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10 Oct 2018
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Detecting within-host interactions using genotype combination prevalence data

Combining epidemiological models with statistical inference can detect parasite interactions

Recommended by based on reviews by Samuel Díaz Muñoz, Erick Gagne and 1 anonymous reviewer

There are several important topics in the study of infectious diseases that have not been well explored due to technical difficulties. One such topic is pursued by Alizon et al. in “Modelling coinfections to detect within-host interactions from genotype combination prevalences” [1]. Both theory and several important examples have demonstrated that interactions among co-infecting strains can have outsized impacts on disease outcomes, transmission dynamics, and epidemiology. Unfortunately, empirical data on pathogen interactions and their outcomes is often correlational making results difficult to decipher.
The analytical framework developed by Alizon et al. [1] infers the presence and strength of pathogen interactions through their impact on transmission dynamics using a novel application of Approximate Bayesian Computation (ABC)-regression to epidemiological data. Traditional analytic approaches identify pathogen interactions when the observed distribution of pathogens among hosts differ from ‘neutral’ expectations. However, deviations from this expectation are not only a result of inter-strain interactions but can be caused by many ecological interactions, such as heterogeneity in host contact networks. To overcome this difficulty, Alizon et al [1] develop an analytical framework that incorporates explicit epidemiological models to allow inference of interactions among strains of Human Papillomaviruses (HPV) even with other ecological interactions that impact the distribution of strains among hosts. Alizon et al also demonstrate that using more of the available data, including the specific combination of strains present in hosts and knowledge of the connectivity of the hosts (i.e., super-spreaders), leads to more accurate inferences of the strength and direction of within-host interactions among coinfecting strains. This method successfully identified data generated from models with high and moderate inter-strain interaction intensity when the host population was homogeneous and was only slightly less successful when the host population was heterogeneous (super-spreaders present). By comparison, some previously published analytical methods could identify only some inter-strain interactions in datasets generated from models with homogeneous host populations, but host heterogeneity obscured these interactions.
This manuscript makes seamless connections between basic viral biology and its epidemiological consequences by tying them together with realistic models, illustrating the fundamental utility of biological modeling. This analytical framework provides crucial tools for experimentalists, facilitating collaborations with theoreticians to better understand the epidemiological consequences of co-infections. In addition, the method is simple enough to be applied by a broad base of experimentalists to the many pathogens where co-infections are common. Thus, this paper has the potential to impact several research fields and public health practice. Those attempting to apply this method should note the potential limitations noted by the authors. For example, it is not designed to detect the mechanisms of inter-strain interactions (there is no within host component of the models) but to identify the existence of interactions through patterns indicative of these interactions while ruling out other sources that could cause the pattern. This approach is likely to be most accurate when strain identification within hosts is precise and unbiased - which is unlikely in many systems where samples are taken only from symptomatic cases and strain detection is not sufficiently sensitive – and when host contact networks can be reasonably estimated. Importantly, a priori knowledge of the set of possible epidemiological models is needed for accurate parameter estimates, which may be true for several prominent pathogens, but not be so for many other pathogens and symbionts. We look forward to future extensions of this framework where this restriction is relaxed. Alizon et al. [1] have provided a framework that will facilitate theoretical and empirical work on the impact of coinfections on infectious disease and should shape future public health data collection standards.


[1] Alizon, S., Murall, C.L., Saulnier, E., & Sofonea, M.T. (2018). Detecting within-host interactions using genotype combination prevalence data. bioRxiv, 256586, ver. 3 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/256586

Detecting within-host interactions using genotype combination prevalence dataSamuel Alizon, Carmen Lía Murall, Emma Saulnier, Mircea T Sofonea<p>Parasite genetic diversity can provide information on disease transmission dynamics but most methods ignore the exact combinations of genotypes in infections. We introduce and validate a new method that combines explicit epidemiological modelli...Eco-immunology & Immunity, Epidemiology, Host-parasite interactions, Statistical ecologyDustin Brisson Samuel Díaz Muñoz, Erick Gagne2018-02-01 09:23:26 View
30 May 2024
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Disentangling the effects of eutrophication and natural variability on macrobenthic communities across French coastal lagoons

Untangling Eutrophication Effects on Coastal Lagoon Ecosystems

Recommended by ORCID_LOGO based on reviews by Kaylee P. Smit, Matthew J. Pruden and Kendyl Wright

Disentangling the effects on ecosystem structure and functioning of natural and human-induced impacts in transitional waters is a great challenge in coast ecology. This is due to the observation that the ecosystems of transitional waters are naturally dynamic systems with characteristics of stressed systems. For example, the benthic communities present low species richness and high abundance of species with a high tolerance to variations, e.g., salinity. This general observation is known as the paradigm of the “Transitional Waters Quality Paradox” (Zaldívar et al., 2008) derived from the previously described “Estuarine Quality Paradox” (Elliott and Quintino, 2007). 

In Jones et al. (2024) “Disentangling the effects of eutrophication and natural variability on macrobenthic communities across French coastal lagoons”, a great diversity of lagoons is analyzed to disentangle the effects of eutrophication from those of natural environmental variability on benthic macroinvertebrates and understanding the links between environmental variables affecting benthic macroinvertebrates. These authors use a very elegant set of numerical approaches, including correlograms, linear models and variance partitioning. They apply this suite to a dataset of macrobenthic invertebrate abundances and environmental variables from 29 Mediterranean coastal lagoons in France.

