small population sizes suggest competition should be weak and may allow overlap in niche space. We found some niche overlap, yet clear partitioning in diet trophic level (δ15N values from vibrissae), spatial niche space (horizontal and vertical telemetry data) and circadian activity patterns (timing of dives) between males of each species, suggesting competition may remain an active driver of niche partitioning amongst individuals even in small, peripheral populations. Consistent with individual specialisation theory, broad niches of populations were associated with high levels of individual specialisation for both species, despite putative low competition. Specialists in isotopic space were not necessarily specialists in spatial niche space, further emphasising their diverse individual strategies for niche partitioning. Males of each species displayed distinct foraging modes, with Australian fur seals primarily benthic and New Zealand fur seals primarily epipelagic, though unexpectedly high individual specialisation for New Zealand fur seals might suggest marginal populations provide exceptions to the pattern generally observed amongst other fur seals.

Imprints of indirect interactions on a resource-mediated ant-plant network across different levels of network organization

Indirect interactions are pivotal in the evolution of interacting species and the assembly of populations and communities. Nevertheless, despite recently being investigated in plant-animal mutualism at the community level, indirect interactions have not been studied in resource-mediated mutualisms involving plant individuals that share different animal species as partners within a population (i.e., individual-based networks). Here, we analyzed an individual-based ant-plant network to evaluate how resource properties affect indirect interaction patterns and how changes in indirect links leave imprints in the network across multiple levels of network organization. Using complementary analytical approaches, we described the patterns of indirect interactions at the micro-, meso-, and macro-scale. We predicted that plants offering intermediate levels of nectar quantity and quality interact with more diverse ant assemblages. The increased number of ant species would cause a higher potential for indirect interactions in all scales evaluated. We found that nectar properties modified patterns of indirect interactions of plant individuals that share mutualistic partners, leaving imprints across different network scales. To our knowledge, this is the first study tracking indirect interactions in multiple scales within an individual-based network. We show that functional traits of interacting species, such as nectar properties, may lead to changes in indirect interactions, which could be tracked across different levels of the network organization evaluated.

The Spatial Niche and Influencing Factors of Desert Rodents

Resource partitioning may allow species coexistence. Sand dunes in the typical steppe of Alxa Desert Inner Mongolia, China, consisting of desert, shrub, and grass habitats, provide an appropriate system for studies of spatial niche partitioning among small mammals. In this study, the spatial niche characteristics of four rodents, Orientallactaga sibirica, Meriones meridianus, Dipus sagitta, and Phodopus roborovskii, and their responses to environmental changes in the Alxa Desert were studied from 2017 to 2021. Using the capture-mark-recapture method, we tested if desert rodents with different biological characteristics and life history strategies under heterogeneous environmental conditions allocate resources in spatial niches to achieve sympatric coexistence. We investigated the influence of environmental factors on the spatial niche breadth of rodents using random forest and redundancy analyses. We observed that the spatial niche overlap between O. sibirica and other rodents is extremely low (overlap index ≤ 0.14). P. roborovskii had the smallest spatial niche breadth. Spatial niche overlap was observed in two distinct species pairs, M. meridianus and D. sagitta, and P. roborovskii and D. sagitta. The Pielou evenness index of rodent communities is closely related to the spatial distribution of rodents, and the concealment of habitats is a key factor affecting the spatial occupation of rodents.

Recent range shifts of moths, butterflies, and birds are driven by the breadth of their climatic niche

Species are altering their ranges as a response to climate change, but the magnitude and direction of observed range shifts vary considerably among species. The ability to persist in current areas and colonize new areas plays a crucial role in determining which species will thrive and which decline as climate change progresses. Several studies have sought to identify characteristics, such as morphological and life-history traits, that could explain differences in the capability of species to shift their ranges together with a changing climate. These characteristics have explained variation in range shifts only sporadically, thus offering an uncertain tool for discerning responses among species. As long-term selection to past climates have shaped species' tolerances, metrics describing species' contemporary climatic niches may provide an alternative means for understanding responses to on-going climate change. Species that occur in a broader range of climatic conditions may hold greater tolerance to climatic variability and could therefore more readily maintain their historical ranges, while species with more narrow tolerances may only persist if they are able to shift in space to track their climatic niche. Here, we provide a first-filter test of the effect of climatic niche dimensions on shifts in the leading range edges in three relatively well-dispersing species groups. Based on the realized changes in the northern range edges of 383 moth, butterfly, and bird species across a boreal 1,100 km latitudinal gradient over c. 20 years, we show that while most morphological or life-history traits were not strongly connected with range shifts, moths and birds occupying a narrower thermal niche and butterflies occupying a broader moisture niche across their European distribution show stronger shifts towards the north. Our results indicate that the climatic niche may be important for predicting responses under climate change and as such warrants further investigation of potential mechanistic underpinnings.

DNA metabarcoding, diversity partitioning and null models reveal mechanisms of seasonal trophic specialization in a Mediterranean warbler

Optimal Foraging Theory (OFT) predicts that a population's trophic niche expansion should occur in periods of food scarcity as individuals begin to opportunistically exploit sub-optimal food items. However, the Niche Variation Hypothesis (NVH) posits that niche widening may result from increased among-individual differentiation due to food partitioning to avoid competition. We tested these hypotheses through a DNA metabarcoding study of the Sardinian Warbler (Curruca melanocephala) diet over a year. We used null models and the decomposition of beta diversity on among-individual dietary differentiation to infer the mechanisms driving the population's niche variation. Warblers fed frequently on berries, with a peak in late summer and, to a lesser extent, in autumn. Their diet also included a wide range of arthropods, with their prevalence varying among seasons. Consistent with OFT, the population's niche width was narrower in spring/summer when the population was strongly specialized in berries. In winter, the population's niche expanded, possibly reflecting seasonal declines in food abundance. As predicted by NVH, among-individual differentiation tended to be higher in winter, but this was mainly due to increased differences in dietary richness rather than to the partitioning of resources. Overall, our results suggest that within-individual niche does not increase in lean periods, and instead, individuals adopt either a more opportunistic or more specialized foraging strategy. Increased competition in periods of scarcity may help explain such patterns, but instead of showing increased food partitioning as expected from NVH, it may reflect OFT mechanisms on individuals with differential competitive ability to access better food resources.

