Submit a preprint

Latest recommendationsrsstwitter

IdTitleAuthorsAbstractPictureThematic fields▲RecommenderReviewersSubmission date
25 Nov 2022
article picture

Positive fitness effects help explain the broad range of Wolbachia prevalences in natural populations

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

Recommended by based on reviews by 3 anonymous reviewers

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


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

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

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

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

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

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

References

[1] Beckmann JF, Bonneau M, Chen H, Hochstrasser M, Poinsot D, Merçot H, Weill M, Sicard M, Charlat S (2019) The Toxin–Antidote Model of Cytoplasmic Incompatibility: Genetics and Evolutionary Implications. Trends in Genetics, 35, 175–185. https://doi.org/10.1016/j.tig.2018.12.004

[2] Karisto P, Duplouy A, Vries C de, Kokko H (2022) Positive fitness effects help explain the broad range of Wolbachia prevalences in natural populations. bioRxiv, 2022.04.11.487824, ver. 5 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2022.04.11.487824

[3] Laven H (1956) Cytoplasmic Inheritance in Culex. Nature, 177, 141–142. https://doi.org/10.1038/177141a0

[4] Perreau J, Zhang B, Maeda GP, Kirkpatrick M, Moran NA (2021) Strong within-host selection in a maternally inherited obligate symbiont: Buchnera and aphids. Proceedings of the National Academy of Sciences, 118, e2102467118. https://doi.org/10.1073/pnas.2102467118

[5] Vavre F, Fleury F, Varaldi J, Fouillet P, Bouletreau M (2000) Evidence for Female Mortality in Wolbachia-Mediated Cytoplasmic Incompatibility in Haplodiploid Insects: Epidemiologic and Evolutionary Consequences. Evolution, 54, 191–200. https://doi.org/10.1111/j.0014-3820.2000.tb00019.x

[6] Zug R, Hammerstein P (2015) Bad guys turned nice? A critical assessment of Wolbachia mutualisms in arthropod hosts. Biological Reviews, 90, 89–111. https://doi.org/10.1111/brv.12098

[7] Zug R, Hammerstein P (2018) Evolution of reproductive parasites with direct fitness benefits. Heredity, 120, 266–281. https://doi.org/10.1038/s41437-017-0022-5

Positive fitness effects help explain the broad range of Wolbachia prevalences in natural populationsPetteri Karisto, Anne Duplouy, Charlotte de Vries, Hanna Kokko<p style="text-align: justify;">The bacterial endosymbiont <em>Wolbachia</em> is best known for its ability to modify its host’s reproduction by inducing cytoplasmic incompatibility (CI) to facilitate its own spread. Classical models predict eithe...Host-parasite interactions, Population ecologyJorge Peña2022-04-12 12:52:55 View
06 Dec 2019
article picture

Does phenology explain plant-pollinator interactions at different latitudes? An assessment of its explanatory power in plant-hoverfly networks in French calcareous grasslands

The role of phenology for determining plant-pollinator interactions along a latitudinal gradient

Recommended by based on reviews by Ignasi Bartomeus, Phillip P.A. Staniczenko and 1 anonymous reviewer

