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22 May 2019
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Sex makes them sleepy: host reproductive status induces diapause in a parasitoid population experiencing harsh winters

The response of interacting species to biotic seasonal cues

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

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

References

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

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

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

Recommended by based on reviews by Aaron Yilmaz and Michael Morris

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

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

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

References:

[1] Depeux C, Branger A, Moulignier T, Moreau J, Lemaître J-F, Dechaume-Moncharmont F-X, Laverre T, Pauhlac H, Gaillard J-M, Beltran-Bech S (2022) Deleterious effects of thermal and water stresses on life history and physiology: a case study on woodlouse. bioRxiv, 2022.09.26.509512., ver. 3 peer-reviewd and recommended by PCI Ecology. https://doi.org/10.1101/2022.09.26.509512

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

[3] Hassall M, Helden A, Goldson A, Grant A (2005) Ecotypic differentiation and phenotypic plasticity in reproductive traits of Armadillidium vulgare (Isopoda: Oniscidea). Oecologia 143: 51–60.​ https://doi.org/10.1007/s00442-004-1772-3

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

References

Fronhofer (2019) From cognition to range dynamics: advancing our understanding of macroe-
cological patterns. Peer Community in Ecology, 100014. doi: https://doi.org/10.24072/pci.ecology.100014

Keith, S. A. and Bull, J. W. (2017) Animal culture impacts species' capacity to realise climate-driven range shifts. Ecography, 40: 296-304. doi: https://doi.org/10.1111/ecog.02481

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: https://doi.org/10.31234/osf.io/z4p6s

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
03 Feb 2023
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The role of climate change and niche shifts in divergent range dynamics of a sister-species pair

Drivers of range expansion in a pair of sister grackle species

Recommended by ORCID_LOGO based on reviews by 2 anonymous reviewers

The spatial distribution of a species is driven by both biotic and abiotic factors that may change over time (Soberón & Nakamura, 2009; Paquette & Hargreaves, 2021).  Therefore, species ranges are dynamic, especially in humanized landscapes where changes occur at high speeds (Sirén & Morelli, 2020). The distribution of many species is being reduced because of human impacts; however, some species are expanding their distributions, even over their niche (Lustenhouwer & Parker, 2022). One of the factors that may lead to a geographic niche expansion is behavioral flexibility (Mikhalevich et al., 2017), but the mechanisms determining range expansion through behavioral changes are not fully understood. 

The PCI Ecology study by Summers et al. (2023) uses a very large database on the current and historic distribution of two species of grackles that have shown different trends in their distribution. The great-tailed grackle has largely expanded its range over the 20th century, while the range of the boat-tailed grackle has remained very similar. They take advantage of this differential response in the distribution of the two species and run several analyses to test whether it was a change in habitat availability, in the realized niche, in habitat connectivity or in in the other traits or conditions that previously limited the species range, what is driving the observed distribution of the species. The study finds a change in the niche of great-tailed grackle, consistent with the high behavioral flexibility of the species.

The two reviewers and I have seen a lot of value in this study because 1) it addresses a very timely question, especially in the current changing world; 2) it is a first step to better understanding if behavioral attributes may affect species’ ability to change their niche; 3) it contrasts the results using several complementary statistical analyses, reinforcing their conclusions; 4) it is based on the preregistration Logan et al (2021), and any deviations from it are carefully explained and justified in the text and 5) the limitations of the study have been carefully discussed. It remains to know if the boat-tailed grackle has more limited behavioral flexibility than the great-tailed grackle, further confirming the results of this study.
 
References

Logan CJ, McCune KB, Chen N, Lukas D (2021) Implementing a rapid geographic range expansion - the role of behavior and habitat changes. http://corinalogan.com/Preregistrations/gxpopbehaviorhabitat.html

Lustenhouwer N, Parker IM (2022) Beyond tracking climate: Niche shifts during native range expansion and their implications for novel invasions. Journal of Biogeography, 49, 1481–1493. https://doi.org/10.1111/jbi.14395

Mikhalevich I, Powell R, Logan C (2017) Is behavioural flexibility evidence of cognitive complexity? How evolution can inform comparative cognition. Interface Focus, 7, 20160121. https://doi.org/10.1098/rsfs.2016.0121

