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bioRxiv2018

Host-parasite interaction explains variation in prevalence of avian haemosporidians at the community level

Parasites are a selective force that shape host community structure and dynamics, but host communities can also influence parasitism. Understanding the dual nature from host-parasite interactions can be facilitated by quantifying the variation in parasite prevalence (i.e. the proportion of infected host individuals in a population) among host species and then comparing that variation to other ecological factors that are known to also shape host communities. Avian haemosporidian parasites (e.g. Plasmodium and Haemoproteus) are abundant and widespread representing an excellent model for the study of host-parasite interactions. Several geographic and environmental factors have been suggested to determine prevalence of avian haemosporidians in bird communities. However, much remains to be known regarding whether host and parasite traits, represented by phylogenetic distances among species and degree of specialization in host-parasite relationships, can influence parasite prevalence. The aims of this study were to analyze factors affecting prevalence in a bird community and to test whether the degree of parasite specialization on their hosts is determined by host traits. Our statistical analyses suggest that prevalence is mainly determined by the interaction between host species and parasite lineages where tolerance and/or susceptibility to parasites plays an essential role. Additionally, we found that although some of the parasite lineages infected a low number of bird species, the species they infected were distantly related and therefore the parasites themselves should not be considered typical host specialists. Prevalence was higher for generalist than for specialist parasites in some, but not all, host species. These results suggest that prevalence mainly results from the interaction between host immune defences and parasite exploitation strategies wherein the result of an association between particular parasite lineages and particular host species is idiosyncratic.

ecology↗

bioRxiv2018

Plasmid transfer is biased towards close kin in bacteria from natural populations.

Plasmids play a key role in microbial ecology and evolution, yet the determinants of plasmid transfer rates are poorly understood. Here we investigate the importance of genetic similarity between naturally co-occurring Escherichia coli isolates in the transfer of two plasmids (narrow-host-range R1 and broad-host-range RP4). We uncovered extensive variability, spanning over five orders of magnitude, in the ability of isolates to donate and receive plasmids. Overall, transfer was strongly biased towards clone-mates, but not correlated to genetic distance between donors and recipients. Transfer was limited by the presence of a functional restriction-modification system in recipients, thus bias towards kin might be explained by sharing of identical restriction systems. Such conjugation within lineages sets the stage for longer-term pair-wise coevolutionary interactions between plasmids and bacterial hosts.

ecology↗

bioRxiv2018

Spatiotemporal patterns of dunlin (Calidris alpina) in continental lakes of the Iberian Peninsula

Spatiotemporal dynamics may present different levels of regional or local stability, generally attributed to local habitat and landscape factors, reflecting the tolerances and ecological requirements of the populations. In this study, we examined the variations of dunlin abundance and occurrence in twenty-three wetlands of the \"La Mancha Humeda\" Biosphere Reserve, central Spain, between October 2010 and July 2017. In addition, we observed the variations of local abundance in the lakes of the Manjavacas lagoon complex, seeking to understand the factors that determine the local movements of the wintering individuals. Eleven lakes had records of dunlin, but most of individuals (ca. 90%) were observed in the Manjavacas Lagoon Complex (Alcahozo and Manjavacas lakes). The preference for this complex associated with temporal variations of abundance between the Alcahozo and Manjavacas lagoons possibly reflects the specific characteristics of the invertebrate community available as prey, especially for the presence of anostracans and copepods. The results of this study are a first step in understanding the factors that lead this species to select continental wetlands as wintering sites.

ecology↗

bioRxiv2018

Variable Effects on Growth and Defence Traits for Plant Ecotypic Differentiation and Phenotypic Plasticity along Elevation Gradients

