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bioRxiv2018

The return of the trophic chain: fundamental vs realized interactions in a simple arthropod food web

The mathematical theory describing small assemblages of interacting species (community modules or motifs) has proved to be essential in understanding the emergent properties of ecological communities. These models use differential equations to study pairwise interactions between species. However, as community modules become more complex, it is not certain that all potential interactions will be effectively realized. Here, we use community modules to experimentally explore whether the number of trophic links among species scales with community complexity (i.e., by adding species known to feed on each other from pair-wise trials). To investigate this question, we used a simple mite community present in avocado orchards (Persea americana), composed of two predators (Euseius stipulatus and Neoseiulus californicus), one herbivore as shared prey (Oligonychus perseae), and pollen of Carpobrotus edulis as an alternative food resource. These configurations enabled the potential for (intraguild) predation and (apparent) competition to be expressed. Using a series of controls, we assessed whether the presence of one species affected the survival of another, or its conversion of food into offspring). We found that increasing the number of potential interactions did not result in more complex realized community modules. Instead, all communities were reduced to one or two linear trophic chains. Our results show that trophic links assumed to occur when species are assembled in pairs do not necessarily occur when other components of the community are present. Consequently, food-web structure may be unrealistic in theoretical community modules that are parameterized based on pair-wise interactions observed when alternative prey is absent. This further suggests the need for empirical research to work in concert with theoretical approaches to develop more realistic and predictive food-web models.

ecology↗

bioRxiv2018

Combined effect of matrix quality and spatial heterogeneity on biodiversity decline

The land-sparing/land-sharing debate remains an oversimplified framework to evaluate landscape management strategies that aim to reconcile food production and biodiversity conservation. Still, biodiversity-yield curves, on which the framework has relied, provide valuable qualitative information on biodiversitys sensitivity to agricultural practices, and much research has studied this relationship. But the potential effect of landscape configuration on biodiversitys response to intensification has rarely been considered; besides, studies have often taken yield as an indicator of agricultural management and have generalized conclusions from studying particular taxonomic groups. In this work we adapt a metacommunity model to analyze factors that shape biodiversitys response to agricultural intensification while addressing some of the simplifications of the land-sparing/land-sharing dichotomy. In particular, we study species richness decline in landscapes encompassing a combined gradient in matrix quality and configurational heterogeneity of habitat patches, and considering community dynamics. We found that species richness along an intensification gradient shifts from following a robust response to presenting an abrupt decline, as landscape heterogeneity increases, as stricter survival thresholds are applied to species or as habitat area is reduced. Our work highlights the interdependent effects of heterogeneity, habitat availability and matrix quality on biodiversity and contributes to a nuanced understanding of ecological and landscape factors that enable a robust response of biodiversity in the face of spatiotemporal perturbations.

ecology↗

bioRxiv2018

When parasites are selected to kill the young

The impact of infectious disease is often very different in juveniles and adults, but theory has focused on the drivers of stage-dependent defense in hosts rather than the potential for stage-dependent virulence evolution. Stage-structure has the potential to be important to the evolution of pathogens because it exposes parasites to heterogeneous environments in terms of both host characteristics and transmission routes. We develop a stage-structured (juvenile-adult) epidemiological model and examine the evolutionary outcomes of stage-specific virulence under the classic assumption of a transmission-virulence trade-off. We show that selection on virulence against adults remains consistent with the classic theory. However, the evolution of juvenile virulence is sensitive to both demography and transmission pathway with higher virulence against juveniles being favored either when the transmission pathway is assortative (juveniles preferentially interact together) and the juvenile stage is short, or in contrast when the transmission pathway is disassortative and the juvenile stage is long. These results highlight the potentially profound effects of host stage-structure on determining parasite virulence in nature. This new perspective may have broad implications for both understanding and managing disease severity. Impact summaryUnderstanding the evolution of parasite virulence remains one of the most important questions in evolutionary ecology. Virulence is often very different in young and old hosts, but previous theory has presumed that these differences are attributed to adaptation in host defense rather than parasite adaptation. However, stage-structure within host populations can expose parasites to heterogeneous environments, which may lead to differential selection on parasite virulence (stage-specific virulence). Surprisingly, no study has investigated the effects of hosts stage-structure on the evolution of stage-specific virulence. We present a theoretical analysis to examine when selection can favor higher virulence against juveniles (juvenile-virulence) versus adults (adult-virulence). Our key result is that higher juvenile-virulence is selected for either when the transmission is assortative within age classes and maturation is slow, or when the transmission is disassortative (occurring predominantly between-classes) and maturation is relatively fast. These at first sight contrasting outcomes can be understood as adaptation to the exploitation of the more available host stage. Although the data on assortativity in infectious disease systems is limited, empirical studies for the virulence of Great Island Virus in guillemots (Uria aalge) and for salmon louse in pink salmon (Oncorhynchus gorbuscha) are consistent with our predictions. Our work provides testable predictions for stage-specific virulence and presents a novel mechanism that may explain variation in virulence in nature. There are also management implications for conservation, public health, vaccination programs, and farming to understanding the drivers of stage dependent virulence.

