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01 Mar 2023
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Effects of adaptive harvesting on fishing down processes and resilience changes in predator-prey and tritrophic systems

Adaptive harvesting, “fishing down the food web”, and regime shifts

Recommended by based on reviews by Pierre-Yves HERNVANN and 1 anonymous reviewer

The mean trophic level of catches in world fisheries has generally declined over the 20th century, a phenomenon called "fishing down the food web" (Pauly et al. 1998). Several mechanisms have been proposed to explain this decline including the collapse of, or decline in, higher trophic level stocks leading to the inclusion of lower trophic level stocks in the fishery. Fishing down the food web may lead to a reduction in the resilience, i.e., the capacity to rebound from change, of the fished community, which is concerning given the necessity of resilience in the face of climate change. 

The practice of adaptive harvesting, which involves fishing stocks based on their availability, can also result in a reduction in the average trophic level of a fishery (Branch et al. 2010). Adaptive harvesting, similar to adaptive foraging, can affect the resilience of fisheries. Generally, adaptive foraging acts as a stabilizing force in communities (Valdovinos et al. 2010), however it is not clear how including harvesters as the adaptive foragers will affect the resilience of the system.

Tromeur and Loeuille (2023) analyze the effects of adaptively harvesting a trophic community. Using a system of ordinary differential equations representing a predator-prey model where both species are harvested, the researchers mathematically analyze the impact of increasing fishing effort and adaptive harvesting on the mean trophic level and resilience of the fished community. This is achieved by computing the equilibrium densities and equilibrium allocation of harvest effort.  In addition, the researchers numerically evaluate adaptive harvesting in a tri-trophic system (predator, prey, and resource). The study focuses on the effect of adaptively distributing harvest across trophic levels on the mean trophic level of catches, the propensity for regime shifts to occur, the ability to return to equilibrium after a disturbance, and the speed of this return. 

The results indicate that adaptive harvesting leads to a decline in the mean trophic level of catches, resulting in “fishing down the food web”. Furthermore, the study shows that adaptive harvesting may harm the overall resilience of the system. Similar results were observed numerically in a tri-trophic community.

While adaptive foraging is generally a stabilizing force on communities, the researchers found that adaptive harvesting can destabilize the harvested community. One of the key differences between adaptive foraging models and the model presented here, is that the harvesters do not exhibit population dynamics. This lack of a numerical response by the harvesters to decreasing population sizes of their stocks leads to regime shifts. The realism of a fishery that does not respond numerically to declining stock is debatable, however it is very likely that there will a least be significant delays due to social and economic barriers to leaving the fishery, that will lead to similar results.

This study is not unique in demonstrating the ability of adaptive harvesting to result in “fishing down the food web”. As pointed out by the researchers, the same results have been shown with several different model formulations (e.g., age and size structured models). Similarly, this study is not unique to showing that increasing adaptation speeds decreases the resilience of non-linear predator-prey systems by inducing oscillatory behaviours. Much of this can be explained by the destabilising effect of increasing interaction strengths on food webs (McCann et al. 1998). 

By employing a straightforward model, the researchers were able to demonstrate that adaptive harvesting, a common strategy employed by fishermen, can result in a decline in the average trophic level of catches, regime shifts, and reduced resilience in the fished community. While previous studies have observed some of these effects, the fact that the current study was able to capture them all with a simple model is notable. This modeling approach can offer insight into the role of human behavior on the complex dynamics observed in fisheries worldwide.


Branch, T. A., R. Watson, E. A. Fulton, S. Jennings, C. R. McGilliard, G. T. Pablico, D. Ricard, et al. 2010. The trophic fingerprint of marine fisheries. Nature 468:431–435.

Tromeur, E., and N. Loeuille. 2023. Effects of adaptive harvesting on fishing down processes and resilience changes in predator-prey and tritrophic systems. bioRxiv 290460, ver 5 peer-reviewed and recommended by PCI Ecology.

McCann, K., A. Hastings, and G.R. Huxel. 1998. Weak trophic interactions and the balance of nature. Nature 395: 794-798.

Pauly, D., V. Christensen, J. Dalsgaard, R. Froese, and F. Torres Jr. 1998. Fishing down marine food webs. Science 279:860–86.

Valdovinos, F.S., R. Ramos-Jiliberto, L. Garay-Naravez, P. Urbani, and J.A. Dunne. 2010. Consequences of adaptive behaviour for the structure and dynamics of food webs. Ecology Letters 13: 1546-1559.

Effects of adaptive harvesting on fishing down processes and resilience changes in predator-prey and tritrophic systemsEric Tromeur, Nicolas Loeuille<p>Many world fisheries display a declining mean trophic level of catches. This "fishing down the food web" is often attributed to reduced densities of high-trophic-level species. We show here that the fishing down pattern can actually emerge from...Biodiversity, Community ecology, Food webs, Foraging, Population ecology, Theoretical ecologyAmanda Lynn Caskenette2022-05-03 21:09:35 View
09 Nov 2023
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Mark loss can strongly bias estimates of demographic rates in multi-state models: a case study with simulated and empirical datasets

Marks lost in action, biased estimations

Recommended by ORCID_LOGO based on reviews by Olivier Gimenez, Devin Johnson and 1 anonymous reviewer

Capture-Mark-Recapture (CMR) data are commonly used to estimate ecological variables such as abundance, survival probability, or transition rates from one state to another (e.g. from juvenile to adult, or migration from one site to another). Many studies have shown how estimations can be affected by neglecting one aspect of the population under study (e.g. the heterogeneity in survival between individuals) or one limit of the methodology itself (e.g. the fact that observers might not detect an individual although it is still alive). Strikingly, very few studies have yet assessed the robustness of one fundamental assumption of all CMR-based inferences: marks are supposed definitive and immutable. If they are not, how are estimations affected? Addressing this issue is the main goal of the paper by Touzalin et al. (2023), and they did a very nice work. But, because the answer is not that simple, it also calls for further investigations.