Along ecological gradients, ecotypes generally evolve as the result of local adaptation to a specific environment to maximize organisms fitness. Alongside ecotypic differentiation, phenotypic plasticity, as the ability of a single genotype to produce different phenotypes under different environmental conditions, can also evolve for favouring increased organisms performance in different environments. Currently, there is a lack in our understanding of how varying habitats may contribute to the differential contribution of ecotypic differentiation and plasticity in growth versus defence traits. Using reciprocal transplant-common gardens along steep elevation gradients, we evaluated patterns of ecotypic differentiation and phenotypic plasticity of two coexisting but unrelated plant species, Cardamine pratensis and Plantago major. For both species, we observed ecotypic differentiation accompanied by plasticity in growth related traits. Plants grew faster and produced more biomass when placed at low elevation. In contrast, we observed fixed ecotypic differentiation for defence and resistance traits. Generally, low elevation ecotypes produced higher chemical defences regardless of the growing elevation. Yet, some plasticity was observed for specific compounds, such as indole glucosinolates. We speculate that ecotypic differentiation in defence traits is maintained by costs of chemical defence production, while plasticity in growth traits is regulated by temperature driven growth response maximization.

ecology↗

bioRxiv2018

The biggest losers: Habitat isolation deconstructs complex food webs from top to bottom

Habitat fragmentation is threatening global biodiversity. To date, there is only limited understanding of how habitat fragmentation or any alteration to the spatial structure of a landscape in general, affects species diversity within complex ecological networks such as food webs. Here, we present a dynamic and spatially-explicit food web model which integrates complex food web dynamics at the local scale and species-specific dispersal dynamics at the landscape scale, allowing us to study the interplay of local and spatial processes in metacommunities. We explore how habitat fragmentation, defined as a decrease of habitat availability and an increase of habitat isolation, affects the species diversity patterns of complex food webs (-, {beta}-,{gamma} -diversity), and specifically test whether there is a trophic dependency in the effect of habitat fragmentation on species diversity. In our model, habitat isolation is the main driver causing species loss and diversity decline. Our results emphasise that large-bodied consumer species at high trophic positions go extinct faster than smaller species at lower trophic levels, despite being superior dispersers that connect fragmented landscapes better. We attribute the loss of top species to a combined effect of higher biomass loss during dispersal with increasing habitat isolation in general, and the associated energy limitation in highly fragmented landscapes, preventing higher trophic levels to persist. To maintain trophic-complex and species-rich communities calls for effective conservation planning which considers the interdependence of trophic and spatial dynamics as well as the spatial context of a landscape and its energy availability.

ecology↗

bioRxiv2018

The geometry of habitat fragmentation: effects of distribution patterns on short-term species persistence

Land-use changes cause habitat loss and fragmentation and are thus important drivers of anthropogenic biodiversity change. However, there is an ongoing debate about how fragmentation per se affects biodiversity in a given amount of habitat. We illustrate why it is important to distinguish two different aspects of fragmentation to resolve this debate: (i) geometric fragmentation effects, which exclusively arise from the spatial distributions of species and habitat fragments, and (ii) demographic fragmentation effects due to reduced fragment size, increased isolation, or edge effects. While most empirical studies are primarily interested in quantifying demographic fragmentation effects, geometric effects are typically invoked only as post-hoc explanations of biodiversity responses to fragmentation per se. Here, we present an approach to quantify geometric fragmentation effects on species persistence probability. We illustrate this approach using spatial simulations where we systematically varied the initial abundances and distribution patterns (i.e. random, aggregated, and regular) of species as well as habitat amount and fragmentation per se. As expected, we found no geometric fragmentation effects when species were randomly distributed. However, when species were aggregated, we found positive effects of fragmentation per se on persistence probability for a large range of scenarios. For regular species distributions, we found weakly negative geometric effects. These findings are independent of the ecological mechanisms which generate non-random species distributions. Our study helps to reconcile seemingly contradictory results of previous fragmentation studies. Since intraspecific aggregation is a ubiquitous pattern in nature, our findings imply widespread positive geometric fragmentation effects. This expectation is supported by many studies that find positive effects of fragmentation per se on species occurrences and diversity after controlling for habitat amount. We outline how to disentangle geometric and demographic effects of fragmentation, which is critical for predicting the response of biodiversity to landscape change.

ecology↗

bioRxiv2018

The relative influence of niche versus neutral processes on Ediacaran communities

