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30 Mar 2021
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Do the more flexible individuals rely more on causal cognition? Observation versus intervention in causal inference in great-tailed grackles

From cognition to range dynamics – and from preregistration to peer-reviewed preprint

Recommended by based on reviews by Laure Cauchard and 1 anonymous reviewer

In 2018 Blaisdell and colleagues set out to study how causal cognition may impact large scale macroecological patterns, more specifically range dynamics, in the great-tailed grackle (Fronhofer 2019). This line of research is at the forefront of current thought in macroecology, a field that has started to recognize the importance of animal behaviour more generally (see e.g. Keith and Bull (2017)). Importantly, the authors were pioneering the use of preregistrations in ecology and evolution with the aim of improving the quality of academic research.

Now, nearly 3 years later, it is thanks to their endeavour of making research better that we learn that the authors are “[...] unable to speculate about the potential role of causal cognition in a species that is rapidly expanding its geographic range.” (Blaisdell et al. 2021; page 2). Is this a success or a failure? Every reader will have to find an answer to this question individually and there will certainly be variation in these answers as becomes clear from the referees’ comments. In my opinion, this is a success story of a more stringent and transparent approach to doing research which will help us move forward, both methodologically and conceptually.


Fronhofer (2019) From cognition to range dynamics: advancing our understanding of macroe-
cological patterns. Peer Community in Ecology, 100014. doi:

Keith, S. A. and Bull, J. W. (2017) Animal culture impacts species' capacity to realise climate-driven range shifts. Ecography, 40: 296-304. doi:

Blaisdell, A., Seitz, B., Rowney, C., Folsom, M., MacPherson, M., Deffner, D., and Logan, C. J. (2021) Do the more flexible individuals rely more on causal cognition? Observation versus intervention in causal inference in great-tailed grackles. PsyArXiv, ver. 5 peer-reviewed and recommended by Peer community in Ecology. doi:

Do the more flexible individuals rely more on causal cognition? Observation versus intervention in causal inference in great-tailed gracklesBlaisdell A, Seitz B, Rowney C, Folsom M, MacPherson M, Deffner D, Logan CJ<p>Behavioral flexibility, the ability to change behavior when circumstances change based on learning from previous experience, is thought to play an important role in a species’ ability to successfully adapt to new environments and expand its geo...PreregistrationsEmanuel A. Fronhofer2020-11-27 09:49:55 View
04 May 2021
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Are the more flexible great-tailed grackles also better at behavioral inhibition?

Great-tailed grackle research reveals need for researchers to consider their own flexibility and test limitations in cognitive test batteries.

Recommended by based on reviews by Pizza Ka Yee Chow and Alex DeCasian

In the article, "Are the more flexible great-tailed grackles also better at behavioral inhibition?", Logan and colleagues (2021) are setting an excellent standard for cognitive research on wild-caught animals. Using a decent sample (N=18) of wild-caught birds, they set out to test the ambiguous link between behavioral flexibility and behavioral inhibition, which is supported by some studies but rejected by others. Where this study is more thorough and therefore also more revealing than most extant research, the authors ran a battery of tests, examining both flexibility (reversal learning and solution switching) and inhibition (go/no go task; detour task; delay of gratification) through multiple different test series. They also -- somewhat accidentally -- performed their experiments and analyses with and without different criteria for correctness (85%, 100%). Their mistakes, assumptions and amendments of plans made during preregistration are clearly stated and this demonstrates the thought-process of the researchers very clearly.