When and why would mark loss bias estimation? In at least two situations. First, when estimating survival rates: if an individual loses its mark, it will be considered as dead, hence death rates will be overestimated. Second, more subtly, when estimating transition rates: if one individual loses its mark at the specific moment where its state changes, then a transition will be missed in data. The history of the marked individual would then be split into two independent CMR sequences as if there were two different individuals, including one which died.

Touzalin et al. (2023) thoroughly studied these two situations by estimating ecological parameters on 1) well-thought simulated datasets, that cover a large range of possible situations inspired from a nice compilation of hundreds of estimations from fish and bats studies, and 2) on their own bats dataset, for which they had various sources of information about mark losses, i.e. different mark types on the same individuals, including mark based on genotypes, and marks found on the soil in the place where bats lived. Their main findings from the simulated datasets are that there is a general trend for underestimation of survival and transition rates if mark loss is not accounting for in the model, as it would be intuitively expected. However, they also showed from the bats dataset that biases do not show any obvious general trend, suggesting complex interactions between different ecological processes and/or with the estimation procedure itself.

The results by Touzalin et al. (2023) strongly suggest that mark loss should systematically be included in models estimating parameters from CMR data. In addition to adapt the inferential models, the authors also recommend considering either a double marking, or even a single but ‘permanent’ mark such as one based on the genotypes. However, the potential gain of a double marking or of the use of genotypes is still to be evaluated both in theory and practice, and it seems to be not that obvious at first sight. First because double marking can be costly for experimenters but also for the marked animals, especially as several studies showed that marks can significantly affect survival or recapture rates. Second because multiple sources of errors can affect genotyping, which would result in wrong individual assignations especially in populations with low genetic diversity or high inbreeding, or no individual assignation at all, which would increase the occurrence of missing data in CMR datasets. Touzalin et al. (2023) supposed in their paper that there were no genotyping errors, but one can doubt it to be true in most situations. They have now important and interesting other issues to address.


Frédéric Touzalin, Eric J. Petit, Emmanuelle Cam, Claire Stagier, Emma C. Teeling, Sébastien J. Puechmaille (2023) Mark loss can strongly bias demographic rates in multi-state models: a case study with simulated and empirical datasets. BioRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Ecology.

Mark loss can strongly bias estimates of demographic rates in multi-state models: a case study with simulated and empirical datasetsFrédéric Touzalin, Eric J. Petit, Emmanuelle Cam, Claire Stagier, Emma C. Teeling, Sébastien J. Puechmaille<p style="text-align: justify;">1. The development of methods for individual identification in wild species and the refinement of Capture-Mark-Recapture (CMR) models over the past few decades have greatly improved the assessment of population demo...Conservation biology, DemographySylvain Billiard2022-04-12 18:49:34 View
25 Nov 2022
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Positive fitness effects help explain the broad range of Wolbachia prevalences in natural populations

Population dynamics of Wolbachia symbionts playing Dr. Jekyll and Mr. Hyde

Recommended by based on reviews by 3 anonymous reviewers

"Good and evil are so close as to be chained together in the soul"
Robert Louis Stevenson, Dr. Jekyll and Mr. Hyde

Maternally inherited symbionts—microorganisms that pass from a female host to her progeny—have two main ways of increasing their own fitness. First, they can increase the fecundity or viability of infected females. This “positive fitness effects” strategy is the one commonly used by mutualistic symbionts, such as Buchnera aphidicola—the bacterial endosymbiont of the pea aphid, Acyrthosiphon pisum [4]. Second, maternally inherited symbionts can manipulate the reproduction of infected females in a way that enhances symbiont transmission at the expense of host fitness. A famous example of this “reproductive parasitism” strategy is the cytoplasmic incompatibility (CI) [3] induced by bacteria of the genus Wolbachia in their arthropod and nematode hosts. CI works as a toxin-antidote system, whereby the sperm of infected males is modified in a lethal way (toxin) that can only be reverted if the egg is also infected (antidote) [1]. As a result, CI imposes a kind of conditional sterility on their hosts: while infected females are compatible with both infected and uninfected males, uninfected females experience high offspring mortality if (and only if) they mate with infected males [7].

These two symbiont strategies (positive fitness effects versus reproductive parasitism) have been traditionally studied separately, both empirically and theoretically. However, it has become clear that the two strategies are not mutually exclusive, and that a reproductive parasite can simultaneously act as a mutualist—an infection type that has been dubbed “Jekyll and Hyde” [6], after the famous novella by Robert Louis Stevenson about kind scientist Dr. Jekyll and his evil alter ego, Mr. Hyde. In important previous work, Zug and Hammerstein [7] analyzed the consequences of positive fitness effects on the dynamics of different kind of infections, including “Jekyll and Hyde” infections characterized by CI and other reproductive parasitism strategies. Building on this and related modeling framework, Karisto et al. [2] re-investigate and expand on the interplay between positive fitness effects and reproductive parasitism in Wolbachia infections by focusing on CI in both diplodiploid and haplodiploid populations, and by paying particular attention to the mathematical assumption structure underlying their results.

