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02 Jan 2024
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Mt or not Mt: Temporal variation in detection probability in spatial capture-recapture and occupancy models

Useful clarity on the value of considering temporal variability in detection probability

Recommended by ORCID_LOGO based on reviews by Dana Karelus and Ben Augustine

As so often quoted, "all models are wrong; more specifically, we always neglect potentially important factors in our models of ecological systems. We may neglect these factors because no-one has built a computational framework to include them; because including them would be computationally infeasible; or because we don't have enough data.  When considering whether to include a particular process or form of heterogeneity, the gold standard is to fit models both with and without the component, and then see whether we needed the component in the first place ​-- that is, whether including that component leads to an important difference in our conclusions. However, this approach is both tedious and endless, because there are an infinite number of components that we could consider adding to any given model.

Therefore, thoughtful exercises that evaluate the importance of particular complications under a realistic range of simulations and a representative set of case studies are extremely valuable for the field. While they cannot provide ironclad guarantees, they give researchers a general sense of when they can (probably) safely ignore some factors in their analyses. This paper by Sollmann (2024) shows that for a very wide range of scenarios, temporal and spatiotemporal variability in the probability of detection have little effect on the conclusions of spatial capture-recapture and occupancy models.  The author is thoughtful about when such variability may be important, e.g. when variation in detection and density is correlated and thus confounded, or when variation is driven by animals' behavioural responses to being captured.

Reference

Sollmann R (2024). Mt or not Mt: Temporal variation in detection probability in spatial capture-recapture and occupancy models. bioRxiv, 2023.08.08.552394, ver. 2 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2023.08.08.552394

Mt or not Mt: Temporal variation in detection probability in spatial capture-recapture and occupancy modelsRahel Sollmann<p>State variables such as abundance and occurrence of species are central to many questions in ecology and conservation, but our ability to detect and enumerate species is imperfect and often varies across space and time. Accounting for imperfect...Euring Conference, Statistical ecologyBenjamin Bolker Dana Karelus, Ben Augustine, Ben Augustine 2023-08-10 09:18:56 View
30 Sep 2020
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How citizen science could improve Species Distribution Models and their independent assessment

Citizen science contributes to SDM validation

Recommended by based on reviews by Maria Angeles Perez-Navarro and 1 anonymous reviewer

Citizen science is becoming an important piece for the acquisition of scientific knowledge in the fields of natural sciences, and particularly in the inventory and monitoring of biodiversity (McKinley et al. 2017). The information generated with the collaboration of citizens has an evident importance in conservation, by providing information on the state of populations and habitats, helping in mitigation and restoration actions, and very importantly contributing to involve society in conservation (Brown and Williams 2019). An obvious advantage of these initiatives is the ability to mobilize human resources on a large territorial scale and in the medium term, which would otherwise be difficult to finance. The resulting increasing information then can be processed with advanced computational techniques (Hochachka et al 2012; Kelling et al. 2015), thus improving our interpretation of the distribution of species. Specifically, the ability to obtain information on a large territorial scale can be integrated into studies based on Species Distribution Models SDMs. One of the common problems with SDMs is that they often work from species occurrences that have been opportunistically recorded, either by professionals or amateurs. A great challenge for data obtained from non-professional citizens, however, remains to ensure its standardization and quality (Kosmala et al. 2016). This requires a clear and effective design, solid volunteer training, and a high level of coordination that turns out to be complex (Brown and Williams 2019). Finally, it is essential to perform a quality validation following scientifically recognized standards, since they are often conditioned by errors and biases in obtaining information (Bird et al. 2014). There are two basic approaches to obtain the necessary data for this validation: getting it from an external source (external validation), or allocating a part of the database itself (internal validation or cross-validation) to this function.
Matutini et al. (2020) in his work 'How citizen science could improve Species Distribution Models and their independent assessment' shows a novel application of the data generated by a citizen science initiative ('Un Dragon dans mon Jardin') by providing an external source for the validation of SDMs, as a tool to construct habitat suitability maps for nine species of amphibians in western France. Importantly, 'Un Dragon dans mon Jardin' contains standardized presence-absence data, the approximation recognized as the most robust (Guisan, et al. 2017). The SDMs to be validated, in turn, were based on opportunistic information obtained by citizens and professionals. The result shows the usefulness of this external data source by minimizing the overestimation of model accuracy that is obtained with cross-validation with the internal evaluation dataset. It also shows the importance of properly filtering the information obtained by citizens by determining the threshold of sampling effort.
The destiny of citizen science is to be integrated into the complex world of science. Supported by the increasing level of the formation of society, it is becoming a fundamental piece in the scientific system dedicated to the study of biodiversity and its conservation. After funding for scientists specialized in the recognition of biodiversity has been cut back, we are seeing a transformation of the activity of these scientists towards the design, coordination, training and verification of programs for the acquisition of field information obtained by citizens. A main goal is that a substantial part of this information will eventually get integrated into the scientific system, and rigorous verification process a fundamental element for such purpose, as shown by Matutini et al. (2020) work.

References

[1] Bird TJ et al. (2014) Statistical solutions for error and bias in global citizen science datasets. Biological Conservation 173: 144-154. doi: 10.1016/j.biocon.2013.07.037
[2] Brown ED and Williams BK (2019) The potential for citizen science to produce reliable and useful information in ecology. Conservation Biology 33: 561-569. doi: 10.1111/cobi.13223
[3] Guisan A, Thuiller W and Zimmermann N E (2017) Habitat Suitability and Distribution Models: With Applications in R. The University of Chicago Press. doi: 10.1017/9781139028271
[4] Hochachka WM, Fink D, Hutchinson RA, Sheldon D, Wong WK and Kelling S (2012) Data-intensive science applied to broad-scale citizen science. Trens Ecol Evol 27: 130-137. doi: 10.1016/j.tree.2011.11.006
[5] Kelling S, Fink D, La Sorte FA, Johnston A, Bruns NE and Hochachka WM (2015) Taking a ‘Big Data’ approach to data quality in a citizen science project. Ambio 44(Supple. 4):S601-S611. doi: 10.1007/s13280-015-0710-4
[6] Kosmala M, Wiggins A, Swanson A and Simmons B (2016) Assessing data quality in citizen science. Front Ecol Environ 14: 551–560. doi: 10.1002/fee.1436
[7] Matutini F, Baudry J, Pain G, Sineau M and Pithon J (2020) How citizen science could improve Species Distribution Models and their independent assessment. bioRxiv, 2020.06.02.129536, ver. 4 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/2020.06.02.129536
[8] McKinley DC et al. (2017) Citizen science can improve conservation science, natural resource management, and environmental protection. Biological Conservation 208:15-28. doi: 10.1016/j.biocon.2016.05.015

