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bioRxiv2016

Density dependence in demography and dispersal generates fluctuating invasion speeds

Density dependence plays an important role in population regulation and is known to generate temporal fluctuations in population density. However, the ways in which density dependence affects spatial population processes, such as species invasions, are less understood. While classical ecological theory suggests that invasions should advance at a constant speed, empirical work is illuminating the highly variable nature of biological invasions, which often exhibit non-constant spreading speeds even in simple, controlled settings. Here, we explore endogenous density dependence as a mechanism for inducing variability in biological invasions with a set of population models that incorporate density dependence in demographic and dispersal parameters. We show that density dependence in demography at low population densities--i.e., an Allee effect--combined with spatiotemporal variability in population density behind the invasion front can produce fluctuations in spreading speed. The density fluctuations behind the front can arise from either overcompensatory population growth or from density-dependent dispersal, both of which are common in nature. Our results demonstrate that simple rules can generate complex spread dynamics, and highlight a novel source of variability in biological invasions that may aid in ecological forecasting.

Ecology↗

bioRxiv2016

Investigating the potential of opportunistic sighting data to inform wildlife conservation strategies

Abundance and space use are key population-level parameters used to inform management and conservation decisions of rare and elusive species, for which monitoring resources can be limited, potentially affecting quality of model-based inference. Recently-developed methods that integrate multiple data sources arising from the same ecological process have typically been focused on data from well-defined sampling protocols, i.e. structured data sets. Despite a rapid increase in availability of large datasets, the value of unstructured or opportunistic data to improve inference about spatial ecological processes is, however, unclear. Using spatial capture-recapture (SCR) methods, we jointly analyze opportunistic recovery of biological samples, traditional SCR data resulting from systematic sampling of hair traps and rub trees, and satellite telemetry data, collected on a reintroduced brown bear population in the central Alps. We compared the precision of sex-specific estimates of density and space use derived from models using combinations of data sources ranging from traditional SCR to a fully integrated SCR model that includes both telemetry and opportunistic data. Estimates of density and space use were more precise when unstructured data were added compared to estimates from a classical SCR model. Our results demonstrate that citizen science data lend itself naturally to integration with in the SCR framework and highlight the value of opportunistic data for improving inference about space use, and in turn, of abundance and density. When individual identity and location can be obtained from opportunistic observations, such data are informative about space use and thus have the potential to improve estimates of movement and density using SCR methods. This is particularly relevant in studies of rare or elusive species, where the amount of SCR encounters is usually small, but also budget restrictions and the difficulty of collaring animals limit the number of individuals for which telemetry information is available. Spatially-referenced opportunistic data thus potentially increase both the geographic extent of a study and the number of individuals with available spatial information, providing an improved understanding of how individuals are distributed and how they use space - fundamental components for calibrating conservation management actions.

Ecology↗

bioRxiv2016

Scrounging by foragers can resolve the paradox of enrichment

Theoretical models of predator-prey system predict that sufficient enrichment of prey can generate large amplitude limit cycles, paradoxically causing a high risk of extinction (the paradox of enrichment). While real ecological communities contain many gregarious species whose foraging behaviour should be influenced by socially transmitted information, few theoretical studies have examined the possibility that social foraging might be a resolution of the paradox. I considered a predator population in which individuals play the producer-scrounger foraging game both in a one-prey-one-predator system and a two-prey-one-predator system. I analysed the stability of a coexisting equilibrium point in the former one-prey system and that of non-equilibrium dynamics of the latter two-prey system. The result showed that social foraging can stabilise both systems and thereby resolves the paradox of enrichment when scrounging behaviour is prevalent in predators. This suggests a previously neglected mechanism underlying a powerful effect of group-living animals on sustainability of ecological communities.