Logan et al. (2021) show that inhibition in great-tailed grackles is a multi-faceted construct, and demonstrate that the traditional go/no go task likely tests a very different aspect of inhibition than the detour task, which was never linked to any of their flexibility measures. Their comprehensive Bayesian analyses held up the results of some of the frequentist statistics, indicating a consistent relationship between flexibility and inhibition, with more flexible individuals also showing better inhibition (in the go/no go task). This same model, combined with inconsistencies in the GLM analyses (depending on the inclusion or exclusion of an outlier), led them to recommend caution in the creation of arbitrary thresholds for "success" in any cognitive tasks. Their accidental longer-term data collection also hinted at patterns of behaviour that shorter-term data collection did not. Of course, researchers have to decide on success criteria in order to conduct experiments, but in the same way that frequentist statistics are acknowledged to have flaws, the setting of success criteria must be acknowledged as inherently arbitrary. Where possible, researchers could reveal novel, biologically salient patterns by continuing beyond the point where a convenient success criterion has been reached. This research also underscores that tests may not be examining the features we expected them to measure, and are highly sensitive to biological and ecological variation between species as well as individual variation within populations.

To me, this study is an excellent argument for pre-registration of research (registered as Logan et al. 2019 and accepted by Vogel 2019), as the authors did not end up cherry-picking only those results or methods that worked. The fact that some of the tests did not "work", but was still examined, added much value to the study. The current paper is a bit densely written because of the comprehensiveness of the research. Some editorial polishing would likely make for more elegant writing. However, the arguments are clear, the results novel, and the questions thoroughly examined. The results are important not only for cognitive research on birds, but are potentially valuable to any cognitive scientist. I recommend this article as excellent food for thought.


Logan CJ, McCune K, Johnson-Ulrich Z, Bergeron L, Seitz B, Blaisdell AP, Wascher CAF. (2019) Are the more flexible individuals also better at inhibition?  In principle acceptance by PCI Ecology of the version on 6 Mar 2019

Logan CJ, McCune KB, MacPherson M, Johnson-Ulrich Z, Rowney C, Seitz B, Blaisdell AP, Deffner D, Wascher CAF (2021) Are the more flexible great-tailed grackles also better at behavioral inhibition? PsyArXiv, ver. 7 peer-reviewed and recommended by Peer community in Ecology.

Vogel E (2019) Adapting to a changing environment: advancing our understanding of the mechanisms that lead to behavioral flexibility. Peer Community in Ecology, 100016. 

Are the more flexible great-tailed grackles also better at behavioral inhibition?Logan CJ, McCune KB, MacPherson M, Johnson-Ulrich Z, Rowney C, Seitz B, Blaisdell AP, Deffner D, Wascher CAF<p style="text-align: justify;">Behavioral flexibility (hereafter, flexibility) should theoretically be positively related to behavioral inhibition (hereafter, inhibition) because one should need to inhibit a previously learned behavior to change ...PreregistrationsAliza le Roux2020-12-04 13:57:07 View
27 Nov 2023
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Modeling Tick Populations: An Ecological Test Case for Gradient Boosted Trees

Gradient Boosted Trees can deliver more than accurate ecological predictions

Recommended by ORCID_LOGO based on reviews by 2 anonymous reviewers

Tick-borne diseases are an important burden on public health all over the globe, making accurate forecasts of tick population a key ingredient in a successful public health strategy. Over long time scales, tick populations can undergo complex dynamics, as they are sensitive to many non-linear effects due to the complex relationships between ticks and the relevant (numerical) features of their environment.

But luckily, capturing complex non-linear responses is a task that machine learning thrives on. In this contribution, Manley et al. (2023) explore the use of Gradient Boosted Trees to predict the distribution (presence/absence) and abundance of ticks across New York state.

This is an interesting modelling challenge in and of itself, as it looks at the same ecological question as an instance of a classification problem (presence/absence) or of a regression problem (abundance). In using the same family of algorithm for both, Manley et al. (2023) provide an interesting showcase of the versatility of these techniques. But their article goes one step further, by setting up a multi-class categorical model that estimates jointly the presence and abundance of a population. I found this part of the article particularly elegant, as it provides an intermediate modelling strategy, in between having two disconnected models for distribution and abundance, and having nested models where abundance is only predicted for the present class (see e.g. Boulangeat et al., 2012, for a great description of the later).

