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Does evolution design robust food webs?

Theoretical works that use a dynamical approach to study the ability of ecological communities to resist perturbations are largely based on randomly generated ecosystem structures. In contrast, we propose here to asses the robustness of food webs drawn from ecological and evolutionary processes with the use of community evolution models. In a first part, with the use of Adaptive Dynamics theoretical framework, we generate a variety of diversified food webs by solely sampling different richness levels of the environment as a control parameter, and obtain networks that satisfactory compare with empirical data. This allows us to highlight the complex, structuring role of the environmental richness during the evolutionary emergence of food webs. In a second part, we study the short-term ecological responses of food webs to swift changes in their customary environmental richness condition. We reveal a strong link between the environmental conditions that attended food webs evolutionary constructions and their robustness to environmental perturbations. When focusing on emergent properties of our evolved food webs, especially connectance, we highlight results that seem to contradict the current paradigm. Among these food webs, the most connected appear to be the less robust to sudden depletion of the environmental richness that constituted their evolutionary environment. Otherwise, we appraise the \"adaptation\" of food webs, by examining how they perform after being suddently immersed in an environment of modified richness level, in comparison with a trophic network that experienced this latter environmental condition all along its evolution.

ecology↗

Regulation of community functional composition across taxonomic variation by resource-consumer dynamics

High-throughput sequencing techniques such as metagenomic and metatranscriptomic technologies allow cataloging of functional characteristics of microbial community members as well as their taxonomic identity. Such studies have found that a communitys composition in terms of ecologically relevant functional traits or guilds can be conserved more strictly across varying settings than taxonomic composition is. I use a standard ecological resource-consumer model to examine the dynamics of traits relevant to resource consumption, and analyze determinants of functional composition. This model demonstrates that interaction with essential resources can regulate the community-wide abundance of ecologically relevant traits, keeping them at consistent levels despite large changes in the abundances of the species housing those traits in response to changes in the environment, and across variation between communities in species composition. Functional composition is shown to be able to track differences in environmental conditions faithfully across differences in community composition. Mathematical conditions on consumers vital rates and functional responses sufficient to produce conservation of functional community structure across taxonomic differences are presented.

ecology↗

On a mechanistic process of macroparasite aggregation

Parasite aggregation, a recurring pattern in macroparasite infections, is considered one of the "laws" of parasite ecology. Few hosts have a large number of parasites while most hosts have a low number of parasites. Phenomenological models of host-parasite systems thus use the negative-binomial distribution. However, to infer the mechanisms of aggregation, a mechanistic model that does not make any a priori assumptions is essential. Here we formulate a mechanistic model of parasite aggregation in hosts without assuming a negative-binomial distribution. Our results show that a simple model of parasite accumulation still results in an aggregated pattern, as shown by the derived mean and variance of the parasite distribution. By incorporating the derived statistics in host-parasite interactions, we can predict how aggregation affects the population dynamics of the hosts and parasites through time. Thus, our results can directly be applied to observed data as well as can inform the designing of statistical sampling procedures. Overall, we have shown how a plausible mechanistic process can result in the often observed phenomenon of parasite aggregation occurring in numerous ecological scenarios, thus providing a basis for a "law" of ecology.

ecology↗

Laws of diversity and variation in microbial communities

How coexistence of many species is maintained is a fundamental and unanswered question in ecology. Coexistence is a puzzle because we lack a quantitative understanding of the variation in species presence and abundance. Whether variation in ecological communities is driven by deterministic or random processes is one of the most controversial issues in ecology. Here, we study the variation of species presence and abundance in microbial communities from a macroecological standpoint. We identify three novel, fundamental, and universal macroecological laws that characterize the fluctuation of species abundance across communities and over time. These three laws -- in addition to predicting the presence and absence of species, diversity and other commonly studied macroecological patterns -- allow to test mechanistic models and general theories aiming at describing the fundamental processes shaping microbial community composition and dynamics. We show that a mathematical model based on environmental stochasticity quantitatively predicts the three macroecological laws, as well as non-stationary properties of community dynamics.