Trophic downgrading of an adaptable carnivore in an urbanising landscape

Urbanisation critically alters wildlife habitat and resource distribution, leading to shifts in trophic dynamics. The loss of apex predators in human-transformed landscapes can result in changes in the ecological roles of the remaining mesocarnivores. Decreased top-down control together with increased bottom-up forcing through greater availability of anthropogenic foods can result in a predation paradox. Understanding these changes is important for conserving ecological function and biodiversity in rapidly urbanising systems. Here, we use stable isotope analysis to provide insight into longer term changes in trophic position, niche width and overlap of an elusive, medium-sized urban adapter, the caracal (Caracal caracal) in and around the city of Cape Town, South Africa. Using fur samples (n = 168) from individuals along a gradient of urbanisation we find that overall caracals have a broad isotopic dietary niche that reflects their large variation in resource use. When accounting for underlying environmental differences, the intensity of anthropogenic pressure, measured using the Human Footprint Index (HFI), explained variation in both food subsidy use (δ13C values) and trophic status (δ15N values). The significantly higher δ13C values (P < 0.01) and lower δ15N values (P < 0.001) of caracals in more urbanised areas suggest that predator subsidy consumption occurs via predictable, anthropogenic resource subsidies to synanthropic prey. These prey species are predominantly primary consumers, resulting in shifts in diet composition towards lower trophic levels. Further, caracals using areas with higher HFI had narrower isotope niches than those in less impacted areas, likely due to their hyperfocus on a few lower trophic level prey species. This pattern of niche contraction in urban areas is retained when accounting for caracal demographics, including sex and age. The removal of apex predators in human-transformed landscapes together with reliable resource availability, including abundant prey, may paradoxically limit the ecological influence of the remaining predators, and bring about a degree of predator trophic downgrading. The dampening of top-down control, and thus ecosystem regulation, likely points to widespread disruption of trophic dynamics in rapidly developing areas globally.

Nodulation number tempers the relative importance of stochastic processes in the assembly of soybean root-associated communities

Identifying the ecological forces that structure root-associated microbial communities is an essential step toward more sustainable agriculture. Legumes are widely utilized as model plants to study selective forces and their functioning in plant-microbial interactions owing to their ability to establish mutualism with rhizobia. Root nodules act as symbiotic organs to optimize the cost-benefit balance in this mutualistic relationship by modulating the number of nodules. However, it is not known whether the number of nodules is related to the structure of root-associated bacterial communities. Here, the root-associated bacterial communities of soybean grown in native soil by means of soybean cultivars with super- or normal nodulation were investigated across four developmental stages. We compared ecological processes between communities and found decreased relative importance of neutral processes for super-nodulating soybean, although the overall structures resembled those of normal-nodulating soybean. We identified the generalist core bacterial populations in each root-associated compartment, that are shared across root-associated niches, and persist through developmental stages. Within core bacterial species, the relative abundances of bacterial species in the rhizosphere microbiome were linked to host-plant functional traits and can be used to predict these traits from microbes using machine learning algorithms. These findings broaden the comprehensive understanding of the ecological forces and associations of microbiotas in various root-associated compartments and provide novel insights to integrate beneficial plant microbiomes into agricultural production to enhance plant performance.

Parallel shifts in trout feeding morphology suggest rapid adaptation to alpine lake environments

Eco-evolutionary interactions following ecosystem change provide critical insight into the ability of organisms to adapt to shifting resource landscapes. Here we explore evidence for the rapid parallel evolution of trout feeding morphology following eco-evolutionary interactions with zooplankton in alpine lakes stocked at different points in time in the Wind River Range (Wyoming, USA). In this system, trout predation has altered the zooplankton species community and driven a decrease in average zooplankton size. In some lakes that were stocked decades ago, we find shifts in gill raker traits consistent with the hypothesis that trout have rapidly adapted to exploit available smaller-bodied zooplankton more effectively. We explore this morphological response in multiple lake populations across two species of trout (cutthroat trout, Oncorhynchus clarkii, and golden trout Oncorhynchus aguabonita) and examine the impact of resource availability on morphological variation in gill raker number among lakes. Furthermore, we present genetic data to provide evidence that historically stocked cutthroat trout populations likely derive from multiple population sources, and incorporate variation from genomic relatedness in our exploration of environmental predictors of feeding morphology. These findings describe rapid adaptation and eco-evolutionary interactions in trout and document an evolutionary response to novel, contemporary ecosystem change.

Linking changes in individual specialization and population niche of space use across seasons in the great evening bat (Ia io)

BACKGROUND

The niche breadth of an animal population comprises both within-individual and between-individual variation (individual specialization). Both components can be used to explain changes in population niche breadth, and this has been extensively investigated in dietary niche dimension studies. However, little is known about how changes in food resources or environmental factors across seasons affect changes in individual and population space use within the same population.

METHODS

In this study, we used micro-GPS loggers to capture the space use of individuals and of a population of the great evening bat (Ia io) in summer and autumn. We used I. io as a model to investigate how individual spatial niche breadth and spatial individual specialization affect changes in population niche breadth (home range and core area sizes) across seasons. Additionally, we explored the drivers of individual spatial specialization.

RESULTS

We found that the population home range and the core area of I. io did not increase in autumn when insect resources were reduced. Moreover, I. io showed different specialization strategies in the two seasons: higher spatial individual specialization in summer and lower individual specialization but broader individual niche breadth in autumn. This trade-off may maintain the dynamic stability of the population spatial niche breadth across seasons and facilitate the population response to changes in food resources and environmental factors.

CONCLUSIONS

Like diet, spatial niche breadth of a population also may be determined by a combination of individual niche breadth and individual specialization. Our work provides new insights into the evolution of niche breadth from the spatial dimension.

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.

Seasonal variation of population and individual dietary niche in the avivorous bat, Ia io

The variation in niche breadth can affect how species respond to environmental and resource changes. However, there is still no clear understanding of how seasonal variability in food resources impacts the variation of individual dietary diversity, thereby affecting the dynamics of a population's dietary niche breadth. Optimal foraging theory (OFT) and the niche variation hypothesis (NVH) predict that when food resources are limited, the population niche breadth will widen or narrow due to increased within-individual dietary diversity and individual specialization or reduced within-individual dietary diversity, respectively. Here, we used DNA metabarcoding to examine the composition and seasonality of diets of the avivorous bat Ia io. Furthermore, we investigated how the dietary niches changed among seasons and how the population niche breadth changed when the availability of insect resources was reduced in autumn. We found that there was differentiation in dietary niches among seasons and a low degree of overlap, and the decrease of insect resource availability and the emergence of ecological opportunities of nocturnal migratory birds might drive dietary niche shifts toward birds in I. io. However, the population's dietary niche breadth did not broaden by increasing the within-individual dietary diversity or individual specialization, but rather became narrower by reducing dietary diversity via predation on bird resources that served as an ecological opportunity when insect resources were scarce in autumn. Our findings were consistent with the predictions of OFT, because birds as prey for bats provided extremely different resources from those of insects in size and nutritional value. Our work highlights the importance of size and quality of prey resources along with other factors (i.e., physiological, behavioral, and life-history traits) in dietary niche variation.

