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bioRxiv2019

Ecological niche differentiation in soil cyanobacterial communities across the globe

Cyanobacteria are key organisms in the evolution of life on Earth, but their distribution and environmental preferences in terrestrial ecosystems remain poorly understood. This lack of knowledge is particularly evident for two recently discovered non-photosynthetic cyanobacterial classes, Melainabacteria and Sericytochromatia, limiting our capacity to predict how these organisms and the important ecosystem functions they perform will respond to ongoing global change. Here, we conducted a global field survey covering a wide range of vegetation types and climatic conditions to identify the environmental factors associated with the distribution of soil cyanobacterial communities. Network analyses revealed three major clusters of cyanobacterial phylotypes, each one dominated by members of one of the extant classes of Cyanobacteria (Oxyphotobacteria, Melainabacteria and Sericytochromatia), suggesting that species within these taxonomic groups share similar environmental preferences. Melainabacteria appear mostly in acidic and humid ecosystems, especially forests, Oxyphotobacteria are prevalent in arid and semiarid areas, and Sericytochromatia are common in hyperarid oligotrophic environments. We used this information to construct a global atlas of soil cyanobacteria. Our results provide novel insights into the ecology and biogeography of soil cyanobacteria and highlight how their global distribution could change in response to increased aridity, a landmark feature of climate change in terrestrial ecosystems worldwide. Significance statementCyanobacteria have shaped the history of life on Earth and can be important photosynthesizers and nitrogen fixers in terrestrial ecosystems worldwide. The recent discovery of two non-photosynthetic classes has advanced our understanding of their evolution, but their distribution and environmental preferences remain poorly described. Using a global survey conducted across 237 locations on six continents, we identified three main groups of soil cyanobacteria with contrasting environmental preferences: acidic and humid ecosystems, arid and semiarid areas, and hyperarid oligotrophic ecosystems. We then constructed the first global atlas of soil cyanobacteria, an important advance in our understanding of the ecology and biogeography of these functionally important organisms.

ecology↗

bioRxiv2019

Invasive Siberian chipmunks Eutamias sibiricus in Italy: a socio-ecological analysis indicates that they could, and should, be removed

BACKGROUNDEradication of invasive alien species is a form of pest control linked to biodiversity conservation that usually involves killing animals. Squirrels are prominent among invasive alien species in Italy with four species introduced. Three of them are included within the list of alien species of European concern and their eradication and control is recommended. However, their local control is not an easy task, being highly appreciated by the general public. We propose a socio-ecological approach to evaluate the feasibility of eradicating Siberian chipmunks (Eutamias sibiricus) populations. We performed a structured questionnaire to assess the social perception of invasive Siberian chipmunks in urban parks where they occur and to identify groups of visitors who might oppose eradication. We also carried out geographic profiling to test for the spatial expansion of chipmunk populations. RESULTSOverall, park visitors regarded chipmunks positively and appreciated to see them, but human-chipmunk interactions were still rare. We did not identify any group of visitors with a strong attachment to chipmunks, who might oppose future control programs. Geographic profiling showed that chipmunks in Valeggio sul Mincio are starting to expand outside of their introduction site. CONCLUSIONSData from questionnaires show that chipmunks eradication, coupled with adequate communication initiatives, might be feasible. Moreover, geographic profiling indicates that time for a rapid removal is running out. Socio-ecological approaches, combining the analysis of structured questionnaires administered to stakeholders and statistical modeling of pest observations, could be a valuable tool to decide the feasibility and the urgency of invasive pest control.

ecology↗

bioRxiv2019

Evaluating environmental and ecological landscape characteristics relevant to urban resilience across gradients of land-sharing-sparing and urbanity

Within urban landscape planning, debate continues around the relative merits of land-sparing (compaction) and land-sharing (sprawl) scenarios. Using part of Greater Manchester (UK) as a case-study, we present a landscape approach to mapping green infrastructure and variation in social-ecological-environmental conditions as a function of land sparing and sharing. We do so for the landscape as a whole as well as for areas of high and low urbanity. Results imply potential trade-offs between land-sparing-sharing scenarios relevant to characteristics critical to urban resilience such as landscape connectivity and diversity, air quality, surface temperature, and access to green space. These trade-offs may be particularly complex due to the parallel influence of patch attributes such as land-cover and size and imply that both ecological restoration and spatial planning have a role to play in reconciling tensions between land-sparing and sharing strategies.