Through this suite of analyses, they demonstrate the strong complexity of the mechanisms interplaying in a situation of eutrophication on lagoon macrobenthos. The mechanisms involved are direct, like toxicity, or indirect, for example, through modifications of the sediment's biogeochemistry. Such a result on the different interactions involved is very important in the context of the search for indicators to define ecosystem status. Improving the definition of metrics is essential in environmental management decisions.


Elliott, M. and Quintino, V. (2007) The estuarine quality paradox, environmental homeostasis and the difficulty of detecting anthropogenic stress in naturally stressed areas. Marine Pollution Bulletin 54, 640–645.

Jones et al. (2024) Disentangling the effects of eutrophication and natural variability on macrobenthic communities across French coastal lagoons bioRxiv, 2022.08.18.504439, ver. 4 peer-reviewed and recommended by Peer Community in Ecology.

Zaldívar, J. (2008). Eutrophication in transitional waters: an overview.

Disentangling the effects of eutrophication and natural variability on macrobenthic communities across French coastal lagoonsAuriane G. Jones, Gauthier Schaal, Aurélien Boyé, Marie Creemers, Valérie Derolez, Nicolas Desroy, Annie Fiandrino, Théophile L. Mouton, Monique Simier, Niamh Smith, Vincent Ouisse<p style="text-align: justify;">Coastal lagoons are transitional ecosystems that host a unique diversity of species and support many ecosystem services. Owing to their position at the interface between land and sea, they are also subject to increa...Biodiversity, Community ecology, Ecosystem functioning, Marine ecologyNathalie Niquil Matthew J. Pruden2023-09-08 11:26:01 View
24 May 2024
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Effects of water nutrient concentrations on stream macroinvertebrate community stoichiometry: a large-scale study

The influence of water phosphorus and nitrogen loads on stream macroinvertebrate community stoichiometry

Recommended by ORCID_LOGO based on reviews by Thomas Guillemaud, Jun Zuo and 1 anonymous reviewer

The manuscript by Beck et al. (2024) investigates the effects of water phosphorus and nitrogen loads on stream macroinvertebrate community stoichiometry across France. Utilizing data from over 1300 standardized sampling events, this research finds that community stoichiometry is significantly influenced by water phosphorus concentration, with the strongest effects at low nitrogen levels.

The results demonstrate that the assumptions of Ecological Stoichiometry Theory apply at the community level for at least two dominant taxa and across a broad spatial scale, with probable implications for nutrient cycling and ecosystem functionality.

This manuscript contributes to ecological theory, particularly by extending Ecological Stoichiometry Theory to include community-level interactions, clarifying the impact of nutrient concentrations on community structure and function, and informing nutrient management and conservation strategies.

In summary, this study not only addresses a gap in community-level stoichiometric research but also delivers crucial empirical support for advancing ecological science and promoting environmental stewardship.


Beck M, Billoir E, Usseglio-Polatera P, Meyer A, Gautreau E and Danger M (2024) Effects of water nutrient concentrations on stream macroinvertebrate community stoichiometry: a large-scale study. bioRxiv, 2024.02.01.574823, ver. 2 peer-reviewed and recommended by Peer Community in Ecology.

Effects of water nutrient concentrations on stream macroinvertebrate community stoichiometry: a large-scale studyMiriam Beck, Elise Billoir, Philippe Usseglio-Polatera, Albin Meyer, Edwige Gautreau, Michael Danger<p>Basal resources generally mirror environmental nutrient concentrations in the elemental composition of their tissue, meaning that nutrient alterations can directly reach consumer level. An increased nutrient content (e.g. phosphorus) in primary...Community ecology, Ecological stoichiometryHuihuang Chen Thomas Guillemaud, Jun Zuo, Anonymous2024-02-02 10:14:01 View
06 Oct 2020
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Does space use behavior relate to exploration in a species that is rapidly expanding its geographic range?

Explore and move: a key to success in a changing world?

Recommended by based on reviews by Joe Nocera, Marion Nicolaus and Laure Cauchard

Changes in the spatial range of many species are one of the major consequences of the profound alteration of environmental conditions due to human activities. Some species expand, sometimes spectacularly during invasions; others decline; some shift. Because these changes result in local biodiversity loss (whether local species go extinct or are replaced by colonizing ones), understanding the factors driving spatial range dynamics appears crucial to predict biodiversity dynamics. Identifying the factors that shape individual movement is a main step towards such understanding. The study described in this preregistration (McCune et al. 2020) falls within this context by testing possible links between individual exploration behaviour and movements related to daily space use in an avian study model currently rapidly expanding, the great-tailed grackle (Quiscalus mexicanus).