Interpreting past trophic ecology of a threatened alpine parrot, kea Nestor notabilis, from museum specimens

When ecosystems are under severe pressure or environments change, trophic position and intraspecific niche width may decrease or narrow, signalling that conservation action is required. In New Zealand, alpine and subalpine ecosystems have been extensively modified through farming since 19th-century European settlement, with consequences for indigenous species such as the kea Nestor notabilis. We investigated feather stable isotope values in the kea and predicted a lower trophic position in modern kea populations, to reflect reduced lowland habitat and a mixed diet with more plant material. We predicted that size and sex would influence trophic values in this sexually dimorphic species, with larger birds more likely to have a high protein diet. We examined potential dietary changes in 68 museum collected kea from 1880s to 2000s, first recording accession details including provenance and sex and measuring culmen length. We used bulk carbon and nitrogen stable isotope analyses (BSIAs) of feathers and a further feather subset using compound-specific stable isotope analyses of amino acids (CSIA-AA) to obtain isotopic values and estimate trophic position. BSIA showed δ¹⁵ N values in kea feathers declined through time and could indicate that early century kea were highly omnivorous, with δ¹⁵ N values on average higher than in modern kea. Variance in δ¹⁵ N values was greater after 1950, driven by a few individuals. Few differences between males and females were evident, although females in the south region had lower δ¹⁵ N values. There was a tendency for large male birds to have higher trophic values, perhaps reflecting dominant male bird behaviour noted in historical records. Nonetheless, CSIA-AA performed on a subset of the data suggested that variation in BSIA is likely due to baseline changes rather than relative trophic position which may be more homogenous than these data indicate. Although there was more variability in modern kea, we suggest caution in interpretation. Stable isotope data, particularly CSIA-AA, from museum specimens can reveal potential change in ecological networks as well as sexually dimorphic feeding patterns within species. The data can reveal temporal and regional variation in species trophic position and changes in ecosystem integrity to inform conservation decision-making.

Hidden diversity: comparative functional morphology of humans and other species

Gastrointestinal (GI) morphology plays an important role in nutrition, health, and epidemiology; yet limited data on GI variation have been collected since 1885. Here we demonstrate that students can collect reliable data sets on gut morphology; when they do, they reveal greater morphological variation for some structures in the GI tract than has been documented in the published literature. We discuss trait variability both within and among species, and the implications of that variability for evolution and epidemiology. Our results show that morphological variation in the GI tract is associated with each organ's role in food processing. For example, the length of many structures was found to vary significantly with feeding strategy. Within species, the variability illustrated by the coefficients of variation suggests that selective constraints may vary with function. Within humans, we detected significant Pearson correlations between the volume of the liver and the length of the appendix (t-value = 2.5278, df = 28, p = 0.0174, corr = 0.4311) and colon (t-value = 2.0991, df = 19, p = 0.0494, corr = 0.4339), as well as between the lengths of the small intestine and colon (t-value = 2.1699, df = 17, p = 0.0445, corr = 0.4657), which are arguably the most vital organs in the gut for nutrient absorption. Notably, intraspecific variation in the small intestine can be associated with life history traits. In humans, females demonstrated consistently and significantly longer small intestines than males (t-value₁₅ = 2.245, p = 0.0403). This finding supports the female canalization hypothesis, specifically, increased female investment in the digestion and absorption of lipids.

DNA metabarcoding suggests adaptive seasonal variation of individual trophic traits in a critically endangered fish

Dietary studies are critical for understanding foraging strategies and have important applications in conservation and habitat management. We applied a robust metabarcoding protocol to characterize the diet of the critically endangered freshwater fish Zingel asper (the Rhone streber). We conducted modelling and simulation analyses to identify and characterize some of the drivers of individual trophic trait variation in this species. We found that population density and ontogeny had minor effects on the trophic niche of Z. asper. Instead, our results suggest that the majority of trophic niche variation was driven by seasonal variation in ecological opportunity. The total trophic niche width of Z. asper seasonally expanded to include a broader range of prey. Furthermore, null model simulations revealed that the increase of between-individual variation in autumn indicates that Z. asper become more opportunistic relative to summer and spring, rather than being associated with a seasonal specialization of individuals. Overall, our results suggest an adaptive variation of individual trophic traits in Z. asper: the species mainly consumes a few ephemeropteran taxa (Baetis fuscatus and Ecdyonurus) but seems to be capable of adapting its foraging strategy to maintain its body condition. This study illustrates how metabarcoding data obtained from faeces can be validated and combined with individual-based modelling and simulation approaches to explore inter- and intrapopulational individual trophic traits variation and to test hypotheses in the conventional analytic framework of trophic ecology.

Effective specialist or jack of all trades? Experimental evolution of a crop pest in fluctuating and stable environments

Understanding pest evolution in agricultural systems is crucial for developing effective and innovative pest control strategies. Types of cultivation, such as crop monocultures versus polycultures or crop rotation, may act as a selective pressure on pests' capability to exploit the host's resources. In this study, we examined the herbivorous mite Aceria tosichella (commonly known as wheat curl mite), a widespread wheat pest, to understand how fluctuating versus stable environments influence its niche breadth and ability to utilize different host plant species. We subjected a wheat-bred mite population to replicated experimental evolution in a single-host environment (either wheat or barley), or in an alternation between these two plant species every three mite generations. Next, we tested the fitness of these evolving populations on wheat, barley, and on two other plant species not encountered during experimental evolution, namely rye and smooth brome. Our results revealed that the niche breadth of A. tosichella evolved in response to the level of environmental variability. The fluctuating environment expanded the niche breadth by increasing the mite's ability to utilize different plant species, including novel ones. Such an environment may thus promote flexible host-use generalist phenotypes. However, the niche expansion resulted in some costs expressed as reduced performances on both wheat and barley as compared to specialists. Stable host environments led to specialized phenotypes. The population that evolved in a constant environment consisting of barley increased its fitness on barley without the cost of utilizing wheat. However, the population evolving on wheat did not significantly increase its fitness on wheat, but decreased its performance on barley. Altogether, our results indicated that, depending on the degree of environmental heterogeneity, agricultural systems create different conditions that influence pests' niche breadth evolution, which may in turn affect the ability of pests to persist in such systems.

