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14 Jan 2025
Delayed dichromatism in waterfowl as a convenient tool for assessing vital ratesAdrien Tableau, Iain Henderson, Sébastien Reeber, Matthieu Guillemain, Jean-François Maillard, Alain Caizergues https://doi.org/10.1101/2024.06.04.597326A cost-effective and non-invasive approach to estimating population dynamics in waterfowlRecommended by Huihuang Chen based on reviews by 2 anonymous reviewersThis article highlights a novel non-invasive method based on the "apparent sex ratios" that exploits delayed sexual importance in waterfowl populations. Unlike traditional capture-mark-recapture (CMR) technique, which is costly, invasive, and may disturb the target species, this method infers key population dynamics, such as adult survival rate and recruitment rate, by monitoring sex ratios in counts conducted during winter. Juvenile males that resemble adult females before molting provide a unique opportunity to estimate these vital rates. This method is cost-effective, minimizes disturbance to the species, and is particularly suitable for studying protected or invasive species. References Adrien Tableau, Iain Henderson, Sébastien Reeber, Matthieu Guillemain, Jean-François Maillard, Alain Caizergues (2024) Delayed dichromatism in waterfowl as a convenient tool for assessing vital rates. bioRxiv, ver.3 peer-reviewed and recommended by PCI Ecology https://doi.org/10.1101/2024.06.04.597326 | Delayed dichromatism in waterfowl as a convenient tool for assessing vital rates | Adrien Tableau, Iain Henderson, Sébastien Reeber, Matthieu Guillemain, Jean-François Maillard, Alain Caizergues | <p>Monitoring the number of individuals is by far the most popular strategy for studying the environmental factors that determine population dynamics and for measuring the effectiveness of management actions aimed at population recovery, control o... | Biological control, Conservation biology, Demography, Life history, Population ecology, Statistical ecology | Huihuang Chen | 2024-06-07 17:39:34 | View | ||
14 Jan 2025
Cool topoclimates promote cold-adapted plant diversity in temperate mountain forests.Jeremy Borderieux, Emiel De Lombaerde, Karen De Pauw, Pieter Sanczuk, Pieter Vangansbeke, Thomas Vanneste, Pieter De Frenne, Jean-Claude Gégout, Josep M. Serra- Diaz https://doi.org/10.32942/X2XC8TForest microclimate in mountains and its impact on plant community: Still a question of shade, but this time it’s not coming from the canopyRecommended by Romain Bertrand based on reviews by Martin Macek and 2 anonymous reviewersRecently, microclimate has gained significant momentum [1], as evidenced by the increasing number of studies and the emergence of a dedicated scientific community coordinating research efforts [2]. Several factors underpin this trend, including advances in technology that have made microclimate monitoring [3] and ecological contextualization [4] more accessible, as well as improvements in computational methods that facilitate modeling at unprecedented scales [5]. But the growing emphasis on microclimate is primarily driven by their ecological relevance, as microclimate represent the actual climate conditions experienced by organisms [1]. This makes them more suitable than macroclimate data for understanding and predicting biodiversity responses to climate change [6]. While macroclimate data remain a common tool in ecology, they often represent generalized climatic conditions over large spatial scales. These data are typically derived from statistical models calibrated on observations collected at meteorological stations [7], which are usually located at 2 meters above the ground in open areas and at elevations compatible with human activities. Such characteristics limit the applicability of macroclimate data for understanding biodiversity responses, particularly at finer spatial scales. This is especially true in forest ecosystems, where microclimate results from the filtering of macroclimate conditions by forest habitats [8]. A simple walk in a forest during summer highlights this filtering, with the cooling effect of canopy shading and tree packing being clearly perceptible. If humans can sense these variations, they likely influence forest biodiversity. In fact, microclimates are crucial for defining the thermal niches of understory plant species [9] and understanding plant community reshuffling in response to climate warming [10]. In mountainous areas, topography adds further complexity to microclimates. The drop in temperature with elevation, known as the elevation-temperature lapse rate, is familiar, but topography also drives fine-scale variations [11]. Solar radiation hitting forest varies with aspect and hillshade, creating localized temperature differences. For example, equator-facing slopes receive more sunlight, while west-facing slopes are sunlit during the warmest part of the day. Consequently, in the northern hemisphere, southwest-facing slopes generally exhibit warmer temperatures, longer growing seasons, and shorter snow cover durations [12]. Thus, both topography and forest canopy shape the understory microclimate experienced by organisms in temperate mountainous forests. Is biodiversity more influenced by topography- or canopy-induced temperature buffering? While this question may not seem particularly interesting at first glance, understanding the underlying mechanisms of microclimate is crucial for guiding biodiversity conservation decisions in the face of climate change [13]. Poleward-facing slopes, valley bottoms, and dense canopies buffer warm episodes by creating cooler, more humid habitats that can serve as refugia for biodiversity [12]. Both buffering processes are valuable for conservation, but topography-induced buffering is generally more stable over the long term [14]. In contrast, canopy buffering is more vulnerable to human management, disturbances, and the ongoing acceleration of climate change, which is expected to drive tree mortality and lead to canopy opening [15]. Identifying the dominant buffering process in a