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At least 1,621 records · Page 90Linked to original sources

bioRxiv2017

Pre-dispersal conditions and presence of opposite sex modulate density dependence and sex bias of dispersal

Density-dependent dispersal (DDD) has been demonstrated in many species and has several ecological and evolutionary consequences. Yet we know little about how robust DDD is to the various conditions experienced by individuals. In this study, we use three independent experiments on laboratory populations of Drosophila melanogaster to examine the effects of pre-dispersal adult density, sex of the dispersers and presence of mates on the robustness of DDD patterns. We show that DDD can be greatly affected by both pre-dispersal density and interaction between the sexes. Moreover, the direction of sex-biased dispersal can reverse completely due to an interaction between the pre-dispersal and dispersal densities. We also show that interaction between the sexes can lead to negative DDD at the population level, even if, by themselves, neither sex exhibits DDD. Finally, we discuss potential implications of our results for processes like evolutionary rescue from extinctions and genetic divergence of populations.

ecology↗

bioRxiv2017

Species-specific adaptations determine how aridity and biotic interactions drive the assembly of dryland plant communities

O_LIDespite being a core ecological question, disentangling individual and interacting effects of plant-plant interactions, abiotic factors and species-specific adaptations as drivers of community assembly is challenging. Studies addressing this issue are growing rapidly, but they generally lack empirical data regarding species interactions and local abundances, or cover a narrow range of environmental conditions.\nC_LIO_LIWe analysed species distribution models and local spatial patterns to isolate the relative importance of key abiotic (aridity) and biotic (facilitation and competition) drivers of plant community assembly in drylands worldwide. We examined the relative importance of these drivers along aridity gradients and used information derived from the niches of species to understand the role that species-specific adaptations to aridity play in modulating the importance of community assembly drivers.\nC_LIO_LIFacilitation, together with aridity, was the major driver of plant community assembly in global drylands. Due to community specialization, the importance of facilitation as an assembly driver decreased with aridity, and became non significant at the border between arid and semiarid climates. Under the most arid conditions, competition affected species abundances in communities dominated by specialist species. Due to community specialization, the importance of aridity in shaping dryland plant communities peaked at moderate aridity levels.\nC_LIO_LISynthesis: We showed that competition is an important driver of community assembly even under harsh environments, and that the effect of facilitation collapses as driver of species relative abundances under high aridity because of the specialization of the species pool to extremely dry conditions. Our findings pave the way to develop more robust species distribution models aiming to predict the consequences of ongoing climate change on community assembly in drylands, the largest biome on Earth.\nC_LI

ecology↗

bioRxiv2017

Phytoplankton functional types: A trait perspective

Phytoplankton functional types are groupings of many species into a smaller number of types according to their ecological or biogeochemical role. Models describe phytoplankton functional types by a set of traits that determine their growth rates or fitness. Traits for functional types are often determined from observations on a small number of species under laboratory conditions. Functional types can be composed of a large number of species with very different trait values, so the representation of a type by an average trait value may not be appropriate. A potential solution is to estimate trait values from observations of the aggregate biomass of phytoplankton functional types in natural populations. We report on some recent efforts to extract trait values from time-series data using Bayesian statistical models and discuss some challenges of this approach.

ecology↗

bioRxiv2017

Faster carbon accumulation in global forest soils

Comparing soil organic carbon (SOC) stocks across space and time is a fundamental issue in global ecology. However, the conventional approach fails to determine SOC stock in an equivalent volume of mineral-soil, and therefore, SOC stock changes can be under- or overestimates if soils swell or shrink during forest development or degradation. Here, we propose to estimate SOC stock as the product of mineral-soil mass in an equivalent mineral-soil volume and SOC concentration expressed as g C Kg-1 mineral-soil. This method enables researchers to compare SOC stocks across space and time. Our results show an unaccounted SOC accumulation of 2.4 - 10.1 g C m-2 year-1 in the 1m surface mineral-soils in global forests. This unaccounted SOC amounts to an additional C sink of 0.12 - 0.25 Pg C year-1, which equals 30 - 62% of the previously estimated annual SOC accumulation in global forests. This finding suggests that forest soils are stronger C sinks than previously recognized.

