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28 Sep 2020
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The dynamics of spawning acts by a semelparous fish and its associated energetic costs

Extreme weight loss: when accelerometer could reveal reproductive investment in a semelparous fish species

Recommended by ORCID_LOGO based on reviews by Aidan Jonathan Mark Hewison, Loïc Teulier and 1 anonymous reviewer

Continuous observation of animal behaviour could be quite a challenge in the field, and the situation becomes even more complicated with aquatic species mostly active at night. In such cases, biologging techniques are real game changers in ecology, behavioural ecology or eco-physiology. An accelerating number of methodological applications of these tools in natural condition are thus published each year [1]. Biologging is not limited to movement ecology. For instance, fine grain information about energy expenditure can be inferred from body acceleration [2], and accelerometers has already proven useful in monitoring reproductive costs in some fish species [3,4]. The first part of the study by Tentelier et al. [5] is in line with this growing literature. It describes measurements of energy expenditure during reproduction in a fish species, Allis shad (Alosa Alosa), based on tail beat frequency and occurrence of spawning acts. The study has been convincingly conducted, and the results are important for fish biologists. But this is not the whole story: the authors added to this otherwise classical study a very original and insightful analysis which deserves closer interest.
Tentelier et al. propose to use static accelerometer to monitor change in body roundness through the reproductive season. These semelparous fish first mature and built up reserves in the Atlantic Ocean and migrate into fresh water to reproduce. Contrary to iteroparous species, female shads do not have to strategically preserve energy for future reproduction. The females die few days after spawning having exhausted their energetic reserves: they typically lose almost half of their body mass during the spawning season. The beautiful idea in this study was to track down information about this dramatic slimming in the accelerometer data. Indeed, the accelerometer was attached on the side of the fish (close to the dorsal fin). A change in its angle with the vertical plane could be correlated with the change in roundness, the angle declining with the female thinning. Accelerometers have already been used to record body posture [6] but, in the present study, the novelty was to monitor the change in body shape.
Unfortunately, the data by Tentelier et al. are inconclusive so far. Broadly speaking, the accelerometer angle recorded declined through the spawning season, indicating an average slimming of the females, but there was no correlation between the change in angle and the mass loss at the individual level. This was partly due to the fact that the dorsal position of the accelerometer was not optimized to measures egg laying whose effects are mostly observable on ventral side.
Yet, this nice idea deserves more scrutiny. The method seems to be sensitive enough to detect inflation of swim bladder, the gas-filled organ helping the fish to control their position in the water column, as the accelerometer angle increased when the fish stayed close to the water surface. Additional works and proper calibration are certainly needed to validate the use of accelerometer angle as a proxy for body roundness. The actual data were not strong enough to justify a standalone publication on the subject, but it would have been shame to lose traces of such analysis and keep it in the file drawer. This is why I strongly support its report as a side question in a broader study. Science progresses not only with neat conclusive studies but also when unexpected (apparently anecdotal) observations stimulate new researches.


[1] Börger L, Bijleveld AI, Fayet AL, Machovsky‐Capuska GE, Patrick SC, Street GM and Vander Wal E. (2020) Biologging special feature. J. Anim. Ecol. 89, 6–15. 10.1111/1365-2656.13163
[2] Wilson RP et al. (2020) Estimates for energy expenditure in free‐living animals using acceleration proxies: A reappraisal. J. Anim. Ecol. 89, 161–172. 10.1111/1365-2656.13040
[3] Tsuda Y, Kawabe R, Tanaka H, Mitsunaga Y, Hiraishi T, Yamamoto K and Nashimoto K. (2006) Monitoring the spawning behaviour of chum salmon with an acceleration data logger. Ecol. Freshw. Fish 15, 264–274. 10.1111/j.1600-0633.2006.00147.x
[4] Sakaji H, Hamada K, Naito Y. 2018 Identifying spawning events of greater amberjack using accelerometers. Mar. Biol. Res. 14, 637–641. 10.1080/17451000.2018.1492140
[5] Tentelier C, Bouchard C, Bernardin A, Tauzin A, Aymes J-C, Lange F, Récapet C, Rives J (2020) The dynamics of spawning acts by a semelparous fish and its associated energetic costs. bioRxiv, 436295. doi: 10.1101/436295 ver. 7 peer-reviewed and recommended by PCI Ecology. 10.1101/436295
[6] Brown DD, Kays R, Wikelski M, Wilson R, Klimley AP. 2013 Observing the unwatchable through acceleration logging of animal behavior. Anim. Biotelemetry 1, 20. 10.1186/2050-3385-1-20

The dynamics of spawning acts by a semelparous fish and its associated energetic costsCédric Tentelier, Colin Bouchard, Anaïs Bernardin, Amandine Tauzin, Jean-Christophe Aymes, Frédéric Lange, Charlotte Recapet, Jacques Rives<p>1. During the reproductive season, animals have to manage both their energetic budget and gamete stock. In particular, for semelparous capital breeders with determinate fecundity and no parental care other than gametic investment, the depletion...Behaviour & Ethology, Freshwater ecology, Life historyFrancois-Xavier Dechaume-Moncharmont2020-06-04 15:18:56 View
07 Oct 2019
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Which pitfall traps and sampling efforts should be used to evaluate the effects of cropping systems on the taxonomic and functional composition of arthropod communities?

On the importance of experimental design: pitfall traps and arthropod communities

Recommended by ORCID_LOGO based on reviews by Cécile ALBERT and Matthias Foellmer