How citizen science could improve Species Distribution Models and their independent assessmentFlorence Matutini, Jacques Baudry, Guillaume Pain, Morgane Sineau, Josephine Pithon<p>Species distribution models (SDM) have been increasingly developed in recent years but their validity is questioned. Their assessment can be improved by the use of independent data but this can be difficult to obtain and prohibitive to collect....Biodiversity, Biogeography, Conservation biology, Habitat selection, Spatial ecology, Metacommunities & Metapopulations, Species distributions, Statistical ecologyFrancisco Lloret2020-06-03 09:36:34 View
04 Apr 2023
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Data stochasticity and model parametrisation impact the performance of species distribution models: insights from a simulation study

Species Distribution Models: the delicate balance between signal and noise

Recommended by ORCID_LOGO based on reviews by Alejandra Zarzo Arias and 1 anonymous reviewer

Species Distribution Models (SDMs) are one of the most commonly used tools to predict where species are, where they may be in the future, and, at times, what are the variables driving this prediction. As such, applying an SDM to a dataset is akin to making a bet: that the known occurrence data are informative, that the resolution of predictors is adequate vis-à-vis the scale at which their impact is expressed, and that the model will adequately capture the shape of the relationships between predictors and predicted occurrence.

In this contribution, Lambert & Virgili (2023) perform a comprehensive assessment of different sources of complications to this process, using replicated simulations of two synthetic species. Their experimental process is interesting, in that both the data generation and the data analysis stick very close to what would happen in "real life". The use of synthetic species is particularly relevant to the assessment of SDM robustness, as they enable the design of species for which the shape of the relationship is given: in short, we know what the model should capture, and can evaluate the model performance against a ground truth that lacks uncertainty.

Any simulation study is limited by the assumptions established by the investigators; when it comes to spatial data, the "shape" of the landscape, both in terms of auto-correlation and in where the predictors are available. Lambert & Virgili (2023) nicely circumvent these issues by simulating synthetic species against the empirical distribution of predictors; in other words, the species are synthetic, but the environment for which the prediction is made is real. This is an important step forward when compared to the use of e.g. neutral landscapes (With 1997), which can have statistical properties that are not representative of natural landscapes (see e.g. Halley et al., 2004).

A striking point in the study by Lambert & Virgili (2023) is that they reveal a deep, indeed deeper than expected, stochasticity in SDMs; whether this is true in all models remains an open question, but does not invalidate their recommendation to the community: the interpretation of outcomes is a delicate exercise, especially because measures that inform on the goodness of the model fit do not capture the predictive quality of the model outputs. This preprint is both a call to more caution, and a call to more curiosity about the complex behavior of SDMs, while also providing a sensible template to perform future analyses of the potential issues with predictive models.


References

Halley, J. M., et al. (2004) “Uses and Abuses of Fractal Methodology in Ecology: Fractal Methodology in Ecology.” Ecology Letters, vol. 7, no. 3, pp. 254–71. https://doi.org/10.1111/j.1461-0248.2004.00568.x.

Lambert, Charlotte, and Auriane Virgili (2023). Data Stochasticity and Model Parametrisation Impact the Performance of Species Distribution Models: Insights from a Simulation Study. bioRxiv, ver. 2 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2023.01.17.524386

With, Kimberly A. (1997) “The Application of Neutral Landscape Models in Conservation Biology. Aplicacion de Modelos de Paisaje Neutros En La Biologia de La Conservacion.” Conservation Biology, vol. 11, no. 5, pp. 1069–80. https://doi.org/10.1046/j.1523-1739.1997.96210.x.

Data stochasticity and model parametrisation impact the performance of species distribution models: insights from a simulation studyCharlotte Lambert, Auriane Virgili<p>Species distribution models (SDM) are widely used to describe and explain how species relate to their environment, and predict their spatial distributions. As such, they are the cornerstone of most of spatial planning efforts worldwide. SDM can...Biogeography, Habitat selection, Macroecology, Marine ecology, Spatial ecology, Metacommunities & Metapopulations, Species distributions, Statistical ecologyTimothée Poisot2023-01-20 09:43:51 View
26 Mar 2025
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Code-sharing policies are associated with increased reproducibility potential of ecological findings

Ensuring reproducible science requires policies

Recommended by ORCID_LOGO based on reviews by Francisco Rodriguez-Sanchez and Veronica Cruz

Researchers do not live in a vacuum, and the social context we live in affects how we do science. On one hand, increased competition for scarce funding creates the wrong incentives to do fast analysis, leading sometimes to poorly checked results that accumulate errors (Fraser et al. 2018). On the other hand, the actual challenges the world faces require more than ever robust scientific evidence that can be used to tackle the current rapid human-induced environmental change. Moreover, scientists' credibility is at stake at this moment where the global flow of information can be politically manipulated, and accessing reliable sources of information is paramount for society. At the crossroads of these challenges is scientific reproducibility. Making our results transparent and reproducible ensures that no perverse incentives can compromise our findings, that results can be reliably applied to solve relevant problems, and that we regain societal credibility in the scientific process. Unfortunately, in ecology and evolution, we are still far from publishing open, transparent, and reproducible papers (Maitner et al. 2024). Understanding which factors promote increased use of good practices regarding reproducibility is hence very welcome.