ecology↗

bioRxiv2017

Soil community assembly varies across body sizes in a tropical forest

The relative influence of deterministic niche-based (i.e. abiotic conditions, biotic interactions) and stochastic-distance dependent neutral processes (i.e. demography, dispersal) in shaping communities has been extensively studied for various organisms, but is far less explored jointly across the tree of life, in particular in soil environments. Here, using a thorough DNA-based census of the whole soil biota in a large tropical forest plot, we show that soil aluminium, topography, and plant species identity are all important drivers of soil richness and community composition. Body size emerges as an important feature of the comparative ecology of the different taxa at the studied spatial scale, with microorganisms being more importantly controlled by environmental factors, while soil mesofauna rather display random spatial distribution. We infer that niche-based processes contribute differently to community assembly across trophic levels due to spatial scaling. Body size could hence help better quantifying important properties of multitrophic assemblages.

ecology↗

bioRxiv2017

Metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis

Assessing diet variability is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fieldwork to biostatistics, resulting in the detection of false negatives, false positives or low taxonomic resolution. We detail a rigorous metabarcoding approach based on a short COI minibarcode and two-step PCR protocol enabling the all at once taxonomic identification of bats and their arthropod preys for several hundreds of samples. Our study includes faecal pellets collected in France from 357 bats representing 16 species, as well as insect mock communities that mimic bat meals of known composition, negative and positive controls. All samples were analysed using three replicates. We compare the efficiency of DNA extraction methods and we evaluate the effectiveness of our protocol using identification success, taxonomic resolution, sensitivity, and amplification biases. Our parallel identification strategy of predators and preys reduces the risk of mis-assigning preys to wrong predators and decreases the number of molecular steps. Controls and replicates enable to filter the data and limit the risk of false positives, hence guaranteeing high confidence results for both prey occurrence and bat species identification. We validate 551 COI variants from arthropod including 18 orders, 117 family, 282 genus and 290 species. Our method therefore provides a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing chirosurveillance and conservation strategies.

ecology↗

bioRxiv2017

Estimating the footprint of pollution on coral reefs using models of species turn-over

Ecological communities typically change along gradients of human impact, though it is difficult to estimate the footprint of impacts for diffuse threats like pollution. Here we develop a joint model of benthic habitats on lagoonal coral reefs and use it to infer change in benthic composition along a gradient of distance from logging operations. The model estimates both changes in abundances of benthic groups and their compositional turn-over, a type of beta-diversity. We detect compositional turnover across the gradient and use the model to predict the footprint of turbidity impacts from logging. We then apply the model to predict impacts of recent logging activities, finding recent impacts to be small, because recent logging has occurred far from lagoonal reefs. Our model can be used more generally to estimate the footprint of human impacts on ecosystems and evaluate the benefits of conservation actions for ecosystems.

ecology↗

bioRxiv2017

Measuring the gut microbiome in birds: comparison of faecal and cloacal sampling

The gut microbiomes of birds and other animals are increasingly being studied in ecological and evolutionary contexts. While methods for preserving samples and processing high-throughput sequence data to characterise bacterial communities have received considerable attention, there has been little evaluation of non-invasive sampling methods. Numerous studies on birds and reptiles have made inferences about gut microbiota using cloacal sampling, however, it is not known whether the bacterial community of the cloaca provides an accurate representation of the avian gut microbiome. We examined the accuracy with which cloacal swabs and faecal samples measure the microbiota in three different parts of the gastrointestinal tract (ileum, caecum, and colon) using a case study on juvenile ostriches, Struthio camelus, and high-throughput 16S rRNA sequencing. We found that faeces were significantly better than cloacal swabs in representing the bacterial community of the colon. Cloacal samples had a higher abundance of Gammaproteobacteria and fewer Clostridia relative to the gut and faecal samples. However, both faecal and cloacal samples were poor representatives of the microbial communities in the caecum and ileum. Furthermore, the accuracy of the sampling methods in measuring the abundance of different bacterial taxa was highly variable: Bacteroidetes was the most highly correlated phylum between all three gut sections and both methods, whereas colonic Actinobacteria correlated strongly only with faecal samples. This study demonstrates that sampling methods can have significant effects on the inferred gut microbiome in studies of birds. Based on our results, we recommend sampling faeces, whenever possible, as this provides the most accurate assessment of the colon microbiome. The fact that neither sampling technique portrayed the bacterial community of the ileum or the caecum illustrates the difficulty in non-invasively monitoring gut bacteria located further up in the gastrointestinal tract. These results have important implications for the interpretation of avian gut microbiome studies.