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When be Temperate: On the Fitness Benefits of Lysis vs. Lysogeny

Bacterial viruses, i.e., bacteriophage or phage, can infect and lyse their bacterial hosts, releasing new viral progeny. In addition to the lytic pathway, certain bacteriophage (i.e., temperate bacteriophage) can also initiate lysogeny, a latent mode of infection in which the viral genome is integrated into and replicated with the bacterial chromosome. Subsequently, the integrated viral genome, i.e., the prophage, can induce and restart the lytic pathway. Here, we explore the relationship between infection mode, ecological context, and viral fitness, in essence asking: when should viruses be temperate? To do so, we use network loop analysis to quantify fitness in terms of network paths through the life history of an infectious pathogen that start and end with infected cells. This analysis reveals that temperate strategies, particularly those with direct benefits to cellular fitness, should be favored at low host abundances. This finding applies to a spectrum of mechanistic models of phage-bacteria dynamics spanning both explicit and implicit representations of intracellular infection dynamics. However, the same analysis reveals that temperate strategies, in and of themselves, do not provide an advantage when infection imposes a cost to cellular fitness. Hence, we use evolutionary invasion analysis to explore when temperate phage can invade microbial communities with circulating lytic phage. We find that lytic phage can drive down niche competition amongst microbial cells, facilitating the subsequent invasion of latent strategies that increase cellular resistance and/or immunity to infection by lytic viruses - notably this finding holds even when the prophage comes at a direct fitness cost to cellular reproduction. Altogether, our analysis identifies broad ecological conditions that favor latency and provide a principled framework for exploring the impacts of ecological context on both the short- and long-term benefits of being temperate.

ecology↗

Herbivore intraspecific variation and evolutionary divergence drive trophic cascade strength

AO_SCPLOWBSTRACTC_SCPLOWTrophic cascades--the indirect effect of predators on non-adjacent lower trophic levels--are important drivers of the structure and dynamics of ecological communities. However, the influence of intraspecific trait variation on the strength of trophic cascade remains largely unexplored, which limits our understanding of the mechanisms underlying ecological networks. Here we experimentally investigated how intraspecific difference among herbivore lineages specialized on different host plants influences the strength of trophic cascade in a terrestrial tritrophic system. We found that the occurrence and strength of the trophic cascade are strongly influenced by herbivores lineage and host-plant specialization but are not associated with density-dependent effects mediated by the growth rate of herbivore populations. Our findings stress the importance of intraspecific heterogeneities and evolutionary specialization as drivers of the strength of trophic cascades and underline that intraspecific variation should not be overlooked to decipher the joint influence of evolutionary and ecological factors on the functioning of multi-trophic interactions.

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Stabilization of extensive fine-scale diversity by spatio-temporal chaos

It has become recently apparent that the diversity of microbial life extends far below species level to the finest scales of genetic differences. Remarkably, extensive fine-scale diversity can coexist spatially. How is this diversity stable on long timescales despite selective or ecological differences and other evolutionary processes? Most work has focused on stable coexistence or assumed ecological neutrality. We present an alternative: extensive diversity maintained by ecologically-driven spatio-temporal chaos, with no assumptions about niches or other specialist differences between strains. We study generalized Lotka-Volterra models with anti-symmetric correlations in the interactions inspired by multiple pathogen strains infecting multiple host strains. Generally, these exhibit chaos with increasingly wild population fluctuations driving extinctions. But the simplest spatial structure, many identical islands with migration between them, stabilizes a diverse chaotic state. Some types (sub-species) go globally extinct, but many persist for times exponentially long in the number of islands. All persistent types have episodic local blooms to high abundance, crucial for their persistence as, for many, their average population growth rate is negative. Snapshots of the distribution of abundances show a power-law at intermediate abundances that is essentially indistinguishable from the neutral theory. But the dynamics of the large populations are much faster than birth-death fluctuations. We argue that this spatio-temporally chaotic \"phase\" should exist in a wide range of models, and that even in rapidly mixed systems, longer lived spores could similarly stabilize a diverse chaotic phase.

ecology↗

Reconstruction of plant-pollinator networks from observational data

Empirical measurements of ecological networks such as food webs and mutualistic networks are often rich in structure but also noisy and error-prone, particularly for rare species for which observations are sparse. Focusing on the case of plant-pollinator networks, we here describe a Bayesian statistical technique that allows us to make accurate estimates of network structure and ecological metrics from such noisy observational data. Our method yields not only estimates of these quantities, but also estimates of their statistical errors, paving the way for principled statistical analyses of ecological variables and outcomes. We demonstrate the use of the method with an application to previously published data on plant-pollinator networks in the Seychelles archipelago, calculating estimates of network structure, network nestedness, and other characteristics.