Despite the increasing refinement of statistical methods, a robust experimental design is still one of the most important cornerstones to answer ecological and evolutionary questions. However, there is a strong trade-off between a perfect design and its feasibility. A common mantra is that more data is always better, but how much is enough is complex to answer, specially when we want to capture the spatial and temporal variability of a given process. Gardarin and Valantin-Morison [1] make an effort to answer these questions for a practical case: How many pitfalls traps, of which type, and over which extent, do we need to detect shifts in arthropod community composition in agricultural landscapes. There is extense literature on how to approach these challenges using preliminary data in combination with simulation methods [e.g. 2], but practical cases are always welcomed to illustrate the complexity of the decisions to be made. A key challenge in this situation is the nature of simplified and patchy agricultural arthropod communities. In this context, small effect sizes are expected, but those small effects are relevant from an ecological point of view because small increases at low biodiversity may produce large gains in ecosystem functioning [3].
The paper shows that some variables are not important, such as the type of fluid used to fill the pitfall traps. This is good news for potential comparisons among studies using slightly different protocols. However, the bad news are that the sampling effort needed for detecting community changes is larger than the average effort currently implemented. A potential solution is to focus on Community Weighed Mean metrics (CWM; i.e. a functional descriptor of the community body size distribution) rather than on classic metrics such as species richness, as detecting changes on CWM requires a lower sampling effort and it has a clear ecological interpretation linked to ecosystem functioning.
Beyond the scope of the data presented, which is limited to a single region over two years, and hence it is hard to extrapolate to other regions and years, the big message of the paper is the need to incorporate statistical power simulations as a central piece of the ecologist's toolbox. This is challenging, especially when you face questions such as: Should I replicate over space, or over time? The recommended paper is accompanied by the statistical code used, which should facilitate this task to other researchers. Furthermore, we should be aware that some important questions in ecology are highly variable in space and time, and hence, larger sampling effort across space and time is needed to detect patterns. Larger and longer monitoring schemes require a large effort (and funding), but if we want to make relevant ecology, nobody said it would be easy.


[1] Gardarin, A. and Valantin-Morison, M. (2019). Which pitfall traps and sampling efforts should be used to evaluate the effects of cropping systems on the taxonomic and functional composition of arthropod communities? Zenodo, 3468920, ver. 3 peer-reviewed and recommended by PCI Ecology. doi: 10.5281/zenodo.3468920
[2] Johnson, P. C., Barry, S. J., Ferguson, H. M., and Müller, P. (2015). Power analysis for generalized linear mixed models in ecology and evolution. Methods in ecology and evolution, 6(2), 133-142. doi: 10.1111/2041-210X.12306
[3] Cardinale, B. J. et al. (2012). Biodiversity loss and its impact on humanity. Nature, 486(7401), 59-67. doi: 10.1038/nature11148

Which pitfall traps and sampling efforts should be used to evaluate the effects of cropping systems on the taxonomic and functional composition of arthropod communities?Antoine Gardarin and Muriel Valantin-Morison<p>1. Ground dwelling arthropods are affected by agricultural practices, and analyses of their responses to different crop management are required. The sampling efficiency of pitfall traps has been widely studied in natural ecosystems. In arable a...Agroecology, Biodiversity, Biological control, Community ecologyIgnasi Bartomeus2019-01-08 09:40:14 View
24 Mar 2023
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Rapid literature mapping on the recent use of machine learning for wildlife imagery

Review of machine learning uses for the analysis of images on wildlife

Recommended by based on reviews by Falk Huettmann and 1 anonymous reviewer

In the field of ecology, there is a growing interest in machine (including deep) learning for processing and automatizing repetitive analyses on large amounts of images collected from camera traps, drones and smartphones, among others. These analyses include species or individual recognition and classification, counting or tracking individuals, detecting and classifying behavior. By saving countless times of manual work and tapping into massive amounts of data that keep accumulating with technological advances, machine learning is becoming an essential tool for ecologists. We refer to recent papers for more details on machine learning for ecology and evolution (Besson et al. 2022, Borowiec et al. 2022, Christin et al. 2019, Goodwin et al. 2022, Lamba et al. 2019, Nazir & Kaleem 2021, Perry et al. 2022, Picher & Hartig 2023, Tuia et al. 2022, Wäldchen & Mäder 2018).

In their paper, Nakagawa et al. (2023) conducted a systematic review of the literature on machine learning for wildlife imagery. Interestingly, the authors used a method unfamiliar to ecologists but well-established in medicine called rapid review, which has the advantage of being quickly completed compared to a fully comprehensive systematic review while being representative (Lagisz et al., 2022). Through a rigorous examination of more than 200 articles, the authors identified trends and gaps, and provided suggestions for future work. Listing all their findings would be counterproductive (you’d better read the paper), and I will focus on a few results that I have found striking, fully assuming a biased reading of the paper. First, Nakagawa et al. (2023) found that most articles used neural networks to analyze images, in general through collaboration with computer scientists. A challenge here is probably to think of teaching computer vision to the generations of ecologists to come (Cole et al. 2023). Second, the images were dominantly collected from camera traps, with an increase in the use of aerial images from drones/aircrafts that raise specific challenges. Third, the species concerned were mostly mammals and birds, suggesting that future applications should aim to mitigate this taxonomic bias, by including, e.g., invertebrate species. Fourth, most papers were written by authors affiliated with three countries (Australia, China, and the USA) while India and African countries provided lots of images, likely an example of scientific colonialism which should be tackled by e.g., capacity building and the involvement of local collaborators. Last, few studies shared their code and data, which obviously impedes reproducibility. Hopefully, with the journals’ policy of mandatory sharing of codes and data, this trend will be reversed. 


Besson M, Alison J, Bjerge K, Gorochowski TE, Høye TT, Jucker T, Mann HMR, Clements CF (2022) Towards the fully automated monitoring of ecological communities. Ecology Letters, 25, 2753–2775.

Borowiec ML, Dikow RB, Frandsen PB, McKeeken A, Valentini G, White AE (2022) Deep learning as a tool for ecology and evolution. Methods in Ecology and Evolution, 13, 1640–1660.

Christin S, Hervet É, Lecomte N (2019) Applications for deep learning in ecology. Methods in Ecology and Evolution, 10, 1632–1644.

Cole E, Stathatos S, Lütjens B, Sharma T, Kay J, Parham J, Kellenberger B, Beery S (2023) Teaching Computer Vision for Ecology.

Goodwin M, Halvorsen KT, Jiao L, Knausgård KM, Martin AH, Moyano M, Oomen RA, Rasmussen JH, Sørdalen TK, Thorbjørnsen SH (2022) Unlocking the potential of deep learning for marine ecology: overview, applications, and outlook†. ICES Journal of Marine Science, 79, 319–336.

Lagisz M, Vasilakopoulou K, Bridge C, Santamouris M, Nakagawa S (2022) Rapid systematic reviews for synthesizing research on built environment. Environmental Development, 43, 100730.

Lamba A, Cassey P, Segaran RR, Koh LP (2019) Deep learning for environmental conservation. Current Biology, 29, R977–R982.