given area is essential for mapping biodiversity refugia and fully integrating microclimate into conservation strategies. This approach can improve decision-making and actions aimed at promoting biodiversity sustainability in a warming world. The work of Borderieux and colleagues [16] offers new insights into this question through an innovative approach. They focus on temperate forests in a watershed in the Vosges Mountains, where they monitor understory temperature and inventory forest plant communities in separate samplings. Aiming to disentangle the effects of topography and forest canopy on understory temperature and its impact on plant communities, the authors deployed a network of temperature sensors using stratified sampling, balanced according to topography (elevation, aspect, and slope) and canopy cover. They then correlated mean annual temperatures (daily mean and maximum) with topographic factors and canopy cover, considering their potential interactions in a linear model. The contribution of each microclimate component was computed, and their effects on temperatures were mapped. These predictions were then confronted to floristic inventories to test whether topography- and canopy-induced temperature variations explained plant diversity and assemblages. First, the authors demonstrated that local topographic variations, which determine the amount of solar radiation reaching forests in mountainous areas, outweigh the contribution of canopy shading to understory temperatures. This result is surprising, as many previous studies have emphasized the importance of canopy buffering in shaping forest microclimate conditions [8]. However, these studies mostly focused on lowland areas or large scales, where terrain roughness has less influence. It is also unexpected because the authors observed that canopy cover varies at a smaller scale than aspect or topographic position in their study area, creating habitat heterogeneity that could reasonably drive local temperature variations. Nevertheless, the authors found that aspect, heat load, and topographic position induced more variation in microclimate than canopy filtering, significantly allowing deviations from the expected elevation-temperature lapse rate. Second, the topographic effect on understory temperature propagated to biodiversity. The authors found that topography-induced temperature offset explained plant diversity and composition, while canopy-induced temperature offset did not. Specifically, cold topoclimates harbored 30% more species than the average species richness across the inventoried plots. This increase in species richness was primarily due to an increase in cold-adapted species, highlighting the role of cold topoclimates as refugia. It is difficult to assess the extent to which these results are influenced by the specific forest context of the study area chosen by the authors, as there is no clear consensus in previous research regarding the role of topoclimate. For example, Macek et al. (2019) [17] highlighted the predominance of topography in controlling temperature and, consequently, forest community structure in the Czech Republic, while Vandewiele et al. (2023) [18] demonstrated the dominance of canopy control in the German Alps. The forest conditions investigated by Borderieux et al. (2025) were narrow, as they focused mainly on closed forests (more than 80% of the study area and sampling sites exhibiting canopy cover greater than 79%). Given that the canopy buffering effect on temperature increases with canopy cover until plateauing at around 80% [19], this may explain why the authors did not find a strong contribution from the canopy. Nevertheless, the methodology and case presented in their study are both innovative and applicable to other mountainous regions. The work of Borderieux et al. (2025) deserves attention for highlighting a frequently overlooked component of forest microclimate, as canopy filtering is typically regarded as the dominant driver. Topoclimate is a critical factor to consider when protecting cold-adapted forest species in the context of global warming, especially since topographic features are less subject to change than canopy cover. Future research should aim to test this hypothesis across a broader range of forest and topography conditions to identify general patterns, as well as assess the long-term effectiveness of these topographic refugia for biodiversity. It remains unclear whether the cooling effect provided by topoclimate will be sufficient to stabilize climate conditions despite the expected acceleration of climate warming in the coming decades, and whether it will be able to preserve cold-adapted species, which are among the most unique but threatened components of mountain biodiversity. References [1] Kemppinen, J. et al. Microclimate, an important part of ecology and biogeography. Global Ecology and Biogeography 33, e13834 (2024). https://doi.org/10.1111/geb.13834 [2] Lembrechts, J. J. et al. SoilTemp: A global database of near-surface temperature. Global Change Biology 26, 6616–6629 (2020). https://doi.org/10.1111/gcb.15123 [3] Wild, J. et al. Climate at ecologically relevant scales: A new temperature and soil moisture logger for long-term microclimate measurement. Agricultural and Forest Meteorology 268, 40–47 (2019). https://doi.org/10.1016/j.agrformet.2018.12.018 [4] Zellweger, F., Frenne, P. D., Lenoir, J., Rocchini, D. & Coomes, D. Advances in Microclimate Ecology Arising from Remote Sensing. Trends in Ecology & Evolution 34, 327–341 (2019). https://doi.org/10.1016/j.tree.2018.12.012 [5] Haesen, S. et al. ForestTemp – Sub-canopy microclimate temperatures of European forests. Global Change Biology 27, 6307–6319 (2021). https://doi.org/10.1111/gcb.15892 [6] Lembrechts, J. J. et al. Comparing temperature data sources for use in species distribution models: From in-situ logging to remote sensing. Global Ecology and Biogeography 28, 1578–1596 (2019). https://doi.org/10.1111/geb.12974 [7] Fick, S. E. & Hijmans, R. J. WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas. International