Direct submissions to PCI Ecology from bioRxiv.org are possible using the B2J service
Latest recommendations
Id | Title * | Authors * | Abstract * ▲ | Picture * | Thematic fields * | Recommender | Reviewers | Submission date | |
---|---|---|---|---|---|---|---|---|---|
09 Dec 2019
![]() Niche complementarity among pollinators increases community-level plant reproductive successAinhoa Magrach, Francisco P. Molina, Ignasi Bartomeus https://doi.org/10.1101/629931Improving our knowledge of species interaction networksRecommended by Cédric GaucherelEcosystems shelter a huge number of species, continuously interacting. Each species interact in various ways, with trophic interactions, but also non-trophic interactions, not mentioning the abiotic and anthropogenic interactions. In particular, pollination, competition, facilitation, parasitism and many other interaction types are simultaneously present at the same place in terrestrial ecosystems [1-2]. For this reason, we need today to improve our understanding of such complex interaction networks to later anticipate their responses. This program is a huge challenge facing ecologists and they today join their forces among experimentalists, theoreticians and modelers. While some of us struggle in theoretical and modeling dimensions [3-4], some others perform brilliant works to observe and/or experiment on the same ecological objects [5-6]. In this nice study [6], Magrach et al. succeed in studying relatively large plant-pollinator interaction networks in the field, in Mediterranean ecosystems. For the first time to my knowledge, they study community-wide interactions instead of traditional and easier accessible pairwise interactions. On the basis of a statistically relevant survey, they focus on plant reproductive success and on the role of pollinator interactions in such a success. A more reductionist approach based on simpler pairwise interactions between plants and pollinators would not be able to highlight the interaction network structure (the topology) possibly impacting its responses [1,5], among which the reproductive success of some (plant) species. Yet, such a network analysis requires a fine control of probable biases, as those linked to size or autocorrelation between data of various sites. Here, Magrach et al. did a nice work in capturing rigorously the structures and trends behind this community-wide functioning. To grasp possible relationships between plant and pollinator species is a first mandatory step, but the next critical step requires understanding processes hidden behind such relationships. Here, the authors succeed to reach this step too, by starting interpreting the processes at stake in their studied plant-pollinator networks [7]. In particular, the niche complementarity has been demonstrated to play a determinant role in the plant reproductive success, and has a positive impact on it [6]. When will we be able to detect a community-wise process? This is one of my team’s objectives, and we developed new kind of models with this aim. Also, authors focus here on plant-pollinator network, but the next step might be to gather every kind of interactions into a huge ecosystem network which we call the socio-ecosystemic graph [4]. Indeed, why to limit our view to certain interactions only? It will take time to grasp the whole interaction network an ecosystem is sheltering, but this should be our next challenge. And this paper of Magrach et al. [6] is a first fascinating step in this direction. **References** [1] Campbell, C., Yang, S., Albert, R., and Shea, K. (2011). A network model for plant–pollinator community assembly. Proceedings of the National Academy of Sciences, 108(1), 197-202. doi: [10.1073/pnas.1008204108](https://dx.doi.org/10.1073/pnas.1008204108) [2] Kéfi, S., Miele, V., Wieters, E. A., Navarrete, S. A., and Berlow, E. L. (2016). How structured is the entangled bank? The surprisingly simple organization of multiplex ecological networks leads to increased persistence and resilience. PLoS biology, 14(8), e1002527. doi: [10.1371/journal.pbio.1002527](https://dx.doi.org/10.1371/journal.pbio.1002527) [3] Gaucherel, C. (2019). The Languages of Nature. When nature writes to itself. Lulu editions, Paris, France. [4] Gaucherel, C., and Pommereau, F. Using discrete systems to exhaustively characterize the dynamics of an integrated ecosystem. Methods in Ecology and Evolution, 10(9), 1615-1627. doi: [10.1111/2041-210X.13242](https://dx.doi.org/10.1111/2041-210X.13242) [5] Bennett, J. M. et al. (2018). A review of European studies on pollination networks and pollen limitation, and a case study designed to fill in a gap. AoB Plants, 10(6), ply068. doi: [10.1093/aobpla/ply068](https://dx.doi.org/10.1093/aobpla/ply068) [6] Magrach, A., Molina, F. P., and Bartomeus, I. (2020). Niche complementarity among pollinators increases community-level plant reproductive success. bioRxiv, 629931, ver. 7 peer-reviewed and recommended by PCI Ecology. doi: [10.1101/629931](https://dx.doi.org/10.1101/629931) [7] Bastolla, U., Fortuna, M. A., Pascual-García, A., Ferrera, A., Luque, B., and Bascompte, J. (2009). The architecture of mutualistic networks minimizes competition and increases biodiversity. Nature, 458(7241), 1018-1020. doi: [10.1038/nature07950](https://dx.doi.org/10.1038/nature07950) | Niche complementarity among pollinators increases community-level plant reproductive success | Ainhoa Magrach, Francisco P. Molina, Ignasi Bartomeus | <p>Declines in pollinator diversity and abundance have been reported across different regions, with implications for the reproductive success of plant species. However, research has focused primarily on pairwise plant-pollinator interactions, larg... | ![]() | Ecosystem functioning, Interaction networks, Pollination, Terrestrial ecology | Cédric Gaucherel | Nicolas Deguines | 2019-05-07 17:03:23 | View |