Increased knowledge of what factors are determining species interactions are of major importance for our understanding of dynamics and functionality of ecological communities [1]. Currently, when ongoing temperature modifications lead to changes in species temporal and spatial limits the subject gets increasingly topical. A species phenology determines whether it thrive or survive in its environment. However, as the phenologies of different species are not necessarily equally affected by environmental changes, temporal or spatial mismatches can occur and affect the species-species interactions in the network [2] and as such the full network structure.
In this preprint by Manincor et al. [3] the authors explore the effect of phenology overlap on a large network of species interactions in calcareous grasslands in France. They analyze if and how this effect varies along a latitudinal gradient using empirical data on six plant-hoverfly networks. When comparing ecological network along gradients a well-known problem is that the network metrics is dependent on network size [4]. Therefore, instead of focusing on complete network structure the authors here focus on the factors that determine the probability of interactions and interaction frequency (number of visits). The authors use Bayesian Structural Equation Models (SEM) to link the interaction probability and number of visits to phenology overlap and species abundance. SEM is a multivariate technique that can be used to test several hypotheses and evaluate multiple causal relationships using both observed and latent variables to explain some other observed variables. The authors provide a nice description of the approach for this type of study system. In addition, the study also tests whether phenology affects network compartmentalization, by analyzing species subgroups using a latent block model (LBM) which is a clustering method particularly well-suited for weighted networks.
The authors identify phenology overlap as an important determinant of plant-pollinator interactions, but also conclude this factor alone is not sufficient to explain the species interactions. Species abundances was important for number of visits. Plant phenology drives the duration of the phenology overlap between plant and hoverflies in the studied system. This in turn influences either the probability of interaction or the expected number of visits, as well as network compartmentalization. Longer phenologies correspond to lower modularity inferring less constrained interactions, and shorter phenologies correspond to higher modularity inferring more constrained interactions.
What make this study particularly interesting is the presentation of SEMs as an innovative approach to compare networks of different sizes along environmental gradients. The authors show that these methods can be a useful tool when the aim is to understand the structure of plant-pollinator networks and data is varying in complexities. During the review process the authors carefully addressed to the comments from the two reviewers and the manuscript improved during the process. Both reviewers have expertise highly relevant for the research performed and the development of the manuscript. In my opinion this is a highly interesting and valuable piece of work both when it comes to the scientific question and the methodology. I look forward to further follow this research.

References

[1] Pascual, M., and Dunne, J. A. (Eds.). (2006). Ecological networks: linking structure to dynamics in food webs. Oxford University Press.
[2] Parmesan, C. (2007). Influences of species, latitudes and methodologies on estimates of phenological response to global warming. Global Change Biology, 13(9), 1860-1872. doi: 10.1111/j.1365-2486.2007.01404.x
[3] de Manincor, N., Hautekeete, N., Piquot, Y., Schatz, B., Vanappelghem, C. and Massol, F. (2019). Does phenology explain plant-pollinator interactions at different latitudes? An assessment of its explanatory power in plant-hoverfly networks in French calcareous grasslands. Zenodo, 2543768, ver. 4 peer-reviewed and recommended by PCI Ecology. doi: 10.5281/zenodo.2543768
[4] Staniczenko, P. P., Kopp, J. C., and Allesina, S. (2013). The ghost of nestedness in ecological networks. Nature communications, 4, 1391. doi: 10.1038/ncomms2422

Does phenology explain plant-pollinator interactions at different latitudes? An assessment of its explanatory power in plant-hoverfly networks in French calcareous grasslandsNatasha de Manincor, Nina Hautekeete, Yves Piquot, Bertrand Schatz, Cédric Vanappelghem, François Massol<p>For plant-pollinator interactions to occur, the flowering of plants and the flying period of pollinators (i.e. their phenologies) have to overlap. Yet, few models make use of this principle to predict interactions and fewer still are able to co...Interaction networks, Pollination, Statistical ecologyAnna Eklöf2019-01-18 19:02:13 View
10 Jan 2019
article picture

Inferring macro-ecological patterns from local species' occurrences

Upscaling the neighborhood: how to get species diversity, abundance and range distributions from local presence/absence data

Recommended by ORCID_LOGO based on reviews by Kevin Cazelles and 1 anonymous reviewer

How do you estimate the biodiversity of a whole community, or the distribution of abundances and ranges of its species, from presence/absence data in scattered samples?
It all starts with the collector's dilemma: if you double the number of samples, you will not get double the number of species, since you will find many of the same common species, and only a few new rare ones.
This non-additivity has prompted many ecologists to study the Species-Area Relationship. A common theoretical approach has been to connect this spatial pattern to the overall distribution of how common or rare a species can be. At least since Fisher's celebrated log-series [1], ecologists have been trying to, first, infer the shape of the Species Abundance Distribution, and then, use it to predict how many species should be found in a given area or a given number of samples. This has found many applications, from microbial communities to tropical forests, from estimating the number of yet-unknown species to predicting how much biodiversity may be lost if a fraction of the habitat is removed.
In this elegant work, Tovo et al. [2] propose a method that starts only from presence/absence data over a number of samples, and provides the community's diversity, as well as its abundance and range size distributions. This method is simple, analytically explicit, and accurate: the authors test it on the classic Pasoh and Barro Colorado Island tropical forest datasets, and on simulated data. They make a very laudable effort in both explaining its theoretical underpinnings, and proposing a straightforward step-by-step guide to applying it to data.
The core of Tovo et al's method is a simple property: the scale invariance of the Negative Binomial (NB) distribution. Subsampling from a NB gives another NB, where a single parameter has changed. Therefore, if the Species Abundance Distribution is close enough to some NB (which is flexible enough to accommodate all the data here), we can estimate how this parameter changes when going from (1) a single sample to (2) all the available samples, and from there, extrapolate to (3) the entire community.
This principle was first applied by the authors in a previous study [3] that required abundance data in the samples, rather than just presence/absence. Given that binary occurrence data is far more available in a variety of empirical settings, this extension is worthwhile (including its new predictions on range size distributions), and it deserves to be widely known and tested.