ecology↗

bioRxiv2017

Repeated regime shifts in a desert rodent community

While studies increasingly document long-term change in community composition, whether long-term change occurs gradually or via rapid reorganization events remains unclear. We used Latent Dirichlet Allocation (LDA) and a change-point model to examine the long-term dynamics of a desert rodent community undergoing compositional change over a 38-year span. Our approach detected three rapid reorganization events, where changes in the relative abundances of dominant and rare species occurred, and a separate period of increased variance in the structure of the community. These events coincided with time periods--possibly related to climate events--where the total abundance of rodents was extremely low. There are a variety of processes that could link low abundance events with a higher probability of rapid ecological transitions, including higher importance of stochastic processes (i.e., competitive interactions or priority effects) and the removal of structuring effects of competitive dominants or incumbent species. Continued study of the dynamics of community change will provide important information not only on the processes structuring communities, but will also provide guidance for forecasting how communities will undergo change in the future.

ecology↗

bioRxiv2017

Atrazine and amphibians: Data re-analysis and a summary of the controversy

The herbicide atrazine is one of the most commonly used, well studied, and controversial pesticides on the planet. Much of the controversy involves the effects of atrazine on wildlife, particularly amphibians and their non-infectious and infectious diseases, including diseases caused by trematode infections. Here I re-analyze data from authors that were funded by Syngenta Crop Protection, Inc., the company that produces atrazine, and show that even these authors revealed that increasing concentrations of atrazine applied to outdoor mesocosms increases the population growth rate of snails that can transmit trematode parasites to amphibians. These researchers missed this finding in their data because they never calculated population growth rates for the snail populations before they reached a carrying capacity or crashed. These results demonstrate that both Syngenta-funded and non-Syngenta-funded researchers have provided evidence that ecologically relevant concentrations of atrazine are capable of increasing snail populations. Given the controversy surrounding the effects of atrazine on amphibians, I follow this re-analysis with a timeline of some of the most salient events in the history of the atrazine-amphibian controversy.

ecology↗

bioRxiv2017

A global synthesis of phenological responses to climate change

Phenology, or the timing of seasonal activities, is shifting with climate change, resulting in disruptions to the timing of migration and breeding and in emerging asynchronies between interacting species1-5. Recent syntheses have concluded that trophic level1, latitude6, and how phenological responses are measured7 are key to determining the strength of phenological responses to climate change. However, despite these insights, researchers still lack a comprehensive framework that can predict responses to climate change globally and across diverse taxa. For example, little is known about whether phenological shifts are driven by different climatic factors across regions or which ecologically important species characteristics (e.g., body size) predict the strength of phenological responses. Here, we address these questions by synthesizing hundreds of published time series of animal phenology from across the planet. We find that temperature drives phenological responses at mid-latitudes, but precipitation is more important at lower latitudes, likely because these climate factors often drive seasonality in each of these regions. Body size is also negatively associated with the strength of phenological shift, suggesting emerging asynchronies between interacting species that differ in size, such as hosts and ectoparasites and predators and prey. Finally, although there are many compelling biological explanations for spring phenological delays, some examples of delays are associated with short annual records prone to sampling error. As climate change intensifies, our findings arm biologists with predictions concerning which climatic variables and organismal traits drive phenological shifts.

ecology↗

bioRxiv2017

Drones count wildlife more accurately and precisely than humans

Ecologists are increasingly using technology to improve the quality of data collected on wildlife, particularly for assessing the environmental impacts of human activities. Remotely Piloted Aircraft Systems (RPAS; commonly known as drones) are widely touted as a cost-effective way to collect high quality wildlife population data, however, the validity of these claims is unclear. Using life-sized seabird colonies containing a known number of replica birds, we show that RPAS-derived data are, on average, between 43% and 96% more accurate than data from the traditional ground-based collection method. We also demonstrate that counts from this remotely sensed imagery can be semi-automated with a high degree of accuracy. The increased accuracy and precision of RPAS-derived wildlife monitoring data provides greater statistical power to detect fine-scale population fluctuations allowing for more informed and proactive ecological management.