Ecology↗

bioRxiv2016

Hosts, parasites, and their interactions respond to different climatic variables

Aim: Although there is a vast body of literature on the causes of variation in species composition in ecological communities, less effort has been invested in understanding how interactions between these species vary. Since interactions are crucial to the structure and functioning of ecological communities, we need to develop a better understanding of their spatial distribution. Here, we investigate whether species interactions vary more in response to different climate variables, than individual species do. Location: Eurasia. Time period: 2000s. Major taxa: Animalia. Methods: We used a measure of Local Contribution to Beta-Diversity to evaluate the compositional uniqueness of 51 host-parasite communities of rodents and their ectoparasitic fleas across Eurasia, using publicly available data. We measured uniqueness based on the species composition, and based on potential and realized biotic interactions (here, host-parasite interactions). Results: We show that species interactions vary more, across space, than species do. In particular, we show that species interactions respond to some climatic variables that have no effect on species distributions or dissimilarity. Main conclusions: Species interactions capture some degree of variation which is not apparent when looking at species occurrences only. In this system, this appeared as hosts and parasites interacting in different ways as a reponse to different environments, especially the temperature and dryness. We discuss the implications of this finding for the amount of information that should be considered when measuring community dissimilarity.

Ecology↗

bioRxiv2016

Assessing sampling sufficiency of network metrics using bootstrap

Sampling the full diversity of interactions in an ecological community is a highly intensive effort. Recent studies have demonstrated that many network metrics are sensitive to both sampling effort and network size. Here, we develop a statistical framework, based on bootstrap resampling, that aims to assess sampling sufficiency for some of the most widely used metrics in network ecology, namely connectance, nestedness (NODF-nested overlap and decreasing fill) and modularity (using the QuaBiMo algorithm). Our framework can generate confidence intervals for each network metric with increasing sample size (i.e., the number of sampled interaction events, or number of sampled individuals), which can be used to evaluate sampling sufficiency. The sample is considered sufficient when the confidence limits reach stability or lie within an acceptable level of precision for the aims of the study. We illustrate our framework with data from three quantitative networks of plant and frugivorous birds, varying in size from 16 to 115 species, and 17 to 2,745 interactions. These data sets illustrate that, for the same dataset, sampling sufficiency may be reached at different sample sizes depending on the metric of interest. The bootstrap confidence limits reached stability for the two largest networks, but were wide and unstable with increasing sample size for all three metrics estimated based on the smallest network. The bootstrap method is useful to empirical ecologists to indicate the minimum number of interactions necessary to reach sampling sufficiency for a specific network metric. It is also useful to compare sampling techniques of networks in their capacity to reach sampling sufficiency. Our method is general enough to be applied to different types of metrics and networks.

ecology↗

bioRxiv2017

Dynamic species classification of microorganisms across time, abiotic and biotic environments - a sliding window approach

1. Technological advances have greatly simplified to take and analyze digital images and videos, and ecologists increasingly use these techniques for trait, behavioral and taxonomic analyses. The development of techniques to automate biological measurements from the environment opens up new possibilities to infer species numbers, observe presence/absence patterns and recognize individuals based on audio-visual information.\n\n2. Streams of quantitative data, such as temporal species abundances, are processed by machine learning (ML) algorithms into meaningful information. Machine learning approaches learn to distinguish classes (e.g., species) from observed quantitative features (phenotypes), and in-turn predict the distinguished classes in subsequent observations. However, in biological systems, the environment changes, often driving phenotypic changes in behaviour and morphology.\n\n3. Here we describe a framework for classifying species under dynamic biotic and abiotic conditions using a novel sliding window approach. We train a random forest classifier on subsets of the data, covering restricted temporal, biotic and abiotic ranges (i.e. windows). We test our approach by applying the classification framework to experimental microbial communities where results were validated against manual classification. Individuals from one to six ciliate species were monitored over hundreds of generations in dozens of different species combinations and over a temperature gradient. We describe the steps of our classification pipeline and systematically explore the effects of the abiotic and biotic environments as well as temporal effects on classification success.\n\n4. Differences in biotic and abiotic conditions caused simplistic classification approaches to be unsuccessful. In contrast, the sliding window approach allowed classification to be highly successful, because phenotypic differences driven by environmental change could be captured in the learning algorithm. Importantly, automatic classification showed comparable success compared to manual identifications.\n\n5. Our framework allows for reliable classification even in dynamic environmental contexts, and may help to improve long-term monitoring of species from environmental samples. It therefore has application in disciplines with automatic enumeration and phenotyping of organisms such as eco-toxicology, ecology and evolutionary ecology, and broad-scale environmental monitoring.