Paquette A, Hargreaves AL (2021) Biotic interactions are more often important at species’ warm versus cool range edges. Ecology Letters, 24, 2427–2438. https://doi.org/10.1111/ele.13864

Sirén APK, Morelli TL (2020) Interactive range-limit theory (iRLT): An extension for predicting range shifts. Journal of Animal Ecology, 89, 940–954. https://doi.org/10.1111/1365-2656.13150

Soberón J, Nakamura M (2009) Niches and distributional areas: Concepts, methods, and assumptions. Proceedings of the National Academy of Sciences, 106, 19644–19650. https://doi.org/10.1073/pnas.0901637106

Summers JT, Lukas D, Logan CJ, Chen N (2022) The role of climate change and niche shifts in divergent range dynamics of a sister-species pair. EcoEvoRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.32942/osf.io/879pe

The role of climate change and niche shifts in divergent range dynamics of a sister-species pairJeremy Summers, Dieter Lukas, Corina J. Logan, Nancy Chen<p>---This is a POST-STUDY manuscript for the PREREGISTRATION, which received in principle acceptance in 2020 from Dr. Sebastián González (reviewed by Caroline Nieberding, Tim Parker, and Pizza Ka Yee Chow; <a href="https://doi.org/10.24072/pci.ec...Behaviour & Ethology, Biogeography, Dispersal & Migration, Human impact, Landscape ecology, Preregistrations, Species distributionsEsther Sebastián González2022-05-26 20:07:33 View
22 Nov 2021
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Beating your neighbor to the berry patch

When more competitors means less harvested resource

Recommended by ORCID_LOGO based on reviews by Francois Massol, Jeremy Van Cleve and 1 anonymous reviewer

In this paper, Alan R. Rogers (2021) examines the dynamics of foraging strategies for a resource that gains value over time (e.g., ripening fruits), while there is a fixed cost of attempting to forage the resource, and once the resource is harvested nothing is left for other harvesters. For this model, not any pure foraging strategy is evolutionary stable. A mixed equilibrium exists, i.e., with a mixture of foraging strategies within the population, which is still evolutionarily unstable. Nonetheless, Alan R. Rogers shows that for a large number of competitors and/or high harvesting cost, the mixture of strategies remains close to the mixed equilibrium when simulating the dynamics. Surprisingly, in a large population individuals will less often attempt to forage the resource and will instead “go fishing”. The paper also exposes an experiment of the game with students, which resulted in a strategy distribution somehow close to the theoretical mixture of strategies.

The economist John F. Nash Jr. (1950) gained the Nobel Prize of economy in 1994 for his game theoretical contributions. He gave his name to the “Nash equilibrium”, which represents a set of individual strategies that is reached whenever all the players have nothing to gain by changing their strategy while the strategies of others are unchanged. Alan R. Rogers shows that the mixed equilibrium in the foraging game is such a Nash equilibrium. Yet it is evolutionarily unstable insofar as a distribution close to the equilibrium can invade.

The insights of the study are twofold. First, it sheds light on the significance of Nash equilibrium in an ecological context of foraging strategies. Second, it shows that an evolutionarily unstable state can rule the composition of the ecological system. Therefore, the contribution made by the paper should be most significant to better understand the dynamics of competitive communities and their eco-evolutionary trajectories. 

References

Nash JF (1950) Equilibrium points in n-person games. Proceedings of the National Academy of Sciences, 36, 48–49. https://doi.org/10.1073/pnas.36.1.48

Rogers AR (2021) Beating your Neighbor to the Berry Patch. bioRxiv, 2020.11.12.380311, ver. 8 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2020.11.12.380311

 

Beating your neighbor to the berry patchAlan R. Rogers<p style="text-align: justify;">Foragers often compete for resources that ripen (or otherwise improve) gradually. What strategy is optimal in this situation? It turns out that there is no optimal strategy. There is no evolutionarily stable strateg...Behaviour & Ethology, Evolutionary ecology, ForagingFrançois Munoz Erol Akçay, Jorge Peña, Sébastien Lion, François Rousset, Ulf Dieckmann , Troy Day , Corina Tarnita , Florence Debarre , Daniel Friedman , Vlastimil Krivan , Ulf Dieckmann 2020-12-10 18:38:49 View
04 Apr 2023
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Data stochasticity and model parametrisation impact the performance of species distribution models: insights from a simulation study