ADDITIONAL COMMENTS

1) To explain the novelty of the authors' contribution, it is useful to look at competing techniques.
Some ""parametric"" approaches try to infer the whole-community Species Abundance Distribution (SAD) by guessing its functional form (Gaussian, power-law, log-series...) and fitting its parameters from sampled data. The issue is that this distribution shape may not remain in the same family as we increase the sampling effort or area, so the regression problem may not be well-defined. This is where the Negative Binomial's scale invariance is useful.
Other ""non-parametric"" approaches have renounced guessing the whole SAD: they simply try to approximate of its tail of rare species, by looking at how many species are found in only one (or a few) samples. From this, they derive an estimate of biodiversity that is agnostic to the rest of the SAD. Tovo et al. [2] show the issue with these approaches: they extrapolate from the properties of individual samples to the whole community, but do not properly account for the bias introduced by the amount of sampling (the intermediate scale (2) in the summary above).

2) The main condition for all such approaches to work is well-mixedness: each sample should be sufficiently like a lot drawn from the same skewed lottery. As long as that condition applies, finding the best approach is a theoretical matter of probabilities and combinatorics that may, in time, be given a definite answer.
The authors also show that ""well-mixed"" is not as restrictive as it sounds: the method works both on real data (which is never perfectly mixed) and on simulations where species are even more spatially clustered than the empirical data. In addition, the Negative Binomial's scale invariance entails that, if it works well enough at some spatial scale, it will also work at all higher scales (until one reaches the edges of the sufficiently-well-mixed community)

3) One may ask: why the Negative Binomial as a Species Abundance Distribution?
If one wishes for some dynamical explanation, the Negative Binomial can be derived from neutral birth and death process with immigration, as shown by the authors in [3]. But to be applied to data, it should only be able to approximate the empirical distribution well enough (at all relevant scales). Depending on one's taste, this type of probabilistic approaches can be interpreted as:
- purely phenomenological, describing only the observational process of sampling from an existing state of affairs, not the ecological processes that gave rise to that state.
- a null model, from which everything in practice is expected to deviate to some extent.
- or a way to capture the statistical forces that tend to induce stable relationships between different patterns (as long as no ecological process opposes them strongly enough).

References

[1] Fisher, R. A., Corbet, A. S., & Williams, C. B. (1943). The relation between the number of species and the number of individuals in a random sample of an animal population. The Journal of Animal Ecology, 42-58. doi: 10.2307/1411
[2] Tovo, A., Formentin, M., Suweis, S., Stivanello, S., Azaele, S., & Maritan, A. (2019). Inferring macro-ecological patterns from local species' occurrences. bioRxiv, 387456, ver. 2 peer-reviewed and recommended by PCI Ecol. doi: 10.1101/387456
[3] Tovo, A., Suweis, S., Formentin, M., Favretti, M., Volkov, I., Banavar, J. R., Azaele, S., & Maritan, A. (2017). Upscaling species richness and abundances in tropical forests. Science Advances, 3(10), e1701438. doi: 10.1126/sciadv.1701438

Inferring macro-ecological patterns from local species' occurrencesAnna Tovo, Marco Formentin, Samir Suweis, Samuele Stivanello, Sandro Azaele, Amos Maritan<p>Biodiversity provides support for life, vital provisions, regulating services and has positive cultural impacts. It is therefore important to have accurate methods to measure biodiversity, in order to safeguard it when we discover it to be thre...Macroecology, Species distributions, Statistical ecology, Theoretical ecologyMatthieu Barbier2018-08-09 16:44:09 View
21 Feb 2019
article picture

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.