ecology↗

bioRxiv2017

Persistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists

Animal and plant communities in tropical rainforests are known to have high alpha diversity within forests, but low beta diversity between forests. By contrast, it is unknown if the microbial protists inhabiting the same ecosystems exhibit similar biogeographic patterns. To evaluate the biogeographies of soil protists in three lowland Neotropical rainforests using metabarcoding data, we estimated taxa-area and distance-decay relationships for three large protist taxa and their subtaxa, at both the OTU and phylogenetic levels, with presence-absence and abundance based measures, and compared the estimates to null models. High local alpha and low regional beta diversity patterns were persistently found for both the parasitic Apicomplexa and the free-living Cercozoa and Ciliophora, even though they have different ecological functions and different dispersal modes. In comparison to the null models, both OTU and phylogenetic diversities showed spatial structures between forests, but only phylogenetic diversity showed spatial patterns within forests. These results suggest that the biogeographies of macro-and micro-organismal eukaryotes in lowland Neotropical rainforests are partially structured by the same general processes. As with arthropods, the protists high alpha diversity within forests presents problems for estimating their local diversity, and shows that regional diversity cannot be easily estimated because of low turnover between forests.

ecology↗

bioRxiv2017

Anticipating complexity in the deployment of gene drive insects in agriculture

Insects cause substantial losses to agricultural crops each year and require intensive management approaches. Genetic pest management (GPM) has emerged as a viable, non-chemical alternative for managing insect pests. The development of engineered gene drives for agricultural use is promising, though unproven, and has the potential to impact farmers as well as broader socio-ecological systems in several ways. Drawing on lessons from the deployment of other pest control technologies, this paper considers how gene drive insects could intersect with some of the complexities that characterize agricultural systems. The development of gene drives is emerging in a landscape of pest management shaped by past and current approaches, experiences, regulations, public opinion and pest invasions. Because gene drive insects may spread well beyond their release area, stakeholder groups at different spatial scales need to be engaged in decisions about their deployment. This new paradigm both complicates and offers great promise for future pest management efforts.

ecology↗

bioRxiv2017

Genome-Wide SNPs Reveal the Drivers of Gene Flow In An Urban Population of the Asian Tiger Mosquito, Aedes albopictus

Aedes albopictus is a highly invasive disease vector with an expanding worldwide distribution. Genetic assays using low to medium resolution markers have found little evidence of spatial genetic structure even at broad geographic scales, suggesting frequent passive movement along human transportation networks. Here we analysed genetic structure of Ae. albopictus collected from 12 sample sites in Guangzhou, China, using thousands of genome-wide single nucleotide polymorphisms (SNPs). We found evidence for passive gene flow, with distance from shipping terminals being the strongest predictor of genetic distance among mosquitoes. As further evidence of passive dispersal, we found multiple pairs of full-siblings distributed between two sample sites 3.7 km apart. After accounting for geographical variability, we also found evidence for isolation by distance, previously undetectable in Ae. albopictus. These findings demonstrate how large SNP datasets and spatially-explicit hypothesis testing can be used to decipher processes at finer geographic scales than formerly possible. Our approach can be used to help predict new invasion pathways of Ae. albopictus and to refine strategies for vector control that involve the transformation or suppression of mosquito populations.\n\nAuthor SummaryAedes albopictus, the Asian Tiger Mosquito, is a highly invasive disease vector with a growing global distribution. Designing strategies to prevent invasion and to control Ae. albopictus populations in invaded regions requires knowledge of how Ae. albopictus disperses. Studies comparing Ae. albopictus populations have found little evidence of genetic structure even between distant populations, suggesting that dispersal along human transportation networks is common. However, a more specific understanding of dispersal processes has been unavailable due to an absence of studies using high-resolution genetic markers. Here we present a study using high-resolution markers, which investigates genetic structure among 152 Ae. albopictus from Guangzhou, China. We found that human transportation networks, particularly shipping terminals, had an influence on genetic structure. We also found genetic distance was correlated with geographical distance, the first such observation in this species. This study demonstrates how high-resolution markers can be used to investigate ecological processes that may otherwise escape detection. We conclude that strategies for controlling Ae. albopictus will have to consider both passive reinvasion along human transportation networks and active reinvasion from neighbouring regions.

ecology↗

bioRxiv2017

Co-occurring soil bacteria exhibit a robust competitive hierarchy and lack of non-transitive interactions