A fundamental question in community ecology is the relative influence of niche versus neutral processes in determining ecosystem dynamics. The extent to which these processes structured early animal communities is yet to be explored. Here we use spatial point process analyses (SPPA) to determine the influence of niche versus neutral processes on early total-group metazoan paleocommunities from the Ediacaran Period [~]565 million years in age. Preservation of these sessile organisms in large in-situ populations on exposed bedding planes enables inference of the most likely underlying processes governing their spatial distributions by SPPA. We conducted comprehensive spatial mapping of six of the largest Ediacaran paleocommunities in Newfoundland, Canada and Charnwood Forest, UK using LiDAR, photogrammetry and a laser-line probe. For each paleocommunity we determined the best-fit spatial model for each univariate and bivariate species distribution, comparing four sets of spatial models (complete spatial randomness, dispersal, habitat, and combined dispersal with habitat) using goodness-of-fit tests. Random and dispersal models are considered neutral processes while habitat and combined models are considered niche processes. We find the dynamics of these paleocommunities to be dominated by neutral processes, with limited influence from niche processes. Our findings are consistent with community model predictions of when neutral dynamics dominate, but are in stark contrast to the niche-dominated communities of the modern marine realm. Thus, while the underlying processes determining metazoan community assembly appear to have been in place since the appearance of the first macroscopic, complex animals, the dynamics of these early metazoan communities were fundamentally different to those of extant communities.\n\nSignificance statementThe extent to which habitat and dispersal processes structure the earliest animal communities found during the Ediacaran Period [~]565 million years ago, is unknown. In this study we analyse six of the largest and most diverse fossil assemblages from Newfoundland, Canada and Charnwood Forest, UK, using spatial point processes analyses to determine the relative influence of habitat processes (niche) and dispersal processes (neutral) on the spatial distribution of taxa. The vast majority of Ediacaran taxon distributions were controlled by neutral processes, in striking contrast to niche-dominated modern marine ecosystems, but consistent with model predictions of when neutral dynamics dominate communities. Thus the underlying processes determining metazoan community assembly have been in place since the appearance of the first macroscopic, complex animals.

ecology↗

bioRxiv2018

Response of Australian pied oystercatchers Haematopus longirostris to increasing abundance of the beach bivalve prey Donax deltoides

This study measured the response of Australian pied oystercatchers Haematopus longirostris on South Ballina Beach, New South Wales, Australia during a recovery in the stock of the primary prey species Donax deltoides, a large beach clam and commonly known as the pipi. It was predicted that oystercatcher counts would increase when pipi abundance increased (numerical response) and that oystercatcher feeding rates would also increase (functional response). Between Oct 2009 and Mar 2015, mean pipi density increased from c. zero to 30 pipis/m2. Mean oystercatcher feeding rates increased to an asymptote of c. 0.26 pipis/min. Breeding season mean counts of adult-plumage oystercatchers increased from 23 to 43, largely driven by non-territorial birds. Prey size selection was absent, both among different prey types and among pipis > 20 mm. This report provides some insights into the feeding ecology of oystercatchers on sandy ocean beaches that should be valuable in planning future studies.

ecology↗

bioRxiv2018

Local and landscape drivers of aquatic-to-terrestrial subsidies in riparian ecosystems: a worldwide meta-analysis

Cross-boundary fluxes of organisms and matter, termed \"subsidies\", are now recognized to be reciprocal and of roughly equal importance for both aquatic and terrestrial systems, even if terrestrial input to aquatic ecosystems has received most attention. The magnitude of aquatic to terrestrial subsidies is well documented, but the drivers behind these subsidies and their utilization by terrestrial consumers are characteristically local scale studies, limiting the inferences that can be drawn for broader geographic scales. We therefore built and analyzed a database of stable isotope data extracted from 21 studies worldwide, to identify both landscape and local scale variables that may affect the diet of terrestrial predators in riparian ecosystems. Our meta-analysis revealed a greater magnitude of aquatic-to-terrestrial subsidies (> 50%) than previously reported, albeit with large geographic and inter-annual variations. We demonstrated a large effect of landscape-scale factors on aquatic-to-terrestrial subsidies, particularly anthropogenic land use and tree cover. Local human population was the only relevant factor at the local scale. We also found that studies on landscape-scale and anthropogenic land use effects on aquatic-to-terrestrial subsidies are currently strongly under-represented in the ecological literature. Such studies are needed to improve our understanding of how land use and environmental change might influence future patterns of biodiversity and ecosystem function.