Karisto et al. begin by reviewing classic models of Wolbachia infections in diplodiploid populations that assume a “negative fitness effect” (modeled as a fertility penalty on infected females), characteristic of a pure strategy of reproductive parasitism. Together with the positive frequency-dependent effects due to CI (whereby the fitness benefits to symbionts infecting females increase with the proportion of infected males in the population) this results in population dynamics characterized by two stable equilibria (the Wolbachia-free state and an interior equilibrium with a high frequency of Wolbachia-carrying hosts) separated by an unstable interior equilibrium. Wolbachia can then spread once the initial frequency is above a threshold or an invasion barrier, but is prevented from fixing by a proportion of infections failing to be passed on to offspring. Karisto et al. show that, given the assumption of negative fitness effects, the stable interior equilibrium can never feature a Wolbachia prevalence below one-half. Moreover, they convincingly argue that a prevalence greater than but close to one-half is difficult to maintain in the presence of stochastic fluctuations, as in these cases the high-prevalence stable equilibrium would be too close to the unstable equilibrium signposting the invasion barrier.

Karisto et al. then relax the assumption of negative fitness effects and allow for positive fitness effects (modeled as a fertility premium on infected females) in a diplodiploid population. They show that positive fitness effects may result in situations where the original invasion threshold is now absent, the bistable coexistence dynamics are transformed into purely co-existence dynamics, and Wolbachia symbionts can now invade when rare. Karisto et al. conclude that positive fitness effects provide a plausible and potentially testable explanation for the low frequencies of symbiont-carrying hosts that are sometimes observed in nature, which are difficult to reconcile with the assumption of negative fitness effects. 

Finally, Karisto et al. extend their analysis to haplodiploid host populations (where all fertilized eggs develop as females). Here, they investigate two types of cytoplasmic incompatibility: a female-killing effect, similar to the CI effect studied in diplodiploid populations (the “Leptopilina type” of Vavre et al. [5]) and a masculinization effect, where CI leads to the loss of paternal chromosomes and to the development of the offspring as a male (the “Nasonia type” of Vavre et al. [5]). The models are now two-sex, which precludes a complete analytical treatment, in particular regarding the stability of fixed points. Karisto et al. compensate by conducting large numerical analyses that support their claims. Importantly, all main conclusions regarding the interplay between positive fitness effects and reproductive parasitism continue to hold under haplodiploidy. 

All in all, the analysis and results by Karisto et al. suggest that it is not necessary to resort to classical (but depending on the situation, unlikely) mechanisms, such as ongoing invasion or source-sink dynamics, to explain arthropod populations featuring low-prevalent Wolbachia infections. Instead, low-frequency equilibria might be simply due to reproductive parasites conferring beneficial fitness effects, or Wolbachia symbionts playing Dr. Jekyll (positive fitness effects) and Mr. Hyde (cytoplasmatic incompatibility). 


[1] Beckmann JF, Bonneau M, Chen H, Hochstrasser M, Poinsot D, Merçot H, Weill M, Sicard M, Charlat S (2019) The Toxin–Antidote Model of Cytoplasmic Incompatibility: Genetics and Evolutionary Implications. Trends in Genetics, 35, 175–185.

[2] Karisto P, Duplouy A, Vries C de, Kokko H (2022) Positive fitness effects help explain the broad range of Wolbachia prevalences in natural populations. bioRxiv, 2022.04.11.487824, ver. 5 peer-reviewed and recommended by Peer Community in Ecology.

[3] Laven H (1956) Cytoplasmic Inheritance in Culex. Nature, 177, 141–142.

[4] Perreau J, Zhang B, Maeda GP, Kirkpatrick M, Moran NA (2021) Strong within-host selection in a maternally inherited obligate symbiont: Buchnera and aphids. Proceedings of the National Academy of Sciences, 118, e2102467118.

[5] Vavre F, Fleury F, Varaldi J, Fouillet P, Bouletreau M (2000) Evidence for Female Mortality in Wolbachia-Mediated Cytoplasmic Incompatibility in Haplodiploid Insects: Epidemiologic and Evolutionary Consequences. Evolution, 54, 191–200.

[6] Zug R, Hammerstein P (2015) Bad guys turned nice? A critical assessment of Wolbachia mutualisms in arthropod hosts. Biological Reviews, 90, 89–111.

[7] Zug R, Hammerstein P (2018) Evolution of reproductive parasites with direct fitness benefits. Heredity, 120, 266–281.

