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Latest recommendations
Id | Title * | Authors * | Abstract * | Picture * | Thematic fields * | Recommender | Reviewers | Submission date▲ | |
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16 Aug 2024
![]() The distribution of distances to the edge of species coexistenceMario Desallais, Michel Loreau, Jean-François Arnoldi https://doi.org/10.1101/2024.01.21.575550How environmental perturbations affect coexistenceRecommended by Frederik De Laender based on reviews by Thomas Guillemaud, Oscar Godoy, Pablo Lechon and 1 anonymous reviewer Understanding the effects of environmental perturbations on coexistence is a key challenge in ecology, and models have played an important role in structuring our ideas and generating predictions, leading to quantitative hypotheses. In such models, environmental perturbations are often captured by changes in parameter values, such as the intrinsic growth rates of species (1–3). The question then becomes how much one can change these parameters without breaking coexistence and thus losing species (4). References 1. Baert, J.M., Janssen, C.R., Sabbe, K., and De Laender, F. (2016). Per capita interactions and stress tolerance drive stress-induced changes in biodiversity effects on ecosystem functions. Nat. Commun. 7, 12486. https://doi.org/10.1038/ncomms12486 8. Desallais M, Loreau M, Arnoldi J.F. (2024) The distribution of distances to the edge of species coexistence. bioRxiv, ver.4 peer-reviewed and recommended by PCI Ecology https://doi.org/10.1101/2024.01.21.575550 | The distribution of distances to the edge of species coexistence | Mario Desallais, Michel Loreau, Jean-François Arnoldi | <p>In Lotka-Volterra community models, given a set of biotic interactions, recent approaches have analysed the probability of finding a set of species intrinsic growth rates (representing intraspecific demographic features) that will allow coexist... | ![]() | Coexistence, Community ecology, Competition, Facilitation & Mutualism, Interaction networks, Theoretical ecology | Frederik De Laender | 2024-02-15 14:17:32 | View | |
21 Jan 2025
![]() Exploring Rubiaceae fungal endophytes across contrasting tropical forests, tree tissues, and developmental stagesHumberto Castillo-González, Jason C. Slot, Stephanie Yarwood, Priscila Chaverri https://doi.org/10.1101/2024.02.13.580172The hidden diversity of fungal endophytes, associated with Rubiaceae of Costa Rican old-growth forestsRecommended by Melanie Roy based on reviews by Marion Boisseaux and 1 anonymous reviewerEndophytic fungi are expected to be hyperdiverse in tropical forests, and here is an article exploring their diversity, hidden in Rubiaceae leaves, in two old-growth forests of Costa Rica. Humberto Castillo-González et al. not only described their diversity, but also test for the impact of leaf development stage, tissue origin, and site location. They distinguish the different fungal lineages and do identify distinct indicators, showing that specialization of endophytic fungi could be related to other factors in tropical forests. This article is a great example of fungal ecology in the tropics, interacting at fine and large scale with a diversity of hosts. It also invites to discuss the high specialization observed in the tropics, and the ecology of old-growth forests in Costa Rica. References Humberto Castillo-González, Jason C. Slot, Stephanie Yarwood, Priscila Chaverri (2025) Exploring Rubiaceae fungal endophytes across contrasting tropical forests, tree tissues, and developmental stages. bioRxiv, ver.3 peer-reviewed and recommended by PCI Ecology https://doi.org/10.1101/2024.02.13.580172 | Exploring Rubiaceae fungal endophytes across contrasting tropical forests, tree tissues, and developmental stages | Humberto Castillo-González, Jason C. Slot, Stephanie Yarwood, Priscila Chaverri | <p>Fungal endophytes play a pivotal role in tropical forest dynamics, influencing plant fitness through growth stimulation, disease suppression, stress tolerance, and nutrient mobilization. This study investigates the effects of region, leaf devel... | ![]() | Agroecology, Biodiversity, Community ecology, Microbial ecology & microbiology, Mycology, Symbiosis | Melanie Roy | 2024-02-15 22:42:10 | View | |
29 Jun 2024