ecology↗

bioRxiv2017

Population dynamics of mutualism and intraspecific density dependence:how θ-logistic-like density dependence affects mutualistic positive feedback

Mutualism describes the biological phenomenon where two or more species are reciprocally beneficial, regardless of their ecological intimacy or evolutionary history. Classic theory shows that mutualistic benefit must be relatively weak, or else it overpowers the stabilizing influence of intraspecific competition and leads to unrealistic, unbounded population growth. Interestingly, the conclusion that strong positive interactions lead to runaway population growth is strongly grounded in the behavior of a single model. This model [-] the Lotka-Volterra competition model with a sign change to generate mutualism rather than competition between species [-] assumes logistic growth of each species plus a linear interaction term to represent the mutualism. While it is commonly held that the linear interaction term is to blame for the models unrealistic behavior, we show here that a linear mutualism added to a{theta} -logistic model of population growth can prevent unbounded growth. We find that when density dependence is decelerating, the benefit of mutualism at equilibrium is greater than when density dependence is accelerating. Although there is a greater benefit, however, decelerating density dependence tends to destabilize populations whereas accelerating density dependence is always stable. We interpret these findings tentatively, but with promise for the understanding of the population ecology of mutualism by generating several predictions relating growth rates of mutualist populations and the strength of mutualistic interaction.

ecology↗

bioRxiv2017

Thermal adaptation constrains the temperature dependence of ecosystem metabolism

Gross primary production (GPP) is the largest flux in the carbon cycle, yet its response to global warming is highly uncertain. The temperature sensitivity of GPP is directly linked to photosynthetic physiology, but the response of GPP to warming over longer timescales could also be shaped by ecological and evolutionary processes that drive variation community structure and functional trait distributions. Here, we show that selection on photosynthetic traits within and across taxa dampen the effects of temperature on GPP across a catchment of geothermally heated streams. Autotrophs from cold streams had higher photosynthetic rates and after accounting for differences in biomass among sites, rates of ecosystem-level GPP were independent of temperature, despite a 20 {o}C thermal gradient. Our results suggest that thermal adaptation constrains the long-term temperature dependence of GPP, and highlights the importance of considering physiological, ecological and evolutionary mechanisms when predicting how ecosystem-level processes respond to warming.

ecology↗

bioRxiv2017

Dramatic differences in gut bacterial densities help to explain the relationship between diet and habitat in rainforest ants

Abundance is a key parameter in microbial ecology, and important to estimates of potential metabolite flux, impacts of dispersal, and sensitivity of samples to technical biases such as laboratory contamination. However, modern amplicon-based sequencing techniques by themselves typically provide no information about the absolute abundance of microbes. Here, we use fluorescence microscopy and quantitative PCR as independent estimates of microbial abundance to test the hypothesis that microbial symbionts have enabled ants to dominate tropical rainforest canopies by facilitating herbivorous diets, and compare these methods to microbial diversity profiles from 16S rRNA amplicon sequencing. Through a systematic survey of ants from a lowland tropical forest, we show that the density of gut microbiota varies across several orders of magnitude among ant lineages, with median individuals from many genera only marginally above detection limits. Supporting the hypothesis that microbial symbiosis is important to dominance in the canopy, we find that the abundance of gut bacteria is positively correlated with stable isotope proxies of herbivory among canopy-dwelling ants, but not among ground-dwelling ants. Notably, these broad findings are much more evident in the quantitative data than in the 16S rRNA sequencing data. Our results help to resolve a longstanding question in tropical rainforest ecology, and have broad implications for the interpretation of sequence-based surveys of microbial diversity.

