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Id | Title * ▼ | Authors * | Abstract * | Picture * | Thematic fields * | Recommender | Reviewers | Submission date | |
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14 Jun 2024
Hierarchizing multi-scale environmental effects on agricultural pest population dynamics: a case study on the annual onset of Bactrocera dorsalis population growth in Senegalese orchardsCécile Caumette, Paterne Diatta, Sylvain Piry, Marie-Pierre Chapuis, Emile Faye, Fabio Sigrist, Olivier Martin, Julien Papaïx, Thierry Brévault, Karine Berthier https://doi.org/10.1101/2023.11.10.566583Uncovering the ecology in big-data by hierarchizing multi-scale environmental effectsRecommended by Elodie Vercken based on reviews by Kévin Tougeron and Jianqiang SunAlong with the generalization of open-access practices, large, heterogeneous datasets are becoming increasingly available to ecologists (Farley et al. 2018). While such data offer exciting opportunities for unveiling original patterns and trends, they also raise new challenges regarding how to extract relevant information and actually improve our knowledge of complex ecological systems, beyond purely descriptive correlations (Dietze 2017, Farley et al. 2018). In this work, Caumette et al. (2024) develop an original ecoinformatics approach to relate multi-scale environmental factors to the temporal dynamics of a major pest in mango orchards. Their method relies on the recent tree-boosting method GPBoost (Sigrist 2022) to hierarchize the influence of environmental factors of heterogeneous nature (e.g., orchard composition and management; landscape structure; climate) on the emergence date of the oriental fruit fly, Bactrocera dorsalis. As boosting methods allows the analysis of high-dimensional data, they are particularly adapted to the exploration of such datasets, to uncover unexpected, potentially complex dependencies between ecological dynamics and multiple environmental factors (Farley et al. 2018). In this article, Caumette et al. (2024) make a special effort to guide the reader step by step through their complex analysis pipeline to make it broadly understandable to the average ecologist, which is no small feat. I particularly welcome this commitment, as making new, cutting-edge analytical methods accessible to a large community of science practitioners with varying degrees of statistical or programming expertise is a major challenge for the future of quantitative ecology. The main result of Caumette et al. (2024) is that temperature and humidity conditions both at the local and regional scales are the main predictors of B. dorsalis emergence date, while orchard management practices seem to have relatively little influence. This suggests that favourable climatic conditions may allow the persistence of small populations of B. dorsalis over the dry season, which may then act as a propagule source for early re-infestations. However, as the authors explain, the resulting regression model is not designed for predictive purposes and should not at this stage be used for decision-making in pest management. Its main interest rather resides in identifying potential key factors favoring early infestations of B. dorsalis, and help focusing future experimental field studies on the most relevant levers for integrated pest management in mango orchards. In a wider perspective, this work also provides a convincing proof-of-concept for the use of boosting methods to identify the most influential factors in large, multivariate datasets in a variety of ecological systems. It is also crucial to keep in mind that the current exponential growth in high-throughput environmental data (Lucivero 2020) could quickly come into conflict with the need to reduce the environmental footprint of research (Mariette et al. 2022). In this context, robust and accessible methods for extracting and exploiting all the information available in already existing datasets might prove essential to a sustainable pursuit of science. References Dietze MC. 2017. Ecological Forecasting. Princeton University Press Mariette J, Blanchard O, Berné O, Aumont O, Carrey J, Ligozat A-L, Lellouch E, Roche P-E, Guennebaud G, Thanwerdas J, Bardou P, Salin G, Maigne E, Servan S, Ben-Ari T 2022. An open-source tool to assess the carbon footprint of research. Environmental Research: Infrastructure and Sustainability, 2022. https://dx.doi.org/10.1088/2634-4505/ac84a4 | Hierarchizing multi-scale environmental effects on agricultural pest population dynamics: a case study on the annual onset of *Bactrocera dorsalis* population growth in Senegalese orchards | Cécile Caumette, Paterne Diatta, Sylvain Piry, Marie-Pierre Chapuis, Emile Faye, Fabio Sigrist, Olivier Martin, Julien Papaïx, Thierry Brévault, Karine Berthier | <p>Implementing integrated pest management programs to limit agricultural pest damage requires an understanding of the interactions between the environmental variability and population demographic processes. However, identifying key environmental ... | Demography, Landscape ecology, Statistical ecology | Elodie Vercken | 2023-12-11 17:02:08 | View | ||
07 Aug 2023