Journal of Climatology 37, 4302–4315 (2017). https://doi.org/10.1002/joc.5086 [8] De Frenne, P. et al. Global buffering of temperatures under forest canopies. Nat Ecol Evol 3, 744–749 (2019). https://doi.org/10.1038/s41559-019-0842-1 [9] Haesen, S. et al. Microclimate reveals the true thermal niche of forest plant species. Ecology Letters 26, 2043–2055 (2023). https://doi.org/10.1111/ele.14312 [10] Zellweger, F. et al. Forest microclimate dynamics drive plant responses to warming. Science 368, 772–775 (2020). https://doi.org/10.1126/science.aba6880 [11] Rolland, C. Spatial and Seasonal Variations of Air Temperature Lapse Rates in Alpine Regions. Journal of climate, 16(7), 1032-1046 (2003). https://doi.org/10.1175/1520-0442(2003)016%3C1032:SASVOA%3E2.0.CO;2 [12] Rita, A. et al. Topography modulates near-ground microclimate in the Mediterranean Fagus sylvatica treeline. Sci Rep 11, 1–14 (2021). https://doi.org/10.1038/s41598-021-87661-6 [13] Bertrand, R., Aubret, F., Grenouillet, G., Ribéron, A. & Blanchet, S. Comment on “Forest microclimate dynamics drive plant responses to warming”. Science 370, eabd3850 (2020). https://doi.org/10.1126/science.abd3850 [14] Hylander, K., Greiser, C., Christiansen, D. M. & Koelemeijer, I. A. Climate adaptation of biodiversity conservation in managed forest landscapes. Conservation Biology 36, e13847 (2022). https://doi.org/10.1111/cobi.13847 [15] McDowell, N. G. & Allen, C. D. Darcy’s law predicts widespread forest mortality under climate warming. Nature Clim Change 5, 669–672 (2015). https://doi.org/10.1038/nclimate2641 [16] Borderieux, J. et al. Cool topoclimates promote cold-adapted plant diversity in temperate mountain forests. Ecoevorxiv, ver. 3( 2024). Peer-reviewed and recommended by PCI Ecology https://doi.org/10.32942/X2XC8T [17] Macek, M., Kopecký, M. & Wild, J. Maximum air temperature controlled by landscape topography affects plant species composition in temperate forests. Landscape Ecol 34, 2541–2556 (2019). https://doi.org/10.1007/s10980-019-00903-x [18] Vandewiele, M. et al. Mapping spatial microclimate patterns in mountain forests from LiDAR. Agricultural and Forest Meteorology 341, 109662 (2023). https://doi.org/10.1016/j.agrformet.2023.109662 [19] Zellweger, F. et al. Seasonal drivers of understorey temperature buffering in temperate deciduous forests across Europe. Global Ecology and Biogeography 28, 1774–1786 (2019). https://doi.org/10.1111/geb.12991
| Cool topoclimates promote cold-adapted plant diversity in temperate mountain forests. | Jeremy Borderieux, Emiel De Lombaerde, Karen De Pauw, Pieter Sanczuk, Pieter Vangansbeke, Thomas Vanneste, Pieter De Frenne, Jean-Claude Gégout, Josep M. Serra- Diaz | <p>Climate strongly influences the composition and diversity of forest plant communities. Recent studies have highlighted the role of tree canopies in shaping understory thermal conditions at small spatial scales (i.e. microclimate), especially in... | Biodiversity, Climate change, Community ecology, Spatial ecology, Metacommunities & Metapopulations, Terrestrial ecology | Romain Bertrand | 2024-07-05 00:17:37 | View | ||
06 Jan 2025
Using informative priors to account for identifiability issues in occupancy models with identification errorsCélian Monchy, Marie-Pierre Etienne, Olivier Gimenez https://doi.org/10.1101/2024.05.07.592917Accounting for false positives and negatives in monitoring data from sensor networks and eDNARecommended by Damaris Zurell based on reviews by Saoirse Kelleher, Jonathan Rose and 2 anonymous reviewersBiodiversity monitoring increasingly relies on modern technologies such as sensor networks and environmental DNA. These high-throughput methods allow biodiversity assessments with unprecedented detail and are especially useful to detect rare and secretive species that are otherwise difficult to observe with traditional survey-based methods. False negatives through imperfect detection are a typical problem in survey data and depend on intrinsic characteristics of the species, site characteristics of the survey site as well as survey characteristics (Guillera 2017). While imperfect detection might be reduced in modern sensor data and eDNA data, also these types of data are by no means error-free and may bare other challenges. In particular, the bioinformatics and image classification approaches used for species identification from these data can induce a higher rate of false positives than would be expected in expert-based survey data (Hartig et al. 2024). Occupancy models (or occupancy-detection models) have been widely used to map species distributions by fitting a hierarchical model that estimates the paramaters of both the species-environment relationship and an observation submodel. They account for false negatives by inferring detectability from the detection history of a survey location, for example from replicate visits or multiple observers (Guillera 2017). These basic occupancy-detection models assume no false positive errors in the data. Other authors have proposed extensions for false positives that typically rely on unambiguous (known truth) information for some sites or observations (Chambert et al. 2015). In their preprint, Monchy et al. (2024) propose an extension of classic occupancy models that considers a two-step observation process modelling the detection probability at occupied sites and the associated identification probability, separated into the true positive identification rate and the true negative identification rate. Using a simulation approach, the authors compare the effectiveness of a frequentist (maximum likelihood-based) and Bayesian approach for parameter estimation and identifiability, and additionally test the effectiveness of different priors (from non-informative to highly informative). Results of the maximum-likelihood approach indicated biased parameter estimates and identifiability problems. In the Bayesian approach, inclusion of prior information greatly reduces biases in parameter estimates, especially in detection and positive identification rate. Importantly, informative