Populations of western North American monkeyflowers accrue niche breadth primarily via genotypic divergence in environmental optima

Niche breadth, the range of environments that individuals, populations, and species can tolerate, is a fundamental ecological and evolutionary property, yet few studies have examined how niche breadth is partitioned across biological scales. We use a published dataset of thermal performance for a single population from each of 10 closely related species of western North American monkeyflowers (genus Mimulus) to investigate whether populations achieve broad thermal niches through general purpose genotypes, specialized genotypes with divergent environmental optima, and/or variation among genotypes in the degree of generalization. We found the strongest relative support for the hypothesis that populations with greater genetic variation for thermal optimum had broader thermal niches, and for every unit increase in among-family variance in thermal optimum, population-level thermal breadth increased by 0.508°C. While the niche breadth of a single genotype represented up to 86% of population-level niche breadth, genotype-level niche breadth had a weaker positive effect on population-level breadth, with every 1°C increase in genotypic thermal breadth resulting in a 0.062°C increase in population breadth. Genetic variation for thermal breadth was not predictive of population-level thermal breadth. These findings suggest that populations of Mimulus species have achieved broad thermal niches primarily through genotypes with divergent thermal optima and to a lesser extent via general-purpose genotypes. Future work examining additional biological hierarchies would provide a more comprehensive understanding of how niche breadth partitioning impacts the vulnerabilities of individuals, populations, and species to environmental change.

Correlating gut microbial membership to brown bear health metrics

The internal mechanisms responsible for modulating physiological condition, particularly those performed by the gut microbiome (GMB), remain under-explored in wildlife. However, as latitudinal and seasonal shifts in resource availability occur, the myriad micro-ecosystem services facilitated by the GMB may be especially important to wildlife health and resilience. Here, we use brown bears (Ursus arctos) as an ecological model to quantify the relationship between wildlife body condition metrics that are commonly used to assess individual and population-level health and GMB community composition and structure. To achieve these aims, we subsampled brown bear fecal samples collected during United States National Park Service research activities at three National Parks and Preserves (Katmai, Lake Clark, and Gates of the Arctic) and extracted microbial DNA for 16S rRNA amplicon sequencing and microbial taxonomic classification. We analyzed GMB communities using alpha diversity indices, subsequently using Spearman’s correlation analysis to examine relationships between alpha diversity and brown bear health metrics. We found no differences in GMB composition among bears with differing body conditions, nor any correlations between alpha diversity and body condition. Our results indicate that GMB composition reflects diverse foraging strategies while allowing brown bears to achieve similar body condition outcomes.

Linking sexual size dimorphism to trophic niche partitioning in a generalist predator

Sexual size dimorphism is a common phenomenon in mammals, and researchers have been trying to demonstrate the evolutionary causes leading to sexual dimorphism. Two main hypotheses emerged: (1) the sexual selection hypothesis and (2) the sexual competition hypothesis (also called resource partitioning hypothesis). Here, we attempted to link sexual dimorphism in fishers ( Pekania pennanti (Erxleben, 1777)) with their fall diet using stable isotope profiling and body and skull measurements. We used the carcasses of 39 fishers which were caught in eastern Québec during fall 2014 by volunteer trappers as well as several potential prey items ranging from small rodents to cervids. We expected minimal niche overlap between sexes, as males should be able to exploit different prey species than females. We also expected to observe an effect of age class (adults vs. juveniles) on trophic niche. As expected, we found great evidence of sexual dimorphism in both body mass and skull measurements: males were heavier and longer than females and had a larger zygomatic and intracanine width and a longer skull. While proportions of prey in diet according to sex and age did not vary greatly, we found some evidence of niche partitioning using Layman's metrics. Indeed, females tended to have a less diversified and more similar diet compared to one another, whereas males showed more diversified and contrasted diets. Despite our limited sample size, our findings provide partial support to the sexual competition hypothesis, as the difference in body and skull size based on sex could have evolved to lessen intraspecific competition in fishers.

Improving stable isotope assessments of inter- and intra-species variation in coral reef fish trophic strategies

Fish have one of the highest occurrences of individual specialization in trophic strategies among Eukaryotes. Yet, few studies characterize this variation during trophic niche analysis, limiting our understanding of aquatic food web dynamics. Stable isotope analysis (SIA) with advanced Bayesian statistics is one way to incorporate this individual trophic variation when quantifying niche size. However, studies using SIA to investigate trophodynamics have mostly focused on species- or guild-level (i.e., assumed similar trophic strategy) analyses in settings where source isotopes are well-resolved. These parameters are uncommon in an ecological context. Here, we use Stable Isotope Bayesian Ellipses in R (SIBER) to investigate cross-guild trophodynamics of 11 reef fish species within an oceanic atoll. We compared two- (δ 15N and δ 13C) versus three-dimensional (δ 15N, δ 13C, and δ 34S) reconstructions of isotopic niche space for interpreting guild-, species-, and individual-level trophic strategies. Reef fish isotope compositions varied significantly among, but also within, guilds. Individuals of the same species did not cluster together based on their isotope values, suggesting within-species specializations. Furthermore, while two-dimensional isotopic niches helped differentiate reef fish resource use, niche overlap among species was exceptionally high. The addition of δ 34S and the generation of three-dimensional isotopic niches were needed to further characterize their isotopic niches and better evaluate potential trophic strategies. These data suggest that δ 34S may reveal fluctuations in resource availability, which are not detectable using only δ 15N and δ 13C. We recommend that researchers include δ 34S in future aquatic food web studies.

The Trophic Niche of Two Sympatric Species of Salamanders (Plethodontidae and Salamandridae) from Italy

Simple Summary

Studies on species’ trophic niches are essential to understand the characteristics of species’ ecology and life traits, as well as to improve conservation strategies. In the absence of competitors, species realize their trophic niche including in their diet the most profitable food resources. In the presence of competitors, species modify their preferences to reduce competition and maintain the highest benefits at the same time. In this study, we assessed the trophic niche of two species of salamanders coexisting in a forested area of Italy and evaluated which might be the mechanisms that these two species adopted to reduce competition. We found that the Italian cave salamander (Speleomantes italicus) mostly consumed flying prey with a hard cuticle, while the fire salamander (Salamandra salamandra) preferred worm-like and soft-bodied prey. In conclusion, we hypothesize that in our case, the two species of salamanders did not have to change their prey preference in order to avoid competition, but divergences in metabolism and behavioral traits likely worked as natural deterrent.