Movement and exploration: which direction(s) for the link between exploration and dispersal?
Individuals are known to differ in their tendency to explore the environment (Réale et al. 2007; Wolf and Weissing 2012) and therefore in their motivation to move. Accordingly, exploration has been shown to relate to dispersal behaviour, i.e. movements between breeding sites (Dingemanse et al. 2003, Le Galliard et al. 2011, Rasmussen and Belk 2012; reviews in Cote et al. 2010, Ronce et al. 2012). Yet, the mechanisms underlying this link often remain unclear, due to the correlative nature of the data. A classical assumption is that dispersers may benefit from a high capacity to explore, allowing them to familiarize quicker with their new environment once reached, thus alleviating dispersal costs (Bonte et al. 2012). The association between dispersal and exploration would in this case result from selection for this combination of traits (Ronce et al. 2012), even though dispersal event itself may be independent from (and precede the effect of) exploration behaviour. Alternatively (but not exclusively), dispersal may simply be the final outcome of longer movements by individuals exploring larger ranges (Badyaev et al. 1996, Schliehe-Diecks et al. 2012). In the absence of easy ways to manipulate dispersal behaviour, on the one hand, and exploration tendency, on the other hand, investigating detailed, small-scale individual movements in relation to exploration should thus shed light on which processes may yield the observed relations between exploration as an individual personality trait and large-scale, long-term movements, such as dispersal, underlying species range dynamics.
In this project, the exploration behaviour of grackles will be measured in controlled conditions using standardized tests in captivity (McCune et al. 2019) before individuals are released and their daily space use behaviour will then be measured using remote tracking over long time periods (McCune et al. 2020). Importantly, these coupled measures will be obtained for individuals captured in three different populations: within the historical range of the species, in the middle of its expanding range and at the edge of the range (McCune et al. 2020). Therefore, the project will test (i) whether daily space use of individuals is linked to their intrinsic exploration tendency and (ii) whether space use differs between individuals from different populations along the expanding range. The preregistration echoes a complementary project by the same team that will focus on exploration and test (iii) whether exploration tendency differs between individuals from these different populations. Taken together, these three analyses will therefore provide solid background information to assess the role of exploration in the individuals’ decisions leading to movement and range dynamics in this species.
As underlined in the preregistration, previous studies addressing the links between individual exploration behaviour and movements have mostly focused on dispersal. A first type of studies have (as will be done here) measured exploration behaviour of individuals, often in captivity (Dingemanse et al. 2003, Korsten et al. 2013) but also in the wild (Rasmussen and Belk 2012, Debeffe et al. 2013), and related these measures to subsequent dispersal behaviour. The (often implicit) underlying assumption is that more exploratory individuals will be more likely to move further, explore different habitats and thus end up breeding farther than less explorative ones. In other words, exploration tendency precedes and drives dispersal. Sometimes, exploratory behaviour is measured on individuals of known dispersal status, i.e. after the dispersal event (Hoset et al. 2011), in which case selection for certain exploration phenotypes among dispersers may already have occurred. Besides this first approach, another type of studies have measured ‘exploration’ behaviour under the form of prospecting movements of individuals and linked these movements to subsequent dispersal (often in the context of habitat selection). While these studies were in the past based on direct thus potentially biased observations (Reed et al. 1999), they now rely more and more on technological advances using (miniaturized) remote tracking devices (Ponchon et al. 2013) that provide far more complete and unbiased movement data, and sometimes also complementary measures of individuals’ internal state. In this case, the implicit assumption is that individuals prospecting farther and/or in more habitat patches will be more likely to settle in a site located farther away from their departure site, because of a more exhaustive sampling of possible sites allowing individuals to identify higher-quality sites (Badyaev et al. 1996). In other words, exploration tendency would not directly lead to higher movements or longer distances, but would allow individuals to optimize their habitat choice among more numerous options, thus leading to an increased dispersal probability or distance; the relation between exploration and dispersal would thus be indirect. Prospecting studies address more closely the underlying mechanisms of movement; however, they cannot easily separate intrinsic individual exploratory tendency from the prospecting movements themselves, with potential feedback effects of the information already gathered on future exploration of other sites or patches, thus on subsequent movements.
By focusing on individual daily space use movements as a mechanistic approach to understand large-scale movements potentially involved in colonization and range expansion, the grackle study described in this preregistration (McCune et al. 2020) will thus contribute to bridge the knowledge gaps between exploration and dispersal. By linking exploration measures obtained from a battery of standardized tests conducted in controlled conditions to individual daily space use and movements recorded in the wild, the grackle project is set in between previous studies addressing the links between exploration and dispersal: it will document exploration in a separate and independent context with respect to the movements themselves, and it will use a mechanistic view of detailed movements by the same individuals in the wild to explore potential implications for dispersal and range expansion. Testing differences between the three study populations over the species range will indeed inform about potential large-scale, population implications of among-individual variation in the link between exploration and movements. Because this study will only measure already settled adult individuals whose previous history is unknown, there will nevertheless be no direct possible exploration of the link with either previous or subsequent dispersal behaviour. Thus, the potential links studied here relate more directly to post-dispersal benefits of exploration for an optimal exploitation of the new environment. Yet, if exploration is a life-long personality trait linked to daily movement patterns, it may also relate to natal dispersal movements in young individuals.

Evolutionary and conservation perspectives
If the results of the project reveal that exploration tendency and daily space use movements are indeed linked, and that individuals from populations across the species range differ in these traits, new questions will emerge. A first question would be whether such among-individual differences are at the origin of range expansion or rather one of its consequences since, again, we deal with correlative data here. In other words, individuals may differ in exploration tendency, and this may confer them different ability to move around, find and colonize new habitats; or individuals may show differences in exploration following arrival in a new habitat, either because more explorative individuals gain fitness benefits and are thus selected, or because of behavioural plasticity and post-colonization adjustment of exploration behaviour when facing new ecological and social conditions in the new environment. Another open question relates to the link between daily space use and dispersal: is dispersal a by-product of higher daily movements that allow individuals to discover new favorable places where to settle? Exploring this link could involve measuring just fledged individuals before natal dispersal occurs and/or individuals chosen according to their own dispersal history, and this would then imply long-term population monitoring as an efficient (but constraining) tool to address such questions. Finally, assessing the fitness consequences of the link between exploration and space use behaviour, and whether these consequences differ between populations along the range expansion, would also be needed to understand the contribution of this link to the invasion success of this species.
The study model chosen for this project is a rapidly expanding species. Importantly, however, and as emphasized in the preregistration, documenting links between exploration and daily space use patterns as well as differences between populations with different trajectories can provide crucial information in general to understand population persistence in response to global climate and landscape changes, both regarding invasion ability or extinction risk. The information should be key to assess the probability that a species may decline, persist or expand in studies addressing biodiversity and community dynamics in a changing world.