Sanchez-Tojar and colleagues (2025) conducted a (reproducible) analysis of code and data-sharing practices (a cornerstone of scientific reproducibility) in journals with and without explicit policies regarding data and code deposition. The gist is that having policies in place increases data and code sharing. Doing science about how we do science (meta-science) is important to understand which actions drive our behavior as scientists. This paper highlights that in the absence of strong societal or personal incentives to share code and data, clear policies can catalyze this process. However, in my opinion, policies are a needed first step to consolidate a more permanent change in researchers' behavior regarding reproducible science, but policies alone will not be enough to fix the problem if we do not change also the cultural values around how we publish science. Appealing to inner values, and recognizing science needs to be reproducible to ensure potential errors are easily spotted and corrected requires a deep cultural change. 

References

Fraser, Hannah, Tim Parker, Shinichi Nakagawa, Ashley Barnett, and Fiona Fidler. "Questionable research practices in ecology and evolution." PloS one 13, no. 7 (2018): e0200303. https://doi.org/10.1371/journal.pone.0200303

Maitner, Brian, Paul Efren Santos Andrade, Luna Lei, Jamie Kass, Hannah L. Owens, George CG Barbosa, Brad Boyle et al. "Code sharing in ecology and evolution increases citation rates but remains uncommon." Ecology and Evolution 14, no. 8 (2024): e70030. https://doi.org/10.1002/ece3.70030

Alfredo Sánchez-Tójar, Aya Bezine, Marija Purgar, Antica Culina (2025) Code-sharing policies are associated with increased reproducibility potential of ecological findings. EcoEvoRxiv, ver.4 peer-reviewed and recommended by PCI Ecology. https://doi.org/10.32942/X21S7H

Code-sharing policies are associated with increased reproducibility potential of ecological findingsAlfredo Sánchez-Tójar, Aya Bezine, Marija Purgar, Antica Culina<p>Software code (e.g., analytical code) is increasingly recognized as an important research output because it improves transparency, collaboration, and research credibility. Many scientific journals have introduced code-sharing policies; however,...Meta-analyses, Preregistrations, Statistical ecologyIgnasi Bartomeus2024-12-11 10:33:13 View
06 Jan 2021
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Comparing statistical and mechanistic models to identify the drivers of mortality within a rear-edge beech population

The complexity of predicting mortality in trees

Recommended by based on reviews by Lisa Hülsmann and 2 anonymous reviewers

One of the main issues of forest ecosystems is rising tree mortality as a result of extreme weather events (Franklin et al., 1987). Eventually, tree mortality reduces forest biomass (Allen et al., 2010), although its effect on forest ecosystem fluxes seems not lasting too long (Anderegg et al., 2016). This controversy about the negative consequences of tree mortality is joined to the debate about the drivers triggering and the mechanisms accelerating tree decline. For instance, there is still room for discussion about carbon starvation or hydraulic failure determining the decay processes (Sevanto et al., 2014) or about the importance of mortality sources (Reichstein et al., 2013). Therefore, understanding and predicting tree mortality has become one of the challenges for forest ecologists in the last decade, doubling the rate of articles published on the topic (*). Although predicting the responses of ecosystems to environmental change based on the traits of species may seem a simplistic conception of ecosystem functioning (Sutherland et al., 2013), identifying those traits that are involved in the proneness of a tree to die would help to predict how forests will respond to climate threatens.
Modelling tree mortality is complex, involving multiple factors acting simultaneously at different scales, from tree genetics to ecosystem dynamics and from microsite conditions to global climatic events. Therefore, taking into account different approaches to reduce uncertainty of the predictions is needed (Bugmann et al., 2019). Petit-Cailleux et al. (2020) uses statistical and process-based models to detect the main mortality drivers of a drought- and frost-prone beech population. Particularly, they assessed the intra-individual characteristics of the population, that may play a decisive role explaining the differences in tree vulnerability to extreme weather events. Comparing the results of both analytical approaches, they find out several key factors, such as defoliation, leaf phenology and tree size, that were consistent between them. Even more, the process-based model showed the physiological mechanisms that may explain the individual vulnerability, for instance higher loss of hydraulic conductance may increase the mortality risk of trees with early budburst phenology and large stem diameter. The authors also successfully model annual mortality rate with a linear relationship including only three parameters: loss of conductance, biomass of reserves and late frost days.
This valuable study is a good example of the complexity in understanding and predicting tree mortality. The authors carried out the ambitious commitment of studying the inter-annual variation in mortality with 14-year dataset. However, it might be not enough time to control for the dependence of temporal data to soundly model mortality rate. The authors also acknowledge that the use of two approaches increases the knowledge from different perspectives, but at the same time comparing their results is difficult because the parameters used are not identical. Particularly, process-based models tend to consider the same microclimatic conditions for every tree in the population, and may produce inconsistences with statistical models. Alternatively, individual-based modelling might overcome some of the incompatibilities between the approaches (Zhu et al., 2019).

(*) Number (and percentage) of articles found in Web of Sciences after searching (December the 10th, 2020) “tree mortality”: from 163 (0.006%) in 2010 to 412 (0.013%) in 2020.

References

Allen et al. (2010). A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forests. Forest ecology and management, 259(4), 660-684. doi: https://doi.org/10.1016/j.foreco.2009.09.001
Anderegg et al. (2016). When a tree dies in the forest: scaling climate-driven tree mortality to ecosystem water and carbon fluxes. Ecosystems, 19(6), 1133-1147. doi: https://doi.org/10.1007/s10021-016-9982-1
Bugmann et al. (2019). Tree mortality submodels drive simulated long‐term forest dynamics: assessing 15 models from the stand to global scale. Ecosphere, 10(2), e02616. doi: https://doi.org/10.1002/ecs2.2616
Franklin, J. F., Shugart, H. H. and Harmon, M. E. (1987) Death as an ecological process: the causes, consequences, and variability of tree mortality. BioScience, 37, 550–556. doi: https://doi.org/10.2307/1310665
Petit-Cailleux, C., Davi, H., Lefèvre, F., Garrigue, J., Magdalou, J.-A., Hurson, C., Magnanou, E. and Oddou-Muratorio, S. (2020) Comparing statistical and mechanistic models to identify the drivers of mortality within a rear-edge beech population. bioRxiv, 645747, ver 7 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/645747
Reichstein et al. (2013). Climate extremes and the carbon cycle. Nature, 500(7462), 287-295. doi: https://doi.org/10.1038/nature12350
Sevanto, S., Mcdowell, N. G., Dickman, L. T., Pangle, R., and Pockman, W. T. (2014). How do trees die? A test of the hydraulic failure and carbon starvation hypotheses. Plant, cell & environment, 37(1), 153-161. doi: https://doi.org/10.1111/pce.12141
Sutherland et al. (2013). Identification of 100 fundamental ecological questions. Journal of ecology, 101(1), 58-67. doi: https://doi.org/10.1111/1365-2745.12025
Zhu, Y., Liu, Z., and Jin, G. (2019). Evaluating individual-based tree mortality modeling with temporal observation data collected from a large forest plot. Forest Ecology and Management, 450, 117496. doi: https://doi.org/10.1016/j.foreco.2019.117496