ecology↗

bioRxiv2018

Construction, validation and application of nocturnal pollen transport networks in an agro-ecosystem: a comparison using microscopy and DNA metabarcoding

O_LIMoths are globally relevant as pollinators but nocturnal pollination remains poorly understood. Plant-pollinator interaction networks are traditionally constructed using either flower-visitor observations or pollen-transport detection using microscopy. Recent studies have shown the potential of DNA metabarcoding for detecting and identifying pollen-transport interactions. However, no study has directly compared the realised observations of pollen-transport networks between DNA metabarcoding and conventional light microscopy.\nC_LIO_LIUsing matched samples of nocturnal moths, we construct pollen-transport networks using two methods: light microscopy and DNA metabarcoding. Focussing on the feeding mouthparts of moths, we develop and provide reproducible methods for merging DNA metabarcoding and ecological network analysis to better understand species-interactions.\nC_LIO_LIDNA metabarcoding detected pollen on more individual moths, and detected multiple pollen types on more individuals than microscopy, but the average number of pollen types per individual was unchanged. However, after aggregating individuals of each species, metabarcoding detected more interactions per moth species. Pollen-transport network metrics differed between methods, because of variation in the ability of each to detect multiple pollen types per moth and to separate morphologically-similar or related pollen. We detected unexpected but plausible moth-plant interactions with metabarcoding, revealing new detail about nocturnal pollination systems.\nC_LIO_LIThe nocturnal pollination networks observed using metabarcoding and microscopy were similar, yet distinct, with implications for network ecologists. Comparisons between networks constructed using metabarcoding and traditional methods should therefore be treated with caution. Nevertheless, the potential applications of metabarcoding for studying plant-pollinator interaction networks are encouraging, especially when investigating understudied pollinators such as moths.\nC_LI

ecology↗

bioRxiv2018

Wild Steps in a Semi-wild Setting? Habitat Selection and Behavior of European Bison reintroduced to an Anthropogenic Landscape

Recently, several wild or semi-wild herds of European bison have been reintroduced across Europe. It is essential for future successful bison reintroductions to know how the European bison use different habitats, which environmental parameters drive their habitat selection, and whether their habitat use and behavioural patterns in new reintroduction sites differ from habitats where European bison have been roaming freely for a long time.\n\nHere, we address these questions for a 40-ha enclosed site that has been inhabited by semi-free ranging European bison since 2012. The site, Vorup Meadows, is adjacent to the Guden[a] river in Denmark and consists of human-modified riparian meadows. During 2013 we monitored the behavioural pattern and spatial use of the 11 bison present and in parallel carried out floristic analyses to assess habitat structure and food quality in the enclosure. We tested habitat use and selection against environmental parameters such as habitat characteristics, plant community traits, topography, and management area (release area vs. meadow area) using linear regression and spatial models.\n\nThe bison herd had comparable diurnal activity patterns as observed in previous studies on free-roaming bison herds. Topography emerged as the main predictor of the frequency of occurrence in our spatial models, with high-lying drier areas being used more. Bison did not prefer open areas over areas with tree cover when accounting for habitat availability. However, they spent significantly more time in the release area, a former agricultural field with supplementary fodder, than expected from availability compared to the rest of the enclosure, a meadow with tree patches. We wish to increase awareness of possible long-term ethological effects of the release site and the management protocols accomplished here that might reduce the ecological impact by the bison in the target habitat, and thereby compromise or even oppose the conservation goals of the conservation efforts.