Badayev, A. V., Martin, T. E and Etges, W. J. 1996. Habitat sampling and habitat selection by female wild turkeys: ecological correlates and reproductive consequences. Auk 113: 636-646. doi:
Bonte, D. et al. 2012. Costs of dispersal. Biological Reviews 87: 290-312. doi:
Cote, J., Clobert, J., Brodin, T., Fogarty, S. and Sih, A. 2010. Personality-dependent dispersal: characterization, ontogeny and consequences for spatially structured populations. Philosophical Transactions of the Royal Society B 365: 4065-4576. doi:
Debeffe, L., Morellet, N., Cargnelutti, B., Lourtet, B., Coulon, A., Gaillard, J.-M., Bon, R. and Hewison A. J. M. 2013. Exploration as a key component of natal dispersal: dispersers explore more than philopatric individuals in roe deer. Animal Behaviour 86: 143-151. doi:
Dingemanse, N. J., Both, C., van Noordwijk, A. J., Rutten, A. L. and Drent, P. J. 2003. Natal dispersal and personalities in great tits (Parus major). Proceedings of the Royal Society B 270: 741-747. doi:
Hoset, K. S., Ferchaud, A.-L., Dufour, F., Mersch, D., Cote, J. and Le Galliard, J.-F. 2011. Natal dispersal correlates with behavioral traits that are not consistent across early life stages. Behavioral Ecology 22: 176–183. doi:
Korsten, P., van Overveld, T., Adriaensen, F. and Matthysen, E. 2013. Genetic integration of local dispersal and exploratory behaviour in a wild bird. Nature Communications 4: 2362. doi:
Le Galliard, J.-F., Rémy, A., Ims, R. A. and Lambin, X. 2011. Patterns and processes of dispersal behaviour in arvicoline rodents. Molecular Ecology 21: 505-523. doi:
McCune K, Ross C, Folsom M, Bergeron L, Logan CJ. 2020. Does space use behavior relate to exploration in a species that is rapidly expanding its geographic range? In principle acceptance by PCI Ecology of the version on 23 Sep 2020
McCune K, MacPherson M, Rowney C, Bergeron L, Folsom M, Logan CJ. 2019. Is behavioral flexibility linked with exploration, but not boldness, persistence, or motor diversity? ( In principle acceptance by PCI Ecology of the version on 27 Mar 2019
Ponchon, A., Grémillet, D., Doligez, B., Chambert, T., Tveraa, T., González-Solís, J. and Boulinier, T. 2013. Tracking prospecting movements involved in breeding habitat selection: insights, pitfalls and perspectives. Methods in Ecology and Evolution 4: 143-150. doi:
Rasmussen, J. E. and Belk, M. C. 2012. Dispersal behavior correlates with personality of a North American fish. Current Zoology 58: 260–270. doi:
Réale, D., Reader, S. M., Sol, D., McDougall, P. T. and Dingemanse, N. J. 2007. Integrating animal temperament within ecology and evolution. Biological Reviews 82: 291-318. doi:
Reed, J. M., Boulinier, T., Danchin, E. and Oring, L. W. 1999. Informed dispersal: prospecting by birds for breeding sites. Current Ornithology 15: 189-259. doi:
Ronce, O. and Clobert, J. 2012. Dispersal syndromes. pp. 119-138 In Dispersal Ecology and Evolution (eds. Clobert, J., Baguette, M., Benton, T. G. and Bullock, J. M.), pp. 119-138. Oxford University Press.
Schliehe-Diecks, S., Eberle, M. and Kappeler, P. M. 2012. Walk the line - dispersal movements of gray mouse lemurs (Microcebus murinus). Behavioral Ecology and Sociobiology 66: 1175-1185. doi:
Wolf, M. and Weissing, F. J. 2012. Animal personalities: consequences for ecology and evolution. Trends in Ecology and Evolution 27: 452-461. doi:

Does space use behavior relate to exploration in a species that is rapidly expanding its geographic range?Kelsey B. McCune, Cody Ross, Melissa Folsom, Luisa Bergeron, Corina LoganGreat-tailed grackles (Quiscalus mexicanus) are rapidly expanding their geographic range (Wehtje 2003). Range expansion could be facilitated by consistent behavioural differences between individuals on the range edge and those in other parts of th...Behaviour & Ethology, Biological invasions, Conservation biology, Habitat selection, Phenotypic plasticity, Preregistrations, Spatial ecology, Metacommunities & MetapopulationsBlandine Doligez2019-09-30 19:27:40 View
31 Aug 2023
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Assessing species interactions using integrated predator-prey models

Addressing the daunting challenge of estimating species interactions from count data

Recommended by ORCID_LOGO and ORCID_LOGO based on reviews by 2 anonymous reviewers

Trophic interactions are at the heart of community ecology. Herbivores consume plants, predators consume herbivores, and pathogens and parasites infect, and sometimes kill, individuals of all species in a food web. Given the ubiquity of trophic interactions, it is no surprise that ecologists and evolutionary biologists strive to accurately characterize them. 