![]() Reassessment of French breeding bird population sizes using citizen science and accounting for species detectabilityJean Nabias, Luc Barbaro, Benoit Fontaine, Jérémy Dupuy, Laurent Couzi, Clément Vallé, Romain Lorrillière https://hal.science/hal-04478371Reassessment of French breeding bird population sizes: from citizen science observations to nationwide estimatesRecommended by Nigel YoccozEstimating populations size of widespread, common species in a relatively large and heterogeneous country like France is difficult for several reasons, from having a sample covering well the diverse ecological gradients to accounting for detectability, the fact that absence of a species may represent a false negative, the species being present but not detected. Bird communities have been the focus of a very large number of studies, with some countries like the UK having long traditions of monitoring both common and rare species. Nabias et al. use a large, structured citizen science project to provide new estimates of common bird species, accounting for detectability and using different habitat and climate covariates to extrapolate abundance to non-sampled areas. About 2/3 of the species had estimates higher than what would have been expected using a previous attempt at estimating population size based in part on expert knowledge and projected using estimates of trends to the period covered by the citizen science sampling. Some species showed large differences between the two estimates, which could be in part explained by accounting for detectability. This paper uses what is called model-based inference (as opposed to design-based inference, that uses the design to make inferences about the whole population; Buckland et al. 2000), both in terms of detectability and habitat suitability. The estimates obtained depend on how well the model components approximate the underlying processes, which in a complex dataset like this one is not easy to assess. But it clearly shows that detectability may have substantial implications for the population size estimates. This is of course not new but has rarely been done at this scale and using a large sample obtained on many species. Interesting further work could focus on testing the robustness of the model-based approach by for example sampling new plots and compare the expected values to the observed values. Such a sampling could be stratified to maximize the discrimination between expected low and high abundances, at least for species where the estimates might be considered as uncertain, or for which estimating population sizes is deemed important. References Buckland, S. T., Goudie, I. B. J., & Borchers, D. L. (2000). Wildlife Population Assessment: Past Developments and Future Directions. Biometrics, 56(1), 1-12. https://doi.org/10.1111/j.0006-341X.2000.00001.x Nabias, J., Barbaro, L., Fontaine, B., Dupuy, J., Couzi, L., et al. (2024) Reassessment of French breeding bird population sizes using citizen science and accounting for species detectability. HAL, ver. 2 peer-reviewed and recommended by Peer Community in Ecology. https://hal.science/hal-04478371 | Reassessment of French breeding bird population sizes using citizen science and accounting for species detectability | Jean Nabias, Luc Barbaro, Benoit Fontaine, Jérémy Dupuy, Laurent Couzi, Clément Vallé, Romain Lorrillière | <p style="text-align: justify;">Higher efficiency in large-scale and long-term biodiversity monitoring can be obtained through the use of Essential Biodiversity Variables, among which species population sizes provide key data for conservation prog... | ![]() | Biogeography, Macroecology, Spatial ecology, Metacommunities & Metapopulations, Species distributions, Statistical ecology | Nigel Yoccoz | 2024-02-26 18:10:27 | View | |
26 Aug 2024
![]() Easy, fast and reproducible Stochastic Cellular Automata with choucaAlexandre Génin, Guillaume Dupont, Daniel Valencia, Mauro Zucconi, M. Isidora Ávila-Thieme, Sergio A. Navarrete, Evie A. Wieters https://doi.org/10.1101/2023.11.08.566206An R package for flexible and fast Stochastic Cellular Automata modelingRecommended by Samuel AlizonStochastic Cellular Automata (SCA) are a popular modelling tool because in, spite of their simplicity, they can generate a variety of spatial patterns. This makes them particularly appreciated, for instance, to validate the insights of analytical or semi-analytical spatial models that make simplifying assumptions, e.g. moment equations models. A first limit to SCA are that as soon as details are added to the model, reproducibility issues may occur. Computation speed is also an issue, especially for large populations. The work by Génin et al. addresses these two issues through the development of an R package, chouca. The use of the package is designed to be as smooth as possible: users only need to define the type of possible