16 Jun 2023
![]() Colonisation debt: when invasion history impacts current range expansionThibaut Morel-Journel, Marjorie Haond, Lana Duan, Ludovic Mailleret, Elodie Vercken https://doi.org/10.1101/2022.11.13.516255Combining stochastic models and experiments to understand dispersal in heterogeneous environmentsRecommended by Joaquín HortalDispersal is a key element of the natural dynamics of meta-communities, and plays a central role in the success of populations colonizing new landscapes. Understanding how demographic processes may affect the speed at which alien species spread through environmentally-heterogeneous habitat fragments is therefore of key importance to manage biological invasions. This requires studying together the complex interplay of dispersal and population processes, two inextricably related phenomena that can produce many possible outcomes. Stochastic models offer an opportunity to describe this kind of process in a meaningful way, but to ensure that they are realistic (sensu Levins 1966) it is also necessary to combine model simulations with empirical data (Snäll et al. 2007). Morel-Journel et al. (2023) put together stochastic models and experimental data to study how population density may affect the speed at which alien species spread through a heterogeneous landscape. They do it by focusing on what they call ‘colonisation debt’, which is merely the impact that population density at the invasion front may have on the speed at which the species colonizes patches of different carrying capacities. They investigate this issue through two largely independent approaches. First, a stochastic model of dispersal throughout the patches of a linear, 1-dimensional landscape, which accounts for different degrees of density-dependent growth. And second, a microcosm experiment of a parasitoid wasp colonizing patches with different numbers of host eggs. In both cases, they compare the velocity of colonization of patches with lower or higher carrying capacity than the previous one (i.e. what they call upward or downward gradients). Their results show that density-dependent processes influence the speed at which new fragments are colonized is significantly reduced by positive density dependence. When either population growth or dispersal rate depend on density, colonisation debt limits the speed of invasion, which turns out to be dependent on the strength and direction of the gradient between the conditions of the invasion front, and the newly colonized patches. Although this result may be quite important to understand the meta-population dynamics of dispersing species, it is important to note that in their study the environmental differences between patches do not take into account eventual shifts in the scenopoetic conditions (i.e. the values of the environmental parameters to which species niches’ respond to; Hutchinson 1978, see also Soberón 2007). Rather, differences arise from variations in the carrying capacity of the patches that are consecutively invaded, both in the in silico and microcosm experiments. That is, they account for potential differences in the size or quality of the invaded fragments, but not on the costs of colonizing fragments with different environmental conditions, which may also determine invasion speed through niche-driven processes. This aspect can be of particular importance in biological invasions or under climate change-driven range shifts, when adaptation to new environments is often required (Sakai et al. 2001; Whitney & Gabler 2008; Hill et al. 2011). The expansion of geographical distribution ranges is the result of complex eco-evolutionary processes where meta-community dynamics and niche shifts interact in a novel physical space and/or environment (see, e.g., Mestre et al. 2020). Here, the invasibility of native communities is determined by niche variations and how similar are the traits of alien and native species (Hui et al. 2023). Within this context, density-dependent processes will build upon and heterogeneous matrix of native communities and environments (Tischendorf et al. 2005), to eventually determine invasion success. What the results of Morel-Journel et al. (2023) show is that, when the invader shows density dependence, the invasion process can be slowed down by variations in the carrying capacity of patches along the dispersal front. This can be particularly useful to manage biological invasions; ongoing invasions can be at least partially controlled by manipulating the size or quality of the patches that are most adequate to the invader, controlling host populations to reduce carrying