priors for the identification process are a by-product of the classifiers that are developed for processing the eDNA data or sensor data. For example, species identification from acoustic sensors is based on image classifiers trained on labelled bird song spectrograms (Kahl et al. 2021) and as part of the evaluation of the classifier, the true positive rate (sensitivity) is routinely being estimated and could thus be readily used in occupancy models accounting for false positives. Thus, the approach proposed by Monchy et al. (2024) is not only highly relevant for biodiversity assessments based on novel sensor and eDNA data but also provides very practical solutions that do not require additional unambiguous data but recycle data that are already available in the processing pipeline. Applying their framework to real-world data will help reducing biases in biodiversity assessments and through improved understanding of the detection process it could also help optimising the design of sensor networks. References Thierry Chambert, David A. W. Miller, James D. Nichols (2015), Modeling false positive detections in species occurrence data under different study designs. Ecology, 96: 332-339. https://doi.org/10.1890/14-1507.1 Gurutzeta Guillera-Arroita (2017) Modelling of species distributions, range dynamics and communities under imperfect detection: advances, challenges and opportunities. Ecography, 40: 281-295. https://doi.org/10.1111/ecog.02445 Florian Hartig, Nerea Abrego, Alex Bush, Jonathan M. Chase, Gurutzeta Guillera-Arroita, Mathew A. Leibold, Otso Ovaskainen, Loïc Pellissier, Maximilian Pichler, Giovanni Poggiato, Laura Pollock, Sara Si-Moussi, Wilfried Thuiller, Duarte S. Viana, David I. Warton, Damaris Zurell D, Douglas W. Yu (2024) Novel community data in ecology - properties and prospects. Trends in Ecology & Evolution, 39: 280-293. https://doi.org/10.1016/j.tree.2023.09.017 Stefan Kahl, Connor M. Wood, Maximilian Eibl, Holger Klinck (2021) BirdNET: A deep learning solution for avian diversity monitoring. Ecological Informatics, 61: 101236. https://doi.org/10.1016/j.ecoinf.2021.101236 Célian Monchy, Marie-Pierre Etienne, Olivier Gimenez (2024) Using informative priors to account for identifiability issues in occupancy models with identification errors. bioRxiv, ver.3 peer-reviewed and recommended by PCI Ecology https://doi.org/10.1101/2024.05.07.592917 | Using informative priors to account for identifiability issues in occupancy models with identification errors | Célian Monchy, Marie-Pierre Etienne, Olivier Gimenez | <p> Non-invasive monitoring techniques like camera traps, autonomous recording units and environmental DNA are increasingly used to collect data for understanding species distribution. These methods have prompted the development of statistica... | Statistical ecology | Damaris Zurell | 2024-05-11 12:04:10 | 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 Bornette based on reviews by Thomas Guillemaud and John GriffinThis 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 | |
16 Dec 2024
From fear to food: predation risk shapes deer behaviour, their resources and forest vegetationJean-Louis Martin, Simon Chamaillé-Jammes, Anne Salomon, Devana Veronica Gomez Pourroy, Mathilde Schlaeflin, Soizic Le Saout, Annick Lucas, Ilham Bentaleb, Simon Chollet, Jake Pattison, Soline Martin-Blangy , Anthony J. Gaston https://hal.science/hal-04381108v5A multidimensional exploration of predator-prey dynamicsRecommended by Gloriana Chaverri based on reviews by Thomas Guillemaud and 2 anonymous reviewersIn the preprint "From Fear to Food: Predation Risk Shapes Deer Behaviour, Their Resources, and Forest Vegetation", Martin et al. provide a comprehensive examination of the intricate interplay between predation risk, deer behavior, and forest ecosystems. The study offers notable insights into the "ecology of fear," as it takes advantage of an extensive dataset that reflects decades of dedicated research effort. The authors’ approach combines behavioral ecology, plant community analysis, and stable isotope studies, making this work a significant contribution to our understanding of complex ecological phenomena. One of the most striking aspects of this study is the scale and richness of the dataset. The authors used data collected over multiple decades, spanning various experimental contexts, including islands with and without predators, hunting, and culling histories. These datasets are invaluable, as such long-term, geographically diverse studies are rare. The inclusion of both behavioral observations (e.g., flight initiation distances) and ecological outcomes (e.g., vegetation recovery) underscores the effort to provide a holistic understanding of these ecological interactions. The results are not only scientifically robust but also conceptually significant. They challenge simplistic assumptions about predator-prey relationships by illustrating how both the presence and absence of predation risk can have lasting effects on ecosystems. For example, the findings that culling restores vegetation but creates behavioral shifts in deer populations emphasize the complexity of ecological restoration efforts. These results invite further exploration into how behavioral adaptations to predation risk may alter long-term ecosystem trajectories. In conclusion, Martin et al.'s preprint represents a significant advancement in understanding predator-prey interactions and their cascading effects on ecosystems. The study’s comprehensive dataset and integrative approach provide a model for future research in ecological and behavioral sciences. It is a commendable contribution to the field, with implications for both theoretical ecology and practical conservation. References Jean-Louis Martin, Simon Chamaillé-Jammes, Anne Salomon, Devana Veronica Gomez Pourroy, Mathilde Schlaeflin, Soizic Le Saout, Annick Lucas, Ilham Bentaleb, Simon Chollet, Jake Pattison, Soline Martin-Blangy , Anthony J. Gaston (2024) From fear to food: predation risk shapes deer behaviour, their resources and forest vegetation . HAL, ver.6 peer-reviewed and recommended by PCI Ecology https://hal.science/hal-04381108v5 | From fear to food: predation risk shapes deer behaviour, their resources and forest vegetation | Jean-Louis Martin, Simon Chamaillé-Jammes, Anne Salomon, Devana Veronica Gomez Pourroy, Mathilde Schlaeflin, Soizic Le Saout, Annick Lucas, Ilham Bentaleb, Simon Chollet, Jake Pattison, Soline Martin-Blangy , Anthony J. Gaston | <p>The “ecology of fear” posits that predation risk shapes the behaviour of large herbivores, their foraging patterns, their habitat selection and their consequent effect on forest ecology. To test some of these predictions we used the extensive e... | Behaviour & Ethology, Biodiversity, Community ecology, Ecosystem functioning, Food webs, Foraging, Habitat selection, Herbivory, Population ecology | Gloriana Chaverri | 2024-01-10 14:07:13 | View | ||