Heather pollen is not necessarily a healthy diet for bumble beesClément Tourbez, Irène Semay, Apolline Michel, Denis Michez, Pascal Gerbaux, Antoine Gekière, Maryse Vanderplanck https://doi.org/10.5281/zenodo.8192036The importance of understanding bee nutritionRecommended by Ignasi Bartomeus based on reviews by Cristina Botías and 1 anonymous reviewerContrasting with the great alarm on bee declines, it is astonishing how little basic biology we know about bees, including on abundant and widespread species that are becoming model species. Plant-pollinator relationships are one of the cornerstones of bee ecology, and researchers are increasingly documenting bees' diets. However, we rarely know which effects feeding on different flowers has on bees' health. This paper (Tourbez et al. 2023) uses an elegant experimental setting to test the effect of heather pollen on bumblebees' (Bombus terrestris) reproductive success. This is a timely question as heather is frequently used by bumblebees, and its nectar has been reported to reduce parasite infections. In fact, it has been suggested that bumblebees can medicate themselves when infected (Richardson et al. 2014), and the pollen of some Asteraceae has been shown to help them fight parasites (Gekière et al. 2022). The starting hypothesis is that heather pollen contains flavonoids that might have a similar effect. Unfortunately, Tourbez and collaborators do not support this hypothesis, showing a negative effect of heather pollen, in particular its flavonoids, in bumblebees offspring, and an increase in parasite loads when fed on flavonoids. This is important because it challenges the idea that many pollen and nectar chemical compounds might have a medicinal use, and force us to critically analyze the effect of chemical compounds in each particular case. The results open several questions, such as why bumblebees collect heather pollen, or in which concentrations or pollen mixes it is deleterious. A limitation of the study is that it uses micro-colonies, and extrapolating this to real-world conditions is always complex. Understanding bee declines require a holistic approach starting with bee physiology and scaling up to multispecies population dynamics. References Gekière, A., Semay, I., Gérard, M., Michez, D., Gerbaux, P., & Vanderplanck, M. 2022. Poison or Potion: Effects of Sunflower Phenolamides on Bumble Bees and Their Gut Parasite. Biology, 11(4), 545. https://doi.org/10.3390/biology11040545 Richardson, L.L., Adler, L.S., Leonard, A.S., Andicoechea, J., Regan, K.H., Anthony, W.E., Manson, J.S., & Irwin, R.E. 2015. Secondary metabolites in floral nectar reduce parasite infections in bumblebees. Proceedings of the Royal Society of London B: Biological Sciences 282 (1803), 20142471. https://doi.org/10.1098/rspb.2014.2471 Tourbez, C., Semay, I., Michel, A., Michez, D., Gerbaux, P., Gekière A. & Vanderplanck, M. 2023. Heather pollen is not necessarily a healthy diet for bumble bees. Zenodo, ver 3, reviewed and recommended by PCI Ecology. https://doi.org/10.5281/zenodo.8192036 | Heather pollen is not necessarily a healthy diet for bumble bees | Clément Tourbez, Irène Semay, Apolline Michel, Denis Michez, Pascal Gerbaux, Antoine Gekière, Maryse Vanderplanck | <p>There is evidence that specialised metabolites of flowering plants occur in both vegetative parts and floral resources (i.e., pollen and nectar), exposing pollinators to their biological activities. While such metabolites may be toxic to bees, ... | Botany, Chemical ecology, Host-parasite interactions, Pollination, Zoology | Ignasi Bartomeus | 2023-04-10 21:22:34 | View | ||
07 Oct 2024
Guidance framework to apply best practices in ecological data analysis: Lessons learned from building Galaxy-EcologyColine Royaux, Jean-Baptiste Mihoub, Marie Jossé, Dominique Pelletier, Olivier Norvez, Yves Reecht, Anne Fouilloux, Helena Rasche, Saskia Hiltemann, Bérénice Batut, Marc Eléaume, Pauline Seguineau, Guillaume Massé, Alan Amossé, Claire Bissery, Romain Lorrilliere, Alexis Martin, Yves Bas, Thimothée Virgoulay, Valentin Chambon, Elie Arnaud, Elisa Michon, Clara Urfer, Eloïse Trigodet, Marie Delannoy, Gregoire Loïs, Romain Julliard, Björn Grüning, Yvan Le Bras https://doi.org/10.32942/X2G033Best practices for ecological analysis are required to act on concrete challengesRecommended by Timothée Poisot based on reviews by Nick Isaac and 1 anonymous reviewerA core challenge facing ecologists is to work through an ever-increasing amount of data. The accelerating decline in biodiversity worldwide, mounting pressure of anthropogenic impacts, and increasing demand for actionable indicators to guide effective policy means that monitoring will only intensify, and rely on tools that can generate even more information (Gonzalez et al., 2023). How, then, do we handle this new volume and diversity of data? This is the question Royaux et al. (2024) are tackling with their contribution. By introducing both a conceptual ("How should we think about our work?") and an operational ("Here is a tool to do our work with") framework, they establish a series of best practices for the analysis of ecological data. It is easy to think about best practices in ecological data analysis in its most proximal form: is it good statistical practice? Is the experimental design correct? These have formed the basis of many recommendations over the years (see e.g. Popovic et al., 2024, for a recent example). But the contribution of Royaux et al. focuses on a different part of the analysis pipeline: the computer science (and software engineering) aspect of it. As data grows in volume and complexity, the code needed to handle it follows the same trend. It is not a surprise, therefore, to see that the demand for programming skills in ecologists has doubled recently (Feng et al., 2020), prompting calls to make computational literacy a core component of undergraduate education (Farrell & Carrey, 2018). But beyond training, an obvious way to make computational analysis ecological data more reliable and effective is to build better tools. This is