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bioRxiv2019

The ecological and epidemiological consequences of reproductive interference between the vectors Aedes aegypti and Aedes albopictus

Vector ecology is integral to understanding the transmission of vector-borne diseases, with processes such as reproduction and competition pivotal in determining vector presence and abundance. The arbovirus vectors Aedes aegypti and Aedes albopictus compete as larvae, but this mechanism is insufficient to explain patterns of coexistence and exclusion. Inviable interspecies matings - known as reproductive interference - is another candidate mechanism. Here, we analyse mathematical models of mosquito population dynamics and epidemiology which include two Aedes-specific features of reproductive interference. First, as these mosquitoes use hosts to find mates, reproductive interference will only occur if the same host is visited. Host choice will, in turn, be determined by functional responses to host availability. Second, females can become sterilised after mis-mating with heterospecifics. We find that a species with an affinity for a shared host will suffer more from reproductive interference than a less selective competitor. Costs from reproductive interference can be \"traded-off\" against costs from larval competition, leading to competitive outcomes difficult to predict from empirical evidence. Sterilisations of a self-limiting species can counter-intuitively lead to higher densities than a competitor suffering less sterilisation. We identify that functional responses and reproductive interference mediate a concomitant relationship between vector ecological dynamics and epidemiology. Competitors with opposite functional responses can maintain disease where human hosts are rare, due to vector coexistence facilitated by a reduced cost from reproductive interference. Our work elucidates the relative roles of the competitive mechanisms governing Aedes populations and the associated epidemiological consequences.

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bioRxiv2019

Simple study designs in ecology produce inaccurate estimates of biodiversity responses

O_LIEcologists use a wide range of study designs to estimate the impact of interventions or threats but there are no quantitative comparisons of their accuracy. For example, while it is accepted that simpler designs, such as After (sampling sites post-impact without a control), Before-After (BA) and Control-Impact (CI), are less robust than Randomised Controlled Trials (RCT) and Before-After Control-Impact (BACI) designs, it is not known how much less accurate they are.\nC_LIO_LIWe simulate a step-change response of a population to an environmental impact using empirically-derived estimates of the major parameters. We use five ecological study designs to estimate the effect of this impact and evaluate each one by determining the percentage of simulations in which they accurately estimate the direction and magnitude of the environmental impact. We also simulate different numbers of replicates and assess several accuracy thresholds.\nC_LIO_LIWe demonstrate that BACI designs could be 1.1-1.5 times more accurate than RCTs, 2.9-4.1 times more accurate than BA, 3.8-5.6 times more accurate than CI, and 6.8-10.8 times more accurate than After designs, when estimating to within {+/-}30% of the true effect (depending on the sample size). We also found that increasing sample size substantially increases the accuracy of BACI designs but only increases the precision of simpler designs around a biased estimate; only by using more robust designs can accuracy increase. Modestly increasing replication of both control and impact sites also increased the accuracy of BACI designs more than substantially increasing replicates in just one of these groups.\nC_LIO_LIWe argue that investment into using more robust designs in ecology, where possible, is extremely worthwhile given the inaccuracy of simpler designs, even when using large sample sizes. Based on our results we propose a weighting system that quantitatively ranks the accuracy of studies based on their study design and the number of replicates used. We hope these accuracy weights enable researchers to better account for study design in evidence synthesis when assessing the reliability of a range of studies using a variety of designs.\nC_LI

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bioRxiv2019

The scaling of genome size and cell size limits maximum rates of photosynthesis with implications for ecological strategies