Nakagawa S, Lagisz M, Francis R, Tam J, Li X, Elphinstone A, Jordan N, O’Brien J, Pitcher B, Sluys MV, Sowmya A, Kingsford R (2023) Rapid literature mapping on the recent use of machine learning for wildlife imagery. EcoEvoRxiv, ver. 4 peer-reviewed and recommended by Peer Community in Ecology.

Nazir S, Kaleem M (2021) Advances in image acquisition and processing technologies transforming animal ecological studies. Ecological Informatics, 61, 101212.

Perry GLW, Seidl R, Bellvé AM, Rammer W (2022) An Outlook for Deep Learning in Ecosystem Science. Ecosystems, 25, 1700–1718.

Pichler M, Hartig F Machine learning and deep learning—A review for ecologists. Methods in Ecology and Evolution, n/a.

Tuia D, Kellenberger B, Beery S, Costelloe BR, Zuffi S, Risse B, Mathis A, Mathis MW, van Langevelde F, Burghardt T, Kays R, Klinck H, Wikelski M, Couzin ID, van Horn G, Crofoot MC, Stewart CV, Berger-Wolf T (2022) Perspectives in machine learning for wildlife conservation. Nature Communications, 13, 792.

Wäldchen J, Mäder P (2018) Machine learning for image-based species identification. Methods in Ecology and Evolution, 9, 2216–2225.

Rapid literature mapping on the recent use of machine learning for wildlife imageryShinichi Nakagawa, Malgorzata Lagisz, Roxane Francis, Jessica Tam, Xun Li, Andrew Elphinstone, Neil R. Jordan, Justine K. O’Brien, Benjamin J. Pitcher, Monique Van Sluys, Arcot Sowmya, Richard T. Kingsford<p>1. Machine (especially deep) learning algorithms are changing the way wildlife imagery is processed. They dramatically speed up the time to detect, count, classify animals and their behaviours. Yet, we currently have a very few systematic liter...Behaviour & Ethology, Conservation biologyOlivier GimenezAnonymous2022-10-31 22:05:46 View
18 Dec 2020
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Once upon a time in the far south: Influence of local drivers and functional traits on plant invasion in the harsh sub-Antarctic islands

A meaningful application of species distribution models and functional traits to understand invasion dynamics

Recommended by based on reviews by Paula Matos and Peter Convey

Polar and subpolar regions are fragile environments, where the introduction of alien species may completely change ecosystem dynamics if the alien species become keystone species (e.g. Croll, 2005). The increasing number of human visits, together with climate change, are favouring the introduction and settling of new invaders to these regions, particularly in Antarctica (Hughes et al. 2015). Within this context, the joint use of Species Distribution Models (SDM) –to assess the areas potentially suitable for the aliens– with other measures of the potential to become successful invaders can inform on the need for devoting specific efforts to eradicate these new species before they become naturalized (e.g. Pertierra et al. 2016).
Bazzichetto et al. (2020) use data from a detailed inventory, SDMs and trait data altogether to assess the drivers of invasion success of six alien plants on Possession Island, in the remote sub-Antarctic archipelago of Crozet. SDMs have inherent limitations to describe different aspects of species distributions, including the fundamental niche and, with it, the areas that could host viable populations (Hortal et al. 2012). Therefore, their utility to predict future biological invasions is limited (Jiménez-Valverde et al. 2011). However, they can be powerful tools to describe species range dynamics if they are thoughtfully used by adopting conscious decisions about the techniques and data used, and interpreting carefully the actual implications of their results.
This is what Bazzichetto et al. (2020) do, using General Linear Models (GLM) –a technique well rooted in the original niche-based SDM theory (e.g. Austin 1990)– that can provide a meaningful description of the realized niche within the limits of an adequately sampled region. Further, as alien species share and are similarly affected by several steps of the invasion process (Richardson et al. 2000), these authors model the realized distribution of the six species altogether. This can be done through the recently developed joint-SDM, a group of techniques where the co-occurrence of the modelled species is explicitly taken into account during modelling (e.g. Pollock et al. 2014). Here, the addition of species traits has been identified as a key step to understand the associations of species in space (see Dormann et al. 2018). Bazzichetto et al. (2020) combine their GLM-based SDM for each species with a so-called multi-SDM approach, where they assess together the consistency in the interactions between both species and topographically-driven climate variations, and several plant traits and two key anthropic factors –accessibility from human settlements and distance to hiking paths.
This work is a good example on how a theoretically meaningful SDM approach can provide useful –though perhaps not deep– insights on biological invasions for remote landscapes threatened by biotic homogenization. By combining climate and topographic variables as proxies for the spatial variations in the abiotic conditions regulating plant growth, measures of accessibility, and traits of the plant invaders, Bazzichetto et al. (2020) are able to identify the different effects that the interactions between the potential intensity of propagule dissemination by humans, and the ecological characteristics of the invaders themselves, may have on their invasion success.
The innovation of modelling together species responses is important because it allows dissecting the spatial dynamics of spread of the invaders, which indeed vary according to a handful of their traits. For example, their results show that no all old residents have profited from the larger time of residence in the island, as Poa pratensis is seemingly as dependent of a higher intensity of human activity as the newcomer invaders in general are. According to Bazzichetto et al. trait-based analyses, these differences are apparently related with plant height, as smaller plants disperse more easily. Further, being perennial also provides an advantage for the persistence in areas with less human influence. This puts name, shame and fame to the known influence of plant life history on their dispersal success (Beckman et al. 2018), at least for the particular case of plant invasions in Possession Island.
Of course this approach has limitations, as data on the texture, chemistry and temperature of the soil are not available, and thus were not considered in the analyses. These factors may be critical for both establishment and persistence of small plants in the harsh Antarctic environments, as Bazzichetto et al. (2020) recognize. But all in all, their results provide key insights on which traits may confer alien plants with a higher likelihood of becoming successful invaders in the fragile Antarctic and sub-Antarctic ecosystems. This opens a way for rapid assessments of invasibility, which will help identifying which species in the process of naturalizing may require active contention measures to prevent them from becoming ecological game changers and cause disastrous cascade effects that shift the dynamics of native ecosystems.