precisely what Royaux et al. have achieved. They illustrate their approach through their experience building Galaxy-Ecology, a computing environment for ecological analysis: by introducing a clear taxonomy of computing concepts (data exploration, pre-processing, analysis, representation), with a hierarchy between them (formatting, data correction, anonymization), they show that we can think about the pipeline going from data to results in a way that is more systematized, and therefore more prone to generalization. We may buckle at the idea of yet another ontology, or yet another framework, for our work, but I am convinced that the work of Royaux et al. is precisely what our field needs. Because their levels of atomization (their term for the splitting of complex pipelines into small, single-purpose tasks) are easy to understand, and map naturally onto tasks that we already perform, it is likely to see wide adoption. Solving the big, existential challenges of monitoring and managing biodiversity at the global scale requires the adoption of good practices, and a tool like Galaxy-Ecology goes a long way towards this goal. References Farrell, K.J., and Carey, C.C. (2018). Power, pitfalls, and potential for integrating computational literacy into undergraduate ecology courses. Ecol. Evol. 8, 7744-7751. Feng, X., Qiao, H., and Enquist, B. (2020). Doubling demands in programming skills call for ecoinformatics education. Frontiers in Ecology and the Environment 18, 123-124. | Guidance framework to apply best practices in ecological data analysis: Lessons learned from building Galaxy-Ecology | Coline Royaux, Jean-Baptiste Mihoub, Marie Jossé, Dominique Pelletier, Olivier Norvez, Yves Reecht, Anne Fouilloux, Helena Rasche, Saskia Hiltemann, Bérénice Batut, Marc Eléaume, Pauline Seguineau, Guillaume Massé, Alan Amossé, Claire Bissery, Rom... | <p>Numerous conceptual frameworks exist for best practices in research data and analysis (e.g. Open Science and FAIR principles). In practice, there is a need for further progress to improve transparency, reproducibility, and confidence in ecology... | Statistical ecology | Timothée Poisot | 2024-04-12 10:13:59 | View | ||
13 May 2024
Getting More by Asking for Less: Linking Species Interactions to Species Co-Distributions in MetacommunitiesMatthieu Barbier, Guy Bunin, Mathew A. Leibold https://doi.org/10.1101/2023.06.04.543606Beyond pairwise species interactions: coarser inference of their joined effects is more relevantRecommended by François Munoz based on reviews by Frederik De Laender, Hao Ran Lai and Malyon BimlerBarbier et al. (2024) investigated the dynamics of species abundances depending on their ecological niche (abiotic component) and on (numerous) competitive interactions. In line with previous evidence and expectations (Barbier et al. 2018), the authors show that it is possible to robustly infer the mean and variance of interaction coefficients from species co-distributions, while it is not possible to infer the individual coefficient values. The authors devised a simulation framework representing multispecies dynamics in an heterogeneous environmental context (2D grid landscape). They used a Lotka-Volterra framework involving pairwise interaction coefficients and species-specific carrying capacities. These capacities depend on how well the species niche matches the local environmental conditions, through a Gaussian function of the distance of the species niche centers to the local environmental values. They considered two contrasted scenarios denoted as « Environmental tracking » and « Dispersal limited ». In the latter case, species are initially seeded over the environmental grid and cannot disperse to other cells, while in the former case they can disperse and possibly be more performant in other cells. The direct effects of species on one another are encoded in an interaction matrix A, and the authors further considered net interactions depending on the inverse of the matrix of direct interactions (Zelnik et al., 2024). The net effects are context-dependent, i.e., it involves the environment-dependent biotic capacities, even through the interaction terms can be defined between species as independent from local environment. The results presented here underline that the outcome of many individual competitive interactions can only be understood in terms of macroscopic properties. In essence, the results here echoe the mean field theories that investigate the dynamics of average ecological properties instead of the microscopic components (e.g., McKane et al. 2000). In a philosophical perspective, community ecology has long struggled with analyzing and inferring local determinants of species coexistence from species co-occurrence patterns, so that it was claimed that no universal laws can be derived in the discipline (Lawton 1999). Using different and complementary methods and perspectives, recent research has also shown that species assembly parameter values cannot be unambiguously inferred from species co-occurrences only, even in simple designs where an equilibrium can be reached (Poggiato et al. 2021). Although the roles of high-order competitive interactions and intransivity can lead to species coexistence, the simple view of a single loop of competitive interactions is easily challenged when further interactions and complexity is added (Gallien et al. 2024). But should we put so much emphasis on inferring individual interaction coefficients? In a quest to understand the emerging properties of elementary processes, ecological theory could go forward with a more macroscopic analysis and understanding