A central challenge in plant ecology is to define the major axes of plant functional variation with direct consequences for fitness. Central to the three main components of plant fitness (growth, survival, and reproduction) is the rate of metabolic conversion of CO2 into carbon that can be allocated to various structures and functions. Here we (1) argue that a primary constraint on the maximum rate of photosynthesis per unit leaf area is the size and packing density of cells and (2) show that variation in genome size is a strong predictor of cell sizes, packing densities, and the maximum rate of photosynthesis across terrestrial vascular plants. Regardless of the genic content associated with variation in genome size, the simple biophysical constraints of encapsulating the genome define the lower limit of cell size and the upper limit of cell packing densities, as well as the range of possible cell sizes and densities. Genome size, therefore, acts as a first-order constraint on carbon gain and is predicted to define the upper limits of allocation to growth, reproduction, and defense. The strong effects of genome size on metabolism, therefore, have broad implications for plant biogeography and for other theories of plant ecology, and suggest that selection on metabolism may have a role in genome size evolution.

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bioRxiv2019

Non-production vegetation has a positive effect on ecological processes in agroecosystems

An ever-expanding human population, ongoing global climatic changes, and the spread of intensive farming practices is putting increasing pressure on agroecosystems and the inherent biodiversity they contain. Non-production vegetation elements, such as woody patches, riparian margins, and inter-crop and restoration plantings, are vital for conserving biodiversity in agroecosystems and are therefore considered key to sustaining the biotic and abiotic processes underpinning sustainable and resilient agroecosystems. Despite this critical role, there is a surprising lack of synthesis of which types of non-production vegetation elements drive and/or support ecological processes and the mechanisms by which this occurs. Using a systematic, quantitative literature review of 342 articles, we asked: what are the effects of non-production vegetation elements on agroecosystem processes and how are these processes measured within global agroecosystems? Our literature search focussed on the effects of non-production vegetation related to faunal, weed, disease, and abiotic processes. The majority (61%) of studies showed positive effects on ecological processes: non-production vegetation increased the presence, level or rate of the studied process. However, rather than directly measuring ecosystem processes, 83% of studies inferred processes using proxies for ecosystem function, such as biodiversity and soil physicochemical properties. Studies that directly measured non-production vegetation effects focussed on a limited number of vegetation effects including comparisons of vegetation types, farm-scale configuration, and proximity to vegetation. Moreover, studies directly measuring ecosystem processes were similarly limited, dominated by invertebrate biocontrol, predator and natural enemy spillover, animal movement, and ecosystem cycling. We identify research gaps and present a pathway for future research in understanding the ecosystem components and processes that build resilient, sustainable agroecosystems.

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bioRxiv2019

A Nature-based solution in practice: ecological and economic modelling shows pollinators outperform agrochemicals in oilseed crop production

AO_SCPLOWBSTRATC_SCPLOWNature-based agriculture, reducing dependency on chemical inputs, requires using ecological principles for sustainable agro-ecosystems, balancing ecology, economics and social justice. There is growing evidence that pollinator-dependent crops with high insect pollination service can give higher yields. However, the interacting effects between insect pollination and agricultural inputs on crop yields and farm economics remain to be established to reconcile food production with biodiversity conservation. We investigated the effects of insect pollination and agricultural inputs on oilseed rape (Brassica napus L.). We show that not only yield but also gross margins are 16-40% higher in fields with higher pollinator abundance than in fields with reduced pollinator abundance. This effect is however strongly reduced by pesticides use. Higher yields may be achieved by either increasing agrochemicals (reducing pests) or increasing bee abundance, but crop economic returns was only increased by the latter, because pesticides did not increase yields while their costs reduced gross margins.

