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bioRxiv2018

Identify and predict environmental change effects on tiger mosquitos, Aedes polynesiensis

SO_SCPLOWUMMARYC_SCPLOWTo control mosquito populations for managing vector-borne diseases, a critical need is to identify and predict their response to causal environmental variables. However, most existing attempts rely on linear approaches based on correlation, which cannot apply in complex, nonlinear natural systems, because correlation is neither a necessary nor sufficient condition for causation. Appling empirical dynamic modelling that acknowledges nonlinear dynamics on nine subpopulations of tiger mosquitos from three neighbouring reef islets of the Raiatea atoll, we identified temperature, precipitation, dew point, air pressure, and mean tide level as causal environmental variables. Interestingly, responses of subpopulations in close proximity (100-500 m) differed with respect to their causal environmental variables and the time delay of effect, highlighting complexity in mosquito-environment causality network. Moreover, we demonstrated how to explore the effects of changing environmental variables on number and strength of mosquito outbreaks, providing a new framework for pest control and disease vector ecology.

ecology↗

bioRxiv2018

Evolutionary stability of plant-pollinator networks: efficient communities, hysteresis, and a pollination dilemma

Mutualistic interactions between species such as pollination and plant-mycorrhiza interactions are ubiquitous in nature and essential for ecosystem functioning. Often dozens or even hundreds of species with different degree of specialization form complex networks of interdependence. How the complexity evolved and is maintained are fundamental questions in ecology. Here, we present a new game theoretical approach to model complex mutualistic interactions, which we apply to pollination networks. The theoretical analysis revealed multiple evolutionary stable network structures that form a gradient from generalism toward specialism with increasing availability of pollination service. In particular, we found that efficient communities evolve only under pollination oversupply, but that pollination shortage selects for inefficient network structures due to a pollination dilemma. These results suggest that availability of pollination services is a key factor structuring pollination networks and offer a new explanation for the geographical differences in pollination faunas that have long been recognized by ecologists. The study bridges the gap between network studies, game theory, and the natural history of pollination, which have hitherto been studied largely independently.

ecology↗

bioRxiv2018

Human activity is altering the world’s zoogeographical regions

Human activity leading to both species introductions and extinctions is widely known to influence diversity patterns on local and regional scales. Yet, it is largely unknown whether the intensity of this activity is enough to affect the configuration of biodiversity at broader levels of spatial organization. Zoogeographical regions, or zooregions, are surfaces of the Earth defined by characteristic pools of species, which reflect ecological, historical, and evolutionary processes acting over millions of years. Consequently, it is widely assumed that zooregions are robust and unlikely to change on a human timescale. Here, however, we show that human-mediated introductions and extinctions can indeed reconfigure the currently recognized zooregions of amphibians, mammals, and birds. In particular, introductions homogenize the African and Eurasian zooregions in mammals; reshape boundaries with the reallocation of Oceania to the New World zooregion in amphibians; and divide bird zooregions by increasing biotic heterogeneity. Furthermore, the combined effect of amphibian introductions and extinctions has the potential to divide two zooregions largely representing the Old and the New World. Interestingly, the robustness of zooregions against changes in species composition may largely explain such zoogeographical changes. Altogether, our results demonstrate that human activities can erode the higher-level organization of biodiversity formed over millions of years. Comparable reconfigurations have previously been detectable in Earths history only after glaciations and mass extinction events, highlighting the profound and far-reaching impact of ongoing human activity and the need to protect the uniqueness of biotic assemblages from the effects of future species introductions and extinctions.

ecology↗

bioRxiv2018

Simultaneous detection of invasive signal crayfish, endangered white-clawed crayfish and the crayfish plague pathogen using environmental DNA