Abstract

The trophic niche of a species is one of the fundamental traits of species biology. The ideal trophic niche of a species is realized in the absence of interspecific competition, targeting the most profitable and easy-to-handle food resources. However, when a competitor is present, species adopt different strategies to reduce competition and promote coexistence. In this study, we assessed the potential mechanisms that allow the coexistence of two generalist salamanders: the Italian cave salamander (Speleomantes italicus) and the fire salamander (Salamandra salamandra). We surveyed, in April 2021, a forested area of Emilia-Romagna (Italy) during rainy nights. Analyzing the stomach contents of the captured individuals, we obtained information on the trophic niche of these two sympatric populations. Comparing our results with those of previous studies, we found that the two species did not modify their trophic niche, but that alternative mechanisms allowed their coexistence. Specifically, different prey preferences and predator metabolisms were likely the major factors allowing reduced competition between these two generalist predators.

Long-term manure inputs induce a deep selection on agroecosystem soil antibiotic resistome

Although the enrichment of antibiotic resistance genes (ARGs) in diverse organic soils have been explored, understanding of the ecological processes governing the composition of ARGs in long-term organically fertilized soils still remains limited across typical agricultural regions. Thus, the distribution and assembly of ARG profile in three typical agricultural soils (black soil, fluvo-aquic soil, and red soil) under long-term contrasting fertilization regimes (chemical-only vs organic-only) were investigated using high-throughput qPCR (HT-qPCR). The application of organic manure significantly increased the abundance and number of ARGs across soils, as compared to those with chemical fertilizer. Organic manure application enriched the abundance of mobile genetic elements (MGEs), which were positively associated with ARGs. In addition, it is long-term organic fertilizer that enriched the number and abundance of opportunist and specialist ARGs in the fluvo-aquic and red soils, but not black soils. The number and abundance of most generalist ARGs did not change significantly among different fertilization or soil types. The assembly process of the ARG profiles tends to be more deterministic in organically fertilized soils than in chemically fertilized soils. These results suggest that long-term organic fertilizer application may contribute to the persistence and health risk of the soil antibiotic resistomes (especially specialist ARGs).

Individual-level specialisation and interspecific resource partitioning in bees revealed by pollen DNA metabarcoding

It is increasingly recognised that intraspecific variation in traits, such as morphology, behaviour, or diet is both ubiquitous and ecologically important. While many species of predators and herbivores are known to display high levels of between-individual diet variation, there is a lack of studies on pollinators. It is important to fill in this gap because individual-level specialisation of flower-visiting insects is expected to affect their efficiency as pollinators with consequences for plant reproduction. Accordingly, the aim of our study was to quantify the level of individual-level specialisation and foraging preferences, as well as interspecific resource partitioning, in three co-occurring species of bees of the genus Ceratina (Hymenoptera: Apidae: Xylocopinae), C. chalybea, C. nigrolabiata, and C. cucurbitina. We conducted a field experiment where we provided artificial nesting opportunities for the bees and combined a short-term mark-recapture study with the dissection of the bees' nests to obtain repeated samples from individual foraging females and complete pollen provisions from their nests. We used DNA metabarcoding based on the ITS2 locus to identify the composition of the pollen samples. We found that the composition of pollen carried on the bodies of female bees and stored in the brood provisions in their nests significantly differed among the three co-occurring species. At the intraspecific level, individual females consistently differed in their level of specialisation and in the composition of pollen carried on their bodies and stored in their nests. We also demonstrate that higher generalisation at the species level stemmed from larger among-individual variation in diets, as observed in other types of consumers, such as predators. Our study thus reveals how specialisation and foraging preferences of bees change from the scale of individual foraging bouts to complete pollen provisions accumulated in their nests over many days. Such a multi-scale view of foraging behaviour is necessary to improve our understanding of the functioning of plant-flower visitor communities.

The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs

Environmental degradation has the potential to alter key mutualisms that underlie the structure and function of ecological communities. How microbial communities associated with fishes vary across populations and in relation to habitat characteristics remains largely unknown despite their fundamental roles in host nutrition and immunity. We find significant differences in the gut microbiome composition of a facultative coral-feeding butterflyfish (Chaetodon capistratus) across Caribbean reefs that differ markedly in live coral cover (∼0–30%). Fish gut microbiomes were significantly more variable at degraded reefs, a pattern driven by changes in the relative abundance of the most common taxa potentially associated with stress. We also demonstrate that fish gut microbiomes on severely degraded reefs have a lower abundance of Endozoicomonas and a higher diversity of anaerobic fermentative bacteria, which may suggest a less coral dominated diet. The observed shifts in fish gut bacterial communities across the habitat gradient extend to a small set of potentially beneficial host associated bacteria (i.e., the core microbiome) suggesting essential fish-microbiome interactions may be vulnerable to severe coral degradation.

The gut microbiome composition of the coral-feeding butterflyfish across Caribbean reefs is more variable at degraded reefs. These microbiomes have a lower abundance of Endozoicomonas and a higher diversity of anaerobic fermentative bacteria.

Linking agricultural practices to lizard trophic behaviour: An ecological approach

Among intensive agricultural practices, pesticides, mowing, and heavy agricultural machineries have become an important tool to maximize harvesting and secure animal husbandry. However, they are also cause of agricultural ecosystem decline, often leading to degradation of key micro-habitat features for many species, higher predation risk and lower food availability. We investigated the diet and foraging ecology of the Italian wall lizard in agricultural areas to determine whether different management practices (conventional, organic, and control) can affect (i) the structure of the trophic niche of the species; (ii) prey diversity, the degree of individual specialization, and the overall population feeding strategy; (iii) lizards' health status. Faecal pellets were collected for diet composition analyses, while prey diversity in the environment was estimated by placing adhesive traps. Lizards' body condition did not differ among management type although males from control field resulted slightly larger than those from conventional and organic areas. The species showed a generalist (conventional and organic areas) and mixed (control area) feeding strategy with a preference for coleopterans. Although a different prey diversity was found in control areas compared to organic and conventional ones, diet composition and the importance of specific food items was similar among management types. This may suggest that management activities may have affected the overall prey availability and indirectly influenced lizard trophic behaviour. Our study provides a comprehensive knowledge on the feeding ecology of P. siculus in managed habitats, which may have useful implications for the overall conservation of lizards in agricultural environments.

Evolutionary transitions in diet influence the exceptional diversification of a lizard adaptive radiation

Background

Diet is a key component of a species ecological niche and plays critical roles in guiding the trajectories of evolutionary change. Previous studies suggest that dietary evolution can influence the rates and patterns of species diversification, with omnivorous (animal and plant, ‘generalist’) diets slowing down diversification compared to more restricted (‘specialist’) herbivorous and carnivorous diets. This hypothesis, here termed the “dietary macroevolutionary sink” hypothesis (DMS), predicts that transitions to omnivorous diets occur at higher rates than into any specialist diet, and omnivores are expected to have the lowest diversification rates, causing an evolutionary sink into a single type of diet. However, evidence for the DMS hypothesis remains conflicting. Here, we present the first test of the DMS hypothesis in a lineage of ectothermic tetrapods—the prolific Liolaemidae lizard radiation from South America.