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bioRxiv2019

Human Demographic Outcomes of a Restored Agro-Ecological Balance

As prominent features of the Anthropocene, biodiversity loss and invasive species are exacting serious negative economic, environmental and societal impacts. While the monetary aspects of species invasion are reasonably well assessed, their human and social livelihood outcomes often remain obscure. Here, we empirically demonstrate the (long-term) human demographic consequences of the 1970s invasion of a debilitating pest affecting cassava -a carbohydrate-rich food staple-across sub-Saharan Africa. Successive pest attack in 18 African nations inflicted an 18 {+/-} 29% drop in crop yield, with cascading effects on birth rate (-6%), adult mortality (+4%) and decelerating population growth. The 1981 deliberate release of the parasitic wasp Anagyrus lopezi permanently restored food security and enabled parallel recovery of multiple demographic indices. This analysis draws attention to the societal repercussions of ecological disruptions in subsistence farming systems, providing lessons for efforts to meet rising human dietary needs while safeguarding agro-ecological functionality and resilience during times of global environmental change.

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bioRxiv2019

The balance of interaction types determines the assembly and stability of ecological communities

What determines the assembly and stability of complex communities is a central question in ecology. Past work has suggested that mutualistic interactions are inherently destabilizing. However, this conclusion relies on assuming that benefits from mutualisms never stop increasing. Furthermore, almost all theoretical work focuses on the internal (asymptotic) stability of communities assembled all-at-once. Here, we present a model with saturating benefits from mutualisms and sequentially assembled communities. We show that such communities are internally stable for any level of diversity and any combination of species interaction types. External stability, or resistance to invasion, is thus an important but overlooked measure of stability. We demonstrate that the balance of different interaction types governs community dynamics. Mutualisms may increase external stability and diversity of communities as well as species persistence, depending on how benefits saturate. Ecological selection increases the prevalence of mutualisms, and limits on biodiversity emerge from species interactions. Our results help resolve longstanding debates on the stability, saturation, and diversity of communities.

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bioRxiv2019

Z-scores unite >70 pairwise indices of ecological similarity and association for binary data

Pairwise ecological resemblance, which includes compositional similarity between sites (beta diversity), or associations between species (co-occurrence), can be measured by >70 indices. Classical examples for presence-absence data are Jaccard index or C-score. These can be expressed using contingency table matching components a, b, c and d - the joint presences, presences at only one site/species, and joint absences. Using simulations of point patterns for two species with known magnitude of association, I demonstrate that most of the indices describe this simulated association almost identically, as long as they are calculated as a Z-score, i.e. as deviation of the index from a null expectation. Further, I show that Z-scores estimated resemblance better than raw forms of the indices, particularly in the face of confounding effects of spatial scale and conspecific aggregation. Finally, I show that any single of the matching components, when expressed as Z-score, can be used as an index that performs as good as the classical indices; this also includes joint absences. All this simplifies selection of the \"right\" resemblance index, it underscores the advantage of expressing resemblance as deviation from a null expectation, and it revives the potential of joint absences as a meaningful ecological quantity.

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bioRxiv2019

Beyond the ecology of fear: non-lethal effects of predators are strong whereas those of parasites are diverse

The ecology of fear demonstrates how prey responses to avoid predation cause non-lethal effects at all ecological scales. Parasites also elicit defensive responses in hosts with associated non-lethal effects, which raises the longstanding, yet unresolved question of how non-lethal effects of parasites compare with those of predators. We developed a framework for systematically answering this question for all types of predator and parasite systems. Our framework predicts that trait responses and their non-lethal effects should be strongest from predators and parasites that do not kill individuals to feed on them, but which nevertheless damage fitness. Analysing trait response data on amphibians, which have been well-studied for this area of research, showed that individuals generally responded more directly to short-term predation risks than to parasitism. Apart from studies using amphibians, there have been few direct comparisons of responses to predation and parasitism, and none have incorporated responses to micropredators, parasitoids, or parasitic castrators, or examined their long-term consequences. Addressing these and other data gaps highlighted by our general framework can advance the field toward understanding how non-lethal effects shape real food webs, which contain multiple predator and parasite species.