ecology↗

bioRxiv2018

Prediction of Algal Blooms in the Great Lakes through a Convolution Neural Network of Remote Sensing Data

Harmful algal blooms (HABs) are the proliferation of algae due to eutrophication and have severe repercussions to the ecological balance in many water bodies, due to the toxins the algae produce. Additionally, the identification and prediction of these HABs has been a challenge in the scientific community due to the interactions between both biological and physical processes that cause the HABs. Here, we used remote sensing data to bypass these issues; remote sensing data provides significant information about the coverage of chlorophyll which can be used to locate HABs. Using this indicator of HABs, we trained a Convolution Neural Network (CNN) to identify nine types of algal blooms, using 25 epochs of 900 images, which can predict algal bloom shapes with an 80 percent accuracy. This approach of HAB identification can easily be applied to other aquatic ecosystems where remote sensing data is present.

ecology↗

bioRxiv2018

Immigration from the metacommunity affects bdelloid rotifer community dynamics most

Dispersal is an important driver of local community dynamics. It has been proposed that, for communities composed of microscopic organisms, dispersal could well be the dominant process, outpacing local processes driven by environmental conditions and species interactions. This is because microscopic organisms often reproduce asexually, fostering rapid colonization, and are easily dispersed by water or air current. We studied the case of bdelloid rotifers belonging to the genus Adineta, microscopic asexual animals with dried stages that are easily dispersed by wind to investigate the relative effects of dispersal and local processes on their community dynamics. To this end, we constructed a classic competition model to theoretically examine how spatial and local biodiversity dynamics varied with fitness and dispersal characteristics of bdelloid Adineta species. Next, we compared our predictions with an experimental dataset containing spatio-temporal Adineta community dynamics from the wild. This comparison suggested that immigration from the local meta-community was the most critical parameter under the conditions tested. One Adineta vaga species, abundant in the surrounding area, rapidly colonized our experimental habitats and dominated most of the communities. We also ran the model under different levels of environmental conditions (permissive, intermediate and harsh) to simulate seasonal community variability and found that communities experience important bottlenecks yearly in winter but that the same community re-established. The dissimilarities observed between roof communities suggest differences in adaptation or immigration capacities. Besides their asexual reproduction and extreme desiccation tolerance, a key characteristic of bdelloid ecology identified here, is the spatio-temporal dynamic of abundant bdelloid clones present in the meta-community that rapidly colonize empty patches to establish new populations.

ecology↗

bioRxiv2018

High levels of antibiotic resistance gene expression among birds living in a wastewater treatment plant

Antibiotic resistance is rendering common bacterial infections untreatable. Wildlife can incorporate and disperse antibiotic resistant bacteria in the environment, such as water systems, which in turn serve as reservoirs of resistance genes for human pathogens. We used bulk RNA-sequencing (meta-transcriptomics) to assess the diversity and expression levels of functionally active resistance genes in the microbiome of birds with aquatic behavior. We sampled birds across a range of habitats, from penguins in Antarctica to ducks in a wastewater treatment plant in Australia. This revealed 81 antibiotic resistance genes in birds from all localities, including {beta}-lactam, tetracycline and chloramphenicol resistance in Antarctica, and genes typically associated with multidrug resistance plasmids in areas with high human impact. Notably, birds feeding at a wastewater treatment plant carried the greatest resistance gene burden, suggesting that human waste, even if it undergoes treatment, contributes to the spread of antibiotic resistance genes to the wild. Differences in resistance gene burden also reflected the birds ecology, taxonomic group and microbial functioning. Ducks, which feed by dabbling, carried a higher abundance and diversity of resistance genes than turnstones, avocets and penguins, that usually prey on more pristine waters. In sum, this study helps to reveal the complex factors explaining the distribution of resistance genes and their exchange routes between humans and wildlife.