One thing that Manley et al. (2023) should be commended for is their focus on opening up the black box of machine learning techniques. I have never believed that ML models are more inherently opaque than other families of models, but the focus in this article on explainable machine learning shows how these models might, in fact, bring us closer to a phenomenological understanding of the mechanisms underpinning our observations.

There is also an interesting discussion in this article, on the rate of false negatives in the different models that are being benchmarked. Although model selection often comes down to optimizing the overall quality of the confusion matrix (for distribution models, anyway), depending on the type of information we seek to extract from the model, not all types of errors are created equal. If the purpose of the model is to guide actions to control vectors of human pathogens, a false negative (predicting that the vector is absent at a site where it is actually present) is a potentially more damaging outcome, as it can lead to the vector population (and therefore, potentially, transmission) increasing unchecked.


Boulangeat I, Gravel D, Thuiller W. Accounting for dispersal and biotic interactions to disentangle the drivers of species distributions and their abundances: The role of dispersal and biotic interactions in explaining species distributions and abundances. Ecol Lett. 2012;15: 584-593.

Manley W, Tran T, Prusinski M, Brisson D. (2023) Modeling tick populations: An ecological test case for gradient boosted trees. bioRxiv, 2023.03.13.532443, ver. 3 peer-reviewed and recommended by Peer Community in Ecology.

Modeling Tick Populations: An Ecological Test Case for Gradient Boosted TreesWilliam Manley, Tam Tran, Melissa Prusinski, Dustin Brisson<p style="text-align: justify;">General linear models have been the foundational statistical framework used to discover the ecological processes that explain the distribution and abundance of natural populations. Analyses of the rapidly expanding ...Parasitology, Species distributions, Statistical ecologyTimothée PoisotAnonymous, Anonymous2023-03-23 23:41:17 View
19 Dec 2020
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Hough transform implementation to evaluate the morphological variability of the moon jellyfish (Aurelia spp.)

A new member of the morphometrics jungle to better monitor vulnerable lagoons

Recommended by based on reviews by Julien Claude and 1 anonymous reviewer

In the recent years, morphometrics, the quantitative description of shape and its covariation [1] gained considerable momentum in evolutionary ecology. Using the form of organisms to describe, classify and try to understand their diversity can be traced back at least to Aristotle. More recently, two successive revolutions rejuvenated this idea [1–3]: first, a proper mathematical refoundation of the theory of shape, then a technical revolution in the apparatus able to acquire raw data. By using a feature extraction method and planning its massive use on data acquired by aerial drones, the study by Lacaux and colleagues [4] retraces this curse of events.
The radial symmetry of Aurelia spp. jelly fish, a common species complex, is affected by stress and more largely by environmental variations, such as pollution exposition. Aurelia spp. normally present four gonads so that the proportion of non-tetramerous individuals in a population has been proposed as a biomarker [5,6].
In this study, the authors implemented the Hough transform to largely automate the detection of the gonads in Aurelia spp. Such use of the Hough transform, a long-used approach to identify shapes through edge detection, is new to morphometrics. Here, the Aurelia spp. gonads are identified as ellipses from which aspect descriptors can be derived, and primarily counted and thus can be used to quantify the proportion of individuals presenting body plans disorders.

The sample sizes studied here were too low to allow finer-grained ecophysiological investigations. That being said, the proof-of-concept is convincing and this paper paths the way for an operational and innovative approach to the ecological monitoring of sensible aquatic ecosystems.