Results

Ancestral reconstructions suggest that the stem ancestor was probably insectivorous. The best supported trait model is a diet-dependent speciation rate, with independent extinction rates. Herbivory has the highest net diversification rate, omnivory ranks second, and insectivory has the lowest. The extinction rate is the same for all three diet types and is much lower than the speciation rates. The highest transition rate was from omnivory to insectivory, and the lowest transition rates were between insectivory and herbivory.

Conclusions

Our findings challenge the core prediction of the DMS hypothesis that generalist diets represent an ‘evolutionary sink’. Interestingly, liolaemid lizards have rapidly and successfully proliferated across some of the world’s coldest climates (at high elevations and latitudes), where species have evolved mixed arthropod-plant (omnivore) or predominantly herbivore diets. This longstanding observation is consistent with the higher net diversification rates found in both herbivory and omnivory. Collectively, just like the evolution of viviparity has been regarded as a ‘key adaptation’ during the liolaemid radiation across cold climates, our findings suggest that transitions from insectivory to herbivory (bridged by omnivory) are likely to have played a role as an additional key adaptation underlying the exceptional diversification of these reptiles across extreme climates.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02028-3.

Population niche width is driven by within-individual niche expansion and individual specialization in introduced brook trout in mountain lakes

The width of a population's resource-use niche is determined by individual diet breadth ("within-individual component") and the degree of niche partitioning between individuals ("between-individual component"). The balance between these two factors affects ecological stability and evolutionary trajectories, and may shift as ecological opportunity permits broader population niches. Lakes in California's Sierra Nevada Mountains vary in resource diversity for introduced brook trout (Salvelinus fontinalis) due to elevation, lake morphometry, and watershed features. We compared the relative contributions of within- and between-individual niche components to two measures of the dietary niches of thirteen populations of brook trout: prey taxonomic composition and prey size distribution. For both taxonomic and size diversity of fish diets, population niche width was positively related to both the within- and between-individual components. For taxonomic diversity, the two components increased in parallel, while for size diversity, the between-individual component became more important relative to the within-individual component in populations with the greatest niche widths. Our results support the Niche Variation Hypothesis that populations with broader niches are more heterogeneous among individuals and show that individual niche width and individual specialization can operate in parallel to expand the population niche.

The evolution of trait variance creates a tension between species diversity and functional diversity

It seems intuitively obvious that species diversity promotes functional diversity: communities with more plant species imply more varied plant leaf chemistry, more species of crops provide more kinds of food, etc. Recent literature has nuanced this view, showing how the relationship between the two can be modulated along latitudinal or environmental gradients. Here we show that even without such effects, the evolution of functional trait variance can erase or even reverse the expected positive relationship between species- and functional diversity. We present theory showing that trait-based eco-evolutionary processes force species to evolve narrower trait breadths in more tightly packed, species-rich communities, in their effort to avoid competition with neighboring species. This effect is so strong that it leads to an overall reduction in trait space coverage whenever a new species establishes. Empirical data from land snail communities on the Galápagos Islands are consistent with this claim. The finding that the relationship between species- and functional diversity can be negative implies that trait data from species-poor communities may misjudge functional diversity in species-rich ones, and vice versa.

The positive relationship between species diversity and functional diversity has been shown to vary. Here, the authors use theoretical models and data from Galápagos land snail communities to show how eco-evolutionary processes can force species to evolve narrower trait breadths in more species-rich communities to avoid competition, creating a negative relationship.

Feeding ecology of the endangered toad Bombina pachypus in central Italy

Anurans are generalist opportunistic consumers, but many species show some degree of diet specialization. Within populations, individuals may specialize on specific dietary resources (individual specialization). Indeed, generalist populations may be composed of individuals using the whole range of available resources or by diverse individuals exploiting specific food items. Based on the Niche Variation Hypothesis (NHV) an increase in population niche width may be related to higher incidence of individual specialization. We analysed the feeding ecology of the endangered toad Bombina pachypus (Bonaparte, 1838) in central Italy. Bombina pachypus showed a generalist feeding strategy, wide trophic niche, high individual generalization, and a predominance use of terrestrial resources. The study species inhabits seasonal habitats determining variation in food availability and diversity, and this may have driven toads to be unselective and consume almost any encountered palatable item. The absence of sexual size dimorphism may explain the absence of trophic differentiation between sexes. The analysis of individual feeding traits revealed a week degree of individual specialization positively correlated to niche width partly supporting NHV. The obtained information can be used for the implementation of effective conservation strategies of locally imperilled species, especially those breeding in temporary ponds.

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.

Trophic niche partitioning between two prey and their incidental predators revealed various threats for an endangered species

Documenting trophic niche partitioning and resource use within a community is critical to evaluate underlying mechanisms of coexistence, competition, or predation. Detailed knowledge about foraging is essential as it may influence the vital rates, which, in turn, can affect trophic relationships between species, and population dynamics. The aims of this study were to evaluate resource and trophic niche partitioning in summer/autumn between the endangered Atlantic-Gaspésie caribou (Rangifer tarandus caribou) population, moose (Alces americanus) and their incidental predators, the black bear (Ursus americanus) and coyote (Canis latrans), and to quantify the extent to which these predators consumed caribou. Bayesian isotopic analysis showed a small overlap in trophic niche for the two sympatric ungulates suggesting a low potential for resource competition. Our results also revealed that caribou occupied a larger isotopic niche area than moose, suggesting a greater diversity of resources used by caribou. Not surprisingly, coyotes consumed mainly deer (Odocoileus virginianus), moose, snowshoe hare (Lepus americanus), and occasionally caribou, while bears consumed mainly vegetation and, to a lesser extent, moose and caribou. As coyotes and bears also feed on plant species, we documented trophic niche overlap between caribou and their predators, as searching for similar resources can force them to use the same habitats and thus increase the encounter rate and, ultimately, mortality risk for caribou. Although the decline in the Gaspésie caribou population is mostly driven by habitat-mediated predation, we found evidence that the low level of resource competition with moose, added to the shared resources with incidental predators, mainly bears, may contribute to jeopardize the recovery of this endangered caribou population. Highlighting the trophic interaction between species is needed to establish efficient conservation and management strategies to insure the persistence of endangered populations. The comparison of trophic niches of species sharing the same habitat or resources is fundamental to evaluate the mechanisms of coexistence or competition and eventually predict the consequences of ecosystem changes in the community.