Aquatic Invasive Species (AIS) are important vectors for the introduction of novel pathogens which can, in turn, become drivers of rapid ecological and evolutionary change, compromising the persistence of native species. Conservation strategies rely on accurate information regarding presence and distribution of AIS and their associated pathogens to prevent or mitigate negative impacts, such as predation, displacement or competition with native species for food, space or breeding sites. Environmental DNA is increasingly used as a conservation tool for early detection and monitoring of AIS. We used a novel eDNA high-resolution melt curve (HRM) approach to simultaneously detect the UK endangered native crayfish (Austropotamobius pallipes), the highly invasive signal crayfish (Pacifastacus leniusculus) and their dominant pathogen, Aphanomyces astaci, (causative agent of crayfish plague). We validated the approach with laboratory and field samples in areas with known presence or absence of both crayfish species as well as the pathogen, prior to the monitoring of areas where their presence was unknown. We identified the presence of infected signal crayfish further upstream than previously detected in an area where previous intensive eradication attempts had taken place, and the coexistence of both species in plague free catchments. We also detected the endangered native crayfish in an area where trapping had failed. With this method, we could estimate the distribution of native and invasive crayfish and their infection status in a rapid, cost effective and highly sensitive way, providing essential information for the development of conservation strategies in catchments with populations of endangered native crayfish.

ecology↗

bioRxiv2018

Beta diversity patterns derived from island biogeography theory

The Theory of Island Biogeography (TIB) has been successful in predicting alpha diversity patterns such as species-area relationships and species-abundance distributions. Although beta diversity (i.e. the dissimilarity of community composition) has long been recognized as an important element of the TIB and is crucial for understanding community assembly processes, it has never been formally incorporated into the theory. Here we derive theoretical predictions for the expected pairwise beta diversity values under a species-level neutral scenario where all species have equal colonization and extinction rates. We test these predictions for the avian community composition of 42 islands (and 93 species) in the Thousand Island Lake, China. We find that alpha diversity patterns alone do not distinguish a species-level neutral model from a non-neutral model. In contrast, beta diversity patterns clearly reject a species-level neutral model. We suggest that the presented theoretical integration beta diversity offers a powerful path for testing the presence of neutral processes in ecology and biogeography.

ecology↗

bioRxiv2018

Influence of elevated CO2 on development and food utilization of target armyworm Mythimna separata fed on transgenic Bt maize infected by nitrogen-fixing bacteria

Bt crops will face a new ecological risk of reduced effectiveness against target-insect pests owing to the general decrease in exogenous-toxin content in Bt crops grown under elevated CO2. How to deal with this issue may affect the sustainability of transgenic crops as an effective pest management tool especially under future CO2 raising. In this study, azotobacters, as being one potential biological regulator to enhance crops nitrogen utilization efficiency, were selected and the effects of Bt maize and non-Bt maize infected by Azospirillum brasilense and Azotobacter chroococcum on development and food utilization of target Mythimna separate were studied under ambient and elevated CO2. The results indicated that azotobacter infection significantly increased larval life-span, pupal duration, RCR and AD of M. separata, and significantly decreased RGR, ECD and ECI of M. separata fed on Bt maize; There were opposite trends in development and food utilization of M. separata fed on non-Bt maize infected with azotobacters compared with the buffer control regardless of CO2 level. Presumably, the application of azotobacter infection could make Bt maize facing lower field hazards from the target pest of M. separate, and finally improve the resistance of Bt maize against target lepidoptera pests especially under elevated CO2.\n\nSummary statementElevated CO2 effect on development and food utilization of target armyworm Mythimna separata fed on Bt maize infected by azotobacter, Azospirillum brasilense and Azotobacter chroococcum

ecology↗

bioRxiv2018

Using citizen science data in integrated population models to inform conservation decision-making

Analysis of animal population status and change are core elements of ecological research and critical for prioritizing conservation actions. Traditionally, count-based data from structured surveys have been the main source of information used to estimate trends and changes in populations. In the past decade, advances in integrated population models (IPMs) have allowed these data to be combined with other data sources (e.g., observations of marked individuals). IPMs have allowed researchers to determine the direction and magnitude of a species population trajectory and to test underlying mechanisms. For many species, life-history characteristics (e.g., low site-fidelity), low abundance and/or low detection probability make it difficult to collect sufficient data; thus, IPMs for these species are difficult to employ. We used count data from eBird to estimate population trends for one such species, the tricolored blackbird (Agelaius tricolor). We combined estimates of relative abundance with banding and nesting data. Our joint estimation of demographic rates allowed us to evaluate their individual contributions to the population growth rate. We suggest that investments in increasing reproductive success and recruitment are the most likely conservation strategies to increase the population. The extensive survey efforts of citizen scientists aided the employment of IPMs to inform conservation efforts.\n\nData AccessibilityShould the manuscript be accepted, the data supporting the results will be published along with the manuscript. The eBird data used for analyses in this manuscript may be downloaded from https://ebird.org/data/download.