transitions along with their rates, the parameter values, the number of neighbours, and the initial state of the landscape. The main function returns the population dynamics of each state and even the final state of the landscape. In addition to its flexibility, an asset of chouca resides in its use of the Rcpp package, which compiles the model designed by the user in C++. This allows for high computation speed, which can be further boosted by using parallelising options from R. In their manuscript, the authors use ecological models to illustrate the more advanced possibilities opened by chouca, e.g. in terms of graphical interpretation or even to estimate parameter values by computing likelihood functions (the implementation in R does make it very appropriate for statistical inference in general). The package still has some limitations, and, for example, it currently only applied to 2D rectangular grids and it cannot include elaborate movement processes. However, some of these could be addressed in future releases and chouca already has the potential to become central for SCA modelling, both for beginners and expert users, especially in ecology. References Alexandre Génin, Guillaume Dupont, Daniel Valencia, Mauro Zucconi, M. Isidora Ávila-Thieme, Sergio A. Navarrete, Evie A. Wieters (2024) Easy, fast and reproducible Stochastic Cellular Automata with chouca. bioRxiv, ver.6 peer-reviewed and recommended by Peer Community in Ecology https://doi.org/10.1101/2023.11.08.566206 | Easy, fast and reproducible Stochastic Cellular Automata with chouca | Alexandre Génin, Guillaume Dupont, Daniel Valencia, Mauro Zucconi, M. Isidora Ávila-Thieme, Sergio A. Navarrete, Evie A. Wieters | <p style="text-align: justify;">Stochastic cellular automata (SCA) are models that describe spatial dynamics using a grid of cells that switch between discrete states over time. They are widely used to understand how small-scale processes scale up... | ![]() | Community ecology, Landscape ecology, Spatial ecology, Metacommunities & Metapopulations, Statistical ecology, Theoretical ecology | Samuel Alizon | 2024-03-11 10:54:39 | View | |
26 Aug 2024
![]() Urban Cepaea nemoralis snails are less likely to have nematodes trapped within their shellsMaxime Dahirel, Hannah Reyné, Katrien De Wolf, Dries Bonte https://doi.org/10.1101/2024.03.07.583959Urbanisation linked to a decline in the proportion of snails with trapped nematodes in their shellRecommended by Alison Duncan based on reviews by Robbie Rae and 1 anonymous reviewerUrbanisation modifies species’ habitats affecting their density, distribution, fitness, and behaviour with knock-on effects for their parasites’ abundance and transmission (Bradley & Altizer 2007). A meta-analysis found that changes in resource provisioning due to anthropogenic change can have both positive and negative effects on parasite infection in wildlife populations, but that feeding on urban waste had an effect of reducing infection, especially for helminths and protozoa (Becker, Streicker & Altizer 2015). Another study found that urbanisation reduced ectoparasite load in birds, but had no effect on endoparasites or avian flu (Reid et al. 2024). These changes may be due to novel diets reducing transmission via predation upon trophic hosts (Becker, Streicker & Altizer 2015) or behavioural, leading to more time available to preen (Reid et al. 2024). Less is known about how urbanisation affects invertebrates (but see Lewthwaite et al., 2024) and their parasites. This is important considering that invertebrates are often intermediate hosts of, and/or vector other parasites. Recent work has found that snails and slugs can trap nematodes in their shells to prevent infection (Rae 2017). This newly discovered resistance mechanism reveals that the shell serves an immune defence function. It also provides a record of nematode exposure and documents incidences of resistance to infection as the trapped nematode becomes fixed onto the shell surface (Rae 2017). Dahirel and co-authors exploit this to investigate whether snail-nematode interactions change in response to increasing levels of urbanisation (Dahirel et al. 2024). They explore whether the proportion of Cepaea nemoralis snails with trapped nematodes in their shell changes across an urbanisation gradient. They also explore whether different phenotypic snail traits, notably shell size, colour, band number and fusion explain the likelihood of having trapped nematodes in their shells. An increase in urbanisation was associated with a decrease in the proportion of snails with trapped