Austin, M. P., Nicholls, A. O., and Margules, C. R. (1990). Measurement of the realized qualitative niche: environmental niches of five Eucalyptus species. Ecological Monographs, 60(2), 161-177. doi:
Bazzichetto, M., Massol, F., Carboni, M., Lenoir, J., Lembrechts, J. J. and Joly, R. (2020) Once upon a time in the far south: Influence of local drivers and functional traits on plant invasion in the harsh sub-Antarctic islands. bioRxiv, 2020.07.19.210880, ver. 3 peer-reviewed and recommended by PCI Ecology. doi:
Beckman, N. G., Bullock, J. M., and Salguero-Gómez, R. (2018). High dispersal ability is related to fast life-history strategies. Journal of Ecology, 106(4), 1349-1362. doi:
Croll, D. A., Maron, J. L., Estes, J. A., Danner, E. M., and Byrd, G. V. (2005). Introduced predators transform subarctic islands from grassland to tundra. Science, 307(5717), 1959-1961. doi:
Dormann, C. F., Bobrowski, M., Dehling, D. M., Harris, D. J., Hartig, F., Lischke, H., Moretti, M. D., Pagel, J., Pinkert, S., Schleuning, M., Schmidt, S. I., Sheppard, C. S., Steinbauer, M. J., Zeuss, D., and Kraan, C. (2018). Biotic interactions in species distribution modelling: 10 questions to guide interpretation and avoid false conclusions. Global Ecology and Biogeography, 27(9), 1004-1016. doi:
Jiménez-Valverde, A., Peterson, A., Soberón, J., Overton, J., Aragón, P., and Lobo, J. (2011). Use of niche models in invasive species risk assessments. Biological Invasions, 13(12), 2785-2797. doi:
Hortal, J., Lobo, J. M., and Jiménez-Valverde, A. (2012). Basic questions in biogeography and the (lack of) simplicity of species distributions: Putting species distribution models in the right place. Natureza & Conservação – Brazilian Journal of Nature Conservation, 10(2), 108-118. doi:
Hughes, K. A., Pertierra, L. R., Molina-Montenegro, M. A., and Convey, P. (2015). Biological invasions in terrestrial Antarctica: what is the current status and can we respond? Biodiversity and Conservation, 24(5), 1031-1055. doi:
Pertierra, L. R., Baker, M., Howard, C., Vega, G. C., Olalla-Tarraga, M. A., and Scott, J. (2016). Assessing the invasive risk of two non-native Agrostis species on sub-Antarctic Macquarie Island. Polar Biology, 39(12), 2361-2371. doi:
Pollock, L. J., Tingley, R., Morris, W. K., Golding, N., O'Hara, R. B., Parris, K. M., Vesk, P. A., and McCarthy, M. A. (2014). Understanding co-occurrence by modelling species simultaneously with a Joint Species Distribution Model (JSDM). Methods in Ecology and Evolution, 5(5), 397-406. doi:
Richardson, D. M., Pyšek, P., Rejmánek, M., Barbour, M. G., Panetta, F. D., and West, C. J. (2000). Naturalization and invasion of alien plants: concepts and definitions. Diversity and Distributions, 6(2), 93-107. doi:

Once upon a time in the far south: Influence of local drivers and functional traits on plant invasion in the harsh sub-Antarctic islandsManuele Bazzichetto, François Massol, Marta Carboni, Jonathan Lenoir, Jonas Johan Lembrechts, Rémi Joly, David Renault<p>Aim Here, we aim to: (i) investigate the local effect of environmental and human-related factors on alien plant invasion in sub-Antarctic islands; (ii) explore the relationship between alien species features and their dependence on anthropogeni...Biogeography, Biological invasions, Spatial ecology, Metacommunities & Metapopulations, Species distributionsJoaquín Hortal2020-07-21 21:13:08 View
06 Sep 2019
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Assessing metacommunity processes through signatures in spatiotemporal turnover of community composition

On the importance of temporal meta-community dynamics for our understanding of assembly processes

Recommended by based on reviews by Joaquín Hortal and 2 anonymous reviewers

The processes that trigger community assembly are still in the centre of ecological interest. While prior work mostly focused on spatial patterns of co-occurrence within a meta-community framework [reviewed in 1, 2] recent studies also include temporal patterns of community composition [e.g. 3, 4, 5, 6]. In this preprint [7], Franck Jabot and co-workers extend they prior approaches to quasi neutral community assembly [8, 9, 10] and develop an analytical framework of spatial and temporal diversity turnover. A simple and heuristic path model for beta diversity and an extended ecological drift model serve as starting points. The model can be seen as a counterpart to Ulrich et al. [5]. These authors implemented competitive hierarchies into their neutral meta-community model while the present paper focuses on environmental filtering. Most important, the model and parameterization of four empirical data sets on aquatic plant and animal meta-communities used by Jabot et al. returned a consistent high influence of environmental stochasticity on species turnover. Of course, this major result does not come to a surprise. As typical for this kind of models it depends also to a good deal on the initial model settings. It nevertheless makes a strong conceptual point for the importance of environmental variability over dispersal and richness effects. One interesting side effect regards the impact of richness differences (ΔS). Jabot et al. interpret this as a ‘nuisance variable’ as they do not have a stringent explanation. Of course, it might be a pure statistical bias introduced by the Soerensen metric of turnover that is normalized by richness. However, I suspect that there is more behind the ΔS effect. Richness differences are generally associated with respective differences in total abundances and introduce source – sink dynamics that inevitably shape subsequent colonization – extinction processes. It would be interesting to see whether ΔS alone is able to trigger observed patterns of community assembly and community composition. Such an analysis would require partitioning of species turnover into richness and nestedness effects [11]. I encourage Jabot et al. to undertake such an effort.
The present paper is also another call to include temporal population variability into metapopulation models for a better understanding of the dynamics and triggering of community assembly. In a next step, competitive interactions should be included into the model to infer the relative importance of both factors.