ecology↗

bioRxiv2018

Viral Fitness Across a Continuum from Lysis to Latency

The prevailing paradigm in ecological studies of viruses and their microbial hosts is that the reproductive success of viruses depends on the proliferation of the \"predator\", i.e., the virus particle. Yet, viruses are obligate intracellular parasites, and the virus genome - the actual unit of selection - can persist and proliferate from one cell generation to the next without lysis or the production of new virus particles. Here, we propose a theoretical framework to quantify the invasion fitness of viruses using an epidemiological cell-centric metric that focuses on the proliferation of viral genomes inside cells instead of virus particles outside cells. This cell-centric metric enables direct comparison of viral strategies characterized by obligate killing of hosts (e.g., via lysis), persistence of viral genomes inside hosts (e.g., via lysogeny), and strategies along a continuum between these extremes (e.g., via chronic infections). As a result, we can identify environmental drivers, life history traits, and key feedbacks that govern variation in viral propagation in nonlinear population models. For example, we identify threshold conditions given relatively low densities of susceptible cells and relatively high growth rates of infected cells in which lysogenic and other chronic strategies have higher potential viral reproduction than lytic strategies. Altogether, the theoretical framework helps unify the ongoing study of eco-evolutionary drivers of viral strategies in natural environments.

ecology↗

bioRxiv2018

Historic collections as a tool for assessing the global pollinator crisis

There is increasing concern about the decline of pollinators worldwide. However, despite reports that pollinator declines are widespread, data are scarce and often geographically and taxonomically biased. These biases limit robust inference about any potential pollinator crisis. Non-structured and opportunistic historical specimen collection data provide the only source of historical information which can serve as a baseline for identifying pollinator declines. Specimens historically collected and preserved in museums not only provide information on where and when species were collected, but also contain other ecological information such as species interactions and morphological traits. Here, we provide a synthesis of how researchers have used historical data to identify long-term changes in biodiversity, species abundances, morphology and pollination services. Despite recent advances, we show that information on the status and trends of most pollinators is absent, but we highlight opportunities and limitations to progress the assessment of pollinator declines globally. Finally, we demonstrate different approaches to analysing museum collection data using two contrasting case studies from distinct geographical regions (New Zealand and Spain) for which long-term pollinator declines have never been assessed. There is immense potential for museum specimens to play a central role in assessing the extent of the global pollination crisis.

ecology↗

bioRxiv2018

Heterogeneous Viral Strategies Promote Coexistence in Virus-Microbe Systems

Viruses of microbes, including bacterial viruses (phage), archaeal viruses, and eukaryotic viruses, can influence the fate of individual microbes and entire populations. Here, we model distinct modes of virus-host interactions and study their impact on the abundance and diversity of both viruses and their microbial hosts. We consider two distinct viral populations infecting the same microbial population via two different strategies: lytic and chronic. A lytic strategy corresponds to viruses that exclusively infect and lyse their hosts to release new virions. A chronic strategy corresponds to viruses that infect hosts and then continually release new viruses via a budding process without cell lysis. The chronic virus can also be passed on to daughter cells during cell division. The long-term association of virus and microbe in the chronic mode drives differences in selective pressures with respect to the lytic mode. We utilize invasion analysis of the corresponding nonlinear differential equation model to study the ecology and evolution of heterogenous viral strategies. We first investigate stability of equilibria, and characterize oscillatory and bistable dynamics in some parameter regions. Then, we derive fitness quantities for both virus types and investigate conditions for competitive exclusion and coexistence. In so doing we find unexpected results, including a regime in which the chronic virus requires the lytic virus for survival and invasion.

ecology↗

bioRxiv2018

Cascading Effects of Shrimp Trawling: Increased Benthic Biomass and Increase in Net Primary Production