Global long-term stability of individual dietary specialization in herbivorous mammals

Dietary variation within species has important ecological and evolutionary implications. While theoreticians have debated the consequences of trait variance (including dietary specialization), empirical studies have yet to examine intraspecific dietary variability across the globe and through time. Here, we use new and published serial sampled δ¹³C_enamel values of herbivorous mammals from the Miocene to the present (318 individuals summarized, 4134 samples) to examine how dietary strategy (i.e. browser, mixed-feeder, grazer) affects individual isotopic variation. We find that almost all herbivores, regardless of dietary strategy, are composed of individual specialists. For example, Cormohipparion emsliei (Equidae) from the Pliocene of Florida (approx. 5 Ma) exhibits a δ¹³C_enamel range of 13.4‰, but all individuals sampled have δ¹³C_enamel ranges of less than or equal to 2‰ (mean = 1.1‰). Most notably, this pattern holds globally and through time, with almost all herbivorous mammal individuals exhibiting narrow δ¹³C_enamel ranges (less than or equal to 3‰), demonstrating that individuals are specialized and less representative of their overall species' dietary breadth. Individual specialization probably reduces intraspecific competition, increases carrying capacities, and may have stabilizing effects on species and communities over time. Individual specialization among species with both narrow and broad dietary niches is common over space and time-a phenomenon not previously well recognized or documented empirically.

Variable effects of wolves on niche breadth and density of intraguild competitors

The parallel niche release hypothesis (PNR) indicates that reduced competition with dominant competitors results in greater density and niche breadth of subordinate competitors and which may support an adaptive advantage.We assessed support for the PNR by evaluating relationships between variation in niche breadth and intra- and interspecific density (an index of competition) of wolves (Canis lupus) coyotes (C. latrans), and bobcats (Lynx rufus).We estimated population density (wolf track surveys, coyote howl surveys, and bobcat hair snare surveys) and variability in space use (50% core autocorrelated kernel density home range estimators), temporal activity (hourly and overnight speed), and dietary (isotopic δ13C and δ15N) niche breadth of each species across three areas of varying wolf density in the Upper Peninsula of Michigan, USA, 2010-2019.Densities of wolves and coyotes were inversely related, and increased variability in space use, temporal activity, and dietary niche breadth of coyotes was associated with increased coyote density and decreased wolf density supporting the PNR. Variability in space use and temporal activity of wolves and dietary niche breadth of bobcats also increased with increased intraspecific density supporting the PNR.Through demonstrating decreased competition between wolves and coyotes and increased coyote niche breadth and density, our study provides multidimensional support for the PNR. Knowledge of the relationship between niche breadth and population density can inform our understanding of the role of competition in shaping the realized niche of species.

A 21-Year Survey of Escherichia coli from Bloodstream Infections (BSI) in a Tertiary Hospital Reveals How Community-Hospital Dynamics of B2 Phylogroup Clones Influence Local BSI Rates

This is a longitudinal study comprising 649 Escherichia coli isolates representing all 7,165 E. coli bloodstream infection (BSI) episodes recorded in a hospital (1996 to 2016). Strain analysis included clonal identification (phylogenetic groups/subgroups, STc131 subclades, pulsed-field gel electrophoresis [PFGE], and whole-genome sequencing [WGS]), antibiotic susceptibility (13 antibiotics), and virulence-associated genes (VAGs; 29 genes). The incidence of E. coli BSI increased from 1996 to 2016 (5.5 to 10.8 BSI episodes/1,000 hospitalizations, average 7 to 8/1,000). B2 isolates predominate (53%), with subgroups B2-I (STc131), B2-II, B2-IX, and B2-VI representing 25%, 25%, 14%, and 9%, respectively. Intertwined waves of community-acquired (CA) plus health care-associated and community-onset health care-associated (HCA) and hospital-acquired (HA) episodes of both B2 and non-B2 phylogroups occurred. A remarkable increase was observed only for B2-I-STc131 (C1/C2 subclades), with oscillations for other B2 subgroups and phylogroups throughout the years. Epidemic and persistent clones (comprising isolates with highly similar/identical PFGE types and genomes differing in 6 to 173 single nucleotide polymorphisms [SNPs]) of B2-I (STc131), B2-II (STc73), B2-III (STc127), B2-IX (STc95), and B2-VI (STc12) were recovered from different patients, most at hospital admission, for long periods (2 to 17 years), and extended-spectrum beta-lactamase (ESBL) producers or resistance to ciprofloxacin in B2 isolates was almost restricted to B2-I (STc131) subclade C. STc131 contributed to increasing the B2 rates but only transiently altered the E. coli population structure. The increase of E. coli BSI was determined by waves of CA+HCA BSI episodes that predate the waves of HA BSI. Besides the risk of hospital transmission that led to temporal increases in BSI, this study suggests that E. coli populations/clones from community-based healthy individuals may occasionally have an epidemic structure and provide a source of transmissible strains influencing the HA BSI incidence.

IMPORTANCE Sepsis is the third leading cause of mortality in Western countries and one of the Global Health Threats recognized by the WHO since 2017. Despite Escherichia coli constituting the most common cause of bloodstream infections (BSI), its epidemiology is not fully understood, in part due to the scarcity of local and longitudinal studies. Our work analyzes the long-term dynamics of E. coli causing bacteremia in a single institution and reveals waves of different clonal lineages that emerge periodically and successfully spread afterward in both the community and hospitals. Because the origin of E. coli bloodstream infections is the gut, the microbiota of healthy individuals might occasionally have an epidemic structure, providing a source of E. coli strains to influence the incidence of hospital BSI. The study complements previous fractionated observations focusing on specific E. coli lineages or antibiotic-resistant isolates in the last decades and helps to understand the epidemiology of E. coli BSI and the dynamics of pandemic clones.

Morphology of migration: associations between wing shape, bill morphology and migration in kingbirds (Tyrannus)

Morphology is closely linked to locomotion and diet in animals. In animals that undertake long-distance migrations, limb morphology is under selection to maximize mobility and minimize energy expenditure. Migratory behaviours also interact with diet, such that migratory animals tend to be dietary generalists, whereas sedentary taxa tend to be dietary specialists. Despite a hypothesized link between migration status and morphology, phylogenetic comparative studies have yielded conflicting findings. We tested for evolutionary associations between migratory status and limb and bill morphology across kingbirds, a pan-American genus of birds with migratory, partially migratory and sedentary taxa. Migratory kingbirds had longer wings, in agreement with expectations that selection favours improved aerodynamics for long-distance migration. We also found an association between migratory status and bill shape, such that more migratory taxa had wider, deeper and shorter bills compared to sedentary taxa. However, there was no difference in intraspecific morphological variation among migrants, partial migrants and residents, suggesting that dietary specialization has evolved independently of migration strategy. The evolutionary links between migration, diet and morphology in kingbirds uncovered here further strengthen ecomorphological associations that underlie long-distance seasonal movements in animals.