[1] Kendall, D. G. (1989). A survey of the statistical theory of shape. Statistical Science, 87-99. doi:
[2] Rohlf, F. J., and Marcus, L. F. (1993). A revolution morphometrics. Trends in ecology & evolution, 8(4), 129-132. doi:
[3] Adams, D. C., Rohlf, F. J., and Slice, D. E. (2004). Geometric morphometrics: ten years of progress following the ‘revolution’. Italian Journal of Zoology, 71(1), 5-16. doi:
[4] Lacaux, C., Desolneux, A., Gadreaud, J., Martin-Garin, B. and Thiéry, A. (2020) Hough transform implementation to evaluate the morphological variability of the moon jellyfish (Aurelia spp.). bioRxiv, 2020.03.11.986984, ver. 3 peer-reviewed and recommended by Peer Community in Ecology. doi:
[5] Gershwin, L. A. (1999). Clonal and population variation in jellyfish symmetry. Journal of the Marine Biological Association of the United Kingdom, 79(6), 993-1000. doi:
[6] Gadreaud, J., Martin-Garin, B., Artells, E., Levard, C., Auffan, M., Barkate, A.-L. and Thiéry, A. (2017) The moon jellyfish as a new bioindicator: impact of silver nanoparticles on the morphogenesis. In: Mariottini GL, editor. Jellyfish: ecology, distribution patterns and human interactions. Nova Science Publishers; 2017. pp. 277–292.

Hough transform implementation to evaluate the morphological variability of the moon jellyfish (Aurelia spp.)Céline Lacaux, Agnès Desolneux, Justine Gadreaud, Bertrand Martin-Garin and Alain Thiéry<p>Variations of the animal body plan morphology and morphometry can be used as prognostic tools of their habitat quality. The potential of the moon jellyfish (Aurelia spp.) as a new model organism has been poorly tested. However, as a tetramerous...MorphometricsVincent Bonhomme2020-03-18 17:40:51 View
01 Jun 2018
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Data-based, synthesis-driven: setting the agenda for computational ecology

Some thoughts on computational ecology from people who I’m sure use different passwords for each of their accounts

Recommended by based on reviews by Matthieu Barbier and 1 anonymous reviewer

Are you an ecologist who uses a computer or know someone that does? Even if your research doesn’t rely heavily on advanced computational techniques, it likely hasn’t escaped your attention that computers are increasingly being used to analyse field data and make predictions about the consequences of environmental change. So before artificial intelligence and robots take over from scientists, now is great time to read about how experts think computers could make your life easier and lead to innovations in ecological research. In “Data-based, synthesis-driven: setting the agenda for computational ecology”, Poisot and colleagues [1] provide a brief history of computational ecology and offer their thoughts on how computational thinking can help to bridge different types of ecological knowledge. In this wide-ranging article, the authors share practical strategies for realising three main goals: (i) tighter integration of data and models to make predictions that motivate action by practitioners and policy-makers; (ii) closer interaction between data-collectors and data-users; and (iii) enthusiasm and aptitude for computational techniques in future generations of ecologists. The key, Poisot and colleagues argue, is for ecologists to “engage in meaningful dialogue across disciplines, and recognize the currencies of their collaborations.” Yes, this is easier said than done. However, the journey is much easier with a guide and when everyone involved serves to benefit not only from the eventual outcome, but also the process.


[1] Poisot, T., Labrie, R., Larson, E., & Rahlin, A. (2018). Data-based, synthesis-driven: setting the agenda for computational ecology. BioRxiv, 150128, ver. 4 recommended and peer-reviewed by PCI Ecology. doi: 10.1101/150128

Data-based, synthesis-driven: setting the agenda for computational ecologyTimothée Poisot, Richard Labrie, Erin Larson, Anastasia RahlinComputational ecology, defined as the application of computational thinking to ecological problems, has the potential to transform the way ecologists think about the integration of data and models. As the practice is gaining prominence as a way to...Meta-analyses, Statistical ecology, Theoretical ecologyPhillip P.A. Staniczenko2018-02-05 20:51:41 View
11 Aug 2023
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Implementing Code Review in the Scientific Workflow: Insights from Ecology and Evolutionary Biology

