Remi Vergnon

Bio: Remi Vergnon is an academic researcher from University of Sheffield. The author has contributed to research in topics: Ecological niche & Species diversity. The author has an hindex of 9, co-authored 15 publications receiving 502 citations. Previous affiliations of Remi Vergnon include Wageningen University and Research Centre & Institut de recherche pour le développement.

Niches versus neutrality: uncovering the drivers of diversity in a species-rich community.

Abstract: Ecological models suggest that high diversity can be generated by purely niche-based, purely neutral or by a mixture of niche-based and neutral ecological processes. Here, we compare the degree to which four contrasting hypotheses for coexistence, ranging from niche-based to neutral, explain species richness along a body mass niche axis. We derive predictions from these hypotheses and confront them with species body-mass patterns in a highly sampled marine phytoplankton community. We find that these patterns are consistent only with a mechanism that combines niche and neutral processes, such as the emergent neutrality mechanism. In this work, we provide the first empirical evidence that a niche-neutral model can explain niche space occupancy pattern in a natural species-rich community. We suggest this class of model may be a useful hypothesis for the generation and maintenance of species diversity in other size-structured communities.

Trend analysis of indicators: a comparison of recent changes in the status of marine ecosystems around the world

Abstract: Blanchard, J. L., Coll, M., Trenkel, V. M., Vergnon, R., Yemane, D., Jouffre, D., Link, J. S., and Shin, Y-J. 2010. Trend analysis of indicators: a comparison of recent changes in the status of marine ecosystems around the world. – ICES Journal of Marine Science, 67: 000– 000. Time-series of ecological and exploitation indicators collected from 19 ecosystems were analysed to investigate whether there have been temporal trends in the status of fish communities. Using linear and non-linear statistical methods, trends are reported for six indicators (mean length of fish in the community, mean lifespan, proportion of predatory fish, total biomass of surveyed species, mean trophic level of landings, and inverse fishing pressure), and the redundancy of these indicators across ecosystems is evaluated. The expected direction of change for an ecosystem that is increasingly impacted by fishing is a decline in all indicators. A mixture of negative and positive directions of change is recorded, both within and among all ecosystems considered. No consistent patterns in the redundancy of the ecological indicators across ecosystems emerged from the analyses, confirming that each indicator provided complementary information on ecosystem status. The different trends in indicators may reflect differing historical exploitation patterns, management, and environmental regimes in these systems. Commitment to monitoring programmes and development of system-specific baseline, target, and threshold reference levels are required. Improved understanding of the responsiveness and performance of ecological indicators to management actions are needed to address adequately whether ecosystems are recovering from, or being further impacted by, fishing, and whether management targets are being met. The relative effects of multiple environmental and ecological processes as well as multiple human-induced stressors that characterize exploited ecosystems also need to be quantified.

Emergent neutrality leads to multimodal species abundance distributions

Abstract: Recent analyses of data sampled in communities ranging from corals and fossil brachiopods to birds and phytoplankton suggest that their species abundance distributions have multiple modes, a pattern predicted by none of the existing theories. Here we show that the multimodal pattern is consistent with predictions from the theory of emergent neutrality. This adds to the observations, suggesting that natural communities may be shaped by the evolutionary emergence of groups of similar species that coexist in niches. Such self-organized similarity unifies niche and neutral theories of biodiversity.

Why trees and shrubs but rarely trubs

Abstract: An analysis of the maximum height of woody plant species across the globe reveals that an intermediate size is remarkably rare. We speculate that this may be due to intrinsic suboptimality or to ecosystem bistability with open landscapes favouring shrubs, and closed canopies propelling trees to excessive tallness.

Toward a unifying theory of biodiversity.

Abstract: Ecologists have long agreed that to coexist species must be sufficiently different (1, 2). This worldview was challenged when Stephen Hubbell published his neutral theory of biodiversity showing that species that are essentially equal should also be able to evade competitive exclusion (3). Although this neutral theory inspired a fresh look at biodiversity, it also met resistance as it seemed to violate the deeply held belief that all species are fundamentally different. Interestingly, a harmonious combination of niche differentiation and neutrality can emerge naturally in simulated communities, thus suggesting a way of unifying the niche and neutral view (4). A peculiar prediction of this theory of emergent neutrality is that species should be distributed over niche space in a lumpy way, a pattern that is indeed often observed in nature (5⇓⇓⇓–9). In this view the lumps correspond to niches, while species within lumps are essentially more of the same, reflecting two alternative ways for species to coexist: being sufficiently different or being sufficiently similar (Fig. 1). A study in PNAS now lends important support to this unifying theory by showing its compatibility with Tilman’s widely embraced theory of competition for resources (10). Fig. 1. Simulation of the evolutionary adaptation of species showing the emergence of regularly spaced lumps of near-neutral coexistence. Species move away from the gaps toward the self-organized niches reflected in the lumps. The distance between the lumps corresponds to the niche separation that is theoretically predicted from the classic theory of limiting similarity. Modified with permission from ref. 4; Copyright (2006), National Academy of Sciences, USA. The theoretical prediction that coexistence of two species requires sufficient niche differentiation (2) has become one of the cornerstones of ecology. It also makes intuitive sense. The smaller the niche overlap, the weaker the competition … [↵][1]1To whom correspondence should be addressed. Email: Marten.Scheffer{at}wur.nl. [1]: #xref-corresp-1-1