On the evolution of trophic position

The trophic structure of food webs is primarily determined by the variation in trophic position among species and individuals. Temporal dynamics of food web structure are central to our understanding of energy and nutrient fluxes in changing environments, but little is known about how evolutionary processes shape trophic position variation in natural populations. We propose that trophic position, whose expression depends on both environmental and genetic determinants of the diet variation in individual consumers, is a quantitative trait that can evolve via natural selection. Such evolution can occur either when trophic position is correlated with other heritable morphological and behavioural traits under selection, or when trophic position is a target of selection, which is possible if the fitness effects of prey items are heterogeneously distributed along food chains. Recognising trophic position as an evolving trait, whose expression depends on the food web context, provides an important conceptual link between behavioural foraging theory and food web dynamics, and a useful starting point for the integration of ecological and evolutionary studies of trophic position.

Relationships Among Trophic Niche Width, Morphological Variation, and Genetic Diversity of Hemiculter leucisculus in China

According to the niche variation hypothesis (NVH), the populations with wider niches are phenotypically more variable than those with narrow niches. Giller expanded the NVH, suggesting that the niche width, morphological variation, and genetic diversity are all positively correlated. However, the hypothesis has been a subject of debate and discussion. In the present study, the NVH was tested by analyzing the relationships among trophic niche width, morphological variation, and genetic diversity of Hemiculter leucisculus, a widespread cyprinid fish. The fish samples were collected from six sites across Haihe, the Yellow, and the Yangtze River basins in China. The relationships among trophic niche width, morphological variation, and genetic diversity were analyzed using Pearson correlation at the inter-population level. Our analysis indicated that trophic niche width is significantly positively correlated with morphological variation, which corroborates the NVH. Morphological variation was significantly correlated to genetic diversity. However, no relationship was observed between trophic niche width and genetic diversity. We inferred that the dietary niche of H. leucisculus might change due to the plastic response toward environmental changes rather than due to the genetic variation. We also suggest that the effects of environment and heredity on the niche of the freshwater fish should be quantified separately in further studies.

Nitrogen pollution promotes changes in the niche space of fish communities

Historically, anthropogenic fixed nitrogen has been purposely increased to benefit food production and global development. One consequence of this increase has been to raise concentrations of nitrogen in aquatic ecosystems. To evaluate whether nitrogen pollution promotes changes in the estimates of niche space of fish communities, we examined 16 sites along a Brazilian river basin highly impacted by anthropogenic activities, especially discharge of domestic and industrial sewage from a region with more than 5 million inhabitants. We analysed the carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope ratios of fish species and both autochthonous (periphyton) and allochthonous (course and fine particulate organic matter) basal food resources. To estimate the magnitude of nitrogen pollution, we measured the nitrate and ammonium concentrations at each site. Sampling was conducted in the dry and wet seasons to evaluate the influence of seasonality. Nitrogen pollution generally increased estimates of niche space, and seasonality influenced only the niche estimates of fish communities from polluted sites. In addition, isotopic analyses of nitrogen polluted sites yielded unrealistic estimates of trophic positioning (detritivores at the top of the food web). We conclude that changes in niche space estimates reflect both alterations in baseline isotopic values and differential trophic behaviour among fishes. Our study suggests that under conditions of high pollution, other factors appear to influence isotopic estimates of niche, such as isotopically distinct sources that have not been sampled, and/or differences in δ¹⁵N turnover rates between fish tissue and basal resources, creating isotopic baselines that are challenging to interpret.

Are stable isotope ratios suitable for describing niche partitioning and individual specialization?

As concerns about anthropogenic and natural disturbance grow, understanding animal resource use patterns has been increasingly prioritized to predict how changes in environmental conditions, food web structure, and population dynamics will affect biological resilience. Among the tools used to assess resource use, stable isotope analysis has proliferated in ecological studies, particularly in relation to describing intra- and interspecific variation in trophic interactions. Despite a growing need to disseminate scientific information, the inherent limitations of stable isotope ratios and inappropriate synonymizing of distinct evolutionary and ecological processes may mislead ecological inferences in natural systems. This situation necessitates a re-evaluation of the utility of stable isotope ratios to address certain ecological questions. Here, we assess the efficacy of stable isotope ratios to describe two fundamental ecological processes, niche partitioning and individual specialization. Investigation of these processes has increased substantially in accordance with increased access to stable isotope data. This article discusses the circumstances and approaches that are necessary to evaluate niche partitioning and individual specialization, and outlines key considerations for the associated application of stable isotope ratios.

Competition shapes individual foraging and survival in a desert rodent ensemble

Intraspecific variation, including individual diet variation, can structure populations and communities, but the causes and consequences of individual foraging strategies are often unclear. Interactions between competition and resources are thought to dictate foraging strategies (e.g. specialization vs. generalization), but classical paradigms such as optimal foraging and niche theory offer contrasting predictions for individual consumers. Furthermore, both paradigms assume that individual foraging strategies maximize fitness, yet this prediction is rarely tested. We used repeated stable isotope measurements (δ¹³ C, δ¹⁵ N; N = 3,509) and 6 years of capture-mark-recapture data to quantify the relationship between environmental variation, individual foraging and consumer fitness among four species of desert rodents. We tested the relative effects of intraspecific competition, interspecific competition, resource abundance and resource diversity on the foraging strategies of 349 individual animals, and then quantified apparent survival as function of individual foraging strategies. Consistent with niche theory, individuals contracted their trophic niches and increased foraging specialization in response to both intraspecific and interspecific competition, but this effect was offset by resource availability and individuals generalized when plant biomass was high. Nevertheless, individual specialists obtained no apparent fitness benefit from trophic niche contractions as the most specialized individuals exhibited a 10% reduction in monthly survival compared to the most generalized individuals. Ultimately, this resulted in annual survival probabilities nearly 4× higher for generalists compared to specialists. These results indicate that competition is the proximate driver of individual foraging strategies, and that diet-mediated fitness variation regulates population and community dynamics in stochastic resource environments. Furthermore, our findings show dietary generalism is a fitness maximizing strategy, suggesting that plastic foraging strategies may play a key role in species' ability to cope with environmental change.