A handy “How to” review code for ecologists and evolutionary biologists

Recommended by based on reviews by Serena Caplins and 1 anonymous reviewer

Ivimey Cook et al. (2023) provide a concise and useful “How to” review code for researchers in the fields of ecology and evolutionary biology, where the systematic review of code is not yet standard practice during the peer review of articles. Consequently, this article is full of tips for authors on how to make their code easier to review. This handy article applies not only to ecology and evolutionary biology, but to many fields that are learning how to make code more reproducible and shareable. Taking this step toward transparency is key to improving research rigor (Brito et al. 2020) and is a necessary step in helping make research trustable by the public (Rosman et al. 2022).


Brito, J. J., Li, J., Moore, J. H., Greene, C. S., Nogoy, N. A., Garmire, L. X., & Mangul, S. (2020). Recommendations to enhance rigor and reproducibility in biomedical research. GigaScience, 9(6), giaa056.

Ivimey-Cook, E. R., Pick, J. L., Bairos-Novak, K., Culina, A., Gould, E., Grainger, M., Marshall, B., Moreau, D., Paquet, M., Royauté, R., Sanchez-Tojar, A., Silva, I., Windecker, S. (2023). Implementing Code Review in the Scientific Workflow: Insights from Ecology and Evolutionary Biology. EcoEvoRxiv, ver 5 peer-reviewed and recommended by Peer Community In Ecology.

Rosman, T., Bosnjak, M., Silber, H., Koßmann, J., & Heycke, T. (2022). Open science and public trust in science: Results from two studies. Public Understanding of Science, 31(8), 1046-1062.

Implementing Code Review in the Scientific Workflow: Insights from Ecology and Evolutionary BiologyEdward Ivimey-Cook, Joel Pick, Kevin Bairos-Novak, Antica Culina, Elliot Gould, Matthew Grainger, Benjamin Marshall, David Moreau, Matthieu Paquet, Raphaël Royauté, Alfredo Sanchez-Tojar, Inês Silva, Saras Windecker<p>Code review increases reliability and improves reproducibility of research. As such, code review is an inevitable step in software development and is common in fields such as computer science. However, despite its importance, code review is not...Meta-analyses, Statistical ecologyCorina Logan2023-05-19 15:54:01 View
30 Jan 2020
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Diapause is not selected as a bet-hedging strategy in insects: a meta-analysis of reaction norm shapes

When to diapause or not to diapause? Winter predictability is not the answer

Recommended by based on reviews by Kévin Tougeron, Md Habibur Rahman Salman and 1 anonymous reviewer

Winter is a harsh season for many organisms that have to cope with food shortage and potentially lethal temperatures. Many species have evolved avoidance strategies. Among them, diapause is a resistance stage many insects use to overwinter. For an insect, it is critical to avoid lethal winter temperatures and thus to initiate diapause before winter comes, while making the most of autumn suitable climatic conditions [1,2]. Several cues can be used to appreciate that winter is coming, including day length and temperature [3]. But climate changes, temperatures rise and become more variable from year to year, which imposes strong pressure upon insect phenology [4]. How can insects adapt to changes in the mean and variance of winter onset?
In this paper, Jens Joschinski and Dries Bonte [5] address this question by using a well conducted meta-analysis of 458 diapause reaction norms obtained from 60 primary studies. They first ask first if insect mean diapause timing is tuned to match winter onset. They further ask if insects adapt to climatic unpredictability through a bet-hedging strategy by playing it safe and avoid risk (conservative bet-hedging) or on the contrary by avoiding to put all their eggs in one basket and spread the risk among their offspring (diversified bet-hedging). From published papers, the authors extracted data on mean diapause timing and information on latitude from which they retrieved day length inducing diapause, the date of winter onset and the day length at winter onset.
They found a positive correlation between latitude and the day length inducing diapause. On the contrary they found positive but (very) weak correlation between the date of winter onset and the date of diapause, thus indicating that diapause timing is not as optimally adapted to local environments as expected, particularly at high latitudes. They only found weak correlations between climate unpredictability and variability in diapause timing, and no correlation between climate unpredictability and deviation from optimal diapause timing. Together, these findings go against the hypothesis that insects use diversified or conservative bet-hedging strategies to cope with uncertainty in climatic conditions.
This is what makes the study thought provoking: the results do not match the theory well. Not because of a lack of data or a narrow scope, but because diapause is a complex trait that is determined by a large array of physiological and ecological factors [3]. Determining what are these factors is of particular interest in the face of the current climate change. This study shows what does not determine the timing of insect diapause. Researchers now know where to look at to improve our understanding of this key aspect of insect adaptation to climatic conditions.