Positive fitness effects help explain the broad range of Wolbachia prevalences in natural populationsPetteri Karisto, Anne Duplouy, Charlotte de Vries, Hanna Kokko<p style="text-align: justify;">The bacterial endosymbiont <em>Wolbachia</em> is best known for its ability to modify its host’s reproduction by inducing cytoplasmic incompatibility (CI) to facilitate its own spread. Classical models predict eithe...Host-parasite interactions, Population ecologyJorge Peña2022-04-12 12:52:55 View
03 Jun 2022
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Evolutionary emergence of alternative stable states in shallow lakes

How to evolve an alternative stable state

Recommended by ORCID_LOGO based on reviews by Jean-François Arnoldi and 1 anonymous reviewer

Alternative stable states describe ecosystems that can persist in more than one configuration. An ecosystem can shift between stable states following some form of perturbation. There has been much work on predicting when ecosystems will shift between stable states, but less work on why some ecosystems are able to exist in alternative stable states in the first place. The paper by Ardichvili, Loeuille, and Dakos (2022) addresses this question using a simple model of a shallow lake. Their model is based on a trade-off between access to light and nutrient availability in the water column, two essential resources for the macrophytes they model. They then identify conditions when the ancestral macrophyte will diversify resulting in macrophyte species living at new depths within the lake. The authors find a range of conditions where alternative stable states can evolve, but the range is narrow. Nonetheless, their model suggests that for alternative stable states to exist, one requirement is for there to be asymmetric competition between competing species, with one species being a better competitor on one limiting resource, with the other being a better competitor on a second limiting resource. 

These results are interesting and add to growing literature on how asymmetric competition can aid species coexistence. Asymmetric competition may be widespread in nature, with closely related species often being superior competitors on different resources. Incorporating asymmetric competition, and its evolution, into models does complicate theoretical investigations, but Ardichvili, Loeuille, and Dakos’ paper elegantly shows how substantial progress can be made with a model that is still (relatively) simple.


Ardichvili A, Loeuille N, Dakos V (2022) Evolutionary emergence of alternative stable states in shallow lakes. bioRxiv, 2022.02.23.481597, ver. 3 peer-reviewed and recommended by Peer Community in Ecology.

Evolutionary emergence of alternative stable states in shallow lakesAlice Ardichvili, Nicolas Loeuille, Vasilis Dakos<p style="text-align: justify;">Ecosystems under stress may respond abruptly and irreversibly through tipping points. Although much is explored on the mechanisms that affect tipping points and alternative stable states, little is known on how ecos...Community ecology, Competition, Eco-evolutionary dynamics, Theoretical ecologyTim Coulson2022-03-01 10:54:05 View
24 May 2022
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Controversy over the decline of arthropods: a matter of temporal baseline?

Don't jump to conclusions on arthropod abundance dynamics without appropriate data

Recommended by ORCID_LOGO based on reviews by Gabor L Lovei and 1 anonymous reviewer

Humans are dramatically modifying many aspects of our planet via increasing concentrations of carbon dioxide in the atmosphere, patterns of land-use change, and unsustainable exploitation of the planet’s resources. These changes impact the abundance of species of wild organisms, with winners and losers. Identifying how different species and groups of species are influenced by anthropogenic activity in different biomes, continents, and habitats, has become a pressing scientific question with many publications reporting analyses of disparate data on species population sizes. Many conclusions are based on the linear analysis of rather short time series of organismal abundances.
There has been particular interest in how arthropods are impacted by environmental change, with several recent papers reporting contradictory results. To investigate why these contradictions might arise, Duchenne et al. (2022) conducted an analysis of four published data sets along with a series of experimental analyses of simulated time series to examine the power of widely used statistical analyses to gain inference on temporal trends. Their important paper reveals that accurate inference on dynamics, particularly of species that exhibit large temporal fluctuations in abundance, requires time series that are substantially longer than are typically collected, as well as careful thought as to whether linear models are appropriate. Linear analyses of short time series are susceptible to providing unreliable inference as trends can be strongly influenced by points at either end of the time series. 
Duchenne et al.’s paper provides important insight on the conditions when strong inference on temporal trends of arthropod (and other species) abundances can be made, and when they should be treated with caution. They do not doubt that many insect and arachnid species are changing their abundances, and that patterns in these changes may vary spatially. What their results do say is that we should treat grand claims of population recovery or rapid declines apparently to extinction with caution when they are based on short time series, particularly of species that show significant boom and bust dynamics. In many ways, these results are not unexpected, but it is nice to see such careful and thoughtful analyses and interpretation. More data are required for most arthropod species before clear assessments of abundance trends can be made. Given our reliance on many arthropods for food, pollination, and numerous ecosystem services, and the ability of other species to spread devastating human diseases such as dengue and malaria, it is advisable that we slow our modification of their habitats while additional data are collected to allow us to better characterise the trajectory of arthropod populations to understand what the consequences of our actions on the natural world are likely to be.  

Duchenne F, Porcher E, Mihoub J-B, Loïs G, Fontaine C (2022) Controversy over the decline of arthropods: a matter of temporal baseline? bioRxiv, 2022.02.09.479422, ver. 3 peer-reviewed and recommended by Peer Community in Ecology.

