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bioRxiv2018

Contrasted hybridization patterns between two local populations of European wildcats in France

The European wildcat (Felis silvestris silvestris) is threatened across the totality of its area of distribution by hybridization with the domestic cat F.s. catus. The underlying ecological processes promoting hybridization, remain largely unknown. In France, wildcats are mainly present in the North-East but signs of their presence in the Pyrenees have been recently provided. However, no studies have been carried out in the French Pyrenees to assess the genetic status of wildcats. We have compared a local population of wildcats living in a continuous habitat in the French Pyrenees and a local population of wildcats living in a fragmented habitat in Northeastern France to evaluate how habitat fragmentation influence the population structure of European wildcats. Close kin were not found in the same geographic location contrary to what was observed for females in the Northeastern wildcat population. Furthermore, there was no evidence of hybridization in the Pyrenean wildcats and only one domestic cat raised suspicions while hybridization was categorically detected in northeastern France. The two wildcat populations were significantly differentiated (Fst = 0.08) and the genetic diversity of the Pyrenean wildcats was lower than that of other wildcat populations in France and in Europe. Taken together, these results suggest that habitat fragmentation, and in particular the absence of agricultural fields, may play an important role in lowering the probability of hybridization by reducing the likelihood of contact with domestic cats. Moreover, our results suggest that the French Pyrenean wildcat populations is isolated and may be threatened by a lack of genetic diversity.

ecology↗

bioRxiv2018

Developing a modern data workflow for living data

Data management and publication are core components of the research process. An emerging challenge that has received limited attention in biology is managing, working with, and providing access to data under continual active collection. \"Evolving data\" present unique challenges in quality assurance and control, data publication, archiving, and reproducibility. We developed a evolving data workflow for a long-term ecological study that addresses many of the challenges associated with managing this type of data. We do this by leveraging existing tools to: 1) perform quality assurance and control; 2) import, restructure, version, and archive data; 3) rapidly publish new data in ways that ensure appropriate credit to all contributors; and 4) automate most steps in the data pipeline to reduce the time and effort required by researchers. The workflow uses two tools from software development, version control and continuous integration, to create a modern data management system that automates the pipeline.

ecology↗

bioRxiv2018

Interactions in self-assembled microbial communities saturate with diversity

How the diversity of organisms competing for or sharing resources influences community production is an important question in ecology but has rarely been explored in natural microbial communities. These generally contain large numbers of species making it difficult to disentangle how the effects of different interactions scale with diversity. Here, we show that changing diversity affects measures of community function in relatively simple communities but that increasing richness beyond a threshold has little detectable effect. We generated self-assembled communities with a wide range of diversity by growth of cells from serially diluted seawater on brown algal leachate. We subsequently isolated the most abundant taxa from these communities via dilution-to-extinction in order to compare productivity functions of the entire community to those of individual taxa. To parse the effect of different types of organismal interactions, we developed relative total function (RTF) as an index for positive or negative effects of diversity on community function. Our analysis identified three overall regimes with increasing diversity. At low richness (<12 taxa), potential positive and negative effects of interactions are both weak, while at moderate richness (12-20 taxa), community resource uptake increases but the carbon use efficiency decreases. Finally, beyond 20 taxa, there was no net change in community function indicating a saturation of potential interactions. These data suggest that although more diverse communities had overall greater access to resources, individual taxa within these communities had lower resource availability and reduced carbon use efficiency, indicating that competition due to niche overlap increases with diversity but that these interactions saturate at a specific threshold.

ecology↗

bioRxiv2018

When an insecticide affects the adaptive value of Intraguild predation by an invader