Comparing statistical and mechanistic models to identify the drivers of mortality within a rear-edge beech populationCathleen Petit-Cailleux, Hendrik Davi, François Lefevre, Christophe Hurson, Joseph Garrigue, Jean-André Magdalou, Elodie Magnanou and Sylvie Oddou-Muratorio<p>Since several studies have been reporting an increase in the decline of forests, a major issue in ecology is to better understand and predict tree mortality. The interactions between the different factors and the physiological processes giving ...Climate change, Physiology, Population ecologyLucía DeSoto2019-05-24 11:37:38 View
20 Jun 2019
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Sexual segregation in a highly pagophilic and sexually dimorphic marine predator

Sexual segregation in a sexually dimorphic seabird: a matter of spatial scale

Recommended by based on reviews by Dries Bonte and 1 anonymous reviewer

Sexual segregation appears in many taxa and can have important ecological, evolutionary and conservation implications. Sexual segregation can take two forms: either the two sexes specialise in different habitats but share the same area (habitat segregation), or they occupy the same habitat but form separate, unisex groups (social segregation) [1,2]. Segregation would have evolved as a way to avoid, or at least, reduce intersexual competition.
Testing whether social or habitat segregation is at play necessitates the use of combined approaches to determine the spatial scale at which segregation occurs. This enterprise is even more challenging when studying marine species, which travel over long distances to reach their foraging areas. This is what Barbraud et al. [3] have endeavoured on the snow petrel (Pagodroma nivea), a sexually dimorphic, polar seabird. Studying sexual segregation at sea requires tools for indirect measures of habitat use and foraging tactics. During the incubation period, in a colony based at Pointe Geologie, Adelie land, East Antarctica, the team has equipped birds with GPS loggers to analyse habitat use and foraging behaviour. It has also compared short-, mid-, and long-term stable isotopic profiles, from plasma, blood cells, and feather samples, respectively.
Barbraud et al. [3] could not detect any evidence for sexual segregation in space use. Furthermore, the two sexes showed similar δ13C profiles, illustrating similar foraging latitudes, and indicating no sexual segregation at large spatial scales. Snow petrels all forage exclusively in the sea ice environment formed over the deep Antarctic continental shelf. The authors, however, found other forms of segregation: males consistently foraged at higher sea ice concentrations than females. Males also fed on higher trophic levels than females. Therefore, male and female snow petrels segregate at a smaller spatial scale, and use different foraging tactics and diet specialisations. Females also took shorter foraging trips than males, with higher mass gain that strongly benefit from higher sea ice concentration. Mass gain in males increased with the length of their foraging trip at sea ice areas.
The authors conclude that high sea ice concentration offers the most favourable foraging habitat for snow petrels, and thus that intersexual competition may drive females away from high sea ice areas. This study shows that combining information from different tools provides an elegant way of isolating the potential factors driving sexual segregation and the spatial scales at which it occurs.

References

[1] Conradt, L. (2005). Definitions, hypotheses, models and measures in the study of animal segregation. In Sexual segregation in vertebrates: ecology of the two sexes (Ruckstuhl K.E. and Neuhaus, P. eds). Cambridge University Press, Cambridge, United Kingdom. Pp:11–34.
[2] Ruckstuhl, K. E. (2007). Sexual segregation in vertebrates: proximate and ultimate causes. Integrative and Comparative Biology, 47(2), 245-257. doi: 10.1093/icb/icm030
[3] Barbraud, C., Delord, K., Kato, A., Bustamante, P., & Cherel, Y. (2018). Sexual segregation in a highly pagophilic and sexually dimorphic marine predator. bioRxiv, 472431, ver. 3 peer-reviewed and recommended bt PCI Ecology. doi: 10.1101/472431

Sexual segregation in a highly pagophilic and sexually dimorphic marine predatorChristophe Barbraud, Karine Delord, Akiko Kato, Paco Bustamante, Yves Cherel<p>Sexual segregation is common in many species and has been attributed to intra-specific competition, sex-specific differences in foraging efficiency or in activity budgets and habitat choice. However, very few studies have simultaneously quantif...Foraging, Marine ecologyDenis Réale Dries Bonte, Anonymous2018-11-19 13:40:59 View
14 May 2019
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Field assessment of precocious maturation in salmon parr using ultrasound imaging

OB-GYN for salmon parrs

Recommended by ORCID_LOGO based on reviews by Hervé CAPRA and 1 anonymous reviewer

Population dynamics and stock assessment models are only as good as the data used to parameterise them. For Atlantic salmon (Salmo salar) populations, a critical parameter may be frequency of precocious maturation. Indeed, the young males (parrs) that mature early, before leaving the river to reach the ocean, can contribute to reproduction but have much lower survival rates afterwards. The authors cite evidence of the potentially major consequences of this alternate reproductive strategy. So, to be parameterised correctly, it needs to be assessed correctly. Cue the ultrasound machine.

Through a thorough analysis of data collected on 850 individuals [1], over three years, the authors clearly show that the non-invasive examination of the internal cavity of young fishes to look for gonads, using a portable ultrasound machine, provides reliable and replicable evidence of precocious maturation. They turned into OB-GYN for salmons (albeit for male salmons!) and it worked. While using ultrasounds to detect fish gonads is not a new idea (early attempts for salmonids date back to the 80s [2]), the value here is in the comparison with the classic visual inspection technique (which turns out to be less reliable) and the fact that ultrasounds can now easily be carried out in the field.