of species coexistence in many communities. The authors referred several times to an interesting paper from Schaffer (1981), entitled « Ecological abstraction: the consequences of reduced dimensionality in ecological models ». It proposes that estimating individual species competition coefficients is not possible, but that competition can be assessed at the coarser level of organisation, i.e., between ecological guilds. This idea implies that the dimensionality of the competition equations should be greatly reduced to become tractable in practice. Taking together this claim with the results of the present Barbier et al. (2024) paper, it becomes clearer that the nature of competitive interactions can be addressed through « abstracted » quantities, as those of guilds or the moments of the individual competition coefficients (here the average and the standard deviation). Therefore the scope of Barbier et al. (2024) framework goes beyond statistical issues in parameter inference, but question the way we must think and represent the numerous competitive interactions in a simplified and robust way. References Barbier, Matthieu, Jean-François Arnoldi, Guy Bunin, et Michel Loreau. 2018. « Generic assembly patterns in complex ecological communities ». Proceedings of the National Academy of Sciences 115 (9): 2156‑61. https://doi.org/10.1073/pnas.1710352115 | Getting More by Asking for Less: Linking Species Interactions to Species Co-Distributions in Metacommunities | Matthieu Barbier, Guy Bunin, Mathew A. Leibold | <p>AbstractOne of the more difficult challenges in community ecology is inferring species interactions on the basis of patterns in the spatial distribution of organisms. At its core, the problem is that distributional patterns reflect the ‘realize... | Biogeography, Community ecology, Competition, Spatial ecology, Metacommunities & Metapopulations, Species distributions, Statistical ecology, Theoretical ecology | François Munoz | 2023-10-21 14:14:16 | 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 | ||
20 Feb 2024
Functional trade-offs: exploring the temporal response of field margin plant communities to climate change and agricultural practicesIsis Poinas, Christine N Meynard, Guillaume Fried https://doi.org/10.1101/2023.03.03.530956Unravelling plant diversity in agricultural field margins in France: plant species better adapted to climate change need other agricultures to persistRecommended by Julia Astegiano based on reviews by Ignasi Bartomeus, Clélia Sirami and Diego GurvichAgricultural field margin plants, often referred to as “spontaneous” species, are key for the stabilization of several social-ecological processes related to crop production such as pollination or pest control (Tamburini et al. 2020). Because of its beneficial function, increasing the diversity of field margin flora becomes as important as crop diversity in process-based agricultures such as agroecology. Contrary, supply-dependent intensive agricultures produce monocultures and homogenized environments that might benefit their productivity, which generally includes the control or elimination of the field margin flora (Emmerson et al. 2016, Aligner 2018). Considering that different agricultural practices are produced by (and produce) different territories (Moore 2020) and that they are also been shaped by current climate change, we urgently need to understand how agricultural intensification constrains the potential of territories to develop agriculture more resilient to such change (Altieri et al., 2015). Thus, studies unraveling how agricultural practices' effects on agricultural field margin flora interact with those of climate change is of main importance, as plant strategies better adapted to such social-ecological processes may differ. References Alignier, A., 2018. Two decades of change in a field margin vegetation metacommunity as a result of field margin structure and management practice changes. Agric., Ecosyst. & Environ., 251, 1–10. https://doi.org/10.1016/j.agee.2017.09.013 Altieri, M.A., Nicholls, C.I., Henao, A., Lana, M.A., 2015. Agroecology and the design of climate change-resilient farming systems. Agron. Sustain. Dev. 35, 869–890. https://doi.org/10.1007/s13593-015-0285-2 Emmerson, M., Morales, M. B., Oñate, J. J., Batary, P., Berendse, F., Liira, J., Aavik, T., Guerrero, I., Bommarco, R., Eggers, S., Pärt, T., Tscharntke, T., Weisser, W., Clement, L. & Bengtsson, J. (2016). How agricultural intensification affects biodiversity and ecosystem services. In Adv. Ecol. Res. 55, 43-97. https://doi.org/10.1016/bs.aecr.2016.08.005 Grime, J. P., 1977. Evidence for the existence of three primary strategies in plants and its relevance to ecological and evolutionary theory. The American Naturalist, 111(982), 1169–1194. https://doi.org/10.1086/283244 Grime, J. P., 1988. The C-S-R model of primary plant strategies—Origins, implications and tests. In L. D. Gottlieb & S. K. Jain, Plant Evolutionary Biology (pp. 371–393). Springer Netherlands. https://doi.org/10.1007/978-94-009-1207-6_14 Moore, J., 2020. El capitalismo en la trama de la vida (Capitalism in The Web of Life). Traficantes de sueños, Madrid, Spain. Poinas, I., Fried, G., Henckel, L., & Meynard, C. N., 2023. Agricultural drivers of field margin plant communities are scale-dependent. Bas. App. Ecol. 72, 55-63. https://doi.org/10.1016/j.baae.2023.08.003 Poinas, I., Meynard, C. N., Fried, G., 2024. Functional trade-offs: exploring the temporal response of field margin plant communities to climate change and agricultural practices, bioRxiv, ver. 4 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2023.03.03.530956 Tamburini, G., Bommarco, R., Wanger, T.C., Kremen, C., Van Der Heijden, M.G., Liebman, M., Hallin, S., 2020. Agricultural diversification promotes multiple ecosystem services without compromising yield. Sci. Adv. 6, eaba1715. https://doi.org/10.1126/sciadv.aba1715 | Functional trade-offs: exploring the temporal response of field margin plant communities to climate change and agricultural practices | Isis Poinas, Christine N Meynard, Guillaume Fried | <p style="text-align: justify;">Over the past decades, agricultural intensification and climate change have led to vegetation shifts. However, functional trade-offs linking traits responding to climate and farming practices are rarely analyzed, es... | Agroecology, Biodiversity, Botany, Climate change, Community ecology | Julia Astegiano | 2023-03-04 15:40:35 | View | ||