ecology↗

The effects of resource subsidy duration on detritus-based stream ecosystems: a stream mesocosm experiment

Most of the resource subsidies are temporally variable, and studies have revealed that ecological processes can be mediated by the temporal attributes of subsidies, such as timing and frequency. Less studies have, however, examined the effects of the subsidy duration, an another major temporal attribute, on consumer populations, communities and ecosystem functions. Using an outdoor mesocosm experiment, we demonstrated that, even with the same total amounts, the prolonged subsidy let large-stage fish effectively monopolize the subsidy over small-stage fish, while the pulsed subsidy allowed small-stage fish to increase the ingestion rate of the subsidy. This effect resulted in causing weaker indirect positive effects on in-situ benthic prey and a leaf breakdown rate with the prolonged subsidy than with the pulsed-subsidy although it depended on dominant benthic prey species having different edibility. Increasing evidences have shown that global warming would not only advance, but also prolong the growing seasons, which may, in turn, make subsidies more prolonged. The ecological significance of the subsidy duration might be common in nature, and should be incorporated to better understand ecological processes in spatially and temporally coupled ecosystems.

ecology↗

Relationship between early body condition, energetic reserves and fitness in an iteroparous insect

O_LIInsects are core actors for the balance of many earth ecosystems, as well as an alternative source of food and feed with a low ecological footprint. A comprehensive understanding of their life history requires reliable tools. Body condition constitutes the amount of energy reserves available to a fitness trait after maintenance costs have been accounted for. Body condition is standardly estimated using Body Condition Indexes (BCIs) in vertebrates. In insects the relevance of BCIs is frequently questioned on the basis that they might not accurately reflect neither energy reserves nor fitness.. However, to date no study has tested whether the very concept of body condition is relevant in insects, i.e. whether BCIs accurately reflect the relative energy reserves allocated to fitness traits. C_LIO_LIWe propose that the relevance of using BCIs in insects depends on whether their structural size has a fitness cost. If on the contrary insects only benefit from a larger body size, a simple measurement of body size or mass will predict fitness, but not a BCI. We experimentally manipulated food availability at the larval and adult stage and used total fecundity of females as a fitness proxy of Tenebrio molitor, an important model in physiology, ecology and evolution, and one of the first insects to be considered as a source of food and feed. C_LIO_LIOur results support three key assumptions of the relevance of BCIs in insects: (i) a valid BCI correlated with energy reserves corrected for a given size (i.e. relative energy reserves) and not with absolute measures of energy reserves; (ii) both structural size and body condition positively predict different components of fitness; and, (iii) the effect of body condition was dependent on resource availability, whereby its effect was only apparent and large when food was unrestricted at the larval stage and restricted at the adult stage. C_LIO_LIOverall we demonstrate the relevance of using BCIs in insects. Their use should be generalized to improve fitness readouts in evolution, ecological and physiological studies, as well as improve their husbandry for commercial purposes. C_LI

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THE INFLUENCE OF ECOSYSTEM AND PHYLOGENY ON TROPICAL TREE CROWN SIZE AND SHAPE

1The sizes and shapes of tree crowns are of fundamental importance in ecology, yet understanding the forces that determine them remains elusive. A cardinal question facing ecologists is the degree to which general and non-specific versus ecological and context-dependent processes are responsible for shaping tree crowns. Here, we test this question for the first time across diverse tropical ecosystems. Using trees from 20 plots varying in elevation, precipitation, and ecosystem type (savanna-forest transitions) across the paleo- and neo-tropics, we test the relationship between crown dimensions and tree size. By analyzing these scaling relationships across environmental gradients, biogeographic regions, and phylogenetic distance, we extend Metabolic Scaling Theory (MST) predictions to include how local selective pressures shape variation in crown dimensions. Across all sites, we find strong agreement between mean trends and MST predictions for the scaling of crown size and shape, but large variation around the mean. While MST explained approximately half of the observed variation in tree crown dimensions, we find that local, ecosystem, and phylogenetic predictors account for the half of the residual variation. Crown scaling does not change significantly across regions, but does change across ecosystem types, where savanna tree crowns grow more quickly with tree size than forest tree crowns. Crowns of legumes were wider and larger than those of other taxa. Thus, while MST can accurately describe the central tendency of tree crown size, local ecological conditions and evolutionary history appear to modify the scaling of crown shape. Importantly, our extension of MST incorporating these differences accounts for the mechanisms driving variation in the scaling of crown dimensions across the tropics. These results are critical when scaling the function of individual trees to larger spatial scales or incorporating the size and shape of tree crowns in global biogeochemical models.