Beyond the potentially important consequences of this new technique for the correct assessment of salmon population dynamics, the authors also make the case for the acquisition of more reliable individual-level data in ecological studies, which I applaud.

References.

[1] Nevoux M, Marchand F, Forget G, Huteau D, Tremblay J, and Destouches J-P. (2019). Field assessment of precocious maturation in salmon parr using ultrasound imaging. bioRxiv 425561, ver. 3 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/425561
[2] Reimers E, Landmark P, Sorsdal T, Bohmer E, Solum T. (1987). Determination of salmonids’ sex, maturation and size: an ultrasound and photocell approach. Aquaculture Magazine.13:41-44.

Field assessment of precocious maturation in salmon parr using ultrasound imagingMarie Nevoux, Frédéric Marchand, Guillaume Forget, Dominique Huteau, Julien Tremblay, Jean-Pierre Destouches<p>Salmonids are characterized by a large diversity of life histories, but their study is often limited by the imperfect observation of the true state of an individual in the wild. Challenged by the need to reduce uncertainty of empirical data, re...Conservation biology, Demography, Experimental ecology, Freshwater ecology, Life history, Phenotypic plasticity, Population ecologyJean-Olivier Irisson2018-09-25 17:24:59 View
21 Dec 2020
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Influence of local landscape and time of year on bat-road collision risks

Assessing bat-vehicle collision risks using acoustic 3D tracking

Recommended by ORCID_LOGO based on reviews by Mark Brigham and ?

The loss of biodiversity is an issue of great concern, especially if the extinction of species or the loss of a large number of individuals within populations results in a loss of critical ecosystem services. We know that the most important threat to most species is habitat loss and degradation (Keil et al., 2015; Pimm et al., 2014); the latter can be caused by multiple anthropogenic activities, including pollution, introduction of invasive species and fragmentation (Brook et al., 2008; Scanes, 2018). Roads are a major cause of habitat fragmentation, isolating previously connected populations and being a direct source of mortality for animals that attempt to cross them (Spellberg, 1998).
While most studies have focused on the effect of roads on larger mammals (Bartonička et al., 2018; Litvaitis and Tash, 2008), in recent years many researchers have grown increasingly concerned about the risk of collision between bats and vehicles (Fensome and Mathews, 2016). For example, a recent publication by Medinas et al. (2021) found 509 bat casualties along a 51-km-long transect during a period of 3 years. Their study provides extremely valuable information to asses which factors primarily drive bat mortality on roads, yet it required a substantial investment of time coupled with the difficulty of detecting bat carcasses. Other studies have used acoustic monitoring as a proxy to gauge risk of collision based on estimates of bat density along roads (reviewed in Fensome and Mathews 2016); while the results of such studies are valuable, the number of passes recorded does not necessarily equal collision risk, as many species may simply avoid crossing the roads. Understanding the risk of collisions is of vital importance for adequate planning of road construction, particularly for key sites that harbor threatened bat species or unusually large populations, especially if these are already greatly impacted by other anthropogenic activities (e.g. wind turbines; Kunz et al. 2007) or unusually deadly pathogens (e.g. white-nose syndrome; Blehert et al. 2009).
The study by Roemer et al. (2020) titled “Influence of local landscape and time of year on bat-road collision risks”, is a welcome addition to our understanding of bat collision risk as it employs a more accurate assessment of bat collision risk based on acoustic monitoring and tracking of flight paths. The goal of the study of Roemer and collaborators, which was conducted at 66 study sites in the Mediterranean region, is to provide an assessment of collision risk based on bat activity near roads. They collected a substantial amount of information for several species: more than 30,000 estimated flight trajectories for 21+ species, including Barbastella barbastellus, Myotis spp., Plecotus sp., Rhinolophus ferrumequinum, Miniopterus schreibersii, Pipistrellus spp., Nyctalus leisleri, and others. They assess risk based on estimates of 1) species abundance from acoustic monitoring, 2) direction of flight paths along roads, and 3) bat-vehicle co-occurrence.
Their findings suggest that risk is habitat, species, guild, and season-specific. Roads within forested habitats posed the largest threats for most species, particularly since most flights within these habitats occurred at the zone of collision risk. They also found that bats typically fly parallel to the road axis regardless of habitat type, which they argue supports the idea that bats may use roads as corridors. The results of their study, as expected, also show that the majority of bat passes were detected during summer or autumn, depending on species, yet they provide novel findings of an increase in risky behaviors during autumn, when the number of passes at the zone of collision risk increased significantly. Their results also suggest that mid-range echolocators, a classification that is based on call design and parameters (Frey-Ehrenbold et al., 2013), had a larger portion of flights in the zone at risk, thus potentially making them more susceptible than short and long-range echolocators to collisions with vehicles.
The methods employed by Roemer et al. (2020) could further help us determine how roads pose species and site-specific threats in a diversity of places without the need to invest a significant amount of time locating bat carcasses. Their findings are also important as they could provide valuable information for deciding where new roads should be constructed, particularly if the most vulnerable species are abundant, perhaps due to the presence of important roost sites. They also show how habitats near larger roads could increase threats, providing an important first step for recommendations regarding road construction and maintenance. As pointed out by one reviewer, one possible limitation of the study is that the results are not supported by the identification of carcasses. For example, does an increase in the number of identified flights at the zone of risk really translate into an increase in the number of collisions? Regardless of the latter, the paper’s methods and results are very valuable and provide an important step towards developing additional tools to assess bat-vehicle collision risks.