The outcome of an interaction between individuals of different species depends upon numerous factors such as the age, sex, and even phenotype of the individuals involved and the environment in which they are in. Despite this complexity, biologists often simplify an interaction down to a single number, an interaction coefficient that describes the average outcome of interactions between members of the populations of the species. Models of interacting species tend to be very simple, and interaction coefficients are often estimated from time series of population sizes of interacting species. Although biologists have long known that this approach is often approximate and sometimes unsatisfactory, work on estimating interaction strengths in more complex scenarios, and using ecological data beyond estimates of abundance, is still in its infancy. 

In their paper, Matthieu Paquet and Frederic Barraquand (2023)​ develop a demographic model of a predator and its prey. They then simulate demographic datasets that are typical of those collected by ecologists and use integrated population modelling to explore whether they can accurately retrieve the values interaction coefficients included in their model. They show that they can with good precision and accuracy. The work takes an important step in showing that accurate interaction coefficients can be estimated from the types of individual-based data that field biologists routinely collect, and it paves for future work in this area.

As if often the case with exciting papers such as this, the work opens up a number of other avenues for future research. What happens as we move from demographic models of two species interacting such as those used by Paquet and Barraquand​ to more realistic scenarios including multiple species? How robust is the approach to incorrectly specified process or observation models, core components of integrated population modelling that require detailed knowledge of the system under study? 

Integrated population models have become a powerful and widely used tool in single-species population ecology. It is high time the techniques are extended to community ecology, and this work takes an important step in showing that this should and can be done. I would hope the paper is widely read and cited.


Paquet, M., & Barraquand, F. (2023). Assessing species interactions using integrated predator-prey models. EcoEvoRxiv, ver. 2 peer-reviewed and recommended by Peer Community in Ecology.

Assessing species interactions using integrated predator-prey modelsMatthieu Paquet, Frederic Barraquand<p style="text-align: justify;">Inferring the strength of species interactions from demographic data is a challenging task. The Integrated Population Modelling (IPM) approach, bringing together population counts, capture-recapture, and individual-...Community ecology, Demography, Euring Conference, Food webs, Population ecology, Statistical ecologyTim Coulson Ilhan Özgen-Xian2023-01-05 17:02:22 View
02 Aug 2022
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The effect of dominance rank on female reproductive success in social mammals

When do dominant females have higher breeding success than subordinates? A meta-analysis across social mammals.

Recommended by ORCID_LOGO based on reviews by 2 anonymous reviewers

In this meta-analysis, Shivani et al. [1] investigate 1) whether dominance and reproductive success are generally associated across social mammals and 2) whether this relationship varies according to a) life history traits (e.g., stronger for species with large litter size), b) ecological conditions (e.g., stronger when resources are limited) and c) the social environment (e.g., stronger for cooperative breeders than for plural breeders). Generally, the results are consistent with their predictions, except there was no clear support for this relationship to be conditional on the ecological conditions. considered

As I have previously recommended the preregistration of this study [2,3], I do not have much to add here, as such recommendation should not depend on the outcome of the study. What I would like to recommend is the whole scientific process performed by the authors, from preregistration sent for peer review, to preprint submission and post-study peer review. It is particularly recommendable to notice that this project was a Masters student project, which shows that it is possible and worthy to preregister studies, even for such rather short-term projects. I strongly congratulate the authors for choosing this process even for an early career short-term project. I think it should be made possible for short-term students to conduct a preregistration study as a research project, without having to present post-study results. I hope this study can encourage a shift in the way we sometimes evaluate students’ projects.

I also recommend the readers to look into the whole pre- and post- study reviewing history of this manuscript and the associated preregistration, as it provides a better understanding of the process and a good example of the associated challenges and benefits [4]. It was a really enriching experience and I encourage others to submit and review preregistrations and registered reports!



[1] Shivani, Huchard, E., Lukas, D. (2022). The effect of dominance rank on female reproductive success in social mammals. EcoEvoRxiv, rc8na, ver. 10 peer-reviewed and recommended by Peer Community in Ecology.

[2] Shivani, Huchard, E., Lukas, D. (2020). Preregistration - The effect of dominance rank on female reproductive success in social mammals In principle acceptance by PCI Ecology of the version 1.2 on 07 July 2020.

[3] Paquet, M. (2020) Why are dominant females not always showing higher reproductive success? A preregistration of a meta-analysis on social mammals. Peer Community in Ecology, 100056.

[4] Parker, T., Fraser, H., & Nakagawa, S. (2019). Making conservation science more reliable with preregistration and registered reports. Conservation Biology, 33(4), 747-750.

The effect of dominance rank on female reproductive success in social mammalsShivani, Elise Huchard, Dieter Lukas<p>Life in social groups, while potentially providing social benefits, inevitably leads to conflict among group members. In many social mammals, such conflicts lead to the formation of dominance hierarchies, where high-ranking individuals consiste...Behaviour & Ethology, Meta-analysesMatthieu Paquet2021-10-13 18:26:42 View
03 Oct 2023
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Integrating biodiversity assessments into local conservation planning: the importance of assessing suitable data sources

Biodiversity databases are ever more numerous, but can they be used reliably for Species Distribution Modelling?