ecology↗

bioRxiv2017

PREDICTING COEXISTENCE IN SPECIES WITH CONTINUOUS ONTOGENETIC NICHE SHIFTS AND COMPETITIVE ASYMMETRY

A longstanding problem in ecology is whether structured life cycles impede or facilitate coexistence between species. Theory based on populations with two discrete stages in the life-cycle indicates that coexistence requires at least one species to shift its niche between stages and that each species is a better competitor in one of the niches. However, in many cases, niche shifts are associated with changes in an underlying continuous trait like organism size and we have few predictions for how the conditions for coexistence are affected by this type of ontogenetic dynamics. Here we develop a framework for analyzing species coexistence based on Integral Projection Models (IPMs) that incorporates continuous ontogenetic changes in both the resource niche and competitive ability. We parameterize the model using experimental data from Trinidadian guppies and make predictions about how niche shifts and competitive symmetries allow or prevent species coexistence. Overall, our results show that the effects of competition on fitness depend upon trait-mediated niche-separation, trait-mediated competitive asymmetry in the part of the niche that is shared across body sizes, and the sensitivity of fitness to body size. When all three conditions are considered, we find multiple ecological and evolutionary routes to coexistence. When both species can shift their niche with increasing body size and competition for resources among the species and sizes is symmetric, then the species that shifts its niche to a greater degree with ontogeny will competitively exclude the other species. When competitive ability increases with increasing body size, then the two species can coexist when the better competitor shifts its niche with body size to a lesser degree than the weaker competitior. This region of coexistence shrinks as the better competitor increasingly shifts its niche with increasing size. When both species shift their niches with size, but each is a better competitor on resources used by smaller or larger individuals, then the model predicts an alternative stable state over some range of niche shifts. We discuss how our results provide new insights into species coexistence and the evolutionary consequences of size-structured interspecific competition.

ecology↗

bioRxiv2017

Host traits drive viral life histories across phytoplankton viruses

Viruses are integral to ecological and evolutionary processes, but we have a poor understanding of what drives variation in key traits across diverse viruses. For lytic viruses, burst size, latent period, and genome size are primary characteristics controlling host-virus dynamics. Burst size and latent period are analogous to organismal traits of fecundity and generation time, and genome size affects the size of the virion as well as viral control of host metabolism. Here we synthesize data on these traits for 75 strains of phytoplankton viruses, which play an important role in global biogeochemistry. We find that primary traits of the host (genome size, growth rate) are major ecological drivers, explaining 40-50% of variation in burst size and latent period. We analyze an eco-evolutionary model to explore mechanisms underlying these patterns. We find that burst size may be set by the host genomic resources available for viral construction, while latent period evolves to permit this maximal burst size, modulated by host metabolic rate. These results suggest that general mechanisms may underlie the evolution of diverse viruses, which will facilitate our understanding of viral community processes, ecosystem impacts, and coevolutionary dynamics.

ecology↗

bioRxiv2017

Integrating Telemetry Data Into Spatial Capture-Recapture Modifies Inferences On Multi-Scale Resource Selection

Estimating population size and resource selection functions (RSFs) are common approaches in applied ecology for addressing wildlife conservation and management objectives. Traditionally such approaches have been undertaken separately with different sources of data. Spatial capture-recapture (SCR) provides a framework for jointly estimating density and multi-scale resource selection, and data integration techniques provide opportunities for improving inferences from SCR models. Here we illustrate an application of integrated SCR-RSF modeling to a population of American marten (Martes americana) in alpine forests of northern New England. Spatial encounter data from camera traps were combined with telemetry locations from radio-collared individuals to examine how density and space use varied with spatial environmental features. We compared multi-model inferences between the integrated SCR-RSF model with telemetry and a standard SCR model with no telemetry. The integrated SCR-RSF model supported more complex relationships with spatial variation in third-order resource selection (i.e., individual space use), including selection for areas with shorter distances to mixed coniferous forest and rugged terrain. Both models indicated increased second-order selection (i.e., density) for areas close to mixed coniferous forest, while the integrated SCR-RSF model had a lower effect size due to modulation from spatial variability in space use. Our application of the integrated SCR-RSF model illustrates the improved inferences from spatial encounter data that can be achieved from integrating auxiliary telemetry data. Integrated modeling allows ecologists to join empirical data to ecological theory using a robust quantitative framework to better address conservation and management objectives.

