Estimating 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

The 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

A 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.
https://doi.org/10.1002/ece3.4363

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.
https://doi.org/10.1002/fee.2179
 
Gonzalez, A., Vihervaara, P., Balvanera, P., Bates, A.E., Bayraktarov, E., Bellingham, P.J., Bruder, A., Campbell, J., Catchen, M.D., Cavender-Bares, J., et al. (2023). A global biodiversity observing system to unite monitoring and guide action. Nat. Ecol. Evol., 1-5. 
https://doi.org/10.1038/s41559-023-02171-0
 
Popovic, G., Mason, T.J., Drobniak, S.M., Marques, T.A., Potts, J., Joo, R., Altwegg, R., Burns, C.C.I., McCarthy, M.A., Johnston, A., et al. (2024). Four principles for improved statistical ecology. Methods Ecol. Evol. 15, 266-281.
https://doi.org/10.1111/2041-210X.14270
 
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, 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 (2024) Guidance framework to apply best practices in ecological data analysis: Lessons learned from building Galaxy-Ecology. EcoEvoRxiv, ver.3 peer-reviewed and recommended by PCI Ecology. 
https://doi.org/10.32942/X2G033

Morand et al. (2024) designed convolutional neural networks to predict the occurrences of 38 marine animals worldwide. The environmental predictors were sea surface temperature, chlorophyll concentration, salinity and fifteen others. The time of some of the predictors was chosen to be as close as possible to the time of the observed occurrence.

This approach has previously only been applied to the analysis of the distribution of terrestrial plant species (Botella et al. 2018, Deneu et al. 2021), so the application here to very different marine ecosystems and organisms is a novelty worth highlighting and discussing.

A very interesting feature of PCI Ecology is that reviews are provided with the final manuscript and the present recommendation text.

In the case of the Morand et al. article, the reviewers provided very detailed and insightful comments that deserve to be published and read alongside the article.

The reviewers' comments question the ecological significance and implications of choosing fine temporal and spatial scales in CNN distribution modelling in order to obtain species distribution modelling (SDM).

The main question debated during the review process was whether the CNN modeling approach used here can be defined as a kind of niche modeling.

The fact is that most of the organisms studied here are mobile, and the authors have taken into account precise environmental information at dates close to those of species appearance (for example, "Temperature and chlorophyll values were also included 15 and 5 days before the occurrences"). In doing so, they took into account the fine spatial and temporal scales of species occurrences and environmental conditions, which can be influenced by both environmental preferences and the movement behaviors of individuals. The question then arises: does this approach really represent the ecological niches of the marine organisms selected? Given that most selected organisms may have specific seasonal movement dynamics, the CNN model also learns the individual movement behaviors of organisms over seasons and years. The ecological niche is a broader concept that takes into account all the environmental conditions that enable species to persist over the course of their lives and over generations. This differs from the case of sessile land plants, which must respond to the environmental context only at the points of appearance.

This is not a shortcoming of the methodology proposed here but rather an interesting conceptual issue to be considered and discussed. Modelling the occurrence of individuals at a given time and position can characterize not only the species' niche but also the dynamics of organisms' temporal movements. As a result, the model predicts the position of individuals at a given time, while the niche should also represent the role of environmental conditions faced by individuals at other times in their lives.
A relevant perspective would then be to analyze whether and how the neural network can help disentangle the ranges of environmental conditions defining the niche from those influencing the movement dynamics of individuals.

Another interesting point is that the CNN model is used here as a multi-species classifier, meaning that it provides the ranked probability that a given observation corresponds to one of the 38 species considered in the study, depending on the environmental conditions at the location and time of the observation. In other words, the model provides the relative chance of choosing each of the 38 species at a given time and place. Imagine that you are only studying two species that have exactly the same niche, a standard SDM approach should provide a high probability of occurrence close to 1 in localities where environmental conditions are very and equally suited to both species, while the CNN classifier would provide a value close to 0.5 for both species, meaning that we have an equal chance of choosing one or the other. Consequently, the fact that the probability given by the classifier is higher for a species at a given point than at another point does not (necessarily) mean that the first point presents better environmental conditions for that species but rather that we are more likely to choose it over one of the other species at this point than at another. In fact, the classification task also reflects whether the other 37 species are more or less likely to be found at each point. The classifier, therefore, does not provide the relative probability of occurrence of a species in space but rather a relative chance of finding it instead of one of the other 37 species at each point of space and time.

It is important that an ecologist designing a multi-species classifier for species distribution modelling is well aware of this point and does not interpret the variation of probabilities for a species in space as an indication of more or less suitable habitat for that specific species. On the other hand, predicting the relative probabilities of finding species to a given point at a given time gives an indication of the dynamics of their local co-occurrence. In this respect, the CNN approach is closer to a joint species distribution model (jSDM). As Ovaskainen et al. (2017) mention, "By simultaneously drawing on the information from multiple species, these (jSDM) models allow one to seek community-level patterns in how species respond to their environment". Let's return to the two species example we used above. The fact that the probabilities are 0.5 for both species actually suggests that both species can coexist at the same abundance at this location. In this respect, the CNN multi-species classifier offers promising prospects for the prediction of assemblages and habitats thanks to the relative importance of the most characteristic/dominant species from a species pool. The species pool comprises all classified species and must be sufficiently representative of the ecological diversity of species niches in the area.

Finally, CNN-based species distribution modelling is a powerful and promising tool for studying the distributions of multi-species assemblages as a function of local environmental features but also of the spatial heterogeneity of each feature around the observation point in space and time (Deneu et al. 2021). It allows acknowledging the complex effects of environmental predictors and the roles of their spatial and temporal heterogeneity through the convolution operations performed in the neural network. As more and more computationally intensive tools become available, and as more and more environmental data becomes available at finer and finer temporal and spatial scales, the CNN approach is likely to be increasingly used to study biodiversity patterns across spatial and temporal scales.

References

Botella, C., Joly, A., Bonnet, P., Monestiez, P., and Munoz, F. (2018). Species distribution modeling based on the automated identification of citizen observations. Applications in Plant Sciences, 6(2), e1029. https://doi.org/10.1002/aps3.1029

Deneu, B., Servajean, M., Bonnet, P., Botella, C., Munoz, F., and Joly, A. (2021). Convolutional neural networks improve species distribution modelling by capturing the spatial structure of the environment. PLoS Computational Biology, 17(4), e1008856. https://doi.org/10.1371/journal.pcbi.1008856

Morand, G., Joly, A., Rouyer, T., Lorieul, T., and Barde, J. (2024) Predicting species distributions in the open ocean with convolutional neural networks. bioRxiv, ver.3 peer-reviewed and recommended by PCI Ecology https://doi.org/10.1101/2023.08.11.551418

Ovaskainen, O., Tikhonov, G., Norberg, A., Guillaume Blanchet, F., Duan, L., Dunson, D., ... and Abrego, N. (2017). How to make more out of community data? A conceptual framework and its implementation as models and software. Ecology letters, 20(5), 561-576. https://doi.org/10.1111/ele.12757

As 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