nematodes in their shells. At the same time larger shells were more likely to have trapped nematodes, but this effect did not change across the urbanisation gradient. The authors discuss that reduced nematode encapsulation in urban environments may be due to lower encounter rate due to either fewer nematodes in urban environments, changes in snail behaviour reducing exposure, or alternatively that urban snails were less resistant to nematode infection. It will be interesting to investigate how this resistance mechanism is related to other forms of snail immunity and whether high rates of nematode encapsulation are an indicator of high resistance or high exposure. This will enable nematode trapping to be used as a marker to indicate environments and/or snail populations harbouring high levels of parasitism and further exploitation of museum collections to understand host-parasite interactions in the past (Rae 2017). References Becker, D.J., Streicker, D.G. & Altizer, S. (2015) Linking anthropogenic resources to wildlife-pathogen dynamics: a review and meta-analysis. Ecol Lett, 18, 483-495. https://doi.org/10.1111/ele.12428 Bradley, C.A. & Altizer, S. (2007) Urbanization and the ecology of wildlife diseases. Trends Ecol Evol, 22, 95-102. https://doi.org/10.1016/j.tree.2006.11.001 Maxime Dahirel, Hannah Reyné, Katrien De Wolf, Dries Bonte (2024) Urban Cepaea nemoralis snails are less likely to have nematodes trapped within their shells. bioRxiv, ver.4 peer-reviewed and recommended by PCI Ecology https://doi.org/10.1101/2024.03.07.583959 Lewthwaite, J.M.M., Baiotto, T.M., Brown, B.V., Cheung, Y.Y., Baker, A.J., Lehnen, C., McGlynn, T.P., Shirey, V., Gonzalez, L., Hartop, E., Kerr, P.H., Wood, E. & Guzman, L.M. (2024) Drivers of arthropod biodiversity in an urban ecosystem. Sci Rep, 14, 390. https://doi.org/10.1038/s41598-023-50675-3 Rae, R. (2017) The gastropod shell has been co-opted to kill parasitic nematodes. Sci Rep, 7, 4745. https://doi.org/10.1038/s41598-017-04695-5 Reid, R., Capilla-Lasheras, P., Haddou, Y., Boonekamp, J. & Dominoni, D.M. (2024) The impact of urbanization on health depends on the health metric, life stage and level of urbanization: a global meta-analysis on avian species. Proc Biol Sci, 291, 20240617. https://doi.org/10.1098/rspb.2024.0617 | Urban *Cepaea nemoralis* snails are less likely to have nematodes trapped within their shells | Maxime Dahirel, Hannah Reyné, Katrien De Wolf, Dries Bonte | <p style="text-align: justify;">Urbanisation is a major human-induced environmental change which can impact not only individual species, but also the way these species interact with each other. As a group, terrestrial molluscs interact frequently ... | ![]() | Host-parasite interactions, Human impact | Alison Duncan | 2024-03-11 11:35:15 | 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 | |
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 PoisotA 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 | ||
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 SueurAs 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 | ||
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 | |
07 Feb 2025
![]() In defense of the original Type I functional response: The frequency and population-dynamic effects of feeding on multiple prey at a timeMark Novak, Kyle Edward Coblentz, John P DeLong https://doi.org/10.1101/2024.05.14.594210Revising behavioural assumptions leads to a new appreciation of an old functional response modelRecommended by Frédéric BarraquandThe functional response, describing the relation between predator intake rate and prey density, is a pivotal concept to understand foraging behaviour and its consequences for community dynamics. Holling (1959a) introduced three types of functional responses according to their shapes, labelled I, II and III. The type II, also known as the disc equation (Holling 1959b), has become popular among empiricists and theoreticians alike, due to its ability to describe predator intake saturation. The type III is often used to represent predator switching to other prey species when main prey density is low. Although theoretical works identify the linear functional response used in Lotka-Volterra models as a type I, Holling (1959a)’s type I model actually envisioned that at some threshold prey density, the linear increase in predator intake with prey density would give way to an upper predator intake limit, so that Holling’s type I has a rectilinear shape, with an angle joining straight lines. Ecology students can actually see this rectilinear shape reproduced in