Controversy over the decline of arthropods: a matter of temporal baseline?François Duchenne, Emmanuelle Porcher, Jean-Baptiste Mihoub, Grégoire Loïs, Colin Fontaine<p style="text-align: justify;">Recently, a number of studies have reported somewhat contradictory patterns of temporal trends in arthropod abundance, from decline to increase. Arthropods often exhibit non-monotonous variation in abundance over ti...Conservation biologyTim Coulson2022-02-11 15:44:44 View
31 May 2022
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Sexual coercion in a natural mandrill population

Rare behaviours can have strong effects: evidence for sexual coercion in mandrills

Recommended by ORCID_LOGO based on reviews by Micaela Szykman Gunther and 1 anonymous reviewer

Sexual coercion can be defined as the use by a male of force, or threat of force, which increases the chances that a female will mate with him at a time when she is likely to be fertile, and/or decrease the chances that she will mate with other males, at some cost to the female (Smuts & Smuts 1993). It has been evidenced in a wide range of species and may play an important role in the evolution of sexual conflict and social systems. However, identifying sexual coercion in natural systems can be particularly challenging. Notably, while male behaviour may have immediate consequences on mating success (“harassment”), the mating benefits may be delayed in time (“intimidation”), and in such cases, evidencing coercion requires detailed temporal data at the individual level. Moreover, in some species male aggressive behaviours may be subtle or rare and hence hardly observed, yet still have important effects on female mating probability and fitness. Therefore, investigating the occurrence and consequences of sexual coercion in such species is particularly relevant but studying it in a statistically robust way is likely to require a considerable amount of time spent observing individuals.

In this paper, Smit et al. (2022) test three clear predictions of the sexual coercion hypothesis in a natural population of Mandrills, where severe male aggression towards females is rare: (1) male aggression is more likely on sexually receptive females than on females in other reproductive states, (2) receptive females are more likely to be injured and (3) male aggression directed towards females is positively related to subsequent probability of copulation between those dyads. They also tested an alternative hypothesis, the “aggressive male phenotype” under which the correlation between male aggression towards females and subsequent mating could be statistically explained by male overall aggressivity. In agreement with the three predictions of the sexual coercion hypothesis, (1) male aggression was on average 5 times more likely, and (2) injuries twice as likely, to be observed on sexually receptive females than on females in other reproductive states and (3) copulation between males and sexually receptive females was twice more likely to be observed when aggression by this male was observed on the female before sexual receptivity. There was no support for the aggressive male hypothesis.

The reviewers and I were highly positive about this study, notably regarding the way it is written and how the predictions are carefully and clearly stated, tested, interpreted, and discussed.

This study is a good illustration of a case where some behaviours may not be common or obvious yet have strong effects and likely important consequences and thus be clearly worth studying. More generally, it shows once more the importance of detailed long-term studies at the individual level for our understanding of the ecology and evolution of wild populations.

It is also a good illustration of the challenges faced, when comparing the likelihood of contrasting hypotheses means we need to alter sample sizes and/or the likelihood to observe at all some behaviours. For example, observing copulation within minutes after aggression (and therefore, showing statistical support for “harassment”) is inevitably less likely than observing copulations on the longer-term (and therefore showing statistical support for “intimidation”, when of course effort is put into recording such behavioural data on the long-term). Such challenges might partly explain some apparently intriguing results. For example, why are swollen females more aggressed by males if only aggression before the swollen period seems associated with more chances of mating? Here, the authors systematically provide effect sizes (and confidence intervals) and often describe the effects in an intuitive biological way (e.g., “Swollen females were, on average, about five times more likely to become injured”). This clearly helps the reader to not merely compare statistical significances but also the biological strengths of the estimated effects and the uncertainty around them. They also clearly acknowledge limits due to sample size when testing the harassment hypothesis, yet they provide precious information on the probability of observing mating (a rare behaviour) directly after aggression (already a rare behaviour!), that is, 3 times out of 38 aggressions observed between a male and a swollen female. Once again, this highlights how important it is to be able to pursue the enormous effort put so far into closely and continuously monitoring this wild population.

Finally, this study raises exciting new questions, notably regarding to what extent females exhibit “counter-strategies” in response to sexual coercion, notably whether there is still scope for female mate choice under such conditions, and what are the fitness consequences of these dynamic conflicting sexual interactions. No doubt these questions will sooner than later be addressed by the authors, and I am looking forward to reading their upcoming work.


Smit N, Baniel A, Roura-Torres B, Amblard-Rambert P, Charpentier MJE, Huchard E (2022) Sexual coercion in a natural mandrill population. bioRxiv, 2022.02.07.479393, ver. 5 peer-reviewed and recommended by Peer Community in Ecology.

Smuts BB, Smuts R w. (1993) Male Aggression and Sexual Coercion of Females in Nonhuman Primates and Other Mammals: Evidence and Theoretical Implications. In: Advances in the Study of Behavior (eds Slater PJB, Rosenblatt JS, Snowdon CT, Milinski M), pp. 1–63. Academic Press.

Sexual coercion in a natural mandrill populationNikolaos Smit, Alice Baniel, Berta Roura-Torres, Paul Amblard-Rambert, Marie J. E. Charpentier, Elise Huchard<p style="text-align: justify;">Increasing evidence indicates that sexual coercion is widespread. While some coercive strategies are conspicuous, such as forced copulation or sexual harassment, less is known about the ecology and evolution of inti...Behaviour & EthologyMatthieu Paquet2022-02-11 09:32:49 View
14 Nov 2022
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Estimating abundance of a recovering transboundary brown bear population with capture-recapture models

A new and efficient approach to estimate, from protocol and opportunistic data, the size and trends of populations: the case of the Pyrenean brown bear

Recommended by based on reviews by Tim Coulson, Romain Pigeault and ?