Biological invasions can generate major ecological disturbances, such as changes in species diversity and structure of communities. It is believed that the multicolored Asian ladybeetle, Harmonia axyridis Pallas (Col, Coccinellidae), recognized as one of the most invasive insects in the world, has reduced native coccinellids populations in several areas and is considered as a threat for biodiversity at large. A significant trait, favoring its invasiveness and its dominance over indigenous ladybeetles, is intraguild predation (IGP). IGP has advantageous adaptive value for individuals, removing competitors, potential predators and providing an alternative nutritive resource, when main resources are scarce. Previous research demonstrated that this invasive ladybeetle is highly susceptible to the reduced-risk insecticide novaluron, a chitin synthesis inhibitor, whereas the North American indigenous competitor, Coleomegilla maculata DeGeer (Col, Coccinellidae), is not. Our study explores the adaptive value of IGP for each of the two coccinellids after preying on each others larvae, previously treated with insecticide. Our first hypothesis is that the invasive ladybeetle, susceptible to the insecticide, should lose the adaptive value of IGP, while the native predator not. Our second hypothesis is that the adaptive value of IGP for the invasive predator will be recovered over time, as a result of neutralisation of the insecticide by the intraguild prey (native species). The results support both hypotheses, and show that an insecticide can completely remove the adaptive value of IGP for the invader, while it does not change for the indigenous ladybeetle. Moreover, the study demonstrates that if the intraguild prey (non-susceptible to the insecticide) undergoes molt after being exposed to the insecticide, the adaptive value for the intraguild predator is restored.

ecology↗

bioRxiv2018

Trade-offs in provisioning and stability of multiple ecosystem services in agroecosystems

Changes in land use generate trade-offs in the delivery of ecosystem services in agricultural landscapes. However, we know little about how the stability of ecosystem services responds to landscape composition, and what ecological mechanisms underlie these trade-offs. Here, we develop a model to investigate the dynamics of three ecosystem services in intensively-managed agroecosystems, i.e. pollination-independent crop yield, crop pollination, and biodiversity. Our model reveals trade-offs and synergies imposed by landscape composition that affect not only the magnitude but also the stability of ecosystem service delivery. Trade-offs involving crop pollination are strongly affected by the degree to which crops depend on pollination and by their relative requirement for pollinator densities. We show conditions for crop production to increase with biodiversity and decreasing crop area, reconciling farmers profitability and biodiversity conservation. Our results further suggest that, for pollination-dependent crops, management strategies that focus on maximising yield will often overlook its stability. Given that agriculture has become more pollination-dependent over time, it is essential to understand the mechanisms driving these trade-offs to ensure food security.

ecology↗

bioRxiv2018

Low functional but large soil-related variations in growth trajectories characterise the widespread Neotropical tree Cecropia obtusa Trecul (Urticaceae)

AO_SCPLOWBSTRACTC_SCPLOWO_LITrait-environment relationships have been described at the community level across tree species. However, whether interspecific trait-environment relationships are consistent at the intraspecific level is yet unknown. Moreover, we do not know how consistent is the response between organ vs. whole-tree level. C_LIO_LIWe examined phenotypic variability for 16 functional leaf (dimensions, nutrient, chlorophyll) and wood traits (density) across two soil types, Ferralitic Soil (FS) vs. White Sands (WS), on two sites for 70 adult trees of Cecropia obtusa Trecul (Urticaceae) in French Guiana. Cecropia is a widespread pioneer Neotropical genus that generally dominates early successional forest stages. To understand how soil types impact resource-use through the processes of growth and branching, we examined the architectural development with a retrospective analysis of growth trajectories. We expect soil types to affect both, functional traits in relation to resource acquisition strategy as already described at the interspecific level, and growth strategies due to resource limitations with reduced growth on poor soils. C_LIO_LIFunctional traits were not involved in the soil response, as only two traits-leaf residual water content and K content-showed significant differences across soil types. Soil effects were stronger on growth trajectories, with WS trees having the slowest growth trajectories and less numerous branches across their lifespan. C_LIO_LIThe analysis of growth trajectories based on architectural analysis improved our ability to characterise the response of trees with soil types. The intraspecific variability is higher for growth trajectories than functional traits for C. obtusa, revealing the complementarity of the architectural approach with the functional approach to gain insights on the way trees manage their resources over their lifetime. Soil-related responses of Cecropia functional traits are not the same as those at the interspecific level, suggesting that the effects of the acting ecological processes are different between the two levels. Apart from soil differences, much variation was found across sites, which calls for further investigation of the factors shaping growth trajectories in tropical forests. C_LI

ecology↗

bioRxiv2018

Potential impacts of transport infrastructure and traffic on bird conservation in Swedish Special Protection Areas