ecology↗

bioRxiv2018

Finding the signal in the noise of Citizen Science Observations

While many observations of species are being collected by citizen science projects worldwide, it can be challenging to identify projects collecting data that effectively monitor biodiversity. Over the past several years the allure of taking a \"Big Data\" approach has provided the opportunity to gather massive quantities of observations via the Internet, too often with insufficient information to describe how the observations were made. Information about species populations -- where and when they occur and how many of them are there -- (i.e., the signal) can be lost because insufficient information is gathered to account for the inherent biases in data collection (i.e., the noise). Here we suggest that citizen science projects that have succeeded in motivating large numbers of participants, must consider factors that influence the ecological process that affect species populations as well as the observation process that determines how observations are made. Those citizen science projects that collect sufficient contextual information describing the observation process can be used to generate increasingly accurate information about the distribution and abundance of organisms. We illustrate this using eBird as a case study, describing how this citizen science platform is able to collect vital contextual information on the observation process while maintaining a broad global constituency of participants. We highlight how eBird provides information with which to generate biodiversity indicators -- specifically distribution, abundance, and habitat associations -- across the entire annual cycle, even for populations of long distance migratory birds, a highly challenging taxon.

ecology↗

bioRxiv2018

Regional neutrality evolves through local adaptive niche evolution

Joost Vanoverbeke, Department of Biology, Katholieke Universiteit Leuven, Leuven, Belgium. Abstract: Biodiversity in natural systems can be maintained either because niche differentiation among competitors facilitates stable coexistence or because equal fitness among neutral species allows for their long-term co-occurrence despite a slow drift toward extinction. Whereas the relative importance of these two ecological mechanisms has been well-studied in the absence of evolution, the role of local adaptive evolution in maintaining biological diversity through these processes is less clear. Here we study the contribution of local adaptive evolution to coexistence in a landscape of interconnected patches subject to disturbance. Under these conditions, early colonists to empty patches following disturbance can often adapt to novel local conditions sufficiently fast to prevent successful colonization by other pre-adapted species. Over the long term, the iteration of these local-scale priority effects results in niche convergence of species at the regional scale even though species tend to monopolize local patches. Thus, the dynamics evolve from stable coexistence through niche differentiation to neutral co-occurrence at the landscape level while still maintaining strong local niche differentiation. Our model results show that neutrality can emerge at the regional scale from local, niche-based adaptive evolution, potentially resolving why ecologists often observe neutral distribution patterns at the landscape level despite strong niche divergence among local communities. Our results also demonstrate how local adaptive evolution can shape cryptic eco-evolutionary dynamics and thus alter the regional mechanisms that determine biological diversity and resistance to disturbance.

ecology↗

bioRxiv2018

The host fruit amplifies mutualistic interactions between Ceratitis capitata larvae and associated bacteria.

Background:\n\nThe Mediterranean fruit fly Ceratitis capitata is a major pest in horticulture. The development of fly larvae is mediated by bacterial decay in the fruit tissue. Despite the importance of bacteria on larval development, very little is known about the interaction between bacteria and larvae in their true ecological context. Understanding their relationship and inter-dependence in the host fruit is important for the development of new pest control interfaces to deal with this pest.\n\nResults:\n\nWe find no negative effects on egg hatch or larval development brought about by the bacterial isolates tested. The various symbionts inhabiting the flys digestive system differ in their degree of contribution to the development of fly larvae depending on the given host and their sensitivity to induced inhibition caused by female produced antimicrobial peptides. These differences were observed not only at the genus or species level but also between isolates of the same species. We demonstrate how the microbiota from the mothers gut supports the development of larvae in the fruit host and show that larvae play a major role in spreading the bacterial contagion in the infected fruit itself. In addition, we present (for the first time) evidence for horizontal transfer of bacteria between larvae of different maternal origin that develop together in the same fruit.\n\nConclusions:\n\nLarvae play a major role in the spread and shaping of the microbial population in the fruit. The transfer of bacteria between different individuals developing in the same fruit suggests that the infested fruit serves as a microbial hub for the amplification and spread of bacterial strains between individuals.