References

[1] Bartonička T, Andrášik R, Duľa M, Sedoník J, Bíl M (2018) Identification of local factors causing clustering of animal-vehicle collisions. The Journal of Wildlife Management, 82, 940–947. https://doi.org/10.1002/jwmg.21467
[2] Blehert DS, Hicks AC, Behr M, Meteyer CU, Berlowski-Zier BM, Buckles EL, Coleman JTH, Darling SR, Gargas A, Niver R, Okoniewski JC, Rudd RJ, Stone WB (2009) Bat White-Nose Syndrome: An Emerging Fungal Pathogen? Science, 323, 227–227. https://doi.org/10.1126/science.1163874
[3] Brook BW, Sodhi NS, Bradshaw CJA (2008) Synergies among extinction drivers under global change. Trends in Ecology & Evolution, 23, 453–460. https://doi.org/10.1016/j.tree.2008.03.011
[4] Fensome AG, Mathews F (2016) Roads and bats: a meta-analysis and review of the evidence on vehicle collisions and barrier effects. Mammal Review, 46, 311–323. https://doi.org/10.1111/mam.12072
[5] Frey‐Ehrenbold A, Bontadina F, Arlettaz R, Obrist MK (2013) Landscape connectivity, habitat structure and activity of bat guilds in farmland-dominated matrices. Journal of Applied Ecology, 50, 252–261. https://doi.org/10.1111/1365-2664.12034
[6] Keil P, Storch D, Jetz W (2015) On the decline of biodiversity due to area loss. Nature Communications, 6, 8837. https://doi.org/10.1038/ncomms9837
[7] Kunz TH, Arnett EB, Erickson WP, Hoar AR, Johnson GD, Larkin RP, Strickland MD, Thresher RW, Tuttle MD (2007) Ecological impacts of wind energy development on bats: questions, research needs, and hypotheses. Frontiers in Ecology and the Environment, 5, 315–324. https://doi.org/10.1890/1540-9295(2007)5[315:EIOWED]2.0.CO;2
[8] Litvaitis JA, Tash JP (2008) An Approach Toward Understanding Wildlife-Vehicle Collisions. Environmental Management, 42, 688–697. https://doi.org/10.1007/s00267-008-9108-4
[9] Medinas D, Marques JT, Costa P, Santos S, Rebelo H, Barbosa AM, Mira A (2021) Spatiotemporal persistence of bat roadkill hotspots in response to dynamics of habitat suitability and activity patterns. Journal of Environmental Management, 277, 111412. https://doi.org/10.1016/j.jenvman.2020.111412
[10] Pimm SL, Jenkins CN, Abell R, Brooks TM, Gittleman JL, Joppa LN, Raven PH, Roberts CM, Sexton JO (2014) The biodiversity of species and their rates of extinction, distribution, and protection. Science, 344. https://doi.org/10.1126/science.1246752
[11] Roemer C, Coulon A, Disca T, Bas Y (2020) Influence of local landscape and time of year on bat-road collision risks. bioRxiv, 2020.07.15.204115, ver. 3 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2020.07.15.204115
[12] Scanes CG (2018) Chapter 19 - Human Activity and Habitat Loss: Destruction, Fragmentation, and Degradation. In: Animals and Human Society (eds Scanes CG, Toukhsati SR), pp. 451–482. Academic Press. https://doi.org/10.1016/B978-0-12-805247-1.00026-5
[13] Spellerberg I (1998) Ecological effects of roads and traffic: a literature review. Global Ecology & Biogeography Letters, 7, 317–333. https://doi.org/10.1046/j.1466-822x.1998.00308.x

Influence of local landscape and time of year on bat-road collision risksCharlotte Roemer, Aurélie Coulon, Thierry Disca, and Yves Bas<p>Roads impact bat populations through habitat loss and collisions. High quality habitats particularly increase bat mortalities on roads, yet many questions remain concerning how local landscape features may influence bat behaviour and lead to hi...Behaviour & Ethology, Biodiversity, Conservation biology, Human impact, Landscape ecologyGloriana Chaverri2020-07-20 10:56:29 View
31 Oct 2022
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Ten simple rules for working with high resolution remote sensing data

Preventing misuse of high-resolution remote sensing data

Recommended by ORCID_LOGO based on reviews by Jane Wyngaard and 1 anonymous reviewer

To observe, characterise, identify, understand, predict... This is the approach that researchers follow every day. This sequence is tirelessly repeated as the biological model, the targeted ecosystem and/or the experimental, environmental or modelling conditions change. This way of proceeding is essential in a world of rapid change in response to the frenetic pace of intensifying pressures and forcings that impact ecosystems. To better understand our Earth and the dynamics of its components, to map ecosystems and diversity patterns, and to identify changes, humanity had to demonstrate inventiveness and defy gravity. 

Gustave Hermite and Georges Besançon were the first to launch aloft balloons equipped with radio transmitters, making possible the transmission of meteorological data to observers in real time [1]. The development of aviation in the middle of the 20th century constituted a real leap forward for the frequent acquisition of aerial observations, leading to a significant improvement in weather forecasting models. The need for systematic collection of data as holistic as possible – an essential component for the observation of complex biological systems - has resulted in pushing the limits of technological prowess. 

The conquest of space and the concurrent development of satellite observations has largely contributed to the collection of a considerable mass of data, placing our Earth under the "macroscope" - a concept introduced to ecology in the early 1970s by Howard T. Odum (see [2]), and therefore allowing researchers to move towards a better understanding of ecological systems, deterministic and stochastic patterns … with the ultimate goal of improving management actions [2,3]. Satellite observations have been carried out for nearly five decades now [3] and have greatly contributed to a better qualitative and quantitative understanding of the functioning of our planet, its diversity, its climate... and to a better anticipation of possible future changes (e.g., [4-7]).

This access to rich and complex sources of information, for which both spatial and temporal resolutions are increasingly fine, results in the implementation of increasingly complex computation-based analyses, in order to meet the need for a better understanding of ecological mechanisms and processes, and their possible changes. Steven Levitt stated that "Data is one of the most powerful mechanisms for telling stories". This is so true … Data should not be used as a guide to thinking and a critical judgment at each stage of the data exploitation process should not be neglected. 