07 Nov 2024
A dataset of Zostera marina and Zostera noltei structure and functioning in four sites along the French coast over a period of 18 monthsÉlise Lacoste, Vincent Ouisse, Nicolas Desroy, Lionel Allano, Isabelle Auby, Touria Bajjouk, Constance Bourdier, Xavier Caisey, Marie-Noelle de Casamajor, Nicolas Cimiterra, Céline Cordier, Amélia Curd, Lauriane Derrien, Gabin Droual, Stanislas F. Dubois, Élodie Foucault, Aurélie Foveau, Jean-Dominique Gaffet, Florian Ganthy, Camille Gianaroli, Rachel Ignacio-Cifré, Pierre-Olivier Liabot, Gregory Messiaen, Claire Meteigner, Benjamin Monnier, Robin Van Paemelen, Marine Pasquier, Loic Rigouin, Cla... https://doi.org/10.5281/zenodo.10425140A functional ecology reference database on the populations of two species of Zoostera along french coastsRecommended by Gudrun Bornette based on reviews by Antoine Vernay, Sara PUIJALON and 1 anonymous reviewerSeagrass beds are in a poor state of conservation and the ecological function of these plant communities is poorly assessed. Four zones of eelgrass beds (Zostera marina and Zostera noltei) were described in terms of the morphology of the plant populations and the associated fauna. At the same time, parameters related to the functioning of these ecosystems were quantified (benthic fluxes of oxygen, carbon and nutrients) over a two-year cycle. The article provides the databases collected and provides the main characteristics of these habitats for the measured parameters. The work provides a reference database on the Zoostera beds of french coastal areas, outlining the ecological contrasts between both ecosystems. This database can on the one hand contribute to help management and restoration of these habitats, and on the other hand provide a reference state of their ecology, with a view to long-term monitoring. References Élise Lacoste, Vincent Ouisse, Nicolas Desroy, Lionel Allano, Isabelle Auby, Touria Bajjouk, Constance Bourdier, Xavier Caisey, Marie-Noelle de Casamajor, Nicolas Cimiterra, Céline Cordier, Amélia Curd, Lauriane Derrien, Gabin Droual, Stanislas F. Dubois, Élodie Foucault, Aurélie Foveau, Jean-Dominique Gaffet, Florian Ganthy, Camille Gianaroli, Rachel Ignacio-Cifré, Pierre-Olivier Liabot, Gregory Messiaen, Claire Meteigner, Benjamin Monnier, Robin Van Paemelen, Marine Pasquier, Loic Rigouin, Claire Rollet, Aurélien Royer, Laura Soissons, Aurélien Tancray, Aline Blanchet-Aurigny (2023) A dataset of Zostera marina and Zostera noltei structure and functioning in four sites along the French coast over a period of 18 months.. Zenodo, ver.3 peer-reviewed and recommended by PCI Ecology https://doi.org/10.5281/zenodo.10425140 | A dataset of *Zostera marina* and *Zostera noltei* structure and functioning in four sites along the French coast over a period of 18 months | Élise Lacoste, Vincent Ouisse, Nicolas Desroy, Lionel Allano, Isabelle Auby, Touria Bajjouk, Constance Bourdier, Xavier Caisey, Marie-Noelle de Casamajor, Nicolas Cimiterra, Céline Cordier, Amélia Curd, Lauriane Derrien, Gabin Droual, Stanislas F.... | <p>This manuscript describes the methodology associated with the dataset entitled: A dataset of <em>Zostera marina </em>and <em>Zostera noltei </em>structure and functioning in four sites along the French coast over a period of 18 months. The data... | Biodiversity, Community ecology, Conservation biology, Ecosystem functioning, Marine ecology | Gudrun Bornette | 2023-12-21 11:48:43 | View | ||
07 Nov 2024
Using multiple datasets to account for misalignment between statistical and biological populations for abundance estimationMichelle L. Kissling, Paul M. Lukacs, Kelly Nesvacil, Scott M. Gende, Grey W. Pendleton https://doi.org/10.32942/X2W03TDiving into detection process to solve sampling and abundance issues in a cryptic speciesRecommended by Guillaume Souchay based on reviews by Michael Schaub, Chloé Nater and 1 anonymous reviewerEstimating population parameters is critical for analysis and management of wildlife populations. Drawing inference at the population level requires a robust sampling scheme and information about the representativeness of the studied population (Williams et al. 2002). In their textbook, Williams et al. (see chapter 5, 2002) listed several sampling issues, including both temporal and spatial heterogeneity and especially imperfect detection. Several methods, either sampling-based or model-based can be used to circumvent these issues. In their paper, Kissling et al. (2024) addressed the case of the Kittlitz’s murrelet (Brachyramphus brevirostris), a cryptic ice-associated seabird, combining spatial variation in its distribution, temporal variation in breeding propensity, imperfect detection and logistical challenges to access the breeding area. The Kittlitz’s murrelet is thus the perfect species to illustrate common issues and logistical difficulties to implement a standard sampling scheme. The authors proposed a modelling framework unifying several datasets from different surveys to extract information on each step of the detection process: the spatial match between the targeted population and the sampled population, the probability of presence in the sample area, the probability of availability given