capacity. But further, landscape manipulation of such kind could be used in a preventive way, to account in advance for the effects of the introduction of alien species for agricultural exploitation or biological control, thereby providing an additional safeguard to practices such as the introduction of parasitoids to control plagues. These practical aspects are certainly worth exploring further, together with a more explicit account of the influence of the abiotic conditions and the characteristics of the invaded communities on the success and speed of biological invasions. REFERENCES Hill, J.K., Griffiths, H.M. & Thomas, C.D. (2011) Climate change and evolutionary adaptations at species' range margins. Annual Review of Entomology, 56, 143-159. https://doi.org/10.1146/annurev-ento-120709-144746 Hui, C., Pyšek, P. & Richardson, D.M. (2023) Disentangling the relationships among abundance, invasiveness and invasibility in trait space. npj Biodiversity, 2, 13. https://doi.org/10.1038/s44185-023-00019-1 Hutchinson, G.E. (1978) An introduction to population biology. Yale University Press, New Haven, CT. Levins, R. (1966) The strategy of model building in population biology. American Scientist, 54, 421-431. Mestre, A., Poulin, R. & Hortal, J. (2020) A niche perspective on the range expansion of symbionts. Biological Reviews, 95, 491-516. https://doi.org/10.1111/brv.12574 Morel-Journel, T., Haond, M., Duan, L., Mailleret, L. & Vercken, E. (2023) Colonisation debt: when invasion history impacts current range expansion. bioRxiv, 2022.11.13.516255, ver. 3 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2022.11.13.516255 Snäll, T., B. O'Hara, R. & Arjas, E. (2007) A mathematical and statistical framework for modelling dispersal. Oikos, 116, 1037-1050. https://doi.org/10.1111/j.0030-1299.2007.15604.x Sakai, A.K., Allendorf, F.W., Holt, J.S., Lodge, D.M., Molofsky, J., With, K.A., Baughman, S., Cabin, R.J., Cohen, J.E., Ellstrand, N.C., McCauley, D.E., O'Neil, P., Parker, I.M., Thompson, J.N. & Weller, S.G. (2001) The population biology of invasive species. Annual Review of Ecology and Systematics, 32, 305-332. https://doi.org/10.1146/annurev.ecolsys.32.081501.114037 Soberón, J. (2007) Grinnellian and Eltonian niches and geographic distributions of species. Ecology Letters, 10, 1115-1123. https://doi.org/10.1111/j.1461-0248.2007.01107.x Tischendorf, L., Grez, A., Zaviezo, T. & Fahrig, L. (2005) Mechanisms affecting population density in fragmented habitat. Ecology and Society, 10, 7. https://doi.org/10.5751/ES-01265-100107 Whitney, K.D. & Gabler, C.A. (2008) Rapid evolution in introduced species, 'invasive traits' and recipient communities: challenges for predicting invasive potential. Diversity and Distributions, 14, 569-580. https://doi.org/10.1111/j.1472-4642.2008.00473.x | Colonisation debt: when invasion history impacts current range expansion | Thibaut Morel-Journel, Marjorie Haond, Lana Duan, Ludovic Mailleret, Elodie Vercken | <p>Demographic processes that occur at the local level, such as positive density dependence in growth or dispersal, are known to shape population range expansion, notably by linking carrying capacity to invasion speed. As a result of these process... | ![]() | Biological invasions, Colonization, Dispersal & Migration, Experimental ecology, Landscape ecology, Population ecology, Spatial ecology, Metacommunities & Metapopulations, Theoretical ecology | Joaquín Hortal | Anonymous, Anonymous | 2022-11-16 15:52:08 | View |
27 May 2019
Community size affects the signals of ecological drift and selection on biodiversityTadeu Siqueira, Victor S. Saito, Luis M. Bini, Adriano S. Melo, Danielle K. Petsch, Victor L. Landeiro, Kimmo T. Tolonen, Jenny Jyrkänkallio-Mikkola, Janne Soininen, Jani Heino https://doi.org/10.1101/515098Toward an empirical synthesis on the niche versus stochastic debateRecommended by Eric Harvey based on reviews by Kevin Cazelles and Romain BertrandAs far back as Clements [1] and Gleason [2], the historical schism between deterministic and stochastic perspectives has divided ecologists. Deterministic theories tend to emphasize niche-based processes such as environmental filtering and species interactions as the main drivers of species distribution in nature, while stochastic theories mainly focus on chance colonization, random extinctions and ecological drift [3]. Although the old days when ecologists were fighting fiercely over null models and their adequacy to capture niche-based processes is over [4], the ghost of that debate between deterministic and stochastic perspectives came back to haunt ecologists in the form of the ‘environment versus space’ debate with the development of metacommunity theory [5]. While interest in that question led to meaningful syntheses of metacommunity dynamics in natural systems [6], it also illustrated how context-dependant the answer was [7]. One of the next frontiers in metacommunity ecology is to identify the underlying drivers of this observed context-dependency in the relative importance of ecological processus [7, 8]. References [1] Clements, F. E. (1936). Nature and structure of the climax. Journal of ecology, 24(1), 252-284. doi: 10.2307/2256278 | Community size affects the signals of ecological drift and selection on biodiversity | Tadeu Siqueira, Victor S. Saito, Luis M. Bini, Adriano S. Melo, Danielle K. Petsch, Victor L. Landeiro, Kimmo T. Tolonen, Jenny Jyrkänkallio-Mikkola, Janne Soininen, Jani Heino | <p>Ecological drift can override the effects of deterministic niche selection on small populations and drive the assembly of small communities. We tested the hypothesis that smaller local communities are more dissimilar among each other because of... | Biodiversity, Coexistence, Community ecology, Competition, Conservation biology, Dispersal & Migration, Freshwater ecology, Spatial ecology, Metacommunities & Metapopulations | Eric Harvey | 2019-01-09 19:06:21 | View | ||