ecology↗

bioRxiv2018

Enforced Symmetry: The Necessity of Symmetric Waxing and Waning

This paper demonstrates that the symmetric waxing and waning pat-terns that can be observed in ecological measures such as occupancy and geographic range are created by averaging, rescaling, conditioning and combining different sources of information. Therefore symmetric waxing and waning from the origination of a taxon to the extinction of a taxon in any measure should be treated as the null hypothesis and non-informative.

ecology↗

bioRxiv2018

Disease and climate effects on individuals jointly drive post-reintroduction population dynamics of an endangered amphibian

The emergence of novel pathogens often has dramatic negative effects on previously unexposed host populations. Subsequent disease can drive populations and even species to extinction. After establishment in populations, pathogens can continue to affect host dynamics, influencing the success or failure of species recovery efforts. However, quantifying the effect of pathogens on host populations in the wild is challenging because individual hosts and their pathogens are difficult to observe. Here we use long-term mark-recapture data to describe the dynamics of reintroduced populations of an endangered amphibian (Rana sierrae) and evaluate the success of these recovery efforts in the presence of a recently-emerged pathogen, the amphibian chytrid fungus Batrachochytrium dendrobatidis. We find that high B. dendrobatidis infection intensities are associated with increases in detectability, reductions in survival, and more infected adults. We also find evidence for intensity-dependent survival, with heavily infected individuals suffering higher mortality. These results highlight the need in disease ecology for probabilistic approaches that account for uncertainty in infection intensity using imperfect observational data. Such approaches can advance the understanding of disease impacts on host population dynamics, and in the current study will improve the effectiveness of species conservation actions.

ecology↗

bioRxiv2018

Dynamics of the Previte-Hoffman food web modelwith small immigrations

The ecological dynamics of prey-predator systems are extensively studied over a century. Previte and Hoffman introduced a three species(predator-prey with an omnivore) model in 2013. We demonstrate the asymptotic stability of the Previte and Hoffman modified model adding with small immigration into the prey or predator or omnivore population. A comparison of dynamics is also drawn with immigration and without immigration. It is worth noting that the qualitative dynamics is unchanged among the immigration system over the classical Previte-Hoffman system.

ecology↗

bioRxiv2018

From apparent competition to facilitation, impacts of consumer niche construction on the coexistence and stability of consumer-resource communities.

O_LIIn addition to their direct trophic effects, some consumers have a positive indirect effect on their resource, due to niche construction. A predator can facilitate its prey resource acquisition, through prey transport, or through modifications of nutrient cycling. Other predators defend their prey against other predators, or actively manage it, as in agriculture, which is found in numerous taxa such as humans, but also ants, beetles, fishes and microbes.\nC_LIO_LIHere we investigate the ecological consequences of considering such positive effects in a simple two resource-one predator module, in which the consumer has a positive effect on one of the resources.\nC_LIO_LIWe consider several scenarios, in which the positive effect of the resource is either non costly, ie resulting from a by-product of the consumer phenotype such as nutrient cycling, or costly. The cost either decreases the exploitation of the helped resource or the opportunity to forage the alternative resource.\nC_LIO_LIWe show that by modifying the trophic interactions in the module, niche construction alters the apparent competition between the resources, thereby impacting their coexistence.\nC_LIO_LIWe investigate how the intensity of niche construction impacts species coexistence, the distribution of biomass among the three species, and the stability of the community. When niche construction has little or no cost, it leads to higher consumer and helped resource densities, while decreasing the alternative resource density. Alternatively, when niche construction has a strong cost, the alternative resource can increase in density, niche construction thereby leading to the emergence of facilitative interactions among resource species.\nC_LI

ecology↗

bioRxiv2018

Physiological predictors of reproductive performance in the European Starling (Sturnus vulgaris): I. Univariate analysis