ecology↗

bioRxiv2017

Caterpillars lack a resident gut microbiome

Many animals are inhabited by microbial symbionts that influence their hosts development, physiology, ecological interactions, and evolutionary diversification. However, firm evidence for the existence and functional importance of resident microbiomes in larval Lepidoptera (caterpillars) is lacking, despite the fact that these insects are enormously diverse, major agricultural pests, and dominant herbivores in many ecosystems. Using 16S rRNA gene sequencing and quantitative PCR, we characterized the gut microbiomes of wild leaf-feeding caterpillars in the United States and Costa Rica, representing 124 species from 16 families. Compared with other insects and vertebrates assayed using the same methods, the microbes we detected in caterpillar guts were unusually low-density and highly variable among individuals. Furthermore, the abundance and composition of leaf-associated microbes were reflected in the feces of caterpillars consuming the same plants. Thus, microbes ingested with food are present (though possibly dead or dormant) in the caterpillar gut, but host-specific, resident symbionts are largely absent. To test whether transient microbes might still contribute to feeding and development, we conducted an experiment on field-collected caterpillars of the model species Manduca sexta. Antibiotic suppression of gut bacterial activity did not significantly affect caterpillar weight gain, development, or survival. The high pH, simple gut structure, and fast transit times that typify caterpillar digestive physiology may prevent microbial colonization. Moreover, host-encoded digestive and detoxification mechanisms likely render microbes unnecessary for caterpillar herbivory. Caterpillars illustrate the potential ecological and evolutionary benefits of independence from symbionts, a lifestyle which may be widespread among animals.

ecology↗

bioRxiv2017

The Dynamic Core Microbiome: Structure, Stability And Resistance

The long-term stability of microbiomes is crucial as the persistent occurrence of beneficial microbes and their associated functions ensure host health and well-being. Microbiomes are highly diverse and dynamic, making them challenging to understand. Because many natural systems work as temporal networks, we present an approach that allows identifying meaningful ecological patterns within complex microbiomes: the dynamic core microbiome. On the basis of six marine sponge species sampled monthly over three years, we study the structure, dynamics and stability of their microbiomes. What emerge for each microbiome is a negative relationship between temporal variability and mean abundance. The notion of the dynamic core microbiome allowed us to determine a relevant functional attribute of the microbiome: temporal stability is not determined by the diversity of a hosts microbial assemblages, but rather by the density of those microbes that conform its core microbiome. The core microbial interaction network consisted of complementary members interacting weakly with dominance of comensal and amensal interactions that suggests self-regulation as a key determinant of the temporal stability of the microbiome. These interactions have likely coevolved to maintain host functionality and fitness over ecological, and even evolutionary time scales.

ecology↗

bioRxiv2017

A Comment On Priors For Bayesian Occupancy Models

Understanding patterns of species occurrence and the processes underlying these patterns is fundamental to the study of ecology. One of the more commonly used approaches to investigate species occurrence patterns is occupancy modeling, which can account for imperfect detection of a species during surveys. In recent years, there has been a proliferation of Bayesian modeling in ecology, which includes fitting Bayesian occupancy models. The Bayesian framework is appealing to ecologists for many reasons, including the ability to incorporate prior information through the specification of prior distributions on parameters. While ecologists often intend to choose priors so that they are \"uninformative\"; or \";vague\";, such priors can easily be unintentionally highly informative. Here we report on how the specification of a \"vague\" normally distributed (i.e., Gaussian) prior on coefficients in Bayesian occupancy models can unintentionally influence parameter estimation. Using both simulation and empirical examples, we illustrate how this issue likely compromises inference about species-habitat relationships. While the occurrence of this issue likely depends on the data set, researchers fitting Bayesian occupancy models should conduct sensitivity analyses to ensure intended inference, or use priors other than those most commonly used in the literature. We provide further suggestions for addressing this issue in occupancy studies, and an online tool for exploring this issue under different contexts.

ecology↗

bioRxiv2017

Biomod2EZ - An R script suite for visualizing projected niche model ensembles and reporting statistical results.