[1] Götzenberger, L. et al. (2012). Ecological assembly rules in plant communities—approaches, patterns and prospects. Biological reviews, 87(1), 111-127. doi: 10.1111/j.1469-185X.2011.00187.x
[2] Ulrich, W., & Gotelli, N. J. (2013). Pattern detection in null model analysis. Oikos, 122(1), 2-18. doi: 10.1111/j.1600-0706.2012.20325.x
[3] Grilli, J., Barabás, G., Michalska-Smith, M. J., & Allesina, S. (2017). Higher-order interactions stabilize dynamics in competitive network models. Nature, 548(7666), 210. doi: 10.1038/nature23273
[4] Nuvoloni, F. M., Feres, R. J. F., & Gilbert, B. (2016). Species turnover through time: colonization and extinction dynamics across metacommunities. The American Naturalist, 187(6), 786-796. doi: 10.1086/686150
[5] Ulrich, W., Jabot, F., & Gotelli, N. J. (2017). Competitive interactions change the pattern of species co‐occurrences under neutral dispersal. Oikos, 126(1), 91-100. doi: 10.1111/oik.03392
[6] Dobramysl, U., Mobilia, M., Pleimling, M., & Täuber, U. C. (2018). Stochastic population dynamics in spatially extended predator–prey systems. Journal of Physics A: Mathematical and Theoretical, 51(6), 063001. doi: 10.1088/1751-8121/aa95c7
[7] Jabot, F., Laroche, F., Massol, F., Arthaud, F., Crabot, J., Dubart, M., Blanchet, S., Munoz, F., David, P., and Datry, T. (2019). Assessing metacommunity processes through signatures in spatiotemporal turnover of community composition. bioRxiv, 480335, ver. 3 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/480335
[8] Jabot, F., & Chave, J. (2011). Analyzing tropical forest tree species abundance distributions using a nonneutral model and through approximate Bayesian inference. The American Naturalist, 178(2), E37-E47. doi: 10.1086/660829
[9] Jabot, F., & Lohier, T. (2016). Non‐random correlation of species dynamics in tropical tree communities. Oikos, 125(12), 1733-1742. doi: 10.1111/oik.03103
[10] Datry, T., Bonada, N., & Heino, J. (2016). Towards understanding the organisation of metacommunities in highly dynamic ecological systems. Oikos, 125(2), 149-159. doi: 10.1111/oik.02922
[11] Baselga, A. (2010). Partitioning the turnover and nestedness components of beta diversity. Global ecology and biogeography, 19(1), 134-143. doi: 10.1111/j.1466-8238.2009.00490.x

Assessing metacommunity processes through signatures in spatiotemporal turnover of community compositionFranck Jabot, Fabien Laroche, Francois Massol, Florent Arthaud, Julie Crabot, Maxime Dubart, Simon Blanchet, Francois Munoz, Patrice David, Thibault Datry<p>Although metacommunity ecology has been a major field of research in the last decades, with both conceptual and empirical outputs, the analysis of the temporal dynamics of metacommunities has only emerged recently and still consists mostly of r...Biodiversity, Coexistence, Community ecology, Spatial ecology, Metacommunities & MetapopulationsWerner Ulrich2018-11-29 14:58:54 View
03 Mar 2022
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Artificial reefs geographical location matters more than its age and depth for sessile invertebrate colonization in the Gulf of Lion (NorthWestern Mediterranean Sea)

A longer-term view on benthic communities on artificial reefs: it’s all about location

Recommended by based on reviews by 2 anonymous reviewers

In this study by Blouet, Bramanti, and Guizen (2022), the authors aim to tackle a long-standing data gap regarding research on marine benthic communities found on artificial reefs. The study is well thought out, and should serve as an important reference on this topic going forward.
Artificial reefs (ARs) are increasingly deployed in coastal waters around the world in order to reduce pressure on fisheries or to enhance fisheries stocks, via providing a hard substrate and complex shapes that induce the development of benthic communities, which together with the shape of the ARs themselves can provide areas for fish species to live. Much research has documented the effects of ARs on fish abundance and diversity, and documented over the short-term the benthic communities that settle and grow on ARs. However, there is a clear data gap on longer-term (e.g. greater than 10 years) trends of benthic communities on ARs. As well, any study on ARs must also account for the shape(s) of the ARs themselves, as there are numerous designs deployed, and also consider the depth of the ARs, and the age of the ARs.
The authors used the extensive ARs deployed in the Gulf of Lion in the northwestern Mediterranean to examine the effects of AR shape, depth, age (time since deployment), and location, both at local and wider regional scales, specifically examining the presence and absence of five marine species; 2 gorgonian octocorals, 1 ascidian, 1 annelid, and 1 bryozoan. Results indicate that location influenced the benthic communities above all other factors, suggesting the importance of considering the geographic location in future AR deployment and management of communities. The authors theorize that larval supply processes are important in shaping the observed patterns.
I conclude that this is an important report on AR ecology for several reasons. Firstly, the authors collected data from a variety of benthic species, including species that are habitat-forming but unfortunately perhaps not as focused on as more commercially important species. Secondly, by utilizing ARs deployed from as far back as the mid-1980s, the authors have generated longer-term information on benthic communities on ARs than what is commonly seen in the literature. Finally, the authors should be commended for their clever and hard work to incorporate all of the various factors into their analyses, and elucidating the importance of location. In fairness, this last point represents the only true limitation of the paper, as some of the statistical analyses were limited due to the small numbers of ARs fitting certain categories, and thereby limiting some of the conclusions. Still, it is very rare that a marine experimental ecologist would be in charge of AR deployment designs for 40 years, and the authors cannot be faulted for this shortcoming over which they had no control. On the contrary, the fact that the authors have performed this important work in the face of potentially limited analyses should be recognized. Marine ecology is often strongly limited by a lack of past data. In order to move past this impediment, more excellent work like the current paper is needed, conducted in a wider variety of ecosystems. I hope Blouet et al. (2022) can serve as a template for future work on a wider scale.

Blouet S, Bramanti L, Guizien K (2022) Artificial reefs geographical location matters more than shape, age and depth for sessile invertebrate colonization in the Gulf of Lion (NorthWestern Mediterranean Sea). bioRxiv, 2021.10.08.463669, ver. 4 peer-reviewed and recommended by Peer Community in Ecology.