In this study, the authors report a new method for estimating the abundance of the Pyrenean brown bear population. Precisely, the methodology involved aims to apply Pollock's closed robust design (PCRD) capture-recapture models to estimate population abundance and trends over time. Overall, the results encourage the use of PCRD to study populations' demographic rates, while minimizing biases due to inter-individual heterogeneity in detection probabilities.

Estimating the size and trends of animal population over time is essential for informing conservation status and management decision-making (Nichols & Williams 2006). This is particularly the case when the population is small, geographically scattered, and threatened. Although several methods can be used to estimate population abundance, they may be difficult to implement when individuals are rare, elusive, solitary, largely nocturnal, highly mobile, and/or occupy large home ranges in remote and/or rugged habitats. Moreover, in such standard methods,

  • the population is assumed to be closed both geographically (no immigration nor emigration) and demographically (no births nor deaths) and
  • all individuals are assumed to have identical detection probabilities regardless of their individual attributes (e.g., age, body mass, social status) and habitat features (home-range location and composition) (Otis et al. 1978).

However, these conditions are rarely met in real populations, such as wild mammals (e.g., Bellemain et al. 2005; Solbert et al. 2006), and therefore the risk of underestimating population size can rapidly increase because the assumption of perfect detection of all individuals in the population is violated.

Focusing on the critically endangered Pyrenean brown bear that was close to extinction in the mid-1990s, the study by Vanpe et al. (2022), uses protocol and opportunistic data to describe a statistical modeling exercise to construct mark-recapture histories from 2008 to 2020. Among the data, the authors collected non-invasive samples such as a mixture of hair and scat samples used for genetic identification, as well as photographic trap data of recognized individuals. These data are then analyzed in RMark to provide detection and survival estimates. The final model (i.e. PCRD capture-recapture) is then used to provide Bayesian population estimates. Results show a five-fold increase in population size between 2008 and 2020, from 13 to 66 individuals. Thus, this study represents the first published annual abundance and temporal trend estimates of the Pyrenean brown bear population since 2008.

Then, although the results emphasize that the PCRD estimates were broadly close to the MRS counts and had reasonably narrow associated 95% Credibility Intervals, they also highlight that the sampling effort is different according to individuals. Indeed, as expected, the detection of an individual depends on

  • the intraspecific home range size variation that results in individuals that move the most being most likely to be detected and
  • the mortality rate which is higher on cubs than on adults and subadults (due to infanticide by males, predation, death of the mother, or abandonment).

Overall, the PCRD capture-recapture modelling approach, involved in this study, provides robust estimates of abundance and demographic rates of the Pyrenean brown bear population (with associated uncertainty) while minimizing and considering bias due to inter-individual heterogeneity in detection probabilities.

The authors conclude that mark-recapture provides useful population estimates and urge wildlife ecologists and managers to use robust approaches, such as the RDPC capture-recapture model, when studying large mammal populations. This information is essential to inform management decisions and assess the conservation status of populations.



Bellemain, E.V.A., Swenson, J.E., Tallmon, D., Brunberg, S. and Taberlet, P. (2005). Estimating population size of elusive animals with DNA from hunter-collected feces: four methods for brown bears. Cons. Biol. 19(1), 150-161.

Nichols, J.D. and Williams, B.K. (2006). Monitoring for conservation. Trends Ecol. Evol. 21(12), 668-673.

Otis, D.L., Burnham, K.P., White, G.C. and Anderson, D.R. (1978). Statistical inference from capture data on closed animal populations. Wildlife Monographs (62), 3-135.

Solberg, K.H., Bellemain, E., Drageset, O.M., Taberlet, P. and Swenson, J.E. (2006). An evaluation of field and non-invasive genetic methods to estimate brown bear (Ursus arctos) population size. Biol. Conserv. 128(2), 158-168.

Vanpé C, Piédallu B, Quenette P-Y, Sentilles J, Queney G, Palazón S, Jordana IA, Jato R, Elósegui Irurtia MM, de la Torre JS, and Gimenez O (2022) Estimating abundance of a recovering transboundary brown bear population with capture-recapture models. bioRxiv, 2021.12.08.471719, ver. 4 recommended and peer-reviewed by PCI Ecology.

Estimating abundance of a recovering transboundary brown bear population with capture-recapture modelsCécile Vanpé, Blaise Piédallu, Pierre-Yves Quenette, Jérôme Sentilles, Guillaume Queney, Santiago Palazón, Ivan Afonso Jordana, Ramón Jato, Miguel Mari Elósegui Irurtia, Jordi Solà de la Torre, Olivier Gimenez<p>Estimating the size of small populations of large mammals can be achieved via censuses, or complete counts, of recognizable individuals detected over a time period: minimum detected (population) size (MDS). However, as a population grows larger...Conservation biology, Demography, Population ecologyNicolas BECH2022-01-20 10:49:59 View
15 May 2023
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Behavioral flexibility is manipulable and it improves flexibility and innovativeness in a new context

An experiment to improve our understanding of the link between behavioral flexibility and innovativeness

Recommended by ORCID_LOGO based on reviews by Maxime Dahirel, Andrea Griffin, Aliza le Roux and 1 anonymous reviewer