The ecological impacts of roads and railways extend into the surrounding landscape, leading to habitat degradation and reduced animal densities within an area that is considerably larger than the actual road or railway corridor. For birds, an extensive meta-analysis has pointed at an average of 20% density reduction within 1 km from the infrastructure. I investigated to what extent this density reduction could potentially compromise the habitat quality and conservation value of Swedish Natura 2000 areas designated for the protection of birds (Special Protection Areas; SPAs). A majority (63%) of Swedish SPAs are at least to some extent found within this 1 km potential effect zone. The total overlap between SPA and effect zone is 126,000 ha, or 4.2% of the countrys SPA area. There are however large differences among biogeographical regions. In the southern (continental) and coastal regions combined, 25.8% of the total SPA area fall within the effect zone, representing an estimated 4-7% reduction in bird abundance within SPAs. The probability of overlap with effect zone is higher for larger SPAs. However, the proportion of overlap is higher for smaller SPAs, and accordingly smaller sites can be assumed to experience a greater impact from transport infrastructure and traffic. The impacts on Natura 2000 sites are particularly concerning as this network of protected areas is a cornerstone to maintain and restore biodiversity within EU. I recommend putting a stronger emphasis in the management of Natura 2000 sites on the potential threats to wildlife conservation caused by transport infrastructure and traffic. Special attention should be paid in sites with a large overlap with the effect zone, and in sites hosting particularly vulnerable taxa or habitats. Infrastructure owners and managers should do their best to minimize and compensate for the negative impacts of roads and railways and related traffic in SPAs and other protected areas.

ecology↗

bioRxiv2018

Disturbance During Biofilm Community Succession Promotes Cooperation and Diversity

Diversity-disturbance relationships have found widespread application in ecology, conservation and biodiversity management. In spite of their explanatory power, these conceptual frameworks have yet to be systematically applied to understanding succession in diverse microbial biofilms. Here we investigate community assembly in biofilms formed in replicate microbial bioelectrochemical systems using time-course sequencing of community 16S rRNA genes, corresponding to hundreds of operational taxonomic units (OTUs). For the first time we present a statistical model showing that a simple diversity-disturbance relationship can be used to explain dynamic changes in high diversity biofilm communities. This simple model reveals that succession in these systems is guided towards either a low diversity, generalist-dominated biofilm or a high diversity, cooperative-specialist biofilm, depending on the level of endogenous disturbance measured within the community. The pattern observed shows remarkable symmetry with findings from macro-scale communities such as grasslands, forests and coral reefs.

ecology↗

bioRxiv2018

A shared limiting resource leads to competitive exclusion in a cross-feeding system

Species interactions and coexistence are often highly dependent upon environmental conditions. This is especially true for cross-feeding bacteria that rely on one another for essential nutrients. The addition of a cross-fed nutrient to the environment can release one species from its dependence on another, thereby altering the species interaction and potentially affecting coexistence. Using invasion-from-rare experiments with cross-feeding bacteria, genome-scale metabolic modeling, and classical ecological models, we explored the potential for coexistence when one cross-feeding mutualist becomes independent. We show that whether nutrient addition shifts an interaction from mutualism to commensalism or parasitism depends on whether the limiting nutrient can be metabolized by only one species or by both species. Furthermore, we show that coexistence is only lost when the interaction becomes parasitism, and the obligate species has a slower maximum growth rate. Surprisingly, models suggest that rates of cross-fed nutrient production have a negligible effect. These results contribute to an understanding of how resource changes, whether intentional or not, will manipulate interactions and coexistence in microbial communities.