some texbooks, although not in textbook dynamical models, as they usually transition from Lotka-Volterra models to models with type II response. To many, the rectilinear shape of the original type I looks like a historical curiosity: the type II functional response accounts for intake rate saturation with a more convenient smooth function. Novak et al. (2025) turn this preconception on its head by first pedagogically showing that Holling’s original type I model can be obtained as a limit case of a variant of the celebrated type II model. The derivation follows up earlier work by Sjöberg (1980), which might be unfamiliar to readers outside aquatic ecology. The often untold assumption of the type II functional response model is that searching and handling prey are two exclusive behavioural processes, with predators that can only handle one prey item at a time. Allowing for several prey items to be handled at once while searching, until the predator reaches n prey items, the original type I functional response emerges as a limit case of the « multiprey » functional response as n goes to infinity. Interestingly, the multiprey response looks a lot like the original type I for large yet doable n. Novak et al. (2025) then proceed to look for the prevalence of such multiprey functional response shapes in a large database of functional responses (Uiterwaal et al. 2022). Combining linear type I and multiprey models (the asymptote may not always be visible), they find support for this revised type I hypothesis in about one-third of the cases. Although the type II and III models are still well supported by data, the results do suggest that linearity at low prey density may well be more frequent than one thinks. They complement this analysis by showing that larger predators relative to their prey tend to have larger n in the multiprey response. It is consistent with the hypothesis that the bigger you are relative to your prey, the more prey items you can handle at once. Finally, Novak et al. (2025) investigate the consequences of the multiprey model for community dynamics. They find overall a richer dynamical behaviour than the Lotka-Volterra type I and common parameterizations of the type II, suggesting that observed linearity in some range of prey density does not necessarily translate in simpler dynamical behaviour. Novak et al. (2025) provide here a convincing and pedagogical study showing how seemingly benign behavioural assumptions can in fact profoundly alter the perceived relevance of community dynamics models. As they conclude, their analyses have lessons for future empirical functional response work, which should not necessarily dismiss the type I model and consider perhaps variants to the classical type II and III, as well as for future theoretical analyses, which could generalize this model to multiple prey species, or relax other behavioural assumptions. References Holling, C. S. (1959a). The components of predation as revealed by a study of small-mammal predation of the European Pine Sawfly. The Canadian Entomologist, 91(5), 293-320. https://doi.org/10.4039/Ent91293-5 Holling, C. S. (1959b). Some characteristics of simple types of predation and parasitism. The Canadian Entomologist, 91(7), 385-398. https://doi.org/10.4039/Ent91385-7 Novak, M., Coblentz, K. E., & DeLong, J. P (2025). In defense of the original Type I functional response: The frequency and population-dynamic effects of feeding on multiple prey at a time. bioRxiv, ver.4 peer-reviewed and recommended by PCI Ecology https://doi.org/10.1101/2024.05.14.594210 Sjöberg, S. (1980). Zooplankton feeding and queueing theory. Ecological Modelling, 10(3-4), 215-225. https://doi.org/10.1016/0304-3800(80)90060-5 Uiterwaal, S. F., Lagerstrom, I. T., Lyon, S. R., & DeLong, J. P. (2022). FoRAGE database: A compilation of functional responses for consumers and parasitoids. Ecology, 103(7), e3706. https://doi.org/10.1002/ecy.3706 | In defense of the original Type I functional response: The frequency and population-dynamic effects of feeding on multiple prey at a time | Mark Novak, Kyle Edward Coblentz, John P DeLong | <p>Ecologists differ in the degree to which they consider the linear Type I functional response to be an unrealistic versus sufficient representation of predator feeding rates. Empiricists tend to consider it unsuitably non-mechanistic and theoret... | ![]() | Coexistence, Community ecology, Food webs, Foraging, Population ecology, Theoretical ecology | Frédéric Barraquand | 2024-05-21 03:44:00 | View |
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