Whether individuals are able to cope with new environmental conditions, and whether this ability can be improved, is certainly of great interest in our changing world. One way to cope with new conditions is through behavioral flexibility, which can be defined as “the ability to adapt behavior to new circumstances through packaging information and making it available to other cognitive processes” (Logan et al. 2023). Flexibility is predicted to be positively correlated with innovativeness, the ability to create a new behavior or use an existing behavior in a few situations (Griffin & Guez 2014). 
The post-study manuscript by Logan et al. (2023) proposes to test flexibility manipulability, and the relationship between flexibility and innovativeness. The authors did so with an experimental study on great-tailed grackles (Quiscalus mexicanus), an expanding species in the US, known to be flexible. 
The authors used serial reversal learning to investigate (1) whether behavioral flexibility, as measured by reversal learning using tubes of different shades, is manipulable; (2) whether manipulating (improving/training) behavioral flexibility improves flexibility and innovativeness in new contexts; (3) the type of learning strategy used by the individuals throughout the serial reversals.
The study described in this manuscript was pre-registered in Logan et al. (2019) and received in-principle recommendation on 26 Mar 2019 (Coulon 2019). One hypothesis from this original preregistration will be treated in a separate manuscript.
Among several interesting results, what I found most striking is that flexibility, in this species, seems to be a trait that is acquired by experience (vs. inherent to the individual). This opens exciting interrogations on the role of social learning, and on the impact of rapid environmental changes (which may force the individuals to experiment new ways to access to resources, for example), on individual flexibility and adaptability to new conditions. 

Coulon A (2019) Can context changes improve behavioral flexibility? Towards a better understanding of species adaptability to environmental changes. Peer Community in Ecology, 100019.

Griffin, A. S., & Guez, D. (2014). Innovation and problem solving: A review of common mechanisms. Behavioural Processes, 109, 121–134.

Logan C, Rowney C, Bergeron L, Seitz B, Blaisdell A, Johnson-Ulrich Z, McCune K (2019)
Is behavioral flexibility manipulatable and, if so, does it improve flexibility and problem solving in a new context? In Principle Recommendation 2019. PCI Ecology.

Logan CJ, Lukas D, Blaisdell AP, Johnson-Ulrich Z, MacPherson M, Seitz B, Sevchik A, McCune KB (2023) Behavioral flexibility is manipulable and it improves flexibility and innovativeness in a new context. EcoEcoRxiv, version 5 peer-reviewed and recommended by Peer Community in Ecology.

Behavioral flexibility is manipulable and it improves flexibility and innovativeness in a new contextLogan CJ, Lukas D, Blaisdell AP, Johnson-Ulrich Z, MacPherson M, Seitz BM, Sevchik A, McCune KB<p style="text-align: justify;">Behavioral flexibility, the ability to adapt behavior to new circumstances, is thought to play an important role in a species’ ability to successfully adapt to new environments and expand its geographic range. Howev...Behaviour & Ethology, Preregistrations, ZoologyAurélie Coulon2022-01-13 19:08:52 View
15 Nov 2023
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The challenges of independence: ontogeny of at-sea behaviour in a long-lived seabird

On the road to adulthood: exploring progressive changes in foraging behaviour during post-fledging immaturity using remote tracking

Recommended by based on reviews by Juliet Lamb and 1 anonymous reviewer

In most vertebrate species, the period of life spanning from departure from the growing site until reaching a more advanced life stage (immature or adult) is critical. During this period, juveniles are often highly vulnerable because they have not reached the morphological, physiological and behavioural maturity levels of adults yet and are therefore at high risk of mortality, e.g. through starvation, depredation or competition (e.g. Marchetti & Price 1989, Wunderle 1991, Naef-Daenzer & Grüebler 2016). In line with this, juvenile survival is most often far lower than adult survival (e.g. Wooller et al. 1992). In species with parental care, juveniles have to acquire behavioural independence from their parents and possibly establish their own territory during this period of life. Very often, this is also the period that is least well-known in the life cycle (Cox et al. 2014, Naef-Daenzer & Grüebler 2016) because of reduced accessibility to individuals and/or adoption of low conspicuous behaviours. Therefore, our understanding of how juveniles acquire typical adult behaviours and how this progressively increases their survival prospects is still very limited (Naef-Daenzer & Grüebler 2016), and questions such as the length of this transition period or the cognitive (e.g. learning, memorization) mechanisms involved remain largely unresolved. This is particularly true regarding the acquisition of independent foraging behaviour (Marchetti & Price 1989).

Because direct observations of juvenile behaviours are usually very difficult except in specific situations or at the cost of an enormous effort, the use of remote tracking devices can be particularly appealing in this context (e.g. Ponchon et al. 2013, Kays et al. 2015). Over the past decades, technical advances have allowed the monitoring of not only individuals’ movements at both large and small spatial scales but also their activities and behaviours based on different parameters recording e.g. speed of movement or diving depth (Whitford & Klimley 2019). Device miniaturization has in particular allowed smaller species to be equipped and/or longer periods of time to be monitored (e.g. Naef-Daenzer et al. 2005). This has opened up whole fields of research, and has been particularly used on marine seabirds. In these species, individuals are most often inaccessible when at sea, representing most of the time outside (and even within) the breeding season, and the life cycle of these long-lived species can include an extended immature period (up to many years) during which most of them will remain unseen, until they come back as breeders or pre-breeders (e.g. Wooller et al. 1992, Oro & Martínez-Abraín 2009). Survival has been found to increase gradually with age in these species before reaching high values characteristic of the adult stage. However, the mechanisms underlying this increase are still to be deciphered.