This is what Mahood et al. [8] rightly remind us in their article "Ten simple rules for working with high-resolution remote sensing data" in which they provide the fundamentals to consider when working with data of this nature, a still underutilized resource in several topics, such as conservation biology [3]. In this unconventional article, presented in a pedagogical way, the authors remind different generations of readers how satellite data should be handled and processed. The authors aim to make the readers aware of the most frequent pitfalls encouraging them to use data adapted to their original question, the most suitable tools/methods/procedures, to avoid methodological overkill, and to ensure both ethical use of data and transparency in the research process. While access to high-resolution data is increasingly easy thanks to the implementation of dedicated platforms [4], and because of the development of easy-to-use processing software and pipelines, it is important to take the time to recall some of the essential rules and guidelines for managing them, from new users with little or no experience who will find in this article the recommendations, resources and advice necessary to start exploiting remote sensing data, to more experienced researchers.

References

[1] Jeannet P, Philipona R, and Richner H (2016). 8 Swiss upper-air balloon soundings since 1902. In: Willemse S, Furger M (2016) From weather observations to atmospheric and climate sciences in Switzerland: Celebrating 100 years of the Swiss Society for Meteorology. vdf Hochschulverlag AG. 

[2] Odum HT (2007) Environment, Power, and Society for the Twenty-First Century: The Hierarchy of Energy. Columbia University Press.

[3] Boyle SA, Kennedy CM, Torres J, Colman K, Pérez-Estigarribia PE, Sancha NU de la (2014) High-Resolution Satellite Imagery Is an Important yet Underutilized Resource in Conservation Biology. PLOS ONE, 9, e86908. https://doi.org/10.1371/journal.pone.0086908

[4] Le Traon P-Y, Antoine D, Bentamy A, Bonekamp H, Breivik LA, Chapron B, Corlett G, Dibarboure G, DiGiacomo P, Donlon C, Faugère Y, Font J, Girard-Ardhuin F, Gohin F, Johannessen JA, Kamachi M, Lagerloef G, Lambin J, Larnicol G, Le Borgne P, Leuliette E, Lindstrom E, Martin MJ, Maturi E, Miller L, Mingsen L, Morrow R, Reul N, Rio MH, Roquet H, Santoleri R, Wilkin J (2015) Use of satellite observations for operational oceanography: recent achievements and future prospects. Journal of Operational Oceanography, 8, s12–s27. https://doi.org/10.1080/1755876X.2015.1022050

[5] Turner W, Rondinini C, Pettorelli N, Mora B, Leidner AK, Szantoi Z, Buchanan G, Dech S, Dwyer J, Herold M, Koh LP, Leimgruber P, Taubenboeck H, Wegmann M, Wikelski M, Woodcock C (2015) Free and open-access satellite data are key to biodiversity conservation. Biological Conservation, 182, 173–176. https://doi.org/10.1016/j.biocon.2014.11.048

[6] Melet A, Teatini P, Le Cozannet G, Jamet C, Conversi A, Benveniste J, Almar R (2020) Earth Observations for Monitoring Marine Coastal Hazards and Their Drivers. Surveys in Geophysics, 41, 1489–1534. https://doi.org/10.1007/s10712-020-09594-5

[7] Zhao Q, Yu L, Du Z, Peng D, Hao P, Zhang Y, Gong P (2022) An Overview of the Applications of Earth Observation Satellite Data: Impacts and Future Trends. Remote Sensing, 14, 1863. https://doi.org/10.3390/rs14081863

[8] Mahood AL, Joseph MB, Spiers A, Koontz MJ, Ilangakoon N, Solvik K, Quarderer N, McGlinchy J, Scholl V, Denis LS, Nagy C, Braswell A, Rossi MW, Herwehe L, Wasser L, Cattau ME, Iglesias V, Yao F, Leyk S, Balch J (2021) Ten simple rules for working with high resolution remote sensing data. OSFpreprints, ver. 6 peer-reviewed and recommended by Peer Community in Ecology.  https://doi.org/10.31219/osf.io/kehqz

Ten simple rules for working with high resolution remote sensing dataAdam L. Mahood, Maxwell Benjamin Joseph, Anna Spiers, Michael J. Koontz, Nayani Ilangakoon, Kylen Solvik, Nathan Quarderer, Joe McGlinchy, Victoria Scholl, Lise St. Denis, Chelsea Nagy, Anna Braswell, Matthew W. Rossi, Lauren Herwehe, Leah wasser,...<p>Researchers in Earth and environmental science can extract incredible value from high-resolution (sub-meter, sub-hourly or hyper-spectral) remote sensing data, but these data can be difficult to use. Correct, appropriate and competent use of su...Biogeography, Landscape ecology, Macroecology, Spatial ecology, Metacommunities & Metapopulations, Terrestrial ecologyEric Goberville2021-10-19 21:41:22 View
24 Apr 2025
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Evolutionary rescue in a mixed beech-fir forest: insights from a quantitative-genetics approach in a process-based model

Integrating evolution and ecology in forests: insights from a multi species demogenetic model

Recommended by ORCID_LOGO based on reviews by Silvio Shueler and 3 anonymous reviewers

The study of eco-evolutionary dynamics, i.e. of the inter-twinning between ecological and evolutionary processes when they occur at comparable time scales, is of growing interest in the current context of global change (Carroll, Hendry, Reznick, & Fox, 2007; Govaert et al., 2019). Demo-genetic agent-based models (DG-ABMs) have gained popularity to address this issue because of their abilities to consider feedback loops between ecological and evolutionary processes and to track populations of interacting individuals with adaptive traits variations (Berzaghi et al., 2019; Lamarins et al., 2022). This type of individual- and process-based simulation modelling where interindividual variation in fitness and hence opportunities for selection emerge from demography, which in turn affects the genetic composition of the population over successive generations (feedback loop), is only beginning to be applied to forest trees (Oddou-Muratorio, Hendrik, & Lefèvre, 2020). Examples include studies investigating the dispersal capacity of transgenes in forest landscapes using spatially explicit DG-ABMs with different demographic rates for transgenic and wild-type trees (DiFazio, Slavov, Burczyk, Leonardi, & Strauss, 2004; Kuparinen & Schurr, 2007), the effect of assortative mating and selection on genetic and plastic differentiation along environmental gradients (Soularue et al., 2023) or the interactions and feedback between tree thinning, genetic evolution, and forest stand dynamics, eventually in the context of drought-induced disturbances (Fririon, Davi, Oddou‐Muratorio, Ligot, & Lefèvre, 2024; Godineau et al., 2023).