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bioRxiv2019

Honey bee pollen foraging ecology across an urbanization gradient

Understanding animal foraging ecology requires large samples sizes spanning broad environmental and temporal gradients. For pollinators, this has been hampered by the laborious nature of morphologically identifying pollen. Metagenetic pollen analysis is a solution to this issue, but the field has struggled with poor quantitative performance. Building upon prior laboratory and bioinformatic methods, we applied quantitative multi-locus metabarcoding to characterize the foraging ecology of honey bee colonies situated along an urban-agricultural gradient in central Ohio, USA. In cross-validating a subset of our metabarcoding results using microscopic palynology, we find strong concordance between the molecular and microscopic methods. Our results show that, relative to the agricultural environment, urban and suburban environments were associated with higher taxonomic diversity and temporal turnover of honey bee pollen forage. This is likely reflective of the fine-grain heterogeneity and high beta diversity of urban floral landscapes at the scale of honey bee foraging. Our work also demonstrates the power of honey bees as environmental samplers of floral community composition at large spatial scales, aiding in the distinction of taxa characteristically associated with urban or agricultural land use from those distributed ubiquitously across our landscape gradient.

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bioRxiv2019

Ecological character displacement destabilizes food webs

Ecological character displacement is an adaptive process that generally increases phenotypic diversity. Despite the fact that this diversification is due to an eco-evolutionary feedback between consumers competing for shared resources, its consequences for food-web dynamics have received little attention. Here, I study a model of two consumers competing for two shared resources to examine how character displacement in consumer attack rates affects resource abundances and the resilience of food webs to perturbations. I found that character displacement always strengthened consumer-resource interactions whenever consumers competed for resources that occurred in different habitats. This increase in interaction strength resulted in lower resource abundances and less resilient food webs. This occurred under different evolutionary tradeoffs and in both simple and more realistic foraging scenarios. Taken together, my results show that the adaptive process of character displacement may come with the ecological cost of decreasing food-web resilience.

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bioRxiv2019

A process-based framework for metacommunity ecology

The metacommunity concept has the potential to integrate local and regional dynamics within a general community ecology framework. To this end, the concept must move beyond the discrete archetypes that have largely defined it (e.g. neutral vs. species sorting) and better incorporate local scale species interactions and coexistence mechanisms. Here, we present a fundamental reconception of the framework that explicitly links local coexistence theory to the spatial processes inherent to metacommunity theory, allowing for a continuous range of competitive community dynamics. These dynamics emerge from the three underlying processes that shape ecological communities: 1) density-independent responses to abiotic conditions, 2) density-dependent biotic interactions, and 3) dispersal. Stochasticity is incorporated in the demographic realization of each of these processes. We formalize this framework using a simulation model that explores a wide range of competitive metacommunity dynamics by varying the strength of the underlying processes. Using this model and framework, we show how existing theories, including the traditional metacommunity archetypes, are linked by this common set of processes. We then use the model to generate new hypotheses about how the three processes combine to interactively shape diversity, functioning, and stability within metacommunities. Statement of authorshipThis project was conceived at the sTURN working group, of which all authors are members. PLT developed the framework and model with input from all authors. PLT wrote the model code. PLT and LMG performed the simulations. PLT produced the figures and wrote the first draft with input from LMG and JMC. All authors provided feedback and edits on several versions of the manuscript. Data accessibilityAll code for running the simulation model and producing the figures is archived on Zenodo - https://doi.org/10.5281/zenodo.3833035.

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bioRxiv2019

Phylogenetic and functional diversity have contrasting effects on the ecological functioning of bacterial communities

Quantifying the relative contributions of microbial species to ecosystem functioning is challenging, because of the distinct mechanisms associated with microbial phylogenetic and metabolic diversity. We constructed bacterial communities with different diversity traits and employed exoenzyme activities (EEAs) and total available carbon (TAC) from substrates as proxies of bacterial functioning to test the independent effects of these two aspects of biodiversity. We expected that metabolic diversity, but not phylogenetic diversity would be associated with greater ecological function. Phylogenetically relatedness should intensify species interactions and coexistence, therefore amplifying the influence of metabolic diversity. We examined the effects of each diversity treatment using linear models, while controlling for the other, and found that phylogenetic diversity strongly influenced community functioning, positively and negatively. Metabolic diversity, however, exhibited negative or non-significant relationships with community functioning. When controlling for different substrates, EEAs increased along with phylogenetic diversity but decreased with metabolic diversity. The strength of diversity effects was related to substrate chemistry and the molecular mechanisms associated with each substrates degradation. EEAs of phylogenetically similar groups were strongly affected by within-genus interactions. These results highlight the unique flexibility of microbial metabolic functions that must be considered in further ecological theory development.