Disentangling the importance of ecological niches from stochastic processes across scales

Abstract: Deterministic theories in community ecology suggest that local, niche-based processes, such as environmental filtering, biotic interactions and interspecific trade-offs largely determine patterns of species diversity and composition. In contrast, more stochastic theories emphasize the importance of chance colonization, random extinction and ecological drift. The schisms between deterministic and stochastic perspectives, which date back to the earliest days of ecology, continue to fuel contemporary debates (e.g. niches versus neutrality). As illustrated by the pioneering studies of Robert H. MacArthur and co-workers, resolution to these debates requires consideration of how the importance of local processes changes across scales. Here, we develop a framework for disentangling the relative importance of deterministic and stochastic processes in generating site-to-site variation in species composition (β-diversity) along ecological gradients (disturbance, productivity and biotic interactions) and among biogeographic regions that differ in the size of the regional species pool. We illustrate how to discern the importance of deterministic processes using null-model approaches that explicitly account for local and regional factors that inherently create stochastic turnover. By embracing processes across scales, we can build a more synthetic framework for understanding how niches structure patterns of biodiversity in the face of stochastic processes that emerge from local and biogeographic factors.

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

Abstract: Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research.

Ecological assembly rules in plant communities--approaches, patterns and prospects.

Abstract: Understanding how communities of living organisms assemble has been a central question in ecology since the early days of the discipline. Disentangling the different processes involved in community assembly is not only interesting in itself but also crucial for an understanding of how communities will behave under future environmental scenarios. The traditional concept of assembly rules reflects the notion that species do not co-occur randomly but are restricted in their co-occurrence by interspecific competition. This concept can be redefined in a more general framework where the co-occurrence of species is a product of chance, historical patterns of speciation and migration, dispersal, abiotic environmental factors, and biotic interactions, with none of these processes being mutually exclusive. Here we present a survey and meta-analyses of 59 papers that compare observed patterns in plant communities with null models simulating random patterns of species assembly. According to the type of data under study and the different methods that are applied to detect community assembly, we distinguish four main types of approach in the published literature: species co-occurrence, niche limitation, guild proportionality and limiting similarity. Results from our meta-analyses suggest that non-random co-occurrence of plant species is not a widespread phenomenon. However, whether this finding reflects the individualistic nature of plant communities or is caused by methodological shortcomings associated with the studies considered cannot be discerned from the available metadata. We advocate that more thorough surveys be conducted using a set of standardized methods to test for the existence of assembly rules in data sets spanning larger biological and geographical scales than have been considered until now. We underpin this general advice with guidelines that should be considered in future assembly rules research. This will enable us to draw more accurate and general conclusions about the non-random aspect of assembly in plant communities.

Cryptic species as a window into the paradigm shift of the species concept

Abstract: The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new "species" paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category-which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a "process" counterpart to the long-studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance-based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large-scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.

Multispecies fisheries management and conservation: tactical applications using models of intermediate complexity

Abstract: Stakeholders increasingly expect ecosystem assessments as part of advice on fisheries management. Quantitative models to support fisheries decision-making may be either strategic (‘big picture’, direction-setting and contextual) or tactical (focused on management actions on short timescales), with some strategic models informing the development of tactical models. We describe and review ‘Models of Intermediate Complexity for Ecosystem assessments’ (MICE) that have a tactical focus, including use as ecosystem assessment tools. MICE are context- and question-driven and limit complexity by restricting the focus to those components of the ecosystem needed to address the main effects of the management question under consideration. Stakeholder participation and dialogue is an integral part of this process. MICE estimate parameters through fitting to data, use statistical diagnostic tools to evaluate model performance and account for a broad range of uncertainties. These models therefore address many of the impediments to greater use of ecosystem models in strategic and particularly tactical decision-making for marine resource management and conservation. MICE are capable of producing outputs that could be used for tactical decision-making, but our summary of existing models suggests this has not occurred in any meaningful way to date. We use a model of the pelagic ecosystem in the Coral Sea and a linked catchment and ocean model of the Gulf of Carpentaria, Australia, to illustrate how MICE can be constructed. We summarize the major advantages of the approach, indicate opportunities for the development of further applications and identify the major challenges to broad adoption of the approach.