presence in the sample area and finally, the probability of detection given presence and availability. All these components were part of the framework to estimate abundance and trend for this species. They took advantage of a radiotracking survey during several years to inform spatial match and probability of presence. They performed a behavioural experiment to assess the probability of availability of murrelets given it was present in sampling area, and they used a conventional distance-sampling boat survey to estimate detection of individuals. This is worth noting that the most variable components were the probability of presence in the sample area, with a global mean of 0.50, and the probability of detection given presence and availability ranging from 0.49 to 0.77. The estimated trend for Kittlitz’s murrelet was negative and all the information gathered in this study will be useful for future conservation plan. Coupling a decomposition of the detection process with different data sources was the key to solve problems raised by such “difficult” species, and the paper of Kissling et al. (2024) is a good way to follow for other species, allowing to inform the detection components for the targeted species - and also for our global understanding of detection process, and to infer about the temporal trend of species of conservation concern. References Williams, B. K., Nichols, J. D., and Conroy, M. J. (2002). Analysis and management of animal populations. Academic Press. Michelle L. Kissling, Paul M. Lukacs, Kelly Nesvacil, Scott M. Gende, Grey W. Pendleton (2024) Using multiple datasets to account for misalignment between statistical and biological populations for abundance estimation. EcoEvoRxiv, ver.3 peer-reviewed and recommended by PCI Ecology https://doi.org/10.32942/X2W03T | Using multiple datasets to account for misalignment between statistical and biological populations for abundance estimation | Michelle L. Kissling, Paul M. Lukacs, Kelly Nesvacil, Scott M. Gende, Grey W. Pendleton | <p style="text-align: justify;">A fundamental aspect of ecology is identifying and characterizing population processes. Because a complete census is rare, we almost always use sampling to make inference about the biological population, and the par... | Euring Conference, Population ecology | Guillaume Souchay | 2023-12-28 19:59:21 | View | ||
30 Oct 2024
The importance of sampling design for unbiased estimation of survival using joint live-recapture and live resight modelsMaria C. Dzul, Charles B. Yackulic, William L. Kendall https://doi.org/10.48550/arXiv.2312.13414In the quest for estimating true survivalRecommended by Matthieu Paquet based on reviews by Rémi Fay and 1 anonymous reviewerAccurately estimating survival rate and identifying the drivers of its variation is essential for our understanding of population dynamics and life history strategies (Sæther and Bakke 2000), as well as for population management and conservation (Francis et al. 1998, Doherty et al. 2014). Many studies estimate survival from capture–recapture data using the Cormack–Jolly–Seber (CJS) model (Lebreton et al. 1992). However, survival estimates are confounded with permanent emigration from the study area, which can be particularly problematic for mobile species. This is problematic, not only because CJS models under estimate true survival in populations where permanent emigration occurs (i.e. they estimate “apparent” survival), but also because some factors of interest may affect both survival and emigration (e.g., habitat quality, Paquet et al. 2020), leaving the interpretation of results challenging, for example in terms of management decisions. Several methods have been developed to account for permanent emigration when estimating survival, for example by jointly analyzing CMR data with data on individuals’ locations at each capture/resighting site (to estimate their dispersal distances; Schaub and Royle 2013, Badia Boher et al. 2023), with telemetry data (Powel et al. 2000), mark recovery data (Burnham 1993, Fay et al. 2019), or with live-resight data (Barker 1997). The Barker joint live-recapture/live-resight (JLRLR) model can estimate survival when resight data are continuous over a long interval and from a larger area than the capture recapture data. This model becomes particularly promising with the growing collection of data from citizen science, or remote detection tools (Dzul et al. 2023). However, as pointed out by Dzul et al., this model assumes that resight probability is homogeneous across the area where individuals can move, and this assumption is likely violated for example because of non-random movements or because of non-random location of resighting sites. In their manuscript, Dzul et al. performed a thorough simulation study to evaluate the accuracy of survival estimates from JLRLR models under various study designs regarding the location of resight sites (global, random, fixed including the capture site, and fixed excluding the capture site). They simulated data with varying survival and movement values, varying recapture and resight probabilities, and varying sample sizes. Finally, they also developed and fitted a multi state version of the JLRLR model. They show that JLRLR models performed better than CJS models. Survival estimates were still often biased (either positively or negatively) but they were less biased when sesight sites were randomly located (rather than at fixed locations), when recapture sites were included in the resighting design, and when using the multi state JLRLR model they developed. This study highlights (multistate) JLRLR models as an alternative to CJS models one should consider when auxiliary resight data can be collected. Moreover, it shows the importance of evaluating not only model performance, but also the efficiency of alternative sampling designs before choosing one for our studies. Hopefully, this study will help the authors and other researchers making a more informed and efficient choice of model and design to estimate survival in their study populations. References