24 Jan 2023
Four decades of phenology in an alpine amphibian: trends, stasis, and climatic driversOmar Lenzi, Kurt Grossenbacher, Silvia Zumbach, Beatrice Luescher, Sarah Althaus, Daniela Schmocker, Helmut Recher, Marco Thoma, Arpat Ozgul, Benedikt R. Schmidt https://doi.org/10.1101/2022.08.16.503739Alpine ecology and their dynamics under climate changeRecommended by Sergio Estay based on reviews by Nigel Yoccoz and 1 anonymous reviewerResearch about the effects of climate change on ecological communities has been abundant in the last decades. In particular, studies about the effects of climate change on mountain ecosystems have been key for understanding and communicating the consequences of this global phenomenon. Alpine regions show higher increases in warming in comparison to low-altitude ecosystems and this trend is likely to continue. This warming has caused reduced snowfall and/or changes in the duration of snow cover. For example, Notarnicola (2020) reported that 78% of the world’s mountain areas have experienced a snow cover decline since 2000. In the same vein, snow cover has decreased by 10% compared with snow coverage in the late 1960s (Walther et al., 2002) and snow cover duration has decreased at a rate of 5 days/decade (Choi et al., 2010). These changes have impacted the dynamics of high-altitude plant and animal populations. Some impacts are changes in the hibernation of animals, the length of the growing season for plants and the soil microbial composition (Chávez et al. 2021). Lenzi et al. (2023), give us an excellent study using long-term data on alpine amphibian populations. Authors show how climate change has impacted the reproductive phenology of Bufo bufo, especially the breeding season starts 30 days earlier than ~40 years ago. This earlier breeding is associated with the increasing temperatures and reduced snow cover in these alpine ecosystems. However, these changes did not occur in a linear trend but a marked acceleration was observed until mid-1990s with a later stabilization. Authors associated these nonlinear changes with complex interactions between the global trend of seasonal temperatures and site-specific conditions. Beyond the earlier breeding season, changes in phenology can have important impacts on the long-term viability of alpine populations. Complex interactions could involve positive and negative effects like harder environmental conditions for propagules, faster development of juveniles, or changes in predation pressure. This study opens new research opportunities and questions like the urgent assessment of the global impact of climate change on animal fitness. This study provides key information for the conservation of these populations. References Chávez RO, Briceño VF, Lastra JA, Harris-Pascal D, Estay SA (2021) Snow Cover and Snow Persistence Changes in the Mocho-Choshuenco Volcano (Southern Chile) Derived From 35 Years of Landsat Satellite Images. Frontiers in Ecology and Evolution, 9. https://doi.org/10.3389/fevo.2021.643850 Choi G, Robinson DA, Kang S (2010) Changing Northern Hemisphere Snow Seasons. Journal of Climate, 23, 5305–5310. https://doi.org/10.1175/2010JCLI3644.1 Lenzi O, Grossenbacher K, Zumbach S, Lüscher B, Althaus S, Schmocker D, Recher H, Thoma M, Ozgul A, Schmidt BR (2022) Four decades of phenology in an alpine amphibian: trends, stasis, and climatic drivers.bioRxiv, 2022.08.16.503739, ver. 3 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2022.08.16.503739 Notarnicola C (2020) Hotspots of snow cover changes in global mountain regions over 2000–2018. Remote Sensing of Environment, 243, 111781. https://doi.org/10.1016/j.rse.2020.111781 | Four decades of phenology in an alpine amphibian: trends, stasis, and climatic drivers | Omar Lenzi, Kurt Grossenbacher, Silvia Zumbach, Beatrice Luescher, Sarah Althaus, Daniela Schmocker, Helmut Recher, Marco Thoma, Arpat Ozgul, Benedikt R. Schmidt | <p style="text-align: justify;">Strong phenological shifts in response to changes in climatic conditions have been reported for many species, including amphibians, which are expected to breed earlier. Phenological shifts in breeding are observed i... | Climate change, Population ecology, Zoology | Sergio Estay | Anonymous, Nigel Yoccoz | 2022-08-18 08:25:21 | View | |
29 Aug 2024