Trawling has been shown to cause high mortality of discarded species (bycatch) and short-term ecological disturbance to bottom communities in coastal systems, resulting in lowered benthic biomass. Here we report evidence of a trawling-induced trophic cascade resulting in an increase in biomass of benthic polychaetes after the end of the shrimp trawling season in areas open to trawling in North Carolina (USA). Using comparative measurements of abundance of bycatch species and benthos in open and closed trawling management areas and Ecopath network modeling, we show that trawling in the open area has led to increases in deposit-feeding polychaetes and decreases in bycatch species (fish and crabs) that are benthic predators on the polychaetes. We conclude that proposed management actions to reduce the shrimp trawl fishery effort will influence other net and trap fisheries for southern flounder and blue crabs indirectly, as revealed by our network models, and the proposed trawling ban may lead to improvements in other valuable fisheries.

ecology↗

bioRxiv2018

Spatial Mark-Resight for Categorically MarkedPopulations with an Application to GeneticCapture-Recapture

The estimation of animal population density is a fundamental goal in wildlife ecology and management, commonly met using mark recapture or spatial mark recapture (SCR) study designs and statistical methods. Mark-recapture methods require the identification of individuals; however, for many species and sampling methods, particularly noninvasive methods, no individuals or only a subset of individuals are individually identifiable. The unmarked SCR model, theoretically, can estimate the density of unmarked populations; however, it produces biased and imprecise density estimates in many sampling scenarios typically encountered. Spatial mark-resight (SMR) models extend the unmarked SCR model in three ways: 1) by introducing a subset of individuals that are marked and individually identifiable, 2) introducing the possibility of individual-linked telemetry data, and 3) introducing the possibility that the capture-recapture data from the survey used to deploy the marks can be used in a joint model, all improving the reliability of density estimates. The categorical spatial partial identity model (SPIM) improves the reliability of density estimates over unmarked SCR along another dimension, by adding categorical identity covariates that improve the probabilistic association of the latent identity samples. Here, we combine these two models into a \"categorical SMR\" model to exploit the benefits of both models simultaneously. We demonstrate using simulations that SMR alone can produce biased and imprecise density estimates with sparse data and/or when few individuals are marked. Then, using a fisher (Pekania pennanti) genetic capture-recapture data set, we show how categorical identity covariates, marked individuals, telemetry data, and jointly modeling the capture survey used to deploy marks with the resighting survey all combine to improve inference over the unmarked SCR model. As previously seen in an application of the categorical SPIM to a real-world data set, the fisher data set demonstrates that individual heterogeneity in detection function parameters, especially the spatial scale parameter{sigma} , introduces positive bias into latent identity SCR models (e.g., unmarked SCR, SMR), but the categorical SMR model provides more tools to reduce this positive bias than SMR or the categorical SPIM alone. We introduce the possibility of detection functions that vary by identity category level, which will remove individual heterogeneity in detection function parameters than is explained by categorical covariates, such as individual sex. Finally, we provide efficient SMR algorithms that accommodate all SMR sample types, interspersed marking and sighting periods, and any number of identity covariates using the 2-dimensional individual by trap data in conjunction with precomputed constraint matrices, rather than the 3-dimensional individual by trap by occasion data used in SMR algorithms to date.

ecology↗

bioRxiv2018

The three regimes of spatial recovery

An enduring challenge for ecology is identifying the drivers of ecosystem and population stability. In a spatially explicit context, key features to consider are landscape spatial structure, local interactions, and dispersal. Substantial work has been done on each of these features as a driver of stability, but little is known on the interplay between them. Missing has been a more integrative approach, able to map and identify different dynamical regimes, and thus to predict a systems response to perturbations. Here we first consider a simple scenario, i.e. the recovery of a homogeneous metapopulation from a single localized pulse disturbance. The analysis of this scenario reveals three fundamental recovery regimes: Isolated Regime when dispersal is not significant, Rescue Regime when dispersal mediates recovery, and Mixing Regime when perturbations spread throughout the system. Despite its simplicity, our approach leads to remarkably general predictions. These include the qualitatively different outcomes of various scenarios of habitat fragmentation, the surprising benefits of local extinctions on population persistence at the transition between regimes, and the productivity shifts of metacommunities in a changing environment. This study thus provides context to known results and insight into future directions of research.