17 Dec 2024
Long-term survey of intertidal rocky shore macrobenthic community metabolism and structure after primary successionAline Migné, François Bordeyne, Dominique Davoult https://hal.science/hal-0434775610 years of primary succession in intertidal communities: specific and functional changesRecommended by Gudrun BornetteThis very interesting article describes the changes taking place on artificial substrates placed in an intertidal zone. The study presents an ambitious data set and demonstrates the importance of long-term monitoring to identify community dynamics. In summary, in the short term, the authors observe a phase of complexification of the communities and a peak in productivity, but after a few years, the macro-algae disappear in favour of limpets, a situation that persists after 10 years of monitoring. Monitoring over the short term would lead to an erroneous analysis of the succession patterns and dynamics of the communities, which has important consequences in terms of the recolonisation of artificial substrates in the marine environment. References Aline Migné, François Bordeyne, Dominique Davoult (2023) Long-term survey of intertidal rocky shore macrobenthic community metabolism and structure after primary succession. HAL, ver.2 peer-reviewed and recommended by PCI Ecology https://hal.science/hal-04347756 | Long-term survey of intertidal rocky shore macrobenthic community metabolism and structure after primary succession | Aline Migné, François Bordeyne, Dominique Davoult | <p>Ecological succession involves the transition from opportunistic ephemeral species, which display a minimal variation in functional traits, to slow growing, more functionally diverse, perennial species. The present study aimed in measuring the ... | Biodiversity, Colonization, Community ecology, Ecological successions, Ecosystem functioning, Experimental ecology, Marine ecology | Gudrun Bornette | Thomas Guillemaud, John Griffin, Ignasi Bartomeus, Dilip kumar jha , Abby Gilson , Francisco Arenas, Markus Molis , Matthew Bracken | 2023-12-19 15:39:21 | View | |
07 Feb 2025
![]() In defense of the original Type I functional response: The frequency and population-dynamic effects of feeding on multiple prey at a timeMark Novak, Kyle Edward Coblentz, John P DeLong https://doi.org/10.1101/2024.05.14.594210Revising behavioural assumptions leads to a new appreciation of an old functional response modelRecommended by Frédéric BarraquandThe functional response, describing the relation between predator intake rate and prey density, is a pivotal concept to understand foraging behaviour and its consequences for community dynamics. Holling (1959a) introduced three types of functional responses according to their shapes, labelled I, II and III. The type II, also known as the disc equation (Holling 1959b), has become popular among empiricists and theoreticians alike, due to its ability to describe predator intake saturation. The type III is often used to represent predator switching to other prey species when main prey density is low. Although theoretical works identify the linear functional response used in Lotka-Volterra models as a type I, Holling (1959a)’s type I model actually envisioned that at some threshold prey density, the linear increase in predator intake with prey density would give way to an upper predator intake limit, so that Holling’s type I has a rectilinear shape, with an angle joining straight lines. Ecology students can actually see this rectilinear shape reproduced in some texbooks, although not in textbook dynamical models, as they usually transition from Lotka-Volterra models to models with type II response. To many, the rectilinear shape of the original type I looks like a historical curiosity: the type II functional response accounts for intake rate saturation with a more convenient smooth function. Novak et al. (2025) turn this preconception on its head by first pedagogically showing that Holling’s original type I model can be obtained as a limit case of a variant of the celebrated type II model. The derivation follows up earlier work by Sjöberg (1980), which might be unfamiliar to readers outside aquatic ecology. The often untold assumption of the type II functional response model is that searching and handling prey are two exclusive behavioural processes, with predators that can only handle one prey item at a time. Allowing for several prey items to be handled at once while searching, until the predator reaches n prey items, the original type I functional response emerges as