[1] Dyck, H. V., Bonte, D., Puls, R., Gotthard, K., and Maes, D. (2015). The lost generation hypothesis: could climate change drive ectotherms into a developmental trap? Oikos, 124(1), 54–61. doi: 10.1111/oik.02066
[2] Gallinat, A. S., Primack, R. B., and Wagner, D. L. (2015). Autumn, the neglected season in climate change research. Trends in Ecology & Evolution, 30(3), 169–176. doi: 10.1016/j.tree.2015.01.004
[3] Tougeron, K. (2019). Diapause research in insects: historical review and recent work perspectives. Entomologia Experimentalis et Applicata, 167(1), 27–36. doi: 10.1111/eea.12753
[4] Bale, J. S., and Hayward, S. a. L. (2010). Insect overwintering in a changing climate. Journal of Experimental Biology, 213(6), 980–994. doi: 10.1242/jeb.037911
[5] Joschinski, J., and Bonte, D. (2020). Diapause is not selected as a bet-hedging strategy in insects: a meta-analysis of reaction norm shapes. BioRxiv, 752881, ver. 3 recommended and peer-reviewed by PCI Ecology. doi: 10.1101/752881

Diapause is not selected as a bet-hedging strategy in insects: a meta-analysis of reaction norm shapesJens Joschinski and Dries BonteMany organisms escape from lethal climatological conditions by entering a resistant resting stage called diapause, and it is essential that this strategy remains optimally timed with seasonal change. Climate change therefore exerts selection press...Maternal effects, Meta-analyses, Phenotypic plasticity, Terrestrial ecologyBastien Castagneyrol2019-09-20 11:47:47 View
29 May 2023
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Using integrated multispecies occupancy models to map co-occurrence between bottlenose dolphins and fisheries in the Gulf of Lion, French Mediterranean Sea

Mapping co-occurence of human activities and wildlife from multiple data sources

Recommended by based on reviews by Mason Fidino and 1 anonymous reviewer

Two fields of research have grown considerably over the past twenty years: the investigation of human-wildlife conflicts (e.g. see Treves & Santiago-Ávila 2020), and multispecies occupancy modelling (Devarajan et al. 2020). In their recent study, Lauret et al. (2023) combined both in an elegant methodological framework, applied to the study of the co-occurrence of fishing activities and bottlenose dolphins in the French Mediterranean.

A common issue with human-wildlife conflicts (and, in particular, fishery by-catch) is that data is often only available from those conflicts or interactions, limiting the validity of the predictions (Kuiper et al. 2022). Lauret et al. use independent data sources informing the occurrence of fishing vessels and dolphins, combined in a Bayesian multispecies occupancy model where vessels are "the other species". I particularly enjoyed that approach, as integration of human activities in ecological models can be extremely complex, but can also translate in phenomena that can be captured as one would of individuals of a species, as long as the assumptions are made clearly. Here, the model is made more interesting by accounting for environmental factors (seabed depth) borrowing an approach from Generalized Additive Models in the Bayesian framework. While not pretending to provide (yet) practical recommendations to help conserve bottlenose dolphins (and other wildlife conflicts), this study and the associated code are a promising step in that direction.