ecology↗

bioRxiv2018

Supporting global biodiversity assessment through high-resolution macroecological modelling: Methodological underpinnings of the BILBI framework

AimGlobal indicators of change in the state of terrestrial biodiversity are often derived by intersecting observed or projected changes in the distribution of habitat transformation, or of protected areas, with underlying patterns in the distribution of biodiversity. However the two main sources of data used to account for biodiversity patterns in such assessments - i.e. ecoregional boundaries, and vertebrate species ranges - are typically delineated at a much coarser resolution than the spatial grain of key ecological processes shaping both land-use and biological distributions at landscape scale. Species distribution modelling provides one widely used means of refining the resolution of mapped species distributions, but is limited to a subset of species which is biased both taxonomically and geographically, with some regions of the world lacking adequate data to generate reliable models even for better-known biological groups.\n\nInnovationMacroecological modelling of collective properties of biodiversity (e.g. alpha and beta diversity) as a correlative function of environmental predictors offers an alternative, yet highly complementary, approach to refining the spatial resolution with which patterns in the distribution of biodiversity can be mapped across our planet. Here we introduce a new capability - BILBI (the Biogeographic Infrastructure for Large-scaled Biodiversity Indicators) - which has implemented this approach by integrating advances in macroecological modelling, biodiversity informatics, remote sensing and high-performance computing to assess spatial-temporal change in biodiversity at ~1km grid resolution across the entire terrestrial surface of the planet. The initial implementation of this infrastructure focuses on modelling beta-diversity patterns using a novel extension of generalised dissimilarity modelling (GDM) designed to extract maximum value from sparsely and unevenly distributed occurrence records for over 400,000 species of plants, invertebrates and vertebrates.\n\nMain conclusionsModels generated by BILBI greatly refine the mapping of beta-diversity patterns relative to more traditional biodiversity surrogates such as ecoregions. This capability is already proving of considerable value in informing global biodiversity assessment through: 1) generation of indicators of past-to-present change in biodiversity based on observed changes in habitat condition and protected-area coverage; and 2) projection of potential future change in biodiversity as a consequence of alternative scenarios of global change in drivers and policy options.

ecology↗

bioRxiv2018

Worldwide impacts of past and projected future land-use change on local species richness and the Biodiversity Intactness Index

Although people have modified the world around us throughout human history, the Great Acceleration has seen drivers such as land conversion, exploitation of natural populations, species introductions, pollution and human-induced climate change placing biodiversity under increasing pressure. In this paper we examine 1) how terrestrial species communities have been impacted over the last thousand years of human development and 2) how plausible futures defined by alternative socio-economic scenarios are expected to impact species communities in the future. We use the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) database to model impacts of land-use change and human population on local species richness, community abundance, and biodiversity intactness using a mixed-effects modelling structure. Historical impacts are inferred through projection of model results onto maps of historical land use, provided by the land-use harmonization project, and gridded human population density (HYDE 3.1). Future impacts are explored using the Shared Socio-economic Pathway (SSP) scenarios. These scenarios detail five plausible global futures based upon socio-economic factors such as wealth, population, education, technology, and reliance on fossil fuels, and can be combined with Representative Concentration Pathway (RCP) scenarios to consider climate mitigation strategies. We project model results onto the gridded outputs of six SSP/RCP scenario combinations: SSP1/RCP2.6, SSP2/RCP4.5, SSP3/RCP7.0, SSP4/RCP3.4, SSP4/RCP6.0, and SSP5/RCP8.5. Historical trend lines show that most losses in local biodiversity are relatively recent, with 75% of all loss in both abundance-based Biodiversity Intactness Index and species richness occurring post-1800. Stark regional differences emerge in all future scenarios, with biodiversity in African regions undergoing greater losses than Oceania, North America and the European regions. Although climate change is expected to have severe detrimental impacts to biodiversity - which are not quantified in these results - it is important to consider how the climate change mitigation itself may also impact biodiversity. Our results suggest that strong climate change mitigation through biofuel production will detrimentally impact biodiversity: SSP4/RCP3.4 (with high biofuel mitigation) is predicted to see two times the decrease in abundance-based biodiversity intactness and three times the decrease in local species richness between 2015-2100 as is predicted for SSP4/RCP6.0 (with lower levels of mitigation). SSP4/RCP3.4 forecasts the greatest impact to average local species richness of all the SSP/RCP combinations with an average loss of 13% of local species richness projected to have occurred by 2100. SSP3/RCP7.0 - a scenario describing a globally segregated, and economically protectionist future with low climate change mitigation - has the worst impacts on abundance-based biodiversity intactness with an average loss of 26% of intactness by 2100. However, a brighter future is possible; SSP1/RCP2.6 describes a more sustainable future, where human populations are provided for without further jeopardising environmental integrity - in this scenario we project that biodiversity will recover somewhat, with gains in biodiversity intactness and species richness in many regions of the world by 2100.