ecology↗

A mechanistic, stigmergy model of territory formation in asocial animals: Territorial behavior can dampen disease prevalence but increase persistence

Mechanistic portrayals of how animals form and maintain territories remain rare, and as a discipline, collective movement ecology has tended to focus on synergistic (e.g., migration, shoaling) rather than agonistic or territorial interactions. Here we ask how dynamic territory formation and maintenance might contribute to disease dynamics in an asocial territorial animal for an indirectly transmitted pathogen. We developed a mechanistic individual-based model where stigmergy--the deposition of signals into the environment (e.g., scent marking, scraping)--dictates not only local movement choices and long-term territory formation, but also the risk of pathogen transmission. Based on a variable importance analysis, the length of the infectious period was the single most important variable in predicting outbreak success, maximum prevalence, and outbreak duration. Population size and rate of pathogen decay were also key predictors. We found that territoriality best reduced maximum prevalence in conditions where we would otherwise expect outbreaks to be most successful: slower recovery rates (i.e., longer infectious periods) and higher conspecific densities. However, at high enough densities, outbreak duration became considerably more variable. Our findings therefore support a limited version of the \"territoriality benefits\" hypothesis--where reduced home range overlap leads to reduced opportunities for pathogen transmission, but with the caveat that reduction in outbreak severity may increase the likelihood of pathogen persistence. For longer infectious periods and higher host densities, key trade-offs emerged between the strength of pathogen load, strength of the stigmergy cue, and the rate at which those two quantities decayed; this finding raises interesting questions about the evolutionary nature of these competing processes and the role of possible feedbacks between parasitism and territoriality. This work also highlights the importance of considering social cues as part of the movement landscape in order to improve our understanding of the consequences of individual behaviors on population level outcomes.\n\nAuthor summaryMaking decisions about conservation and disease management relies on our understanding of what allows animal populations to be successful. However, movement ecology, as a field, tends to focus on how animals respond to their abiotic environment. Similarly, disease ecology often focuses on the social behavior of animals without accounting for their individual movement patterns. We developed a simulation model that bridges these two fields by allowing hosts to inform their movement based on the past trajectories of other hosts. As hosts navigate their environment, they leave behind a scent trail while avoiding the scent trails of other individuals. We wanted to know if this means of territory formation could heighten or dampen disease spread when infectious hosts leave pathogens in their wake. We found that territoriality could inhibit disease spread under conditions that we would normally expect pathogens to be most successful: where there are many hosts on the landscape and hosts stay infectious for longer. This work points to how incorporating movement behavior into disease models can provide improved understanding of how diseases spread in wildlife populations; such understanding is particularly important in the face of combatting ongoing and emerging infectious diseases.

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Integrating citizen science data with expert surveys improves the accuracy and range of inference of species distribution models