Costs of reproduction are assumed to be widespread, and to have a physiological basis, but the mechanisms driving decreased survival and future fecundity remain elusive. Our overall goals were to assess whether physiological variables are related to workload ability or immediate fitness consequences and if they mediate future survival or reproductive success. We investigated individual variation in physiological state at two breeding stages (incubation, chick-rearing) in female European starlings (Sturnus vulgaris), for first-and second-broods over two years. Specifically, we measured a suite of 13 physiological traits related to aerobic/metabolic capacity, oxidative stress and muscle damage, intermediary metabolism and energy supply, and immune function. We tested for relationships to traits for workload (e.g. nest visit rate) and fitness (current reproduction, survival and future reproduction).\n\nThere was little co-variation among the 13 physiological traits, either in incubating or chick-rearing birds. There were some systematic differences in incubation versus chick-rearing physiology. Chick-rearing birds had lower hematocrit and plasma creatine kinase but higher hemoglobin, triglyceride and uric acid levels. Only plasma corticosterone was repeatable between incubation and chick-rearing. We assessed relationships in a univariate manner, and found very few significant relationships between incubation or chick-rearing physiology and measures of workload, current productivity, future fecundity or survival. Variability in ecological context may complicate the relationship between physiology and behavior. Additionally, individuals may regulate different aspects of their physiology independently, making detection of physiological mediators of cost of reproduction difficult. In a companion paper (Cohen et al. submitted) we explore the utility of multivariate analysis (Principal Components Analysis, Mahalanobis distance) of the same data to account for potentially complex physiological integration.

ecology↗

bioRxiv2018

The Portal Project: a long-term study of a Chihuahuan desert ecosystem

This is a data paper for the Portal Project, a long-term ecological study of rodents, plants, and ants located in southeastern Arizona, U.S.A. This paper contains an overview of methods and information about the structure of the data files and the relational structure among the files. This is a living data paper and will be updated with new information as major changes or additions are made to the data. All data - along with more detailed data collection protocols and site information - is archived at: https://doi.org/10.5281/zenodo.1215988.

ecology↗

bioRxiv2018

Low incidence of plastic ingestion among three fish species significant for human consumption on the island of Newfoundland, Canada

This study reports the first baselines of plastic ingestion for three fish species that are common food fish in Newfoundland, Canada. Species collections occurred between 2015-2016 for Atlantic cod (Gadus morhua), Atlantic salmon (Salmo salar), and capelin (Mallotus villosus). The frequency of occurrence (%FO) of plastic ingestion for both spawning Atlantic salmon (n=69) and capelin (n=350) was 0%. Of the 1,010 Atlantic cod collected over two years, 17 individuals had ingested plastics, a %FO of 1.68%. This is the only multi-year investigation of plastic ingestion in Atlantic cod for the Northwest Atlantic, and the first for capelin and salmon in the region. Considering the ecological, economic, and cultural importance of these fish species, this study is the beginning of a longitudinal study of plastic ingestion to detect future changes in contamination levels.\n\nHighlightsO_LIIngestion rate (%FO) of plastics in Atlantic cod is 1.68%\nC_LIO_LIIngestion rate (%FO) of plastics in Atlantic salmon and capelin is 0%\nC_LIO_LIFirst study of plastic ingestion rates in Atlantic salmon and capelin\nC_LIO_LIMulti-year baseline of plastic ingestion in Atlantic cod in the Northwest Atlantic\nC_LIO_LIPlastic ingestion rates for three food fish species in Newfoundland, Canada, are low\nC_LI\n\nTermsO_LIFrequency of occurrence (%FO): the number of individuals in a population or group that have ingested plastics (not indicative of the number of particles ingested per individual)\nC_LI

ecology↗

bioRxiv2018

Nothing else matters? A nationwide study of microhabitats drivers at the tree scale