Recommended by ORCID_LOGO based on reviews by 2 anonymous reviewers

Proposing efficient guidelines for biodiversity conservation often requires the use of forecasting tools. Species Distribution Models (SDM) are more and more used to predict how the distribution of a species will react to environmental change, including any large-scale management actions that could be implemented. Their use is also boosted by the increase of publicly available biodiversity databases[1]. The now famous aphorism by George Box "All models are wrong but some are useful"[2] very well summarizes that the outcome of a model must be adjusted to, and will depend on, the data that are used to parameterize it. The question of the reliability of using biodiversity databases to parameterize biodiversity models such as SDM –but the question would also apply to other kinds of biodiversity models, e.g. Population Viability Analysis models[3]– is key to determine the confidence that can be placed in model predictions. This point is often overlooked by some categories of biodiversity conservation stakeholders, in particular the fact that some data were collected using controlled protocols while others are opportunistic. 

In this study[4], the authors use a collection of databases covering a range of species as well as of geographic scales in France and using different data collection and validation approaches as a case study to evaluate the impact of data quality when performing Strategic Environmental Assessment (SEA). Among their conclusions, the fact that a large-scale database (what they call the “country” level) is necessary to reliably parameterize SDM. Besides this and other conclusions of their study, which are likely to be in part specific to their case study –unfortunately for its conservation, biodiversity is complex and varies a lot–, the merit of this work lies in the approach used to test the impact of data on model predictions.


1.  Feng, X. et al. A review of the heterogeneous landscape of biodiversity databases: Opportunities and challenges for a synthesized biodiversity knowledge base. Global Ecology and Biogeography 31, 1242–1260 (2022).

2.  Box, G. E. P. Robustness in the Strategy of Scientific Model Building. in Robustness in Statistics (eds. Launer, R. L. & Wilkinson, G. N.) 201–236 (Academic Press, 1979).

3.  Beissinger, S. R. & McCullough, D. R. Population Viability Analysis. (The University of Chicago Press, 2002).

4.  Ferraille, T., Kerbiriou, C., Bigard, C., Claireau, F. & Thompson, J. D. (2023) Integrating biodiversity assessments into local conservation planning: the importance of assessing suitable data sources. bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Ecology.

Integrating biodiversity assessments into local conservation planning: the importance of assessing suitable data sourcesThibaut Ferraille, Christian Kerbiriou, Charlotte Bigard, Fabien Claireau, John D. Thompson<p>Strategic Environmental Assessment (SEA) of land-use planning is a fundamental tool to minimize environmental impacts of artificialization. In this context, Systematic Conservation Planning (SCP) tools based on Species Distribution Models (SDM)...Biodiversity, Conservation biology, Species distributions, Terrestrial ecologyNicolas Schtickzelle2023-05-11 09:41:05 View
10 Jan 2024
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Beyond variance: simple random distributions are not a good proxy for intraspecific variability in systems with environmental structure

Two paradigms for intraspecific variability

Recommended by ORCID_LOGO based on reviews by Simon Blanchet and Bart Haegeman

Community ecology usually concerns itself with understanding the causes and consequences of diversity at a given taxonomic resolution, most classically at the species level. Yet there is no doubt that diversity exists at all scales, and phenotypic variability within a taxon can be comparable to differences between taxa, as observed from bacteria to fish and trees. The question that motivates an active and growing body of work (e.g. Raffard et al 2019) is not so much whether intraspecific variability matters, but what we get wrong by ignoring it and how to incorporate it into our understanding of communities. There is no established way to think about diversity at multiple nested taxonomic levels, and it is tempting to summarize intraspecific variability simply by measuring species mean and variance in any trait and metric.

In this study, Girard-Tercieux et al (2023a) propose that, to understand its impact on community-level outcomes and in particular on species coexistence, we should carefully distinguish between two ways of thinking about intraspecific variability:

-"unstructured" variation, where every individual's features are like an independent random draw from a species-specific distribution, for instance, due to genetic lottery and developmental accidents

-"structured" variation that is due to each individual encountering a different but enduring microenvironment.

The latter type of variability may still appear complex and random-like when the environment is high-dimensional (i.e. multifaceted, with many different factors contributing to each individual's performance and development). Thus, it is not necessarily "structured" in the sense of being easily understood -- we may need to measure more aspects of the environment than is practical if we want to fully predict these variations.

What distinguishes this "structured" variability is that it is, in a loose sense, inheritable: individuals from the same species that grow in the same microenvironment will have the same performance, in a repeatable fashion. Thus, if each species is best at exploiting at least a fraction of environmental conditions, it is likely to avoid extinction by competition, except in the unlucky case of no propagule reaching any of the favorable sites.
By contrast, drawing each individual's preferences and performance randomly at each generation (from its own species distribution, but independently from other and past individuals) leads to stochastic dynamics, so-called ecological drift, that easily induce a large number of species extinctions.

The core intuition, that the complex spatial structure and high-dimensional nature of the environment plays a key explanatory role in species coexistence, is a running thread through several of the authors' work (e.g. Clark et al 2010), clearly inspired by their focus on tropical forests. This study, by tackling the question of intraspecific determinants of interspecific outcomes, makes a compelling addition to this line of investigation, coming as a theoretical companion to a more data-oriented study (Girard-Tercieux et al 2023b). But I believe it raises a question that is even broader in scope.

This kind of intraspecific variability, due to different individuals growing in different microenvironments, is perhaps most relevant for trees and other sessile organisms, but the distinction made here between "unstructured" and "structured" variability can likely be extended to many other ecological settings.