Information on species habitat associations and distributions, across a wide range of spatial and temporal scales, are a fundamental source of ecological knowledge. However, collecting biological information at relevant scales if often cost prohibitive, although it is essential for framing the broader context of more focused research and conservation efforts. Citizen-science data has been signaled as an increasingly important source of biological information needed to fill in data gaps needed to make more comprehensive and robust inferences on species distributions. However, there are perceived trade-offs of combining highly structured, scientific survey data with largely unstructured, citizen-science data. As a result, the focus of most methodological advances to combine these sources of information has been on treating these sources as independent. The degree to which each source of information is allowed to directly inform a common underlying process (e.g. species distribution) depends on the perceived quality of the data. In this paper, we explore these trade-offs by applying a simplified approach of filtering citizen-science data to resemble structured survey data, and analyze both sources of data under a common framework. To accomplish this, we explored ways of integrating high-resolution survey data on shorebirds in the northern Central Valley of California with observations in eBird for the entire region that were filtered to improve their quality. The integration of survey data with the filtered citizen-science data in eBird resulted in improved inference and predictive ability, and increased the extent and accuracy of inferences on shorebirds for the Central Valley. The structured surveys were found to improve the overall accuracy of ecological inference based only on citizen-science data, by increasing the representation of data collected from high quality habitats for shorebirds (e.g. rice fields). The practical approach we have shown for data integration can be also be used to improve the efficiency of designing biological surveys in the context of larger, citizen-science monitoring efforts, ultimately reducing the financial and time expenditures typically required of monitoring programs and focused research. The simple processing and filtering method we present can be used to integrate other types of data (e.g. camera traps) with more localized efforts (e.g. research projects), ultimately improving our ecological knowledge on the distribution and habitat associations of species of conservation concern worldwide.

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Matching the forecast horizon with the relevant ecologicalprocesses

Most phenomenological, statistical models used to generate ecological forecasts take either a time-series approach, based on long-term data from one location, or a space-for-time approach, based on data describing spatial patterns across environmental gradients. Here we consider how the forecast horizon determines whether more accurate predictions come from the time-series approach, the space-for-time approach, or a combination of the two. We use two simulated case studies to show that forecasts for short and long forecast horizons need to focus on different ecological processes, which are reflected in different kinds of data. In the short-term, dynamics reflect initial conditions and fast processes such as birth and death, and the time-series approach makes the best predictions. In the long-term, dynamics reflect the additional influence of slower processes such as evolutionary and ecological selection, colonization and extinction, which the space-for-time approach can effectively capture. At intermediate time-scales, a weighted average of the two approaches shows promise. However, making this weighted model operational will require new research to predict the rate at which slow processes begin to influence dynamics.

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Network-based metrics of community resilience and dynamics in lake ecosystems

Some ecosystems undergo abrupt transitions to a new regime after passing a tipping point in an exogenous stressor, for example lakes shifting from a clear to turbid eutrophic state in response to nutrient-enrichment. Metrics-based resilience indicators have been developed as early warning signals of these shifts but have not always proved reliable indicators. Alternative approaches focus on changes in the composition and structure of an ecosystem, which can require long-term food-web observations that are typically beyond the scope of monitoring. Here we prototype a network-based algorithm for estimating ecosystem resilience, which reconstructs past ecological networks solely from palaeoecological abundance data. Resilience is estimated using local stability analysis, and eco-net energy: a neural network-based proxy for ecological memory. We test the algorithm on modelled (PCLake+) and empirical (lake Erhai) data. The metrics identify increasing diatom community instability during eutrophication in both cases, with eco-net energy revealing complex eco-memory dynamics. The concept of ecological memory opens a new dimension for understanding ecosystem resilience and regime shifts, with eco-memory potentially increasing ecosystem resilience by allowing past memorised eco-network states to be recovered after disruptions.

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Pollen-feeding Heliconius butterflies host distinctive adult-stage microbiomes