The study by Delord et al. (2023) builds upon the hypothesis that juveniles gradually learn foraging techniques and movement strategies, improving their foraging efficiency, as previous data on flight parameters seemed to show in different long-lived bird species. Yet, these previous studies obtained data over a limited period of time, i.e. a few months at best. Whether these data could capture the whole dynamics of the progressive acquisition of foraging and movement skills can only be assessed by measuring behaviour over a longer time period and comparing it to similar data in adults, to account for seasonal variation in relation to both resource availability and energetic demands, e.g. due to molt.

The present study (Delord et al. 2023) addresses these questions by taking advantage of longer-lasting recordings of the location and activity of juvenile, immature and adult birds obtained simultaneously to investigate changes over time in juvenile behaviour and thereby provide hints about how young progressively acquire foraging skills. This study is performed on Amsterdam albatrosses, a highly endangered long-lived sea bird, with obvious conservation issues (Thiebot et al. 2015). The results show progressive changes in foraging effort over the first two months after departure from the birth colony, but large differences remain between life stages over a much longer time frame. They also reveal strong variations between sexes and over time in the year. Overall, this study, therefore, confirms the need for very long-term data to be collected in order to address the question of progressive behavioural maturation and associated survival consequences in such species with strongly deferred maturity. Ideally, the same individuals should be monitored over different life stages, from the juvenile period up to adulthood, but this would require further technical development to release the issue of powering duration limitation.

As reviewers emphasized in the first review round, one main challenge now remains to ascertain the outcome of the observed behavioural changes in foraging behaviour: we expect them to reflect improvement in foraging skills and thus performance of juveniles over time, but this would need to be tested. Collecting data on foraging efficiency is yet another challenge, that future technical developments may also help overcome. Importantly also, data were available only for individuals that could be caught again because the tracking device had to be retrieved from the bird. Here, a substantial fraction of the loggers (one-fifth) could not be found again (Delord et al. 2023). To what extent the birds for which no data could be obtained are a random sample of the equipped birds would also need to be assessed. The further development of remote tracking techniques allowing data to be downloaded from a long distance should help further exploration of behavioural ontogeny of juveniles while maturing and its survival consequences. Because the maturation process explored here is likely to show very different characteristics (e.g. timing and speed) in smaller / shorter-lived species (see Cox et al. 2014, Naef-Daenzer & Grüebler 2016), the development of miniaturization is also expected to allow further investigation of post-fledging behavioural maturation in a wider range of bird species. Our understanding of this crucial life phase in different types of species should thus continue to progress in the coming years.


Cox W. A., Thompson F. R. III, Cox A. S. & Faaborg J. 2014. Post-fledging survival in passerine birds and the value of post-fledging studies to conservation. Journal of Wildlife Management, 78: 183-193.

Delord K., Weimerskirch H. & Barbraud C. 2023. The challenges of independence: ontogeny of at-sea behaviour in a long-lived seabird. bioRxiv, ver. 6 peer-reviewed and recommended by Peer Community in Ecology.

Kays R., Crofoot M. C., Jetz W. & Wikelski M. 2015. Terrestrial animal tracking as an eye on life and planet. Science, 348 (6240).

Marchetti K: & Price T. 1989. Differences in the foraging of juvenile and adult birds: the importance of developmental constraints. Biological Reviews, 64: 51-70.

Naef-Daenzer B., Fruh D., Stalder M., Wetli P. & Weise E. 2005. Miniaturization (0.2 g) and evaluation of attachment techniques of telemetry transmitters. The Journal of Experimental Biology, 208: 4063–4068.

Naef-Daenzer B. & Grüebler M. U. 2016. Post-fledging survival of altricial birds: ecological determinants and adaptation. Journal of Field Ornithology, 87: 227-250.

Oro D. & Martínez-Abraín A. 2009. Ecology and behavior of seabirds. Marine Ecology, pp.364-389.

Ponchon A., Grémillet D., Doligez B., Chambert T., Tveera T., Gonzàles-Solìs J & Boulinier T. 2013. Tracking prospecting movements involved in breeding habitat selection: insights, pitfalls and perspectives. Methods in Ecology and Evolution, 4: 143-150.

Thiebot J.-B., Delord K., Barbraud C., Marteau C. & Weimerskirch H. 2015. 167 individuals versus millions of hooks: bycatch mitigation in longline fisheries underlies conservation of Amsterdam albatrosses. Aquatic Conservation 26: 674-688.

Whitford M & Klimley A. P. An overview of behavioral, physiological, and environmental sensors used in animal biotelemetry and biologging studies. Animal Biotelemetry, 7: 26.

Wooller R.D., Bradley J. S. & Croxall J. P. 1992. Long-term population studies of seabirds. Trends in Ecology and Evolution, 7: 111-114.

Wunderle J. M. 1991. Age-specific foraging proficiency in birds. Current Ornithology, 8: 273-324.

The challenges of independence: ontogeny of at-sea behaviour in a long-lived seabirdKarine Delord, Henri Weimerskirch, Christophe Barbraud<p style="text-align: justify;">The transition to independent foraging represents an important developmental stage in the life cycle of most vertebrate animals. Juveniles differ from adults in various life history traits and tend to survive less w...Behaviour & Ethology, Foraging, OntogenyBlandine Doligez2021-10-26 07:51:49 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.


[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.

[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.

[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.

[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.

[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.

[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.

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