ecology↗

bioRxiv2018

Three decades of native bee biodiversity surveys at Pinnacles National Park highlight the importance of monitoring natural areas over time

Thousands of species of bees are in global decline, yet research addressing the ecology and status of these wild pollinators lags far behind work being done to address similar impacts on the managed honey bee. This knowledge gap is especially glaring in natural areas, despite knowledge that protected habitats harbor and export diverse bee communities into nearby croplands where their pollination services have been valued at over $3 billion per year. Surrounded by ranches and farmlands, Pinnacles National Park in the Inner South Coast Range of California contains intact Mediterranean chaparral shrubland. This habitat type is among the most valuable for bee biodiversity worldwide, as well as one of the most vulnerable to agricultural conversion, urbanization and climate change. Pinnacles National Park is also one of a very few locations where extensive native bee inventory efforts have been repeated over time. This park thus presents a valuable and rare opportunity to monitor long-term trends and baseline variability of native bees in natural habitats. Fifteen years after a species inventory marked Pinnacles as a biodiversity hotspot for native bees, we resurveyed these native bee communities over two flowering seasons using a systematic, plot-based design. Combining results, we report a total of 450 bee species within this 109km2 natural area of California, including 48 new species records as of 2012 and 95 species not seen since 1999. As far as we are aware, this species richness marks Pinnacles National Park as one of the most densely diverse places known for native bees. We explore patterns of bee diversity across this protected landscape, compare results to other surveyed natural areas, and highlight the need for additional repeated inventories in protected areas over time amid widespread concerns of bee declines.

ecology↗

bioRxiv2018

Prey’s traits mediate a neotropical toad diet

B.O_LIDespite the widespread occurrence of myrmecophagy in anurans it is generally unclear whether ant-specialists feed on ants opportunistically or whether they preferentially select for certain species, potentially favoring specific morphological, ecological, or nutritional traits.\nC_LIO_LIWe flushed 105 stomachs of a lowland neotropical toad, Rhinella alata, and identified each consumed ant to species level. We used linear selectivity to calculate predator preference by comparing the abundances of consumed species to their abundances in the leaf litter community on Barro Colorado Island, Panama. We conducted multiple regression models to test whether linear selectivity or general predator preference related to seven morphological characteristics and two measurements of nutritional content.\nC_LIO_LIRhinella alata preferentially harvested 24 ant species. Other species were either avoided (n=34) or were eaten opportunistically (n=26). We found that R. alata predominantly preys upon large ants that are textured with hair and/or rugosity and preference for prey did not relate to nutrition content. Rhinella alata avoided small ants even if they were hyper abundant in the environment, and preferentially ate chemically-defended and aggressive ants if they were large enough.\nC_LIO_LIWe propose that R. alata prefers large ants because they represent a more efficient prey item in terms of predator handling time and because they are easier to see than are smaller ants. Furthermore, we hypothesize that R. alata predation attempts are more successful when prey are textured because microstructures on the tongue and prey surface may increase prey adhesion.\nC_LIO_LIThe ant specialist R. alata is not specializing on any particular ant species but rather maximizing prey quantity over quality by only eating the largest ants, despite their scarcity in the environment.\nC_LI

ecology↗

bioRxiv2018

Complex stopover and migratory behavior revealed using mechanistic movement models with environmentally driven dynamic parameters

AstractLong distance migration can increase lifetime fitness, but can be costly, incurring increased energetic expenses and higher mortality risks. Stopover and other en route behaviors allow animals to rest and replenish energy stores and avoid or mitigate other hazards during migration. Some animals, such as soaring birds, can subsidize the energetic costs of migration by extracting energy from flowing air. However, it is unclear how these energy sources affect or interact with behavioral processes and stopover in long-distance soaring migrants. To understand these behaviors and the effects of processes that might enhance use of flight subsidies, we developed a flexible mechanistic model to predict how flight subsidies drive migrant behavior and movement processes. The novel modelling framework incorporated time-varying parameters informed by environmental covariates to characterize a continuous range of behaviors during migration. This model framework was fit to GPS satellite telemetry data collected from a large soaring and opportunist foraging bird, the golden eagle (Aquila chrysaetos), during migration in western North America. Fitted dynamic model parameters revealed a clear circadian rhythm in eagle movement and behavior, which was directly related to thermal uplift. Behavioral budgets were complex, however, with evidence for a joint migrating/foraging behavior, resembling a slower paced fly-and-forage migration, which could facilitate efficient refueling while still ensuring migration progress. In previous work, ecological and foraging conditions are normally considered to be the key aspects of stopover location quality, but taxa that can tap energy sources from moving fluids to drive migratory locomotion, such as the golden eagle, may pace migration based on both foraging opportunities and available flight subsidies.