Lepidoptera (butterflies and moths) are diverse and ecologically important, yet we know little about how they interact with microbes as adults. Due to metamorphosis, the form and function of their adult-stage microbiomes might be very different from microbiomes in the larval stage (caterpillars). We studied adult-stage microbiomes of Heliconius and closely related passion-vine butterflies (Heliconiini), which are an important model system in evolutionary biology. To characterize the structure and dynamics of heliconiine microbiomes, we used field collections of wild butterflies, 16S rRNA gene sequencing, quantitative PCR, and shotgun metagenomics. We found that Heliconius harbor simple and abundant bacterial communities that are moderately consistent among conspecific individuals and over time. Heliconiine microbiomes also exhibited a strong signal of host phylogeny, with a major distinction between Heliconius and other butterflies. These patterns were largely driven by differing relative abundances of bacterial phylotypes shared among host species and genera, as opposed to the presence or absence of host-specific phylotypes. We suggest that phylogenetic structure in heliconiine microbiomes arises from conserved host traits that differentially filter microbes from the environment. While the relative importance of different traits remains unclear, our data indicate that pollen-feeding (unique to Heliconius) is not a primary driver. Using shotgun metagenomics, we also discovered trypanosomatids and microsporidia to be prevalent in butterfly guts, raising the possibility of antagonistic interactions between eukaryotic parasites and co-localized gut bacteria. Our discovery of characteristic and phylogenetically structured microbiomes provides a foundation for tests of adult-stage microbiome function, a poorly understood aspect of lepidopteran biology. ImportanceMany insects host microbiomes with important ecological functions. However, the prevalence of this phenomenon is unclear, because in many insect taxa microbiomes have only been studied in part of the life cycle, if at all. A prominent example is the butterflies and moths, in which the composition and functional role of adult-stage microbiomes are largely unknown. We comprehensively characterized microbiomes in adult passion-vine butterflies. Butterfly-associated bacterial communities are generally abundant in guts, consistent within populations, and composed of taxa widely shared among hosts. More closely related butterflies harbor more similar microbiomes, with the most dramatic shift in microbiome composition occurring in tandem with a suite of ecological and life history traits unique to the genus Heliconius. Butterflies are also frequently infected with previously undescribed eukaryotic parasites, which may interact with bacteria in important ways. These findings advance our understanding of butterfly biology and of insect-microbe interactions generally.

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Phenotypic diversity of Methylobacterium associated with rice landraces in Northeast India

The ecology and distribution of many bacteria is strongly associated with specific eukaryotic hosts. However, the impact of such host association on bacterial ecology and evolution is not well understood. Bacteria from the genus Methylobacterium consume plant-derived methanol, and are some of the most abundant and widespread plant-associated bacteria. In addition, many of these species impact plant fitness. To determine the ecology and distribution of Methylobacterium in nature, we sampled bacteria from 36 distinct rice landraces, traditionally grown in geographically isolated locations in North-East (NE) India. These landraces have been selected for diverse phenotypic traits by local communities, and we expected that the divergent selection on hosts may have also generated divergence in associated Methylobacterium strains. We determined the ability of 91 distinct rice-associated Methylobacterium isolates to use a panel of carbon sources, finding substantial variability in carbon use profiles. Consistent with our expectation, across spatial scales this phenotypic variation was largely explained by host landrace identity rather than geographical factors or bacterial taxonomy. However, variation in carbon utilisation was not correlated with sugar exudates on leaf surfaces, suggesting that bacterial carbon use profiles do not directly determine bacterial colonization across landraces. Finally, experiments showed that at least some rice landraces gain an early growth advantage from their specific phyllosphere-colonizing Methylobacterium strains. Together, our results suggest that landrace-specific host-microbial relationships may contribute to spatial structure in rice-associated Methylobacterium in a natural ecosystem. In turn, association with specific bacteria may provide new ways to preserve and understand diversity in one of the most important food crops of the world.

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The diet and feeding behaviour of the black-and-white colobus (Colobus guereza) in the Kalinzu Forest, Uganda

One of the goals for primate feeding ecology is to understand the factors that affect inter- and intra-specific variations. Therefore, a detailed description of basic feeding ecology in as many populations and sites as possible is necessary and warrants further understanding. The black-and-white colobus (Colobus guereza) or guereza is widely distributed in Africa and is one of the well-studied colobines in terms of their feeding; they demonstrate considerable variation in their diets in response to local conditions. We studied the diet of a group of guerezas in the Kalinzu Forest, Uganda, for over 30 consecutive months using behavioural observation (4,308 h total), phenology, and vegetation surveys. A total of 31 plant species were consumed by the study group. This study group was predominantly folivorous; the majority of their feeding time was involved in feeding on young leaves (87%). However, during certain times of the year, fruits and seeds accounted for 45% of monthly feeding time. Young leaves of Celtis durandii were by far the most important food, which constituted 58% of the total feeding records. There was a significant increase in the consumption of fruits and flowers once young leaf availability was low, but their consumption of fruits did not significantly increase even when fruit availability was high. Their monthly dietary diversity increased as the number of available plants with young leaves declined, suggesting that much of the dietary diversity in the study group may be attributable to the young leaf portion of their diet. Our findings may help contribute to a better understanding of the dietary adaptations and feeding ecology of guerezas in response to local environmental conditions.

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