ecology↗

bioRxiv2018

Measuring tolerance to a major fungal pathogen in elite wheat cultivars

O_LITolerance and resistance represent two strategies that hosts evolved to protect themselves from pathogens. Tolerance alleviates the reduction in host fitness due to infection without reducing a pathogens growth, while resistance reduces pathogen growth. We investigated tolerance of wheat to the major fungal pathogen Zymoseptoria tritici in 335 elite wheat cultivars. C_LIO_LIWe used a novel digital phenotyping approach that included 11,152 infected leaves and counted 2,069,048 pathogen fruiting bodies. C_LIO_LIWe discovered a new component of tolerance that is based on the relationship between the green area remaining on a leaf and the number of pathogen fruiting bodies. We found a negative correlation between tolerance and resistance among intolerant cultivars, presenting the first compelling evidence for a tradeoff between tolerance and resistance to plant pathogens. Surprisingly, the tradeoff arises due to limits in the host resources available to the pathogen and not due to metabolic constraints, contrary to what ecological theory suggests. C_LIO_LIThe mechanism underlying this tradeoff may be relevant for many plant diseases in which the amount of host resources available to the pathogen can limit the pathogen population. Our analysis indicates that European wheat breeders may have selected for tolerance instead of resistance to an important pathogen. C_LI

ecology↗

bioRxiv2018

The filtering metaphor revisited: competition and environment jointly structure invasibility and coexistence

Filtering, or the reduction in species diversity that occurs because not all species can persist in all locations, is thought to unfold hierarchically, at large scales due to the environment and at small scales due to competition. However, the ecological effects of competition and the environment are not independent, and observational approaches preclude investigation into their interplay. We use a demographic approach with 30 plant species to experimentally test (i) the effect of competition on species persistence in two soil moisture environments, and (ii) the effect of environmental conditions on the mechanisms underlying competitive coexistence. We find that competitors cause differential persistence of species across environments even when these effects are lacking in the absence of competition, and that the traits that determine persistence depend on the competitive environment. Changing environmental conditions generated idiosyncratic effects on coexistence outcomes, increasing competitive exclusion of some species while promoting coexistence of others. Our results highlight the importance of considering environmental filtering in light of, rather than in isolation from, competition, and challenge community assembly models and approaches to projecting future species distributions.

ecology↗

bioRxiv2018

Universal metabolic constraints on the thermal tolerance of marine phytoplankton

Marine phytoplankton are responsible for over 45% of annual global net primary production. Ocean warming is expected to drive massive reorganisation of phytoplankton communities, resulting in pole-ward range shifts and sharp declines in species diversity, particularly in the tropics. The impacts of warming on phytoplankton species depend critically on their physiological sensitivity to temperature change, characterised by thermal tolerance curves. Local extinctions arise when temperatures exceed species thermal tolerance limits. The mechanisms that determine the characteristics of thermal tolerance curves (e.g. optimal and maximal temperatures) and their variability among the broad physiological diversity of marine phytoplankton are however poorly understood. Here we show that differences in the temperature responses of photosynthesis and respiration establish physiological trade-offs that constrain the thermal tolerance of 18 species of marine phytoplankton, spanning cyanobacteria as well as the red and green super-families. Across all species we found that rates of respiration were more sensitive to increasing temperature and typically had higher optimal temperatures than photosynthesis. Consequently, the fraction of photosynthetic energy available for allocation to growth (carbon-use efficiency) declined exponentially with rising temperatures with a sensitivity that was invariant among the 18 species. Furthermore, the optimal temperature of growth was generally lower than that of photosynthesis and as a result, supra-optimal declines in growth rate were associated with temperature ranges where the carbon-use efficiency exhibited accelerated declines. These highly conserved patterns demonstrate that the limits of thermal tolerance in marine phytoplankton are underpinned by common metabolic constraints linked to the differential temperature responses of photosynthesis and respiration.\n\nSignificance StatementThe impacts of warming on marine phytoplankton depend on their sensitivity to rising temperatures, yet there is currently limited understanding of the mechanisms that limit thermal tolerance among the diversity of marine phytoplankton. Using a comparative study on the dominant, ecologically important lineages of marine phytoplankton - Bacillariophyceae, Dinophyceae, Cyanophyceae, Prasinophyceae, Prymnesiophyceae - we show that rates of respiration are consistently more sensitive to increasing temperature than photosynthesis. Consequently, the fraction of photosynthetic energy available for growth declines with rising temperatures with a sensitivity that is invariant among species. Our results suggest that declines in phytoplankton performance at high temperatures are driven by universal metabolic constrains linked to rising respiratory costs eventually exceeding the supply of reduced carbon from photosynthesis.