a limit case of the « multiprey » functional response as n goes to infinity. Interestingly, the multiprey response looks a lot like the original type I for large yet doable n. Novak et al. (2025) then proceed to look for the prevalence of such multiprey functional response shapes in a large database of functional responses (Uiterwaal et al. 2022). Combining linear type I and multiprey models (the asymptote may not always be visible), they find support for this revised type I hypothesis in about one-third of the cases. Although the type II and III models are still well supported by data, the results do suggest that linearity at low prey density may well be more frequent than one thinks. They complement this analysis by showing that larger predators relative to their prey tend to have larger n in the multiprey response. It is consistent with the hypothesis that the bigger you are relative to your prey, the more prey items you can handle at once. Finally, Novak et al. (2025) investigate the consequences of the multiprey model for community dynamics. They find overall a richer dynamical behaviour than the Lotka-Volterra type I and common parameterizations of the type II, suggesting that observed linearity in some range of prey density does not necessarily translate in simpler dynamical behaviour. Novak et al. (2025) provide here a convincing and pedagogical study showing how seemingly benign behavioural assumptions can in fact profoundly alter the perceived relevance of community dynamics models. As they conclude, their analyses have lessons for future empirical functional response work, which should not necessarily dismiss the type I model and consider perhaps variants to the classical type II and III, as well as for future theoretical analyses, which could generalize this model to multiple prey species, or relax other behavioural assumptions. References Holling, C. S. (1959a). The components of predation as revealed by a study of small-mammal predation of the European Pine Sawfly. The Canadian Entomologist, 91(5), 293-320. https://doi.org/10.4039/Ent91293-5 Holling, C. S. (1959b). Some characteristics of simple types of predation and parasitism. The Canadian Entomologist, 91(7), 385-398. https://doi.org/10.4039/Ent91385-7 Novak, M., Coblentz, K. E., & DeLong, J. P (2025). In defense of the original Type I functional response: The frequency and population-dynamic effects of feeding on multiple prey at a time. bioRxiv, ver.4 peer-reviewed and recommended by PCI Ecology https://doi.org/10.1101/2024.05.14.594210 Sjöberg, S. (1980). Zooplankton feeding and queueing theory. Ecological Modelling, 10(3-4), 215-225. https://doi.org/10.1016/0304-3800(80)90060-5 Uiterwaal, S. F., Lagerstrom, I. T., Lyon, S. R., & DeLong, J. P. (2022). FoRAGE database: A compilation of functional responses for consumers and parasitoids. Ecology, 103(7), e3706. https://doi.org/10.1002/ecy.3706 | In defense of the original Type I functional response: The frequency and population-dynamic effects of feeding on multiple prey at a time | Mark Novak, Kyle Edward Coblentz, John P DeLong | <p>Ecologists differ in the degree to which they consider the linear Type I functional response to be an unrealistic versus sufficient representation of predator feeding rates. Empiricists tend to consider it unsuitably non-mechanistic and theoret... | ![]() | Coexistence, Community ecology, Food webs, Foraging, Population ecology, Theoretical ecology | Frédéric Barraquand | 2024-05-21 03:44:00 | View | |
04 Sep 2019
![]() Gene expression plasticity and frontloading promote thermotolerance in Pocillopora coralsK. Brener-Raffalli, J. Vidal-Dupiol, M. Adjeroud, O. Rey, P. Romans, F. Bonhomme, M. Pratlong, A. Haguenauer, R. Pillot, L. Feuillassier, M. Claereboudt, H. Magalon, P. Gélin, P. Pontarotti, D. Aurelle, G. Mitta, E. Toulza https://doi.org/10.1101/398602Transcriptomics of thermal stress response in coralsRecommended by Staffan Jacob based on reviews by Mar SobralClimate change presents a challenge to many life forms and the resulting loss of biodiversity will critically depend on the ability of organisms to timely respond to a changing environment. Shifts in ecological parameters have repeatedly been attributed to global warming, with the effectiveness of these responses varying among species [1, 2]. Organisms do not only have to face a global increase in mean temperatures, but a complex interplay with another crucial but largely understudied aspect of climate change: thermal fluctuations. Understanding the mechanisms underlying adaptation to thermal fluctuations is thus a timely and critical challenge. References [1] Parmesan, C., & Yohe, G. (2003). A globally coherent fingerprint of climate change impacts across natural systems. Nature, 421(6918), 37–42. doi: 10.1038/nature01286 | Gene expression plasticity and frontloading promote thermotolerance in Pocillopora corals | K. Brener-Raffalli, J. Vidal-Dupiol, M. Adjeroud, O. Rey, P. Romans, F. Bonhomme, M. Pratlong, A. Haguenauer, R. Pillot, L. Feuillassier, M. Claereboudt, H. Magalon, P. Gélin, P. Pontarotti, D. Aurelle, G. Mitta, E. Toulza | <p>Ecosystems worldwide are suffering from climate change. Coral reef ecosystems are globally threatened by increasing sea surface temperatures. However, gene expression plasticity provides the potential for organisms to respond rapidly and effect... | ![]() | Climate change, Evolutionary ecology, Marine ecology, Molecular ecology, Phenotypic plasticity, Symbiosis | Staffan Jacob | 2018-08-29 10:46:55 | View | |