References

[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
02 Aug 2021
article picture

Dynamics of Fucus serratus thallus photosynthesis and community primary production during emersion across seasons: canopy dampening and biochemical acclimation

Towards a better understanding of the effects of self-shading on Fucus serratus populations

Recommended by ORCID_LOGO based on reviews by Gwenael Abril, Francesca Rossi and 1 anonymous reviewer

The importance of the vertical structure of vegetation cover for the functioning, management and conservation of ecosystems has received particular attention from ecologists in the last decades. Canopy architecture has many implications for light extinction coefficient, temperature variation reduction, self-shading which are all key parameters for the structuring and functioning of different ecosystems such as grasslands [1,2], forests [3,4], phytoplankton communities [5, 6], macroalgal populations [7] and even underwater animal forests such as octocoral communities [8].

This research topic, therefore, benefits from a large body of literature and the facilitative role of self-shadowing is no longer in question. However, it is always puzzling to note that some of the most common ecosystems turn out to be amongst the least known. This is precisely the case of the Fucus serratus communities which are widespread in Northeast Atlantic along the Atlantic coast of Europe from Svalbard to Portugal, as well as Northwest Atlantic & Gulf of St. Lawrence, easily accessible at low tide, but which have comparatively received less attention than more emblematic macro-algal communities such as Laminariales.

The lack of attention paid to these most common Fucales is particularly critical as some species such as F. serratus are proving to be particularly vulnerable to environmental change, leading to a predicted northward retreat from its current southern boundary [9].

In the present study [10], the authors showed the importance of the vegetation cover in resisting tide-induced environmental stresses. The canopy of F. serratus mitigates stress levels experienced in the lower layers during emersion, while various acclimation strategies take over to maintain the photosynthetic apparatus in optimal conditions.

They hereby highlight adaptation mechanisms to the extreme environment represented by the intertidal zone. These adaptation strategies were expected and similar mechanisms had been shown at the cellular level previously [11]. The earliest studies on the subject have shown that the structure of the bottom, the movement of water, and light availability all "influence the distribution of Fucaceae and disturb the regularity of their fine zonation, which itself is caused by the most important factor, desiccation", as Zaneveld states in his review [12]. He observed that the causes of the zonal distribution of marine algae are numerous, and identified several points of interest such as the relative period of emersion, the rapidity of desiccation, the loss of water, and the thickness of the cell walls.

The present study thus highlights the existence of facilitative mechanisms associated with F. serratus canopy and nicely confirms previous work with in situ observations. It also highlights the importance of the vegetative cover in combating desiccation and introduces the dampening effect as a facilitating mechanism.

The effect of the vegetation cover can sometimes even be felt beyond its immediate area of influence. A recent study shows that ground-level ozone is significantly reduced by the combined effects of canopy shading and turbulence [4]. Below the canopy, the light intensity becomes sufficiently low which inhibits ozone formation due to the decrease in the rates of hydroxyl radical formation and the rates of conversion of nitrogen dioxide to nitrogen oxide by photolysis. In addition, reductions in light levels associated with foliage promote ozone-destroying reactions between plant-emitted species, such as nitric oxide and/or alkenes, and ozone itself. The reduction in diffusivity slows the upward transport of surface emitted species, partially decoupling the area under the canopy from the rest of the atmosphere.

By analogy with the work of Makar et al [4], and in the light of the results provided by the authors of this study, one may wonder whether the canopy dampening of F. serratus communities (and other common fucoids widely distributed on our coasts) might not also influence atmospheric chemistry, both at the Earth's surface and in the atmospheric boundary layer. The lack of accumulation of reactive oxygen species under the canopy found by the authors is consistent with this hypothesis and suggests that the damping effect of F. serratus may well have much wider consequences than expected.

References

[1] Jurik TW, Kliebenstein H (2000) Canopy Architecture, Light Extinction and Self-Shading of a Prairie Grass, Andropogon Gerardii. The American Midland Naturalist, 144, 51–65. http://www.jstor.org/stable/3083010

[2] Mitchley J, Willems JH (1995) Vertical canopy structure of Dutch chalk grasslands in relation to their management. Vegetatio, 117, 17–27. https://doi.org/10.1007/BF00033256

[3] Kane VR, Gillespie AR, McGaughey R, Lutz JA, Ceder K, Franklin JF (2008) Interpretation and topographic compensation of conifer canopy self-shadowing. Remote Sensing of Environment, 112, 3820–3832. https://doi.org/10.1016/j.rse.2008.06.001