In this study, Devresse et al. (2025) extend the current DG-ABM framework for forest trees by incorporating interspecific interactions within diverse, uneven-aged forests. To this end, they adapted an existing multi-species, process-based forest dynamics model—ForCEEPS (Morin et al., 2021)—enabling the evolution of selected tree functional traits across generations. Their work focuses on three quantitative traits: drought tolerance, shade tolerance, and maximal growth rate. Using this enhanced DG-ABM, the authors investigate the conditions under which evolutionary rescue might occur in a mixed beech-fir forest facing climate change. Their results demonstrate that greater trait variability and higher heritability can mitigate short-term (century-scale) forest cover loss under climate warming. The study also shows that assisted gene flow facilitates species adaptation to climate change, while the introduction of pre-adapted species (assisted migration) may enhance post-disturbance recovery but simultaneously constrain the evolutionary rescue of local species.

This work represents a major interdisciplinary advancement in forest ecology and nicely illustrates how integrating evolutionary processes into ecology-focused models can offer novel insights into forest dynamics. The implementation of genetic variability and inheritance via the infinitesimal model of quantitative genetics, along with its limitations, is described in detail, and the various research questions explored using the coupled DG‑ABM are presented as proof of concept for this successful integration. Beyond its methodological contribution, the study highlights the importance of more integrated approaches to understanding forest responses to climate change—approaches that account for both within- and between-species diversity and that promote nature-based solutions. It also underscores the urgent need for experimental studies exploring the genetic variation and architecture of adaptive traits in forest species to better anticipate and support their adaptive potential in a rapidly changing environment.

 

References

Berzaghi, F., Wright, I. J., Kramer, K., Oddou-Muratorio, S., Bohn, F. J., Reyer, C. P. O., … Hartig, F. (2019). Towards a new generation of trait-flexible vegetation models. Trends in Ecology & Evolution, 35(3), 191–205. https://doi.org/10.1016/j.tree.2019.11.006

Carroll, S. P., Hendry, A. P., Reznick, D. N., & Fox, C. W. (2007). Evolution on ecological time-scales. Functional Ecology, 21(3), 387–393. https://doi.org/10.1111/j.1365-2435.2007.01289.x

Devresse, L., Way, F., Postic, T., de Coligny, F. & Morin, X. (2025) Evolutionary rescue in a mixed beech-fir forest: insights from a quantitative-genetics approach in a process-based model. HAL, ver.4 peer-reviewed and recommended by PCI Ecology. https://hal.science/hal-04575070

DiFazio, S. P., Slavov, G. T., Burczyk, J., Leonardi, S., & Strauss, S. H. (2004). Gene flow from tree plantations and implications for transgenic risk assessment. In Plantation Forest Biotechnology for the 21st Century (pp. 405–422). https://doi.org/10.1016/j.diagmicrobio.2009.10.017

Fririon, V., Davi, H., Oddou‐Muratorio, S., Ligot, G., & Lefèvre, F. (2024). Can Thinning Foster Forest Genetic Adaptation to Drought? A Demo‐Genetic Modelling Approach With Disturbance Regimes. Evolutionary Applications, 17(12). https://doi.org/10.1111/eva.70051

Godineau, C., Fririon, V., Beudez, N., de Coligny, F., Courbet, F., Ligot, G., … Lefèvre, F. (2023). A demo-genetic model shows how silviculture reduces natural density-dependent selection in tree populations. Evolutionary Applications, (March), 1–15. https://doi.org/10.1111/eva.13606

Govaert, L., Fronhofer, E. A., Lion, S., Eizaguirre, C., Bonte, D., Egas, M., … Matthews, B. (2019). Eco-evolutionary feedbacks—Theoretical models and perspectives. Functional Ecology, 33(1), 13–30. https://doi.org/10.1111/1365-2435.13241

Kuparinen, A., & Schurr, F. M. (2007). A flexible modelling framework linking the spatio-temporal dynamics of plant genotypes and populations: Application to gene flow from transgenic forests. Ecological Modelling, 202(3–4), 476–486. https://doi.org/10.1016/j.ecolmodel.2006.11.015

Lamarins, A., Fririon, V., Folio, D., Vernier, C., Daupagne, L., Labonne, J., … Oddou-Muratorio, S. (2022). Importance of interindividual interactions in eco-evolutionary population dynamics: The rise of demo-genetic agent-based models. Evolutionary Applications, 15(12), 1988–2001. https://doi.org/10.1111/eva.13508

Morin, X., Bugmann, H., de Coligny, F., Martin-StPaul, N., Cailleret, M., Limousin, J. M., … Guillemot, J. (2021). Beyond forest succession: A gap model to study ecosystem functioning and tree community composition under climate change. Functional Ecology, 35(4), 955–975. https://doi.org/10.1111/1365-2435.13760

Oddou-Muratorio, S., Hendrik, D., & Lefèvre, F. (2020). Integrating evolutionary, demographic and ecophysiological processes to predict the adaptive dynamics of forest tree populations under global change. Tree Genetics & Genomes, 16(5), 1–22. https://doi.org/10.1007/s11295-020-01451-1

Soularue, J. P., Firmat, C., Caignard, T., Thöni, A., Arnoux, L., Delzon, S., … Kremer, A. (2023). Antagonistic Effects of Assortative Mating on the Evolution of Phenotypic Plasticity along Environmental Gradients. American Naturalist, 202(1), 18–39. https://doi.org/10.1086/724579

Evolutionary rescue in a mixed beech-fir forest: insights from a quantitative-genetics approach in a process-based modelLouis Devresse, Freya Way, Tanguy Postic, François de Coligny, Xavier Morin<p>Questions have been raised about the ability of long-lived organisms, such as trees, to adapt to rapid climate change, and to what extent forest management actions influence the evolutionary responses of tree species. Given the life history of ...Community ecology, Competition, Eco-evolutionary dynamics, Ecosystem functioning, Evolutionary ecology, Theoretical ecologySylvie Oddou-Muratorio2024-05-17 19:33:41 View