Jaume A. Badia-Boher, Joan Real, Joan Lluís Riera, Frederic Bartumeus, Francesc Parés, Josep Maria Bas, and Antonio Hernández-Matías. Joint estimation of survival and dispersal effectively corrects the permanent emigration bias in mark-recapture analyses. (2023) Scientific reports 13, no. 1: 6970. https://doi.org/10.1038/s41598-023-32866-0 Richard J Barker (1997) Joint modeling of live-recapture, tag-resight, and tag-recovery data. Biometrics: 666-677. https://doi.org/10.2307/2533966 Kenneth P. Burnham (1993) Marked Individuals in the Study of Bird Populations (ed. J.D. Lebreton), pp. 199–213. Birkhäuser, Basel Kevin E. Doherty, David E. Naugle, Jason D. Tack, Brett L. Walker, Jon M. Graham, Jeffrey L. Beck (2014) Linking conservation actions to demography: grass height explains variation in greater sage‐grouse nest survival. Wildlife biology 20, no. 6 : 320-325. https://doi.org/10.2981/wlb.00004 Maria C. Dzul, Charles B. Yackulic, William L. Kendall (2023) The importance of sampling design for unbiased estimation of survival using joint live-recapture and live resight models. arXiv, ver.3 peer-reviewed and recommended by PCI Ecology https://doi.org/10.48550/arXiv.2312.13414 Rémi Fay, Stephanie Michler, Jacques Laesser, and Michael Schaub (2019) Integrated population model reveals that kestrels breeding in nest boxes operate as a source population. Ecography 42, no. 12: 2122-2131. https://doi.org/10.1111/ecog.04559 Charles M. Francis, John R. Sauer, Jerome R. Serie (1998) Effect of restrictive harvest regulations on survival and recovery rates of American black ducks. The Journal of Wildlife Management : 1544-1557. https://doi.org/10.2307/3802021 Jean-Dominique Lebreton, Kenneth P. Burnham, Jean Clobert, David R. Anderson (1992) Modeling survival and testing biological hypotheses using marked animals: a unified approach with case studies. Ecological monographs 62.1: 67-118. https://doi.org/10.2307/2937171 Matthieu Paquet, Debora Arlt, Jonas Knape, Matthew Low, Pär Forslund, and Tomas Pärt (2020) Why we should care about movements: Using spatially explicit integrated population models to assess habitat source–sink dynamics. Journal of Animal Ecology 89, no. 12: 2922-2933. https://doi.org/10.1111/1365-2656.13357 Larkin A. Powell, Michael J. Conroy, James E. Hines, James D. Nichols, and David G. Krementz. Simultaneous use of mark-recapture and radiotelemetry to estimate survival, movement, and capture rates. (2000) The Journal of Wildlife Management : 302-313. https://doi.org/10.2307/3803003 Bernt-Erik Sæther, Øyvind Bakke (2000) Avian life history variation and contribution of demographic traits to the population growth rate. Ecology 81.3 : 642-653. https://doi.org/10.1890/0012-9658(2000)081[0642:ALHVAC]2.0.CO;2 Michael Schaub, J. Andrew Royle. Estimating true instead of apparent survival using spatial Cormack–Jolly–Seber models (2014) Methods in Ecology and Evolution 5, no. 12: 1316-1326. https://doi.org/10.1111/2041-210X.12134 | The importance of sampling design for unbiased estimation of survival using joint live-recapture and live resight models | Maria C. Dzul, Charles B. Yackulic, William L. Kendall | <p>Survival is a key life history parameter that can inform management decisions and life history research. Because true survival is often confounded with permanent and temporary emigration from the study area, many studies must estimate apparent ... | Dispersal & Migration, Euring Conference, Population ecology, Statistical ecology | Matthieu Paquet | 2023-12-22 22:31:07 | View | ||
30 Oct 2024
General mechanisms for a top-down origin of the predator-prey power lawOnofrio Mazzarisi, Matthieu Barbier, Matteo Smerlak https://doi.org/10.1101/2024.04.04.588057Rethinking Biomass Scaling in Predators-Preys ecosystemsRecommended by Samir Simon Suweis based on reviews by Samraat Pawar and 1 anonymous reviewerThe study titled “General mechanisms for a top-down origin of the predator-prey power law” provides a fresh perspective on the classic predator-prey biomass relationship often observed in ecological communities. Traditionally, predator-prey dynamics have been examined through a bottom-up lens, where prey biomass and energy availability dictate predator populations. However, this study, which instead explores the possibility of a top-down origin for predator-prey power laws, offers a new dimension to our understanding of ecosystem regulation and raises questions about how predator-driven interactions might influence biomass scaling laws independently of prey abundance. Ecologists have long noted that ecosystems often exhibit sublinear scaling between predator and prey biomasses. This pattern implies that predator biomass does not increase proportionally with prey biomass but at a slower rate, leading to a power-law relationship. Traditional explanations, such as those discussed by Peters (1983) and McGill (2006), have linked this to bottom-up processes, suggesting that increases in prey availability support, but do not fully translate to, larger predator populations due to energy losses in the trophic cascade. However, these explanations assume prey abundance as the principal driver. This new work raises an intriguing question: could density-dependent predator interactions, such as competition and interference, be equally or more important in creating this observed power law? The authors hypothesized that density-dependent predator interactions might independently control predator biomass, even when prey is abundant. To test this, they combined predator and prey biomass dynamics equation based on a modified Lotka-Volterra model with agent-based models (ABMs) on a spatial grid, simulating predator-prey populations under varying environmental gradients and density-dependent conditions. These models allowed them to incorporate predator-specific factors, such as intraspecific competition (predator self-regulation) and predation interference, offering a quantitative framework to observe whether these top-down dynamics could indeed explain the observed biomass scaling independently of prey population