Managing forests to preserve biodiversity requires a good knowledge not only of the factors driving its dynamics but also of the structural elements that actually support biodiversity. Tree-related microhabitats (cavities, cracks, conks of fungi) are tree-borne features that are reputed to support specific biodiversity for at least a part of species life cycles. While several studies have analysed the drivers of microhabitats number and occurrence at the tree scale, they remain limited to a few tree species located in relatively narrow biogeographical ranges. We used a nationwide database of forest reserves where microhabitats were inventoried on more than 22,000 trees. We analysed the effect of tree diameter and living status (alive or dead) on microhabitat number and occurrence per tree, taking into account biogeoclimatic variables and tree genus. We confirmed that larger trees and dead trees bore more microhabitats than their smaller or living counterparts did; we extended these results to a wider range of tree genera and ecological conditions. Contrary to expectations, the total number of microhabitat types per tree barely varied with tree genus - though we did find slightly higher accumulation levels for broadleaves than for conifers - nor did it vary with elevation or soil pH. We observed the same results for the occurrence of individual microhabitat types. However, accumulation levels with diameter and occurrence on dead trees were higher for microhabitats linked with wood decay processes (e.g. dead branches or woodpecker feeding holes) than for other, epixylic, microhabitats such as epiphytes (ivy, mosses and lichens). Promoting large living and dead trees of several tree species may be an interesting, and nearly universal, way to favour microhabitats and enhance the substrates needed to support specific biodiversity. In addition, a better understanding of microhabitat drivers and dynamics at the tree scale may help to better define their role as biodiversity indicators for large-scale monitoring.

ecology↗

bioRxiv2018

Cryptic Dispersal Networks Connect Habitat Patches in ways not Captured by Distance

Species interact with the physical world in complex ways, and life history strategies might cause species to differ in how they experience connectedness of the same landscape. As a consequence, dispersal limitation might be present but not captured by distance-based measures of connectivity. To test these ideas, we surveyed plant communities that associate with serpentine soils but differ in dispersal mode (gravity, animal, or wind), and used satellite imagery to quantify forms of landscape connectivity associated with each dispersal mode. Our data yielded two key insights: First, dispersal limitation appeared to be absent using a conventional distance-based measure of connectivity, but emerged after considering forms of landscape connectivity relevant to each dispersal mode. Second, the landscape variables that emerged as important to each dispersal mode were generally consistent with our predictions based on putative dispersal vectors, and included interactive effects that allude to the altered efficacy of animal dispersal in invaded landscapes. Our results have broad implications for understanding how ecological communities reorganize as landscapes are fragmented, patches are lost, and the function of dispersal life histories is altered.

ecology↗

bioRxiv2018

Seasonality controls the predictive skills of diatom based salinity transfer functions

The value of diatoms as bioindicators of contemporary and palaeolimnological studies through transfer function development has increased in the last decades. While they represent a tremendous advance in (palaeo) ecology, these models also leave behind important sources of uncertainties that are often ignored. In the present study we tackle two of the most important sources of uncertainty in the development of diatom salinity inference models: the effect of secondary variables associated to seasonality and the comparison of conventional cross-validation methods with a validation based on independent datasets. Samples (diatoms and environmental variables) were taken in spring, summer and autumn in the freshwater and brackish ditches of the province of North Holland in 1993 and sampled again different locations of the same province in 2008-2010 to validate the models. We found that the abundance of the dominant species significantly changed between the seasons, leading to inconsistent estimates of species optima and tolerances. A model covering intra-annual variability (all seasons combined) provides averages of species optima and tolerances, reduces the effect of secondary variables due to the seasonality effects, thus providing the strongest relationship between salinity and diatom species. In addition, the all-season model also reduces the edge effects usually found in all unimodal-based calibration methods. While based on cross-validation all four models seem to perform relatively well, a validation with an independent dataset emphasizes the importance of using models covering intra-annual variability to perform realistic reconstructions.

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