Artificial reefs geographical location matters more than its age and depth for sessile invertebrate colonization in the Gulf of Lion (NorthWestern Mediterranean Sea)sylvain blouet, Katell Guizien, lorenzo Bramanti<p>Artificial reefs (ARs) have been used to support fishing activities. Sessile invertebrates are essential components of trophic networks within ARs, supporting fish productivity. However, colonization by sessile invertebrates is possible only af...Biodiversity, Biogeography, Colonization, Ecological successions, Life history, Marine ecologyJames Davis Reimer2021-10-11 10:21:36 View
12 Jun 2019
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Environmental heterogeneity drives tsetse fly population dynamics and control

Modeling jointly landscape complexity and environmental heterogeneity to envision new strategies for tsetse flies control

Recommended by based on reviews by Timothée Vergne and 1 anonymous reviewer

Today, understanding spatio-temporal dynamics of pathogens is pivotal to understand their transmission and controlling them. First, understanding this dynamics can reveal the ecology of their transmission [1]. Indeed, such knowledge, based on data that are quite easy to access, can shed light on transmission modes, which could rely on different animal species that can be spatially distributed in a non-uniform way [2]. This is especially true for pathogens with complex life-cycles, despite that investigating such dynamics is very challenging and rely mostly on mathematical models.
Moreover, this knowledge can also highlight some weak points in a complex web of transmission and therefore allowing us to envision new innovative control strategies. This has been first proposed on human pathogens, where connectivity among populations can be analyzed to identify which connections need to be targeted to stop or slow down an epidemics [3]. However, this idea is increasingly recognized as a promising new approach for pathogens involving vector populations, especially regarding the complexity to decrease on a long-term the abundance of these vector populations [4].
In "Environmental heterogeneity drives tsetse fly population dynamics and control" [5], Cecilia and co-authors have developed a sophisticated spatio-temporal mechanistic model to figure out how local environment, involved within landscape of different complexities, can impact the population dynamics of tsetse flies, an invertebrate species that can serve as a vector for many pathogens of animal and human importance. They found that spatial patches with the lowest temperature mean and the lowest environmental fluctuations can act as refuge for this species, representing therefore preferential targets for disease control.
The reviewers and I agree that the mathematical framework developed address very well an important topic for both ecological and public health literature. More importantly, it shows how fundamental ecological knowledge can drive pathogen control strategies, opening an interesting avenue for cross-disciplinary research on vector-borne diseases.


[1] Grenfell, B. T., Bjørnstad, O. N., & Kappey, J. (2001). Travelling waves and spatial hierarchies in measles epidemics. Nature, 414(6865), 716-723. doi: 10.1038/414716a
[2] Perkins, S. E., Cattadori, I. M., Tagliapietra, V., Rizzoli, A. P., & Hudson, P. J. (2003). Empirical evidence for key hosts in persistence of a tick-borne disease. International journal for parasitology, 33(9), 909-917. doi: 10.1016/S0020-7519(03)00128-0
[3] Colizza, V., Barrat, A., Barthélemy, M., & Vespignani, A. (2006). The role of the airline transportation network in the prediction and predictability of global epidemics. Proceedings of the National Academy of Sciences, 103(7), 2015-2020. doi: 10.1073/pnas.0510525103
[4] Pepin, K. M., Leach, C. B., Marques-Toledo, C., Laass, K. H., Paixao, K. S., et al. (2015) Utility of mosquito surveillance data for spatial prioritization of vector control against dengue viruses in three Brazilian cities. Parasites & Vectors 8, 1–15. doi: 10.1186/s13071-015-0659-y
[5] Cecilia, H., Arnoux, S., Picault, S., Dicko, A., Seck, M. T., Sall, B., Bassène, M., Vreysen, M., Pagabeleguem, S., Bancé, A., Bouyer, J. and Ezanno, P.(2019). Environmental heterogeneity drives tsetse fly population dynamics and control. bioRxiv 493650, ver. 3 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/493650

Environmental heterogeneity drives tsetse fly population dynamics and controlCecilia H, Arnoux S, Picault S, Dicko A, Seck MT, Sall B, Bassene M, Vreysen M, Pagabeleguem S, Bance A, Bouyer J, Ezanno P<p>A spatially and temporally heterogeneous environment may lead to unexpected population dynamics. Knowledge still is needed on which of the local environment properties favour population maintenance at larger scale. For pathogen vectors, such as...Biological control, Population ecology, Spatial ecology, Metacommunities & MetapopulationsBenjamin Roche2018-12-14 12:13:39 View
17 Mar 2021
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Intra and inter-annual climatic conditions have stronger effect than grazing intensity on root growth of permanent grasslands

Resolving herbivore influences under climate variability

Recommended by based on reviews by 3 anonymous reviewers

We know that herbivory can have profound influences on plant communities with respect to their distribution and productivity (recently reviewed by Jia et al. 2018). However, the degree to which these effects are realized belowground in the rhizosphere is far less understood. Indeed, many independent studies and synthesis find that the environmental context can be more important than the direct effects of herbivore activity and its removal of plant biomass (Andriuzzi and Wall 2017, Schrama et al. 2013). In spite of dedicated attention, generalizable conclusions remain a bit elusive (Sitters and Venterink 2015). Picon-Cochard and colleagues (2021) help address this research conundrum in an elegant analysis that demonstrates the interaction between long-term cattle grazing and climatic variability on primary production aboveground and belowground. 

Over the course of two years, Picon-Cochard et al. (2021) measured above and belowground net primary productivity in French grasslands that had been subject to ten years of managed cattle grazing. When they compared these data with climatic trends, they find an interesting interaction among grazing intensity and climatic factors influencing plant growth.  In short, and as expected, plants allocate more resources to root growth in dry years and more to above ground biomass in wet and cooler years. However, this study reveals the degree to which this is affected by cattle grazing. Grazed grasslands support warmer and dryer soils creating feedback that further and significantly promotes root growth over green biomass production.  

The implications of this work to understanding the capacity of grassland soils to store carbon is profound. This study addresses one brief moment in time of the long trajectory of this grazed ecosystem. The legacy of grazing does not appear to influence soil ecosystem functioning with respect to root growth except within the environmental context, in this case, climate. This supports the notion that long-term research in animal husbandry and grazing effects on landscapes is deeded. It is my hope that this study is one of many that can be used to synthesize many different data sets and build a deeper understanding of the long-term effects of grazing and herd management within the context of a changing climate.  Herbivory has a profound influence upon ecosystem health and the distribution of plant communities (Speed and Austrheim 2017), global carbon storage (Chen and Frank 2020) and nutrient cycling (Sitters et al. 2020). The analysis and results presented by Picon-Cochard (2021) help to resolve the mechanisms that underly these complex effects and ultimately make projections for the future.