In my understanding, what matters most in "structured" variability is not so much it stemming from a fixed environment, but rather it being maintained across generations, rather than possibly lost by drift. This difference between variability in the form of "frozen" randomness and in the form of stochastic drift over time is highly relevant in other theoretical fields (e.g. in physics, where it is the difference between a disordered solid and a liquid), and thus, I expect that it is a meaningful distinction to make throughout community ecology.


James S. Clark, David Bell, Chengjin Chu, Benoit Courbaud, Michael Dietze, Michelle Hersh, Janneke HilleRisLambers et al. (2010) "High‐dimensional coexistence based on individual variation: a synthesis of evidence." Ecological Monographs 80, no. 4 : 569-608.

Camille Girard-Tercieux, Ghislain Vieilledent, Adam Clark, James S. Clark, Benoît Courbaud, Claire Fortunel, Georges Kunstler, Raphaël Pélissier, Nadja Rüger, Isabelle Maréchaux (2023a) "Beyond variance: simple random distributions are not a good proxy for intraspecific variability in systems with environmental structure." bioRxiv, ver. 4 peer-reviewed and recommended by Peer Community in Ecology.

Camille Girard‐Tercieux, Isabelle Maréchaux, Adam T. Clark, James S. Clark, Benoît Courbaud, Claire Fortunel, Joannès Guillemot et al. (2023b) "Rethinking the nature of intraspecific variability and its consequences on species coexistence." Ecology and Evolution 13, no. 3 : e9860.

Allan Raffard, Frédéric Santoul, Julien Cucherousset, and Simon Blanchet. (2019) "The community and ecosystem consequences of intraspecific diversity: A meta‐analysis." Biological Reviews 94, no. 2: 648-661.

Beyond variance: simple random distributions are not a good proxy for intraspecific variability in systems with environmental structureCamille Girard-Tercieux, Ghislain Vieilledent, Adam Clark, James S. Clark, Benoit Courbaud, Claire Fortunel, Georges Kunstler, Raphaël Pélissier, Nadja Rüger, Isabelle Maréchaux<p>The role of intraspecific variability (IV) in shaping community dynamics and species coexistence has been intensively discussed over the past decade and modelling studies have played an important role in that respect. However, these studies oft...Biodiversity, Coexistence, Community ecology, Competition, Theoretical ecologyMatthieu Barbier2022-08-07 12:51:30 View
22 May 2019
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Sex makes them sleepy: host reproductive status induces diapause in a parasitoid population experiencing harsh winters

The response of interacting species to biotic seasonal cues

Recommended by and based on reviews by Anne Duplouy and 1 anonymous reviewer

In temperate regions, food abundance and quality vary greatly throughout the year, and the ability of organisms to synchronise their phenology to these changes is a key determinant of their reproductive success. Successful synchronisation requires that cues are perceived prior to change, leaving time for physiological adjustments.
But what are the cues used to anticipate seasonal changes? Abiotic factors like temperature and photoperiod are known for their driving role in the phenology of a wide range of plant an animal species [1,2] . Arguably though, biotic cues directly linked to upcoming changes in food abundance could be as important as abiotic factors, but the response of organisms to these cues remains relatively unexplored.
Biotic cues may be particularly important for higher trophic levels because of their tight interaction with the hosts or preys they depend on. In this study Tougeron and colleagues [3] address this topic using interacting insects, namely herbivorous aphids and the parasitic wasps (or parasitoids) that feed on them. The key finding of the study by Tougeron et al. [3] is that the host morph in which parasitic wasp larvae develop is a major driver of diapause induction. More importantly, the aphid morph that triggers diapause in the wasp is the one that will lay overwintering eggs in autumn at the onset of harsh winter conditions. Its neatly designed experimental setup also provides evidence that this response may vary across populations as host-dependent diapause induction was only observed in a wasp population that originated from a cold area. As the authors suggests, this may be caused by local adaptation to environmental conditions because, relative to warmer regions, missing the time window to enter diapause in colder regions may have more dramatic consequences. The study also shows that different aphid morphs differ greatly in their chemical composition, and points to particular types of metabolites like sugars and polyols as specific cues for diapause induction.
This study provides a nice example of the complexity of biological interactions, and of the importance of phenological synchrony between parasites and their hosts. The authors provide evidence that phenological synchrony is likely to be achieved via chemical cues derived from the host. A similar approach was used to demonstrate that the herbivorous beetle Leptinotarsa decemlineata uses plant chemical cues to enter diapause [4]. Beetles fed on plants exposed to pre-wintering conditions entered diapause in higher proportions than those fed on control plants grown at normal conditions. As done by Tougeron et al. [3], in [4] the authors associated diapause induction to changes in the composition of metabolites in the plant. In both studies, however, the missing piece is to unveil the particular chemical involved, an answer that may be provided by future experiments.
Latitudinal clines in diapause induction have been described in a number of insect species [5]. Correlative studies, in which the phenology of different trophic levels has been monitored, suggest that these clines may in part be governed by lower trophic levels. For example, Phillimore et al. [6] explored the relative contribution of temperature and of host plant phenology on adult flight periods of the butterfly Anthocharis cardamines. Tougeron et al. [3], by using aphids and their associated parasitoids, take the field further by moving from observational studies to experiments. Besides, aphids are not only a tractable host-parasite system in the laboratory, they are important agricultural pests. Improving our basic knowledge of their ecological interactions may ultimately contribute to improving pest control techniques. The study by Tougeron et al. [3] exemplifies the multiple benefits that can be gained from addressing fundamental questions in species that are also directly relevant to society.