ecology↗

bioRxiv2018

Overcome Competitive Exclusion in Ecosystems

Explaining biodiversity in nature is a fundamental problem in ecology. One great challenge is embodied in the so-called competitive exclusion principle1-4: the number of species in steady coexistence cannot exceed the number of resources4-7. In the past five decades, various mechanisms have been proposed to overcome the limit on diversity set by the competitive exclusion principle8-25. Yet, none of the existing mechanisms can generically overcome competitive exclusion at steady state4,26. Here we show that by forming chasing triplets in the predation process among the consumers and resources, the number of coexisting species of consumers can exceed that of resources at steady state, naturally breaking the competitive exclusion principle. Our model can be broadly applicable to explain the biodiversity of many consumer-resource ecosystems and deepen our understanding of biodiversity in nature.

ecology↗

bioRxiv2018

Movement behaviour responses to environment: fast inference of individual variation with a mixed effects model

Like many species, movement patterns of southern elephant seals (Mirounga leonina) are being influenced by long-term environmental change. These seals migrate up to 4000 km from their breeding colonies, foraging for months in a variety of Southern Ocean habitats. Understanding how movement patterns vary with environmental features and how these relationships differ among individuals employing different foraging strategies can provide insight into foraging performance at a population level. We apply new fast-estimation tools to fit mixed effects within a random walk movement model, rapidly inferring among-individual variability in southern elephant seal environment-movement relationships. We found that seals making foraging trips to the sea-ice on or near the Antarctic continental shelf consistently reduced speed and directionality (move persistence) with increasing sea ice coverage and had variable responses to chlorophyll a concentration, whereas seals that foraged pelagically reduced move persistence in regions where circumpolar deep water shoaled. Given future climate scenarios, pelagic foragers may encounter more productive habitat but sea-ice foragers may see reduced habitat availability. Our approach is scalable to large telemetry data sets and allows flexible combinations of mixed effects to be evaluated via model selection, thereby illuminating the ecological context of animal movements that underlie habitat use.

ecology↗

bioRxiv2018

Spatial variation in exploited metapopulations obscures risk of collapse

Unanticipated declines among exploited species have commonly occurred despite harvests that appeared sustainable prior to collapse. This is particularly true in the oceans where spatial scales of management are often mismatched with spatially complex metapopulations. We explore causes, consequences and potential solutions for spatial mismatches in harvested metapopulations in three ways. First, we generate novel theory illustrating when and how harvesting metapopulations increases spatial variability and in turn masks local scale volatility. Second, we illustrate why spatial variability in harvested metapopulations leads to negative consequences using an empirical example of a Pacific herring metapopulation. Finally, we construct a numerical management strategy evaluation model to identify and highlight potential solutions for mismatches in spatial scale and spatial variability. Our results highlight that spatial complexity can promote stability at large scales, however ignoring spatial complexity produces cryptic and negative consequences for people and animals that interact with resources at small scales. Harvesting metapopulations magnifies spatial variability, which creates discrepancies between regional and local trends while increasing risk of local population collapses. Such effects asymmetrically impact locally constrained fishers and predators, which are more exposed to risks of localized collapses. Importantly, we show that dynamically optimizing harvest can minimize local risk without sacrificing yield. Thus, multiple nested scales of management may be necessary to avoid cryptic collapses in metapopulations and the ensuing ecological, social and economic consequences.

ecology↗