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bioRxiv2019

Partitioning environment and space in species-by-site matrices: a comparison of methods for community ecology and macroecology

Community ecologists and macroecologists have long sought to evaluate the importance of environmental conditions in determining species distributions, community composition, and diversity across sites. Different methods have been used to estimate species-environment relationships, but their differences to jointly fit and disentangle spatial autocorrelation and structure remain poorly studied. We compared how methods in four broad families of statistical models estimated the contribution of the environment and space to variation in species binary occurrence and abundance. These methods included distance-based regression, generalized linear models (GLM, and the special case of RDA), generalized additive models (GAM), and tree-based machine learning (ML): regression trees, boosted regression trees (BRT), and random forests. The spatial component of the model consisted of spatial distance (in distance-based regression), Morans Eigenvector Maps (MEM; in GLM and ML), smooth spatial splines (in GAM), or tree-based non-linear modelling of spatial coordinates (in ML). We simulated typical site-by-species data to assess the methods performance in (1) fitting environmental and spatial models, and (2) partitioning the variation explained by environmental and spatial predictors. We observed marked differences in performance mostly caused by imbalanced performance in estimating environmental and spatial effects. Such differences also manifested when analyzing eight different empirical datasets. GLM and BRT with MEMs were generally the most reliable methods for partitioning the variation explained by environmental and spatial effects across a wide range of simulated scenarios. The remaining methods tended to underfit simulated spatial structures, causing underestimation of spatial fractions of variation. Our results suggest that previously overlooked methods for performing variation partitioning, especially tree-based ML, offer flexible approaches to analyze site-by-species matrices. We provide general guidelines on the usefulness of different models under different ecological and sampling scenarios, for species distribution modelling, community ecology, and macroecology.

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bioRxiv2025

A Multi-Taxa Approach to Estuarine Biomonitoring: Assessing Vertebrate Biodiversity and Ecological Continuity using Environmental DNA Metabarcoding in the Rance River (Brittany, France)

Estuaries are ecologically vital yet highly impacted ecosystems that serve as transitional zones between land and sea. Monitoring their biodiversity is essential but challenging due to their dynamic nature and the transient presence of many species. Traditionally actinopterygian monitoring in these systems still relies on conventional and intrusive methods such as gill nets and trawls. Environmental DNA (eDNA) metabarcoding offers a non-invasive, multi-taxa alternative that can complement these traditional approaches. Here, we applied an eDNA-based metabarcoding approach to characterize vertebrate diversity in the Rance Estuary, located in the Brittany Region of France. Water samples were collected from five stations spanning marine to freshwater environments. Special attention was given to two stations located upstream and downstream of the tidal power plant (TPP) dam to assess its potential impact on ecological continuity. We detected a total of 124 distinct vertebrate MOTUs--comprising actinopterygians, birds, mammals, and amphibians. Taxonomic composition followed the estuarine gradient, with Jaccard dissimilarity increasing with distance from the sea and largely driven by species turnover. While taxonomic and phylogenetic diversity remained relatively stable across the vertebrate community, functional diversity revealed an increasing terrestrial influence. For actinopterygians, taxonomic diversity decreased upstream, whereas phylogenetic and functional diversity indicated fine-scale structuring, even among nearby stations. This approach enabled the development of biodiversity metrics and facilitated comparisons with previous actinopterygian monitoring surveys in the same area based on conventional methods (scientific fishing using nets and dredges). Our results emphasise the potential of eDNA for holistic estuarine biomonitoring and establish a valuable baseline for future non-invasive assessments.

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