[4] Makar PA, Staebler RM, Akingunola A, Zhang J, McLinden C, Kharol SK, Pabla B, Cheung P, Zheng Q (2017) The effects of forest canopy shading and turbulence on boundary layer ozone. Nature Communications, 8, 15243. https://doi.org/10.1038/ncomms15243

[5] Shigesada N, Okubo A (1981) Analysis of the self-shading effect on algal vertical distribution in natural waters. Journal of Mathematical Biology, 12, 311–326. https://doi.org/10.1007/BF00276919

[6] Barros MP, Pedersén M, Colepicolo P, Snoeijs P (2003) Self-shading protects phytoplankton communities against H2O2-induced oxidative damage. Aquatic Microbial Ecology, 30, 275–282. https://doi.org/10.3354/ame030275

[7] Ørberg SB, Krause-Jensen D, Mouritsen KN, Olesen B, Marbà N, Larsen MH, Blicher ME, Sejr MK (2018) Canopy-Forming Macroalgae Facilitate Recolonization of Sub-Arctic Intertidal Fauna and Reduce Temperature Extremes. Frontiers in Marine Science, 5. https://doi.org/10.3389/fmars.2018.00332

[8] Nelson H, Bramanti L (2020) From Trees to Octocorals: The Role of Self-Thinning and Shading in Underwater Animal Forests. In: Perspectives on the Marine Animal Forests of the World (eds Rossi S, Bramanti L), pp. 401–417. Springer International Publishing, Cham. https://doi.org/10.1007/978-3-030-57054-5_12

[9] Jueterbock A, Kollias S, Smolina I, Fernandes JMO, Coyer JA, Olsen JL, Hoarau G (2014) Thermal stress resistance of the brown alga Fucus serratus along the North-Atlantic coast: Acclimatization potential to climate change. Marine Genomics, 13, 27–36. https://doi.org/10.1016/j.margen.2013.12.008

[10] Migné A, Duong G, Menu D, Davoult D, Gévaert F (2021) Dynamics of Fucus serratus thallus photosynthesis and community primary production during emersion across seasons: canopy dampening and biochemical acclimation. HAL, hal-03079617, ver. 4 peer-reviewed and recommended by Peer community in Ecology. https://hal.archives-ouvertes.fr/hal-03079617

[11] Lichtenberg M, Kühl M (2015) Pronounced gradients of light, photosynthesis and O2 consumption in the tissue of the brown alga Fucus serratus. New Phytologist, 207, 559–569. https://doi.org/10.1111/nph.13396

[12] Zaneveld JS (1937) The Littoral Zonation of Some Fucaceae in Relation to Desiccation. Journal of Ecology, 25, 431–468. https://doi.org/10.2307/2256204

Dynamics of Fucus serratus thallus photosynthesis and community primary production during emersion across seasons: canopy dampening and biochemical acclimationAline Migné, Gwendoline Duong, Dominique Menu, Dominique Davoult & François Gévaert<p style="text-align: justify;">The brown alga <em>Fucus serratus</em> forms dense stands on the sheltered low intertidal rocky shores of the Northeast Atlantic coast. In the southern English Channel, these stands have proved to be highly producti...Marine ecologyCédric Hubas2021-01-05 16:24:02 View
06 Mar 2020
article picture

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.

References
[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
29 May 2023
article picture

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.

REFERENCES

Devarajan, K., Morelli, T.L. & Tenan, S. (2020), Multi-species occupancy models: review, roadmap, and recommendations. Ecography, 43: 1612-1624. https://doi.org/10.1111/ecog.04957

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. https://doi.org/10.1111/acv.12730

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. https://doi.org/10.32942/osf.io/npd6u

Treves, A. & Santiago-Ávila, F.J. (2020). Myths and assumptions about human-wildlife conflict and coexistence. Conserv. Biol. 34, 811–818.  https://doi.org/10.1111/cobi.13472

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
30 Jan 2020
article picture

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.

References

[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
11 Aug 2023
article picture

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).

References

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. https://doi.org/10.1093/gigascience/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. https://doi.org/10.32942/X2CG64

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. https://doi.org/10.1177/09636625221100686

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
01 Jun 2018
article picture

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.

References

[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