ecology↗

bioRxiv2018

How to build a mycelium: tradeoffs in fungal architectural traits

The fungal mycelium represents the essence of the fungal lifestyle, and understanding how a mycelium is constructed is of fundamental importance in fungal biology and ecology. Previous studies have examined initial developmental patterns or focused on a few strains, often mutants of model species, and frequently grown under non-harmonized growth conditions; these factors currently collectively hamper systematic insights into rules of mycelium architecture. To address this, we here use a broader suite of fungi (31 species including members of the Ascomycota, Basidiomycota and Mucoromycotina), all isolated from the same soil, and test for ten architectural traits under standardized laboratory conditions.\n\nWe find great variability in traits among the saprobic fungal species, and detect several clear tradeoffs in mycelial architecture, for example between internodal length and hyphal diameter. Within the constraints so identified, we document otherwise great versatility in mycelium architecture in this set of fungi, and there was no evidence of trait syndromes as might be expected.\n\nOur results point to an important dimension of fungal properties with likely consequences for coexistence within local communities, as well as for functional complementarity (e.g. decomposition, soil aggregation).

ecology↗

bioRxiv2018

Multivariate methods for testing hypotheses of temporal community dynamics

For ecological research to make important contributions towards understanding and managing temporally-variable global change processes, such as responses to land-use and climatic change, we must have effective and comparable ways to quantify and analyse compositional change over time in biological communities. These changes are the sum of local colonisation and extinction events, or changes in the biomass and relative abundance of taxa within and among samples. We conducted a quantitative review of currently available methods for the analysis of multivariate datasets collected at temporal intervals. This review identified the need for the application of quantitative, hypothesis-based approaches to understand temporal change in community composition, particularly for small datasets with less than 15 temporal replicates. To address this gap, we: (1) conceptually present how temporal patterns in community dynamics can be framed as specific, testable hypotheses; (2) provide three fully-worked case-studies, complete with R code, demonstrating multivariate analysis methods for temporal hypothesis testing and pattern visualisation; and (3) present a road map for testing specific, quantitative hypotheses relating to the underlying mechanisms of temporal community dynamics.

ecology↗

bioRxiv2018

A new model explaining the origin of different topologies in interaction networks

The architecture of interaction networks has been extensively studied in the past decades, and different topologies have been observed in natural systems. Despite several phenomenological explanations proposed, we still understand little of the mechanisms that generate those topologies. Here we present a mechanistic model based on the integrative hypothesis of specialization, which aims at explaining the emergence of topology and specialization in consumer-resource networks. By following three first-principles and adjusting five parameters, our model was able to generate synthetic weighted networks that show the main patterns of topology and specialization observed in nature. Our results prove that topology emergence is possible without network-level selection. In our simulations, the intensity of trade-offs in the performance of each consumer species on different resource species is the main factor driving network topology. We predict that interaction networks with low species diversity and low dissimilarity between resources should have a nested topology, although more diverse networks with large dissimilarity should have a compound topology. Additionally, our results highlight scale as a key factor. Our model generates predictions consistent with ecological and evolutionary theories and real-world observations. Therefore, it supports the IHS as a useful conceptual framework to study the architecture of interaction networks.

ecology↗

bioRxiv2018

Is the predation risk of mate-searching different between the sexes?