19 Mar 2024
![]() How does dispersal shape the genetic patterns of animal populations in European cities? A simulation approachPaul Savary, Cécile Tannier, Jean-Christophe Foltête, Marc Bourgeois, Gilles Vuidel, Aurélie Khimoun, Hervé Moal, Stéphane Garnier https://doi.org/10.32942/X2JS41Gene flow in the city. Unravelling the mechanisms behind the variability in urbanization effects on genetic patterns.Recommended by Aurélie CoulonWorldwide, city expansion is happening at a fast rate and at the same time, urbanists are more and more required to make place for biodiversity. Choices have to be made regarding the area and spatial arrangement of suitable spaces for non-human living organisms, that will favor the long-term survival of their populations. To guide those choices, it is necessary to understand the mechanisms driving the effects of land management on biodiversity. Research results on the effects of urbanization on genetic diversity have been very diverse, with studies showing higher genetic diversity in rural than in urban populations (e.g. Delaney et al. 2010), the contrary (e.g. Miles et al. 2018) or no difference (e.g. Schoville et al. 2013). The same is true for studies investigating genetic differentiation. The reasons for these differences probably lie in the relative intensities of gene flow and genetic drift in each case study, which are hard to disentangle and quantify in empirical datasets. In their paper, Savary et al. (2024) used an elegant and powerful simulation approach to better understand the diversity of observed patterns and investigate the effects of dispersal limitation on genetic patterns (diversity and differentiation). Their simulations involved the landscapes of 325 real European cities, each under three different scenarios mimicking 3 virtual urban tolerant species with different abilities to move within cities while genetic drift intensity was held constant across scenarios. The cities were chosen so that the proportion of artificial areas was held constant (20%) but their location and shape varied. This design allowed the authors to investigate the effect of connectivity and spatial configuration of habitat on the genetic responses to spatial variations in dispersal in cities. The main results of this simulation study demonstrate that variations in dispersal spatial patterns, for a given level of genetic drift, trigger variations in genetic patterns. Genetic diversity was lower and genetic differentiation was larger when species had more difficulties to move through the more hostile components of the urban environment. The increase of the relative importance of drift over gene flow when dispersal was spatially more constrained was visible through the associated disappearance of the pattern of isolation by resistance. Forest patches (usually located at the periphery of the cities) usually exhibited larger genetic diversity and were less differentiated than urban green spaces. But interestingly, the presence of habitat patches at the interface between forest and urban green spaces lowered those differences through the promotion of gene flow. One other noticeable result, from a landscape genetic method point of view, is the fact that there might be a limit to the detection of barriers to genetic clusters through clustering analyses because of the increased relative effect of genetic drift. This result needs to be confirmed, though, as genetic structure has only been investigated with a recent approach based on spatial graphs. It would be interesting to also analyze those results with the usual Bayesian genetic clustering approaches. Overall, this study addresses an important scientific question about the mechanisms explaining the diversity of observed genetic patterns in cities. But it also provides timely cues for connectivity conservation and restoration applied to cities. Delaney, K. S., Riley, S. P., and Fisher, R. N. (2010). A rapid, strong, and convergent genetic response to urban habitat fragmentation in four divergent and widespread vertebrates. PLoS ONE, 5(9):e12767. | How does dispersal shape the genetic patterns of animal populations in European cities? A simulation approach | Paul Savary, Cécile Tannier, Jean-Christophe Foltête, Marc Bourgeois, Gilles Vuidel, Aurélie Khimoun, Hervé Moal, Stéphane Garnier | <p><em>Context and objectives</em></p> <p>Although urbanization is a major driver of biodiversity erosion, it does not affect all species equally. The neutral genetic structure of populations in a given species is affected by both genetic drift a... | ![]() | Biodiversity, Conservation biology, Dispersal & Migration, Eco-evolutionary dynamics, Human impact, Landscape ecology, Molecular ecology, Population ecology, Spatial ecology, Metacommunities & Metapopulations, Terrestrial ecology | Aurélie Coulon | 2023-07-25 19:09:16 | View | |
01 Apr 2019