Flexible reproductive seasonality in Africa-dwelling papionins is associated with low environmental productivity and high climatic unpredictabilityJules Dezeure, Julie Dagorrette, Lugdiwine Burtschell, Shahrina Chowdhury, Dieter Lukas, Larissa Swedell, Elise Huchard https://doi.org/10.1101/2024.05.01.591991Reproductive flexibility shapes primate survival in a changing climate driven by environmental unpredictabilityRecommended by Cédric Sueur based on reviews by 2 anonymous reviewersAs seasonal cycles become increasingly disrupted, our understanding of the ecology and evolution of reproductive seasonality in tropical vertebrates remains limited (Bronson 2009). To predict how changes in seasonality might impact these animals, it is crucial to identify which elements of their varied reproductive patterns are connected to the equally varied patterns of rainfall seasonality (within-year fluctuations) or the significant climatic unpredictability (year-to-year variations) characteristic of the intertropical region. Dezeure et al. (2024) provide a comprehensive examination of reproductive seasonality in papionin monkeys across diverse African environments. By investigating the ecological and evolutionary determinants of reproductive timing, the authors offer novel insights into how climatic factors, particularly environmental unpredictability, shape reproductive strategies in these primates. This study stands out not only for its methodological rigour but also for its contribution to our understanding of how primates adapt their reproductive behaviours to varying environmental pressures. The findings have broad implications, particularly in the context of ongoing climate change, which is expected to increase environmental unpredictability globally. The innovative approach of this paper lies in its multifaceted examination of reproductive seasonality, which integrates data from 21 wild populations of 11 papionin species. The study employs a robust statistical framework, incorporating Bayesian phylogenetic generalised linear mixed models to control for phylogenetic relatedness among species. This methodological choice is crucial because it allows the authors to disentangle the effects of environmental variables from evolutionary history, providing a more accurate picture of how current ecological factors influence reproductive strategies. The study’s focus on environmental unpredictability as a determinant of reproductive seasonality is particularly noteworthy. While previous research has established the importance of environmental seasonality (Janson and Verdolin 2005), this paper breaks new ground by showing that the magnitude of year-to-year variation in rainfall – rather than just the seasonal distribution of rainfall – plays a critical role in determining the intensity of reproductive seasonality. This finding is supported by the significant negative correlation between reproductive seasonality and environmental unpredictability, which the authors demonstrate across multiple populations and species. The results of this study are important for several reasons. First, they challenge the traditional view that reproductive seasonality is primarily driven by within-year environmental fluctuations. By showing that inter-annual variability in rainfall is a stronger predictor of reproductive timing than intra-annual variability, the authors suggest that primates, like papionins, have evolved flexible reproductive strategies to cope with the unpredictable availability of resources. This flexibility is likely an adaptive response to the highly variable environments that many African primates inhabit, where food availability can vary dramatically not just within a year but from year to year. Second, the study highlights the role of reproductive flexibility in the evolutionary success of papionins. The authors provide compelling evidence that species within the Papio genus, for example, exhibit significant variability in reproductive timing both within and between populations. This variability suggests that these species possess a remarkable ability to adjust their reproductive strategies in response to local environmental conditions, which may have contributed to their widespread distribution across diverse habitats in Africa. This finding aligns with the work of Brockman and Schaik (2005), who argued that reproductive flexibility is a key factor in the success of primates in unpredictable environments. The study also contributes to our understanding of the evolutionary transition from seasonal to non-seasonal breeding in primates. The authors propose that the loss of strict reproductive seasonality in some papionin species may represent an adaptive shift toward greater reproductive flexibility. This shift could be driven by the need to maximise reproductive success in environments where the timing of resource peaks is difficult to predict. The authors’ findings support this hypothesis, as they show that populations living in more unpredictable environments tend to have lower reproductive seasonality. The broader implications of this study (Dezeure et al. 2024) extend beyond the specific case of papionin monkeys. The findings have relevance for the study of reproductive strategies in other long-lived, tropical mammals that face similar environmental challenges. As climate change is expected to increase the frequency and intensity of environmental unpredictability, understanding how species have historically adapted to such conditions can provide valuable insights into their potential resilience or vulnerability to future changes. Many primate species are already facing significant threats from habitat loss, hunting, and climate change. By identifying the environmental factors that influence reproductive success, Dezeure et al. (2024) study can help inform conservation strategies aimed at protecting the most vulnerable populations. For example, conservation efforts could focus on maintaining or restoring habitat features that promote reproductive flexibility, such as access to a variety of food resources that peak at different times of the year (Chapman et al.). References Brockman D, Schaik C (2005) Seasonality in Primates: Studies of Living and Extinct Human and Non-Human Primates. Cambridge University Press. https://doi.org/10.1017/CBO9780511542343 Bronson FH (2009) Climate change and seasonal reproduction in mammals. Philos Trans R Soc B Biol Sci 364:3331–3340. https://doi.org/10.1098/rstb.2009.0140 Chapman CA, Gogarten JF, Golooba M, et al Fifty+ years of primate research illustrates complex drivers of abundance and increasing primate numbers. Am J Primatol n/a:e23577. https://doi.org/10.1002/ajp.23577 Jules Dezeure, Julie Dagorrette, Lugdiwine Burtschell, Shahrina Chowdhury, Dieter Lukas, Larissa Swedell, Elise Huchard (2024) Flexible reproductive seasonality in Africa-dwelling papionins is associated with low environmental productivity and high climatic unpredictability. bioRxiv, ver.2 peer-reviewed and recommended by PCI Ecology https://doi.org/10.1101/2024.05.01.591991 Janson C, Verdolin J (2005) Seasonality of primate births in relation to climate. In: Schaik CP van, Brockman DK (eds) Seasonality in Primates: Studies of Living and Extinct Human and Non-Human Primates. Cambridge University Press, Cambridge, pp 307–350 https://doi.org/10.1017/CBO9780511542343.012 | Flexible reproductive seasonality in Africa-dwelling papionins is associated with low environmental productivity and high climatic unpredictability | Jules Dezeure, Julie Dagorrette, Lugdiwine Burtschell, Shahrina Chowdhury, Dieter Lukas, Larissa Swedell, Elise Huchard | <p style="text-align: justify;">At a time when seasonal cycles are increasingly disrupted, the ecology and evolution of reproductive seasonality in tropical vertebrates remains poorly understood. In order to predict how changes in seasonality migh... | Behaviour & Ethology, Evolutionary ecology, Zoology | Cédric Sueur | 2024-05-04 18:57:25 | View | ||
14 Jul 2023
Field margins as substitute habitat for the conservation of birds in agricultural wetlandsMallet Pierre, Béchet Arnaud, Sirami Clélia, Mesléard François, Blanchon Thomas, Calatayud François, Dagonet Thomas, Gaget Elie, Leray Carole, Galewski Thomas https://doi.org/10.1101/2022.05.05.490780Searching for conservation opportunities at the marginsRecommended by Ana S. L. Rodrigues based on reviews by Scott Wilson and Elena D ConcepciónIn a progressively human-dominated planet (Venter et al., 2016), the fate of many species will depend on the extent to which they can persist in anthropogenic landscapes. In Western Europe, where only small areas of primary habitat remain (e.g. Sabatini et al., 2018), semi-natural areas are crucial habitats to many native species, yet they are threatened by the expansion of human activities, including agricultural expansion and intensification (Rigal et al., 2023). A new study by Mallet and colleagues (Mallet et al., 2023) investigates the extent to which bird species in the Camargue region are able to use the margins of agricultural fields as substitutes for their preferred semi-natural habitats. Located in the delta of the Rhône River in Southern France, the Camargue is internationally recognized for its biodiversity value, classified as a Biosphere Reserve by UNESCO and as a Wetland of International Importance under the Ramsar Convention (IUCN & UN-WCMC, 2023). Mallet and colleagues tested three specific hypotheses: that grass strips (grassy field boundaries, including grassy tracks or dirt roads used for moving agricultural machinery) can function as substitute habitats for grassland species; that reed strips along drainage ditches (common in the rice paddy landscapes of the Camargue) can function as substitute habitats to wetland species; and that hedgerows can function as substitute habitats to species that favour woodland edges. They did so by measuring how the local abundances of 14 bird species (nine typical of forest edges, 3 of grasslands, and two of reedbeds) respond to increasing coverage of either the three types of field margins or of the three types of semi-natural habitat. This is an elegant study design, yet – as is often the case with real field data – results are not as simple as expected. Indeed, for most species (11 out of 14) local abundances did not increase significantly with the area of their supposed primary habitat, undermining the assumption that they are strongly associated with (or dependent on) those habitats. Among the three species that did respond positively to the area of their primary habitat, one (a forest edge species) responded positively but not significantly to the area of field margins (hedgerows), providing weak evidence to the habitat compensation hypothesis. For the other two (grassland and a wetland species), abundance responded even more strongly to the area of field margins (grass and reed strips, respectively) than to the primary habitat, suggesting that the field margins are not so much a substitute but valuable habitats in their own right. It would have been good conservation news if field margins were found to be suitable habitat substitutes to semi-natural habitats, or at least reasonable approximations, to most species. Given that these margins have functional roles in agricultural landscapes (marking boundaries, access areas, water drainage), they could constitute good win-win solutions for reconciling biodiversity conservation with agricultural production. Alas, the results are more complicated than that, with wide variation in species responses that could not have been predicted from presumed habitat affinities. These results illustrate the challenges of conservation practice in complex landscapes formed