Devarajan, K., Morelli, T.L. & Tenan, S. (2020), Multi-species occupancy models: review, roadmap, and recommendations. Ecography, 43: 1612-1624.

Kuiper, T., Loveridge, A.J. and Macdonald, D.W. (2022), Robust mapping of human–wildlife conflict: controlling for livestock distribution in carnivore depredation models. Anim. Conserv., 25: 195-207.

Lauret V, Labach H, David L, Authier M, & Gimenez O (2023) Using integrated multispecies occupancy models to map co-occurrence between bottlenose dolphins and fisheries in the Gulf of Lion, French Mediterranean Sea. Ecoevoarxiv, ver. 2 peer-reviewed and recommended by PCI Ecology.

Treves, A. & Santiago-Ávila, F.J. (2020). Myths and assumptions about human-wildlife conflict and coexistence. Conserv. Biol. 34, 811–818.

Using integrated multispecies occupancy models to map co-occurrence between bottlenose dolphins and fisheries in the Gulf of Lion, French Mediterranean SeaValentin Lauret, Hélène Labach, Léa David, Matthieu Authier, Olivier Gimenez<p style="text-align: justify;">In the Mediterranean Sea, interactions between marine species and human activities are prevalent. The coastal distribution of bottlenose dolphins (<em>Tursiops truncatus</em>) and the predation pressure they put on ...Marine ecology, Population ecology, Species distributionsPaul Caplat2022-10-21 11:13:36 View
06 Mar 2020
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A community perspective on the concept of marine holobionts: current status, challenges, and future directions

Marine holobiont in the high throughput sequencing era

Recommended by and based on reviews by Sophie Arnaud-Haond and Aurélie Tasiemski

The concept of holobiont dates back to more than thirty years, it was primarily coined to hypothesize the importance of symbiotic associations to generate significant evolutionary novelties. Quickly adopted to describe the now well-studied system formed by zooxanthella associated corals, this concept expanded much further after the emergence of High-Throughput Sequencing and associated progresses in metabarcoding and metagenomics.
Holobionts – defined as the association between an individual host and its microbiota - are now increasingly described at sea and on land. The opinion article by Dittami et al. [1] provides a synthetic overview of marine holobionts. It retraces the history of the holobiont concept, recalls the main mechanisms underlying the association between hosts and microbial communities, highlights the influence of these symbioses on marine ecosystem functioning, and outlines current tools and future lines of research.
In particular, the article discusses some particularities of marine systems, such as the strong connectivity allowing an exchange of microorganisms and chemical signals between and within holobionts.
The authors advocate the need to bridge the gap between large scale exploration studies and smaller scale mechanistic studies, by conducting interdisciplinary research (combining physiology, biochemistry, ecology, experimentation and computational modeling) on some keystone holobionts.
Finally, one strength of the paper by Dittami et al. [1] is that it places the concept of the holobiont in an applied research framework. Several possible applications of knowledge on host-microbiota interactions are suggested, both in the field of aquaculture and that of monitoring the health of marine ecosystems. This article contains all the necessary elements for someone who would like to jump into the study of the holobionths in the marine world.

[1] Dittami SM, Arboleda E, Auguet J, Bigalke A, Briand E, Cardenas P, Cardini U, Decelle J, Engelen AH, Eveillard D, Gachon CMM, Griffiths SM, Harder T, Kayal E, Kazamia E, Lallier FH, Medina M, Marzinelli E, Morganti T, Núñez Pons L, Prado S, Pintado J, Saha M, Selosse M, Skillings D, Stock W, Sunagawa S, Toulza E, Vorobev A, Leblanc C, Not F. (2020). A community perspective on the concept of marine holobionts: current status, challenges, and future directions. Zenodo, ver. 4 peer-reviewed and recommended by PCI Ecology. doi: 10.5281/zenodo.3696771