![]() The inherent multidimensionality of temporal variability: How common and rare species shape stability patternsJean-François Arnoldi, Michel Loreau, Bart Haegeman https://doi.org/10.1101/431296Diversity-Stability and the Structure of PerturbationsRecommended by Kevin CazellesIn his 1972 paper “Will a Large Complex System Be Stable?” [1], May challenges the idea that large communities are more stable than small ones. This was the beginning of a fundamental debate that still structures an entire research area in ecology: the diversity-stability debate [2]. The most salient strength of May’s work was to use a mathematical argument to refute an idea based on the observations that simple communities are less stable than large ones. Using the formalism of dynamical systems and a major results on the distribution of the eigen values for random matrices, May demonstrated that the addition of random interactions destabilizes ecological communities and thus, rich communities with a higher number of interactions should be less stable. But May also noted that his mathematical argument holds true only if ecological interactions are randomly distributed and thus concluded that this must not be true! This is how the contradiction between mathematics and empirical observations led to new developments in the study of ecological networks. References [1] May, Robert M (1972). Will a Large Complex System Be Stable? Nature 238, 413–414. doi: 10.1038/238413a0 | The inherent multidimensionality of temporal variability: How common and rare species shape stability patterns | Jean-François Arnoldi, Michel Loreau, Bart Haegeman | <p>Empirical knowledge of ecosystem stability and diversity-stability relationships is mostly based on the analysis of temporal variability of population and ecosystem properties. Variability, however, often depends on external factors that act as... | ![]() | Biodiversity, Coexistence, Community ecology, Competition, Interaction networks, Theoretical ecology | Kevin Cazelles | 2018-10-02 14:01:03 | View | |
20 Jan 2025
![]() Regional and local variability in the morphometric traits of two emblematic seagrass species (Zostera marina and Zostera noltei) along the French coastÉlise Lacoste, Aurélien Boyé, Aline Blanchet-Aurigny, Nicolas Desroy, Isabelle Auby, Touria Bajjouk, Constance Bourdier, Nicolas Cimiterra, Céline Cordier, Amélia Curd, Lauriane Derrien, Élodie Foucault, Jean-Dominique Gaffet, Florian Ganthy, Loic Rigouin, Claire Rollet, Laura Soissons, Aurélien Tancray, Vincent Ouisse https://doi.org/10.5281/zenodo.10427767Importance of Scale Considerations in Understanding Seagrass DynamicsRecommended by Antoine VernaySeagrasses, particularly Zostera species, have been the subject of numerous studies due to their widespread distribution across the globe (Short et al., 2007), yet they have been in decline for several years as a result of global environmental changes (Touchette, 2007). While case studies and regional studies have been conducted, there remains a lack of information on how to scale these findings, particularly because of the heterogeneous nature of these habitats. In their study, Lacoste et al. examine the ecosystem trajectories of two Zostera species along a regional gradient spanning sites in the English Channel, the Atlantic Ocean, and the Mediterranean Sea. Their research is based on a recently published database, which offers valuable insights for comparing with other studies and serves as a resource for addressing future questions (Lacoste et al., 2024). This underscores the need for a global database to facilitate the integration of functional responses across studies, thus advancing our understanding of Zostera ecology on a larger scale. The multi-trait approach employed in their study provides a comprehensive view of population dynamics over a 1.5-year period, covering different seasons. Such studies highlight the complex responses of Zostera populations when considering environmental, seasonal, and geographical heterogeneity. Understanding these dynamics raises important questions about modeling, particularly in relation to the development of a more global database as previously mentioned. However, the review process has pointed out that the environmental data should be further refined to more rigorously support the presented results. Some statistical analyses could also benefit from improvements to ensure clearer and more explicit conclusions. These concerns are related to the challenges of sampling, the time required for such efforts, and the need to account for spatiotemporal variability. This study could serve as a foundational step for advancing our understanding of Zostera population dynamics on a global scale. In my opinion, despite the large ongoing scientific efforts, upscaling remains one of the major challenges for functional ecologists (Wood et al., 2024), particularly when plant habitats exhibit the kind of heterogeneity seen in Zostera, as demonstrated by Lacoste et al. in their work. References Élise Lacoste, Aurélien Boyé, Aline Blanchet-Aurigny, Nicolas Desroy, Isabelle Auby, Touria Bajjouk, Constance Bourdier, Nicolas Cimiterra, Céline Cordier, Amélia Curd, Lauriane Derrien, Élodie Foucault, Jean-Dominique Gaffet, Florian Ganthy, Loic Rigouin, Claire Rollet, Laura Soissons, Aurélien Tancray, Vincent Ouisse (2024) Regional and local variability in the morphometric traits of two emblematic seagrass species (Zostera marina and Zostera noltei) along the French coast. Zenodo, ver.3 peer-reviewed and recommended by PCI Ecology https://doi.org/10.5281/zenodo.10427767 Lacoste, E., Ouisse, V., Nicolas, D., Allano, L., Auby, I., Bajjouk, T., Bourdier, C., Caisey, X., de Casamajor, M.