[1] Tauber, M. J., Tauber, C. A., and Masaki, S. (1986). Seasonal Adaptations of Insects. Oxford, New York: Oxford University Press.
[2] Bradshaw, W. E., and Holzapfel, C. M. (2007). Evolution of Animal Photoperiodism. Annual Review of Ecology, Evolution, and Systematics, 38(1), 1–25. doi: 10.1146/annurev.ecolsys.37.091305.110115
[3] Tougeron, K., Brodeur, J., Baaren, J. van, Renault, D., and Lann, C. L. (2019b). Sex makes them sleepy: host reproductive status induces diapause in a parasitoid population experiencing harsh winters. bioRxiv, 371385, ver. 6 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/371385
[4] Izzo, V. M., Armstrong, J., Hawthorne, D., and Chen, Y. (2014). Time of the season: the effect of host photoperiodism on diapause induction in an insect herbivore, Leptinotarsa decemlineata. Ecological Entomology, 39(1), 75–82. doi: 10.1111/een.12066
[5] Hut Roelof A., Paolucci Silvia, Dor Roi, Kyriacou Charalambos P., and Daan Serge. (2013). Latitudinal clines: an evolutionary view on biological rhythms. Proceedings of the Royal Society B: Biological Sciences, 280(1765), 20130433. doi: 10.1098/rspb.2013.0433
[6] Phillimore, A. B., Stålhandske, S., Smithers, R. J., and Bernard, R. (2012). Dissecting the Contributions of Plasticity and Local Adaptation to the Phenology of a Butterfly and Its Host Plants. The American Naturalist, 180(5), 655–670. doi: 10.1086/667893

Sex makes them sleepy: host reproductive status induces diapause in a parasitoid population experiencing harsh wintersTougeron K., Brodeur J., van Baaren J., Renault D. and Le Lann C.<p>When organisms coevolve, any change in one species can induce phenotypic changes in traits and ecology of the other species. The role such interactions play in ecosystems is central, but their mechanistic bases remain underexplored. Upper troph...Coexistence, Evolutionary ecology, Experimental ecology, Host-parasite interactions, PhysiologyAdele Mennerat2018-07-18 18:51:03 View
28 Dec 2022
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Deleterious effects of thermal and water stresses on life history and physiology: a case study on woodlouse

An experimental approach for understanding how terrestrial isopods respond to environmental stressors

Recommended by ORCID_LOGO based on reviews by Aaron Yilmaz and Michael Morris

​​In this article, the authors discuss the results of their study investigating the effects of heat stress and moisture stress on a terrestrial isopod Armadilldium vulgare, the common woodlouse [1]. Specifically, the authors have assessed how increased temperature or decreased moisture affects life history traits (such as growth, survival, and reproduction) as well as physiological traits (immune cell parameters and \( beta \)-galactosidase activity). This article quantitatively evaluates the effects of the two stressors on woodlouse. Terrestrial isopods like woodlouse are sensitive to thermal and moisture stress [2; 3] and are therefore good models to test hypotheses in global change biology and for monitoring ecosystem health.

​An important feature of this study is the combination of experimental, laboratory, and analytical techniques. Experiments were conducted under controlled conditions in the laboratory by modulating temperature and moisture, life history and physiological traits were measured/analyzed and then tested using models. Both stressors had negative impacts on survival and reproduction of woodlouse, and result in premature ageing. Although thermal stress did not affect survival, it slowed woodlouse growth. Moisture stress did not have a detectable effect on woodlouse growth but decreased survival and reproductive success. An important insight from this study is that effects of heat and moisture stressors on woodlouse are not necessarily linear, and experimental approaches can be used to better elucidate the mechanisms and understand how these organisms respond to environmental stress.

​This article is timely given the increasing attention on biological monitoring and ecosystem health.​


[1] Depeux C, Branger A, Moulignier T, Moreau J, Lemaître J-F, Dechaume-Moncharmont F-X, Laverre T, Pauhlac H, Gaillard J-M, Beltran-Bech S (2022) Deleterious effects of thermal and water stresses on life history and physiology: a case study on woodlouse. bioRxiv, 2022.09.26.509512., ver. 3 peer-reviewd and recommended by PCI Ecology.

[2] ​Warburg MR, Linsenmair KE, Bercovitz K (1984) The effect of climate on the distribution and abundance of isopods. In: Sutton SL, Holdich DM, editors. The Biology of Terrestrial Isopods. Oxford: Clarendon Press. pp. 339–367.​

[3] Hassall M, Helden A, Goldson A, Grant A (2005) Ecotypic differentiation and phenotypic plasticity in reproductive traits of Armadillidium vulgare (Isopoda: Oniscidea). Oecologia 143: 51–60.​

Deleterious effects of thermal and water stresses on life history and physiology: a case study on woodlouseCharlotte Depeux, Angele Branger, Theo Moulignier, Jérôme Moreau, Jean-Francois Lemaitre, Francois-Xavier Dechaume-Moncharmont, Tiffany Laverre, Hélène Paulhac, Jean-Michel Gaillard, Sophie Beltran-Bech<p>We tested independently the influences of increasing temperature and decreasing moisture on life history and physiological traits in the arthropod <em>Armadillidium vulgare</em>. Both increasing temperature and decreasing moisture led individua...Biodiversity, Evolutionary ecology, Experimental ecology, Life history, Physiology, Terrestrial ecology, ZoologyAniruddha Belsare2022-09-28 13:13:47 View