Biomod2EZ is a suite of R scripts to use in conjunction with the Biomod2 R package by Thuiller et al. (2016) that is used to create ensemble ecological niche models using up to 11 different modeling techniques. Biomod2EZ adds to the functionality of Biomod2 (Thuiller et al. 2016) by incorporating a report generation feature, detailed script annotation, and sample dataset/tutorial to ease the transition from ecological niche modeling using a Graphical User Interface to the coding environment of the R framework (R Development Core Team, 2016).

ecology↗

bioRxiv2017

Taking the short- or long-chain route: conversion efficiency of alpha linolenic acid to long-chain omega-3 fatty acids in aerial insectivore chicks

Food availability and quality are both critical for growing young animals. In nature, swallows (Tachycineta bicolor) and other aerial insectivores feed on both aquatic insects, which are rich in omega-3 long-chain polyunsaturated fatty acid (LCPUFA) and terrestrial insects, which contain considerably less LCPUFA. Carnivorous mammals and fishes must obtain LCPUFA from diet, as they have lost the capacity to convert the precursor omega-3 ALA into LCPUFA. Thus, the relative value of aquatic versus terrestrial insects depends not only on the fatty acid composition of the prey, but also upon the capacity of consumers to convert ALA into LCPUFA. We used a combination of stable-isotope-labeled fatty acid tracers to ask if, and how efficiently, Tree Swallows can deposit newly synthesized LCPUFA into tissue. Our data show for the first time that Tree Swallows can convert ALA into LCPUFA deposited in liver and skeletal muscle. However, high Tree Swallow demand for LCPUFA combined with low ALA availability in natural terrestrial foods may strain their modest conversion ability. This suggests that while Tree Swallows can synthesize LCPUFA de novo, LCPUFA are ecologically essential nutrients in natural systems. Our findings thus provide mechanistic support for our previous findings and the importance of LCPUFA-rich aquatic insects for Tree Swallows and most likely other aerial insectivores with similar niches.\n\nSummary StatementA stable-isotope-labeled tracer reveals the mechanism for omega-3 long-chain polyunsaturated fatty acid (LCPUFA) limitation in a wild avian insectivore, showing that LCPUFA are an ecologically essential nutrient.

ecology↗

bioRxiv2017

Effects of agrochemicals on disease severity of Acanthostomum burminis infections (Digenea: Trematoda) in the Asian common toad, Duttaphrynus melanostictus

BackgroundAgrochemicals are widely used in many parts of the world posing direct and indirect threats to organisms. Xenobiotic-related disease susceptibility is a common phenomenon and a proposed cause of amphibian declines and malformations. For example, parasitic infections combined with pesticides generally pose greater risk to both tadpoles and adult frogs than either factor alone. Here, we report on experimental effects of lone and combined exposures to cercariae of the digenetic trematode Acanthostomum burminis and ecologically relevant concentrations of (0.5 ppm) four pesticides (insecticides: chlorpyrifos, dimethoate; herbicides: glyphosate, propanil) on the tadpoles and metamorphs of the Asian common toad, Duttaphrynus melanostictus.\n\nResultsAll 48 cercaraie successfully penetrated each host suggesting that the pesticides had no short-term detrimental effect on cercarial penetration abilities. When the two treatments were provided separately, both cercariae and pesticides significantly decreased the survival of tadpoles and metamorphs and increased developmental malformations, such as scoliosis, kyphosis, and skin ulcers. Exposure to cercariae and the two insecticides additively reduced host survival. In contrast, mortality associated with the combination of cercariae and herbicides was less than additive. The effect of cercariae on malformation incidence depended on the pesticide treatment; dimethoate, glyphosate, and propanil reduced the number of cercarial-induced malformations relative to both the control and chlorpyrifos treatments.\n\nConclusionsThese results show that ecologically relevant concentrations of the tested agrochemicals had minimal effects on trematode infections, in contrast to others studies which showed that these same treatments increased the adverse effects of these infections on tadpoles and metamorphs of the Asian common toad. These findings reinforce the importance of elucidating the complex interactions among xenobiotics and pathogens on sentinel organisms that may be indicators of risk to other biota.

ecology↗