Andriuzzi WS, Wall DH. 2017. Responses of belowground communities to large aboveground herbivores: Meta‐analysis reveals biome‐dependent patterns and critical research gaps. Global Change Biology 23:3857-3868. doi:

Chen J, Frank DA. 2020. Herbivores stimulate respiration from labile and recalcitrant soil carbon pools in grasslands of Yellowstone National Park. Land Degradation & Development 31:2620-2634. doi:

Jia S, Wang X, Yuan Z, Lin F, Ye J, Hao Z, Luskin MS. 2018. Global signal of top-down control of terrestrial plant communities by herbivores. Proceedings of the National Academy of Sciences 115:6237-6242. doi:

Picon-Cochard C, Vassal N, Martin R, Herfurth D, Note P, Louault F. 2021. Intra and inter-annual climatic conditions have stronger effect than grazing intensity on root growth of permanent grasslands. bioRxiv, 2020.08.23.263137, version 6 peer-reviewed and recommended by PCI Ecology. doi:

Schrama M, Veen GC, Bakker EL, Ruifrok JL, Bakker JP, Olff H. 2013. An integrated perspective to explain nitrogen mineralization in grazed ecosystems. Perspectives in Plant Ecology, Evolution and Systematics 15:32-44. doi:

Sitters J, Venterink HO. 2015. The need for a novel integrative theory on feedbacks between herbivores, plants and soil nutrient cycling. Plant and Soil 396:421-426. doi:

Sitters J, Wubs EJ, Bakker ES, Crowther TW, Adler PB, Bagchi S, Bakker JD, Biederman L, Borer ET, Cleland EE. 2020. Nutrient availability controls the impact of mammalian herbivores on soil carbon and nitrogen pools in grasslands. Global Change Biology 26:2060-2071. doi:

Speed JD, Austrheim G. 2017. The importance of herbivore density and management as determinants of the distribution of rare plant species. Biological Conservation 205:77-84. doi:

Intra and inter-annual climatic conditions have stronger effect than grazing intensity on root growth of permanent grasslandsCatherine Picon-Cochard, Nathalie Vassal, Raphaël Martin, Damien Herfurth, Priscilla Note, Frédérique Louault<p>Background and Aims: Understanding how direct and indirect changes in climatic conditions, management, and species composition affect root production and root traits is of prime importance for the delivery of carbon sequestration services of gr...Agroecology, Biodiversity, Botany, Community ecology, Ecosystem functioningJennifer Krumins2020-08-30 19:27:30 View
20 Feb 2019
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Differential immune gene expression associated with contemporary range expansion of two invasive rodents in Senegal

Are all the roads leading to Rome?

Recommended by based on reviews by Nadia Aubin-Horth and 1 anonymous reviewer

Identifying the factors which favour the establishment and spread of non-native species in novel environments is one of the keys to predict - and hence prevent or control - biological invasions. This includes biological factors (i.e. factors associated with the invasive species themselves), and one of the prevailing hypotheses is that some species traits may explain their impressive success to establish and spread in novel environments [1]. In animals, most research studies have focused on traits associated with fecundity, age at maturity, level of affiliation to humans or dispersal ability for instance. The “composite picture” of the perfect (i.e. successful) invader that has gradually emerged is a small-bodied animal strongly affiliated to human activities with high fecundity, high dispersal ability and a super high level of plasticity. Of course, the story is not that simple, and actually a perfect invader sometimes – if not often- takes another form… Carrying on to identify what makes a species a successful invader or not is hence still an important research axis with major implications.
In this manuscript, Charbonnel and collaborators [2] provide an interesting opportunity to gain novel insights into our understanding of (the) traits underlying invasion success. They nicely combine the power of Next-Generation Sequencing (NGS) with a clever comparative approach of two closely-related invasive rodents (the house mouse Mus musculus and the black rat Rattus rattus) in a common environment. They use this experimental design to test the appealing hypothesis that pathogens may be actors of the story, and may indirectly explain why some non-native species are so successful in invading novel habitats.
It is generally assumed that the community of pathogens encountered by non-native species in novel environments is different from that of their native area. On the one hand (the enemy-release hypothesis), it can be hypothesized that non-native species, when they arrive into a novel environment, will be relaxed from the pressure imposed by their native pathogens because local pathogens are not adapted (and hence do not infect) to this novel host. Because immune defence against pathogens is highly costly, non-native species establishing into a novel environment could hence reallocate these costs to other functions such as fecundity or dispersal apparatus. This scenario has been termed the “evolution of increased competitive ability” (EICA) hypothesis [3]. On the other hand (the EICA-refined hypothesis [4]), one can assume that invaders will encounter new pathogens in newly established areas, and will allocate energy toward cost-effective immune pathways to permit allocating a non-negligible amount of energy toward other functions. Finally, a last hypothesis (the “immune protection” hypothesis) assumes major changes in pathogen composition between native and invaded areas, which should lead to an overall increase in immune investment by the native species to successfully invade novel environments [4]. This last hypothesis suggests that only non-native species being able to take up the associated costs of immunity will be successful invaders.
The role of immunity in invasion success has yet been poorly investigated, mainly because of the difficulty to simultaneously analyse multiple immune pathways [4]. Charbonnel and collaborators [2] overpass this difficulty by screening all genes expressed (using a whole RNA sequencing approach) in an immune tissue: the spleen. They do so along the invasion routes of two sympatric invasive rodents in Africa and compare anciently and newly invaded areas (respectively). For one of the two species (the house mouse), they found a high number of immune-related genes to be up-regulated in newly invaded areas compared to anciently invaded areas. All categories of immune pathways (costly and cost-effective) were up-regulated, suggesting an overall increase in immune investment in the mouse, which corroborates the “immune protection” hypothesis. For the black rat, patterns of gene expression were somewhat different, with much less pronounced differentiation in gene expression between newly and anciently invaded areas. Among the few differentiated genes, a few were associated to immune responses and some of theses genes were even down-regulated in the newly invaded areas. This pattern may actually corroborate the EICA hypothesis, although it could alternatively suggest that stochastic processes (drift) associated to recent decrease in population size (which is expected during a colonisation event) are more important than selection imposed by pathogens in shaping patterns of immune gene expression.
Overall, this study [2] suggests (i) that immune-related traits are important in predicting invasion success and (ii) that two successful species with a similar invasion history and living in similar environments can use different life-history strategies to reach the same success. This later finding is particularly relevant and intriguing as it suggests that the traits and strategies deployed by species to colonise new habitats might actually be idiosyncratic, and that, if general trends actually emerge in regards of traits predicting the success of invaders, the devil might actually be into the details. Comparative studies are extremely important to identify the general rules and the specificities sustaining actual patterns, but these approaches are yet poorly used in biological invasions (at least empirically). The work presented by Charbonnel and colleagues [2] calls for future comparative studies performed at multiple spatial scales (native vs. non-native areas, anciently vs. recently invaded areas), multiple taxonomic resolutions and across multiple traits (to search for trade-offs), so that the success of invasive species can be properly understood and predicted.