A community perspective on the concept of marine holobionts: current status, challenges, and future directionsSimon M. Dittami, Enrique Arboleda, Jean-Christophe Auguet, Arite Bigalke, Enora Briand, Paco Cárdenas, Ulisse Cardini, Johan Decelle, Aschwin Engelen, Damien Eveillard, Claire M.M. Gachon, Sarah Griffiths, Tilmann Harder, Ehsan Kayal, Elena Kazam...Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. T...Marine ecology, Microbial ecology & microbiology, SymbiosisSophie Arnaud-Haond2019-02-05 17:57:11 View
21 Feb 2019
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Photosynthesis of Laminaria digitata during the immersion and emersion periods of spring tidal cycles during hot, sunny weather

Evaluating physiological responses of a kelp to environmental changes at its vulnerable equatorward range limit

Recommended by based on reviews by 2 anonymous reviewers

Understanding processes at species’ range limits is of paramount importance in an era of global change. For example, the boreal kelp Laminaria digitata, which dominates low intertidal and shallow subtidal rocky reefs in northwestern Europe, is declining in the equatorward portion of its range [1]. In this contribution, Migné and colleagues [2] focus on L. digitata near its southern range limit on the coast of France and use a variety of techniques to paint a complete picture of the physiological responses of the kelp to environmental changes. Importantly, and in contrast to earlier work on the species which focused on subtidal individuals (e.g. [3]), Migné et al. [2] describe responses not only in the most physiologically stressful portion of the species’ range but also in the most stressful portion of its local environment: the upper portion of its zone on the shoreline, where it is periodically exposed to aerial conditions and associated thermal and desiccation stresses.
The authors show that whereas L. digitata possesses mechanisms to protect it from irradiance stress at low tide, these mechanisms are not sufficient to prevent damage to photosynthetic pathways (e.g., reduction in optimal quantum yields of photosystem II). This species experiences severe heat stress associated with mid-day low tides during the summer, and the cumulative damage associated with these stresses is likely associated with the range contraction that is currently underway. Given the important role that L. digitata plays as food and habitat for other organisms, its loss will have cascading impacts on community structure and ecosystem functioning. Understanding the mechanisms underlying these declines is essential to understanding the impacts of climate change on species, communities, and ecosystems.


[1] Raybaud, V., Beaugrand, G., Goberville, E., Delebecq, G., Destombe, C., Valero, M., Davoult, D., Morin, P. & Gevaert, F. (2013). Decline in kelp in west Europe and climate. PloS one, 8(6), e66044. doi: 10.1371/journal.pone.0066044
[2] Delebecq, G., Davoult, D., Menu, D., Janquin, M. A., Migné, A., Dauvin, J. C., & Gevaert, F. (2011). In situ photosynthetic performance of Laminaria digitata (Phaeophyceae) during spring tides in Northern Brittany. CBM-Cahiers de Biologie Marine, 52(4), 405. doi: 10.21411/CBM.A.C9EE91F
[3] Migné, A., Delebecq, G., Davoult, D., Spilmont, N., Menu, D., Janquin, M.-A., and Gevaert, F. (2019). Photosynthesis of Laminaria digitata during the immersion and emersion periods of spring tidal cycles during hot, sunny weather. Hal, 01827565, ver. 4 peer-reviewed and recommended by PCI Ecology. hal-01827565

Photosynthesis of Laminaria digitata during the immersion and emersion periods of spring tidal cycles during hot, sunny weatherAline Migné, Gaspard Delebecq, Dominique Davoult, Nicolas Spilmont, Dominique Menu, Marie-Andrée Janquin and François GévaertThe boreal kelp Laminaria digitata dominates the low intertidal and upper subtidal zones of moderately exposed rocky shores in north-western Europe. Due to ocean warming, this foundation species is predicted to disappear from French coasts in the ...Marine ecologyMatthew Bracken2018-07-02 18:03:11 View