Microbial communities are typically incredibly diverse, and this diversity is thought to play a key role in community function. However, explaining how this diversity can be maintained is a major challenge in ecology. Temporal fluctuations and spatial structure in the environment likely play a key role, but it has also been suggested that the structure of interactions within the community may act as a stabilizing force for species diversity. In particular, if competitive interactions are non-transitive as in the classic rock-paper-scissors game, they can contribute to the maintenance of species diversity; on the other hand, if they are predominantly hierarchical, any observed diversity must be maintained via other mechanisms. Here, we investigate the network of pairwise competitive interactions in a model community consisting of 20 strains of naturally co-occurring soil bacteria. We find that the interaction network is strongly hierarchical and lacks significant non-transitive motifs, a result that is robust across multiple environments. Moreover, in agreement with recently proposed community assembly rules, the full 20-strain competition resulted in extinction of all but three of the most highly competitive strains, indicating that higher order interactions do not play a major role in structuring this community. The lack of non-transitivity and higher order interactions in vitro indicates that other factors, such as temporal or spatial heterogeneity, must be at play in enabling these strains to coexist in nature.

ecology↗

bioRxiv2017

Twenty-five species of frogs in a liter of water: eDNA survey for exploring tropical frog diversity

Rapid environmental change in highly biodiverse tropical regions demands efficient biomonitoring programs. While existing metrics of species diversity and community composition rely on encounter-based survey data, eDNA recently emerged as alternative approach. Costs and ecological value of eDNA-based methods have rarely been evaluated in tropical regions, where high species richness is accompanied by high functional diversity (e.g. the use of different microhabitats by different species and life-stages). We first tested whether estimation of tropical frogs community structure derived from eDNA data is compatible with expert field assessments. Next we evaluated whether eDNA is a financially viable solution for biodiversity monitoring in tropical regions. We applied eDNA metabarcoding to investigate frog species occurrence in five ponds in the Chiquitano dry forest region in Bolivia and compared our data with a simultaneous visual and audio encounter survey (VAES). We found that taxon lists and community structure generated with eDNA and VAES correspond closely, and most deviations are attributable to different species life histories. Cost efficiency of eDNA surveys was mostly influenced by the richness of local fauna and the number of surveyed sites: VAES may be less costly in low-diversity regions, but eDNA quickly becomes more cost-efficient in high-diversity regions with many sites sampled. The results highlight that eDNA is suitable for large-scale biodiversity surveys in high-diversity areas if life history is considered, and certain precautions in sampling, genetic analyses and data interpretation are taken. We anticipate that spatially extensive, standardized eDNA biodiversity surveys will quickly emerge in the future.

ecology↗

bioRxiv2017

Correlations, interactions, and predictability in virus-microbe networks

1Microbes are present in high abundances in the environment and in human-associated microbiomes, often exceeding one million per milliliter. Viruses of microbes are present in even higher abundances and are important in shaping microbial populations, communities, and ecosystems. Given the relative specificity of viral infection, it is essential to identify the functional linkages between viruses and their microbial hosts, particularly given dynamic changes in virus and host abundances. Multiple approaches have been proposed to infer infection networks from time-series of in situ communities, among which correlation-based approaches have emerged as the de facto standard. In this work, we evaluate the accuracy of correlation-based inference methods using an in silico approach. In doing so, we compare predicted networks to actual networks to assess the self-consistency of correlation-based inference. At odds with assumptions underlying its widespread use, we find that correlation is a poor predictor of interactions in the context of viral infection and lysis of microbial hosts. The failure to predict interactions holds for methods which leverage product-moment, time-lagged, and relative-abundance based correlations. In closing, we discuss alternative inference methods, particularly model-based methods, as a means to infer interactions in complex microbial communities with viruses.\n\n2 ImportanceInferring interactions from population time-series is an active and ongoing area of research. It is relevant across many biological systems - in particular in virus-microbe communities, but also in gene regulatory networks, neural networks, and ecological communities broadly. Correlation-based inference - using correlations to predict interactions - is widespread. However, it is well known that \"correlation does not imply causation\". Despite this, many studies apply correlation-based inference methods to experimental time-series without first assessing the potential scope for accurate inference. Here, we find that several correlation-based inference methods fail to recover interactions within in silica virus-microbe communities, raising questions on their relevance when applied in situ.

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