by mosaics of variable land use types. With species not necessarily falling neatly into habitat guilds, it becomes even more challenging to plan strategically how to manage landscapes to optimize their conservation. The results presented here suggest that species’ abundances may be responding to landscape variables not taken into account in the analyses, such as connectivity between habitat patches, or maybe positive and negative edge effects between land use types. That such uncertainties remain even in a well-studied region as the Camargue, and for such a well-studied taxon such as birds, only demonstrates the continued importance of rigorous field studies testing explicit hypotheses such as this one by Mallet and colleagues. References IUCN, & UN-WCMC (2023). Protected Planet. Protected Planet. https://www.protectedplanet.net/en Mallet, P., Béchet, A., Sirami, C., Mesléard, F., Blanchon, T., Calatayud, F., Dagonet, T., Gaget, E., Leray, C., & Galewski, T. (2023). Field margins as substitute habitat for the conservation of birds in agricultural wetlands. bioRxiv, 2022.05.05.490780, ver. 3 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2022.05.05.490780 Rigal, S., Dakos, V., Alonso, H., Auniņš, A., Benkő, Z., Brotons, L., Chodkiewicz, T., Chylarecki, P., de Carli, E., del Moral, J. C. et al. (2023). Farmland practices are driving bird population decline across Europe. Proceedings of the National Academy of Sciences, 120, e2216573120. https://doi.org/10.1073/pnas.2216573120 Sabatini, F. M., Burrascano, S., Keeton, W. S., Levers, C., Lindner, M., Pötzschner, F., Verkerk, P. J., Bauhus, J., Buchwald, E., Chaskovsky, O., Debaive, N. et al. (2018). Where are Europe’s last primary forests? Diversity and Distributions, 24, 1426–1439. https://doi.org/10.1111/ddi.12778 Venter, O., Sanderson, E. W., Magrach, A., Allan, J. R., Beher, J., Jones, K. R., Possingham, H. P., Laurance, W. F., Wood, P., Fekete, B. M., Levy, M. A., & Watson, J. E. M. (2016). Sixteen years of change in the global terrestrial human footprint and implications for biodiversity conservation. Nature Communications, 7, 12558. https://doi.org/10.1038/ncomms12558 | Field margins as substitute habitat for the conservation of birds in agricultural wetlands | Mallet Pierre, Béchet Arnaud, Sirami Clélia, Mesléard François, Blanchon Thomas, Calatayud François, Dagonet Thomas, Gaget Elie, Leray Carole, Galewski Thomas | <p style="text-align: justify;">Breeding birds in agricultural landscapes have declined considerably since the 1950s and the beginning of agricultural intensification in Europe. Given the increasing pressure on agricultural land, it is necessary t... | Agroecology, Biodiversity, Conservation biology, Landscape ecology | Ana S. L. Rodrigues | 2022-05-09 10:48:49 | View | ||
14 May 2019
Field assessment of precocious maturation in salmon parr using ultrasound imagingMarie Nevoux, Frédéric Marchand, Guillaume Forget, Dominique Huteau, Julien Tremblay, Jean-Pierre Destouches https://doi.org/10.1101/425561OB-GYN for salmon parrsRecommended by Jean-Olivier Irisson based on reviews by Hervé CAPRA and 1 anonymous reviewerPopulation dynamics and stock assessment models are only as good as the data used to parameterise them. For Atlantic salmon (Salmo salar) populations, a critical parameter may be frequency of precocious maturation. Indeed, the young males (parrs) that mature early, before leaving the river to reach the ocean, can contribute to reproduction but have much lower survival rates afterwards. The authors cite evidence of the potentially major consequences of this alternate reproductive strategy. So, to be parameterised correctly, it needs to be assessed correctly. Cue the ultrasound machine. Through a thorough analysis of data collected on 850 individuals [1], over three years, the authors clearly show that the non-invasive examination of the internal cavity of young fishes to look for gonads, using a portable ultrasound machine, provides reliable and replicable evidence of precocious maturation. They turned into OB-GYN for salmons (albeit for male salmons!) and it worked. While using ultrasounds to detect fish gonads is not a new idea (early attempts for salmonids date back to the 80s [2]), the value here is in the comparison with the classic visual inspection technique (which turns out to be less reliable) and the fact that ultrasounds can now easily be carried out in the field. Beyond the potentially important consequences of this new technique for the correct assessment of salmon population dynamics, the authors also make the case for the acquisition of more reliable individual-level data in ecological studies, which I applaud. References. [1] Nevoux M, Marchand F, Forget G, Huteau D, Tremblay J, and Destouches J-P. (2019). Field assessment of precocious maturation in salmon parr using ultrasound imaging. bioRxiv 425561, ver. 3 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/425561 | Field assessment of precocious maturation in salmon parr using ultrasound imaging | Marie Nevoux, Frédéric Marchand, Guillaume Forget, Dominique Huteau, Julien Tremblay, Jean-Pierre Destouches | <p>Salmonids are characterized by a large diversity of life histories, but their study is often limited by the imperfect observation of the true state of an individual in the wild. Challenged by the need to reduce uncertainty of empirical data, re... | Conservation biology, Demography, Experimental ecology, Freshwater ecology, Life history, Phenotypic plasticity, Population ecology | Jean-Olivier Irisson | 2018-09-25 17:24:59 | View |
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