-N., Cimiterra, N., Cordier, C., Curd, A., Derrien, L., Droual, G., Dubois, F. S., Foucault, E., Foveau, A., Gaffet, J.-D., Ganthy, F., … Blanchet-Aurigny, A. (2024). A dataset of Zostera marina and Zostera noltei structure and functioning in four sites along the French coast over a period of 18 months. https://doi.org/10.5281/zenodo.14174128 Short, F., Carruthers, T., Dennison, W., & Waycott, M. (2007). Global seagrass distribution and diversity : A bioregional model. Journal of Experimental Marine Biology and Ecology, 350(1), 3‑20. https://doi.org/10.1016/j.jembe.2007.06.012 Touchette, B. W. (2007). The biology and ecology of seagrasses. Journal of Experimental Marine Biology and Ecology, 350(1), 1‑2. https://doi.org/10.1016/j.jembe.2007.06.013 Wood, G. V., Filbee-Dexter, K., Coleman, M. A., Valckenaere, J., Aguirre, J. D., Bentley, P. M., Carnell, P., Dawkins, P. D., Dykman, L. N., Earp, H. S., Ennis, L. B., Francis, P., Franco, J. N., Hayford, H., Lamb, J. B., Ling, S. D., Layton, C., Lis, E., Masters, B., … Wernberg, T. (2024). Upscaling marine forest restoration : Challenges, solutions and recommendations from the Green Gravel Action Group. Frontiers in Marine Science, 11. https://doi.org/10.3389/fmars.2024.1364263 | Regional and local variability in the morphometric traits of two emblematic seagrass species (*Zostera marina* and *Zostera noltei*) along the French coast | Élise Lacoste, Aurélien Boyé, Aline Blanchet-Aurigny, Nicolas Desroy, Isabelle Auby, Touria Bajjouk, Constance Bourdier, Nicolas Cimiterra, Céline Cordier, Amélia Curd, Lauriane Derrien, Élodie Foucault, Jean-Dominique Gaffet, Florian Ganthy, Loic... | <p><em>Z</em>Zostera marina and Zostera noltei are two foundation species that play a crucial role in the functioning of coastal ecosystems. They occur in a wide range of environmental conditions over a large geographical area in the northern hemi... | ![]() | Biogeography, Community ecology, Ecosystem functioning, Marine ecology, Morphometrics, Population ecology | Antoine Vernay | 2023-12-23 15:13:57 | View | |
05 Feb 2020
![]() A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcodingMiriam I Brandt, Blandine Trouche, Laure Quintric, Patrick Wincker, Julie Poulain, Sophie Arnaud-Haond https://doi.org/10.1101/717355A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcodingRecommended by Stefaniya KamenovaHigh-throughput sequencing-based techniques such as DNA metabarcoding are increasingly advocated as providing numerous benefits over morphology‐based identifications for biodiversity inventories and ecosystem biomonitoring [1]. These benefits are particularly apparent for highly-diversified and/or hardly accessible aquatic and marine environments, where simple water or sediment samples could already produce acceptably accurate biodiversity estimates based on the environmental DNA present in the samples [2,3]. However, sequence-based characterization of biodiversity comes with its own challenges. A major one resides in the capacity to disentangle true biological diversity (be it taxonomic or genetic) from artefactual diversity generated by sequence-errors accumulation during PCR and sequencing processes, or from the amplification of non-target genes (i.e. pseudo-genes). On one hand, the stringent elimination of sequence variants might lead to biodiversity underestimation through the removal of true species, or the clustering of closely-related ones. On the other hand, a more permissive sequence filtering bears the risks of biodiversity inflation. Recent studies have outlined an excellent methodological framework for addressing this issue by proposing bioinformatic tools that allow the amplicon-specific error-correction as alternative or as complement to the more arbitrary approach of clustering into Molecular Taxonomic Units (MOTUs) based on sequence dissimilarity [4,5]. But to date, the relevance of amplicon-specific error-correction tools has been demonstrated only for a limited set of taxonomic groups and gene markers. References [1] Porter, T. M., and Hajibabaei, M. (2018). Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis. Molecular Ecology, 27(2), 313–338. doi: 10.1111/mec.14478 | A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcoding | Miriam I Brandt, Blandine Trouche, Laure Quintric, Patrick Wincker, Julie Poulain, Sophie Arnaud-Haond | <p>Environmental metabarcoding is an increasingly popular tool for studying biodiversity in marine and terrestrial biomes. With sequencing costs decreasing, multiple-marker metabarcoding, spanning several branches of the tree of life, is becoming ... | ![]() | Biodiversity, Community ecology, Marine ecology, Molecular ecology | Stefaniya Kamenova | 2019-08-02 20:52:45 | View |
FOLLOW US
MANAGING BOARD
Julia Astegiano
Tim Coulson
Vasilis Dakos
Anna Eklof
Dominique Gravel
François Massol
Ben Phillips
Cyrille Violle