In animals that communicate for pair formation, generally one sex invests more effort in mate searching. Although searching by males is prevalent in most animals, in orthopteran insects and some other taxa females physically move to localise signalling males who are predominantly sedentary. Although the two sexes thus share mate searching effort in orthopterans, their behavioural strategies are different and sexual selection theory predicts that signalling males may be following the riskier strategy and incurring higher costs. However, relative levels of risk posed by the two mate searching strategies remain largely unexplored. Hence, we estimated the relative predation risk experienced in natural populations by signalling males and responding females. We did this by quantifying predation risk as a probability of mortality in the context of acoustic communication in a tree cricket, Oecanthus henryi from its ecologically relevant predator, a lynx spider, Peucetia viridans. Spiders may perceive calling in males and movement in females by their ability to detect both airborne acoustic cues and substrate-borne vibratory cues. Probability of mortality was quantified by partitioning it into three spatial components at which crickets and spiders interact, using a combination of extensive field observations and manipulative experiments in a semi-natural setup. We found no differences in predation risk faced by calling males and responding females, suggesting that direct benefits offered by males to females upon pair formation may better explain shared mate searching effort between the sexes in orthopterans.

ecology↗

bioRxiv2018

pymfinder: a tool for the motif analysis of binary and quantitative complex networks

We developed pymfinder, a new software to analyze multiple aspects of the so-called network motifs--distinct n-node patterns of interaction--for any directed, undirected, unipartite or bipartite network. Unlike existing software for the study of network motifs, pymfinder allows the computation of node- and link-specific motif profiles as well as the analysis of weighted motifs. Beyond the overall characterization of networks, the tools presented in this work therefore allow for the comparison of the \"roles\" of either nodes or links of a network. Examples include the study of the roles of different species and/or their trophic/mutualistic interactions in ecological networks or the roles of specific proteins and/or their activation/inhibition relationships in protein-protein interaction networks. Here, we show how to apply the main tools from pymfinder using a predator-prey interaction network from a marine food web. pymfinder is open source software that can be freely and anonymously downloaded from https://github.com/stoufferlab/pymfinder, distributed under the MIT License (2018).

ecology↗

bioRxiv2018

Osmia bicornis is rarely an adequate regulatory surrogate species. Comparing its acute sensitivity towards multiple insecticides with regulatory Apis mellifera endpoints.

Bee species provide essential ecosystem services and maintain floral biodiversity. However, there is an ongoing decline of wild and domesticated bee species. Since agricultural pesticide use is a key driver of this process, there is a need for a protective risk assessment. To achieve a more protective registration process, two wild bee species, Osmia bicornis and Bombus terrestris, were proposed by the European Food Safety Authority as additional test surrogates. We investigated the acute toxicity (median lethal dose, LD50) of multiple commercial insecticide formulations towards the red mason bee (O. bicornis) and compared these values to honey bee (Apis mellifera) regulatory endpoints. In two thirds of all cases O. bicornis was less sensitive than the honey bee. By applying an assessment factor of 10 on the honey bee endpoint a protective level was achieved for 87% (13 out 15) of all evaluated products. Our results show that O. bicornis as a non-sensitive species is rarely an adequate additional surrogate species for lower tier risk assessment. Given the currently limited database, the honey bee seems sufficiently protective in acute scenarios as long as a reasonable assessment factor is applied. However, additional surrogate species such as O. bicornis and B. terrestris are still relevant for ecologically meaningful higher tier studies.

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