ecology↗

bioRxiv2018

Crops and the seed mass-seed output trade-off in plants

A trade-off between seed mass (SM) and seed output (SO) defines a central axis of ecological variation among plants, with implications for understanding both plant trait evolution and plant responses to environmental change. While an observed negative SM-SO relationship is hypothesized to reflect universal constraints on resource allocation in all plants, domestication has likely fundamentally altered this relationship. Using a dataset of SM and SO for 41 of the world most widespread crops and 1,190 wild plant species, coupled with observational data on these traits in soy (Glycine max) and maize (Zea mays), I show that domestication has systematically rewired SM-SO relationships in crops. Compared to wild plants, virtually all crops express a higher SM for a given SO; this domestication signature is especially prominent in seed crops, and also influences the phylogenetic signal in SM and SO. In maize these traits have become positively related likely due to simultaneous selection for greater SM and SO, while in soy these traits have become decoupled likely due to primary selection for SM only. Evolved relationships between SM and SO in plants have been disrupted by both conscious and unconscious artificial selection, which represents a key aspect of how the functional biology of crops differ fundamentally from wild plants along \"universal\" plant trait spectra.

ecology↗

bioRxiv2018

Ensemble projections of global ocean animal biomass with climate change

Climate change is shifting the abundance and distribution of marine species with consequences for ecosystem functioning, seafood supply, management and conservation. Several approaches for future projection exist but these have never been compared systematically to assess their variability. We conducted standardized ensemble projections including 6 global fisheries and marine ecosystem models, forced with 2 Earth-system models and 4 emission scenarios in a fished and unfished ocean, to derive average trends and associated uncertainties. Without fishing, mean global animal biomass decreased by 5% ({+/-}4%) under low and 17% ({+/-}11%) under high emissions by 2100, primarily driven by increasing temperature and decreasing primary production. These climate-change effects were slightly weaker for larger animals and in a fished ocean. Considerable regional variation ranged from strong biomass increases in high latitudes to strong decreases in mid-low latitudes, with good model agreement on the direction of change but variable magnitude. Uncertainties due to differences among ecosystem or Earth-system models were similar, suggesting equal need for model improvement. Our ensemble projections provide the most comprehensive outlook on potential climate-driven ecological changes in the ocean to date. Realized future trends will largely depend on how fisheries and management adapt to these changes in a changing climate.

ecology↗

bioRxiv2018

Nonlinear Effects of Intraspecific Competition Alter Landscape-Wide Upscaling of Ecosystem Function

A major focus of ecology is to understand and predict ecosystem function across scales. Many ecosystem functions are only measured at local scales, while their effects occur at a landscape level. Here, we investigate how landscape-scale predictions of ecosystem function depend on intraspecific competition, a fine-scale process. Specifically, we experimentally investigated the effect of intraspecific density of shredding macroinvertebrates on associated leaf litter decomposition, a key function in freshwater ecosystems. Across two species, we found that leaf processing rates declined with increasing density following a power law, likely due to interference competition. To demonstrate consequences of this nonlinearity, we upscaled estimates of leaf litter processing from shredder abundance surveys in 10 replicated headwater streams. In accordance with Jensens inequality, applying density-dependent consumption rates reduced estimates of catchment-scale leaf consumption up to 60-fold versus using density-independent rates. Our work highlights the need for spatially-explicit upscaling which accounts for intraspecific interactions.

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