changes. Their results show that density-dependent predator dynamics, particularly at high predator densities, can yield sublinear scaling in predator-prey biomass relationships. This aligns well with empirical data, such as African mammalian ecosystems where predators seem to self-regulate under high prey availability by competing amongst themselves rather than expanding in direct proportion to prey biomass. Such findings support a shift from bottom-up perspectives to a model where top-down processes drive population regulation and biomass scaling. I think that the work by Mazzarisi and collaborators (2024) offers a thought-provoking twist on predator-prey dynamics and suggests that our traditional frameworks may benefit from a broader, more predator-centered focus. References 1. Onofrio Mazzarisi, Matthieu Barbier, Matteo Smerlak (2024) General mechanisms for a top-down origin of the predator-prey power law. bioRxiv, ver.2 peer-reviewed and recommended by PCI Ecology https://doi.org/10.1101/2024.04.04.588057 2. Peters, R. H. (1986). The ecological implications of body size (Vol. 2). Cambridge university press. 3. McGill, B. J. (2006). “A renaissance in the study of abundance.” Science, 314(5801), 770-772. https://doi.org/10.1126/science.1134920 | General mechanisms for a top-down origin of the predator-prey power law | Onofrio Mazzarisi, Matthieu Barbier, Matteo Smerlak | <p style="text-align: justify;">The ratio of predator-to-prey biomass density is not constant along ecological gradients: denser ecosystems tend to have fewer predators per prey, following a scaling relation known as the ``predator-prey power law'... | Allometry, Community ecology, Food webs, Macroecology, Theoretical ecology | Samir Simon Suweis | 2024-04-06 21:04:59 | View | ||
10 Oct 2024
Large-scale spatio-temporal variation in vital rates and population dynamics of an alpine birdChloé R. Nater, Francesco Frassinelli, James A. Martin, Erlend B. Nilsen https://doi.org/10.32942/X2VP6JDo look up: building a comprehensive view of population dynamics from small scale observation through citizen scienceRecommended by Aidan Jonathan Mark Hewison based on reviews by Todd Arnold and 1 anonymous reviewerPopulation ecologists are in the business of decrypting the drivers of variation in the abundance of organisms across space and time (Begon et al. 1986). Comprehensive studies of wild vertebrate populations which provide the necessary information on variations in vital rates in relation to environmental conditions to construct informative models of large-scale population dynamics are rare, ostensibly because of the huge effort required to monitor individuals across ecological contexts and over generations. In this current aim, Nater et al. (2024) are leading the way forward by combining distance sampling data collected through a large-scale citizen science (Fraisl et al. 2022) programme in Norway with state-of-the-art modelling approaches to build a comprehensive overview of the population dynamics of willow ptarmigan. Their work enhances our fundamental understanding of this system and provides evidence-based tools to improve its management (Williams et al. 2002). Even better, they are working for the common good, by providing an open-source workflow that should enable ecologists and managers together to predict what will happen to their favourite model organism when the planet throws its next curve ball. In the case of the ptarmigan, for example, it seems that the impact of climate change on their population dynamics will differ across the species’ distributional range, with a slower pace of life (sensu Stearns 1983) at higher latitudes and altitudes. On a personal note, I have often mused whether citizen science, with its inherent limits and biases, was just another sticking plaster over the ever-deeper cuts in the research budgets to finance long-term ecological research. Here, Nater et al. are doing well to convince me that we would be foolish to ignore such opportunities, particularly when citizens are engaged, motivated, with an inherent capacity for the necessary discipline to employ common protocols in a standardised fashion. A key challenge for us professional ecologists is to inculcate the next generation of citizens with a sense of their opportunity to contribute to a better understanding of the natural world. References Begon, Michael, John L Harper, and Colin R Townsend. 1986. Ecology: individuals, populations and communities. Blackwell Science. Fraisl, Dilek, Gerid Hager, Baptiste Bedessem, Margaret Gold, Pen-Yuan Hsing, Finn Danielsen, Colleen B Hitchcock, et al. 2022. Citizen Science in Environmental and Ecological Sciences. Nature Reviews Methods Primers 2 (1): 64. https://doi.org/10.1038/s43586-022-00144-4 Chloé R. Nater, Francesco Frassinelli, James A. Martin, Erlend B. Nilsen (2024) Large-scale spatio-temporal variation in vital rates and population dynamics of an alpine bird. EcoEvoRxiv, ver.4 peer-reviewed and recommended by PCI Ecology https://doi.org/10.32942/X2VP6J Stearns, S.C. 1983. The influence of size and phylogeny of covariation among life-history traits in the mammals. Oikos, 41, 173–187. https://doi.org/10.2307/3544261 Williams, Byron K, James D Nichols, and Michael J Conroy. 2002. Analysis and Management of Animal Populations. Academic Press. | Large-scale spatio-temporal variation in vital rates and population dynamics of an alpine bird | Chloé R. Nater, Francesco Frassinelli, James A. Martin, Erlend B. Nilsen | <p>Quantifying temporal and spatial variation in animal population size and demography is a central theme in ecological research and important for directing management and policy. However, this requires field sampling at large spatial extents and ... | Biodiversity, Biogeography, Conservation biology, Demography, Euring Conference, Landscape ecology, Life history, Population ecology, Spatial ecology, Metacommunities & Metapopulations, Statistical ecology, Terrestrial ecology | Aidan Jonathan Mark Hewison | 2024-02-02 08:54:06 | View |
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