[1] Jeschke, J. M., & Strayer, D. L. (2006). Determinants of vertebrate invasion success in Europe and North America. Global Change Biology, 12(9), 1608-1619. doi: 10.1111/j.1365-2486.2006.01213.x
[2] Blossey, B., & Notzold, R. (1995). Evolution of increased competitive ability in invasive nonindigenous plants: a hypothesis. Journal of Ecology, 83(5), 887-889. doi: 10.2307/2261425
[3] Charbonnel, N., Galan, M., Tatard, C., Loiseau, A., Diagne, C. A., Dalecky, A., Parrinello, H., Rialle, S., Severac, D., & Brouat, C. (2019). Differential immune gene expression associated with contemporary range expansion of two invasive rodents in Senegal. bioRxiv, 442160, ver. 5 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/442160
[4] Lee, K. A., & Klasing, K. C. (2004). A role for immunology in invasion biology. Trends in Ecology & Evolution, 19(10), 523-529. doi: 10.1016/j.tree.2004.07.012

Differential immune gene expression associated with contemporary range expansion of two invasive rodents in SenegalNathalie Charbonnel, Maxime Galan, Caroline Tatard, Anne Loiseau, Christophe Diagne, Ambroise Dalecky, Hugues Parrinello, Stephanie Rialle, Dany Severac and Carine Brouat<p>Background: Biological invasions are major anthropogenic changes associated with threats to biodiversity and health. What determines the successful establishment of introduced populations still remains unsolved. Here we explore the appealing as...Biological invasions, Eco-immunology & Immunity, Population ecologySimon Blanchet2018-10-14 12:21:52 View
15 Jul 2023
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Evolution of dispersal and the maintenance of fragmented metapopulations

The spatial dynamics of habitat fragmentation drives the evolution of dispersal and metapopulation persistence

Recommended by based on reviews by Eva Kisdi, David Murray-Stoker, Shripad Tuljapurkar and 1 anonymous reviewer

​​​​​The persistence of populations facing the destruction of their habitat is a multifaceted question that has mobilized theoreticians and empiricists alike for decades. As an ecological question, persistence has been studied as the spatial rescue of populations via dispersal into remaining suitable habitats. The spatial aggregation of habitat destruction has been a key component of these studies, and it has been applied to the problem of coexistence by integrating competition-colonization tradeoffs. There is a rich ecological literature on this topic, both from theoretical and field studies (Fahrig 2003). The relationship between life-history strategies of species and their resilience to spatially structured habitat fragmentation is also an important component of conservation strategies through the management of land use, networks of protected areas, and the creation of corridors. In the context of environmental change, the ability of species to adapt to changes in landscape configuration and availability can be treated as an eco-evolutionary process by considering the possibility of evolutionary rescue (Heino and Hanski 2001; Bell 2017). However, eco-evolutionary dynamics considering spatially structured changes in landscapes and life-history tradeoffs remains an outstanding question. Finand et al. (2023) formulate the problem of persistence in fragmented landscapes over evolutionary time scales by studying models for the evolution of dispersal in relation to habitat fragmentation and spatial aggregation. Their simulations were conducted on a spatial grid where individuals can colonize suitable patch as a function of their competitive rank that decreases as a function of their (ii) dispersal distance trait. Simulations were run under fixed habitat fragmentation (proportion of unsuitable habitat) and aggregation, and with an explicit rate of habitat destruction to study evolutionary rescue.

Their results reveal a balance between the selection for high dispersal under increasing habitat fragmentation and selection for lower dispersal in response to habitat aggregation. This balance leads to the coexistence of polymorphic dispersal strategies in highly aggregated landscapes with low fragmentation where high dispersers inhabit aggregated habitats while low dispersers are found in isolated habitats. The authors then integrate the spatial rescue mechanism to the problem of evolutionary rescue in response to temporally increasing fragmentation. There they show how rapid evolution allows for evolutionary rescue through the evolution of high dispersal. They also show the limits to this evolutionary rescue to cases where both aggregation and fragmentation are not too high. Interestingly, habitat aggregation prevents evolutionary rescue by directly affecting the evolutionary potential of dispersal. The study is based on simple scenarios that ignore the complexity of relationships between dispersal, landscape properties, and species interactions. This simplicity is the strength of the study, revealing basic mechanisms that can now be tested against other life-history tradeoffs and species interactions. Finand et al. (2023) provide a novel foundation for the study of eco-evolutionary dynamics in metacommunities exposed to spatially structured habitat destruction. They point to important assumptions that must be made along the way, including the relationships between dispersal distance and fecundity (they assume a positive relationship), and the nature of life-history tradeoffs between dispersal rate and local competitive abilities. 


Bell, G. 2017. Evolutionary Rescue. Annual Review of Ecology, Evolution, and Systematics 48:605–627. 
Fahrig, L. 2003. Effects of Habitat Fragmentation on Biodiversity. Annual Review of Ecology, Evolution, and Systematics 34:487–515. 
Finand, B., T. Monnin, and N. Loeuille. 2023. Evolution of dispersal and the maintenance of fragmented metapopulations. bioRxiv, 2022.06.08.495260, ver. 3 peer-reviewed and recommended by Peer Community in Ecology. 
Heino, M., and I. Hanski. 2001. Evolution of Migration Rate in a Spatially Realistic Metapopulation Model. The American Naturalist 157:495–511.

Evolution of dispersal and the maintenance of fragmented metapopulationsBasile Finand, Thibaud Monnin, Nicolas Loeuille<p>Because it affects dispersal risk and modifies competition levels, habitat fragmentation directly constrains dispersal evolution. When dispersal is traded-off against competitive ability, increased fragmentation is often expected to select high...Colonization, Competition, Dispersal & Migration, Eco-evolutionary dynamics, Spatial ecology, Metacommunities & Metapopulations, Theoretical ecologyFrédéric Guichard2022-06-10 13:51:15 View