Species Distribution Models: the delicate balance between signal and noise

Recommended by ORCID_LOGO based on reviews by Alejandra Zarzo Arias and 1 anonymous reviewer

Species Distribution Models (SDMs) are one of the most commonly used tools to predict where species are, where they may be in the future, and, at times, what are the variables driving this prediction. As such, applying an SDM to a dataset is akin to making a bet: that the known occurrence data are informative, that the resolution of predictors is adequate vis-à-vis the scale at which their impact is expressed, and that the model will adequately capture the shape of the relationships between predictors and predicted occurrence.

In this contribution, Lambert & Virgili (2023) perform a comprehensive assessment of different sources of complications to this process, using replicated simulations of two synthetic species. Their experimental process is interesting, in that both the data generation and the data analysis stick very close to what would happen in "real life". The use of synthetic species is particularly relevant to the assessment of SDM robustness, as they enable the design of species for which the shape of the relationship is given: in short, we know what the model should capture, and can evaluate the model performance against a ground truth that lacks uncertainty.

Any simulation study is limited by the assumptions established by the investigators; when it comes to spatial data, the "shape" of the landscape, both in terms of auto-correlation and in where the predictors are available. Lambert & Virgili (2023) nicely circumvent these issues by simulating synthetic species against the empirical distribution of predictors; in other words, the species are synthetic, but the environment for which the prediction is made is real. This is an important step forward when compared to the use of e.g. neutral landscapes (With 1997), which can have statistical properties that are not representative of natural landscapes (see e.g. Halley et al., 2004).

A striking point in the study by Lambert & Virgili (2023) is that they reveal a deep, indeed deeper than expected, stochasticity in SDMs; whether this is true in all models remains an open question, but does not invalidate their recommendation to the community: the interpretation of outcomes is a delicate exercise, especially because measures that inform on the goodness of the model fit do not capture the predictive quality of the model outputs. This preprint is both a call to more caution, and a call to more curiosity about the complex behavior of SDMs, while also providing a sensible template to perform future analyses of the potential issues with predictive models.


References

Halley, J. M., et al. (2004) “Uses and Abuses of Fractal Methodology in Ecology: Fractal Methodology in Ecology.” Ecology Letters, vol. 7, no. 3, pp. 254–71. https://doi.org/10.1111/j.1461-0248.2004.00568.x.

Lambert, Charlotte, and Auriane Virgili (2023). Data Stochasticity and Model Parametrisation Impact the Performance of Species Distribution Models: Insights from a Simulation Study. bioRxiv, ver. 2 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2023.01.17.524386

With, Kimberly A. (1997) “The Application of Neutral Landscape Models in Conservation Biology. Aplicacion de Modelos de Paisaje Neutros En La Biologia de La Conservacion.” Conservation Biology, vol. 11, no. 5, pp. 1069–80. https://doi.org/10.1046/j.1523-1739.1997.96210.x.

Data stochasticity and model parametrisation impact the performance of species distribution models: insights from a simulation studyCharlotte Lambert, Auriane Virgili<p>Species distribution models (SDM) are widely used to describe and explain how species relate to their environment, and predict their spatial distributions. As such, they are the cornerstone of most of spatial planning efforts worldwide. SDM can...Biogeography, Habitat selection, Macroecology, Marine ecology, Spatial ecology, Metacommunities & Metapopulations, Species distributions, Statistical ecologyTimothée Poisot2023-01-20 09:43:51 View
08 Jan 2020
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Studies of NH4+ and NO3- uptake ability of subalpine plants and resource-use strategy identified by their functional traits

Nitrate or not nitrate. That is the question

Recommended by based on reviews by Vincent Maire and 1 anonymous reviewer

The article by Legay et al. [1] addresses two main issues: the links between belowground and aboveground plant traits and the links between plant strategies (as defined by these traits) and the capacity to absorb nitrate and ammonium. I recommend this work because these are important and current issues. The literature on plant traits is extremely rich and the existence of a leaf economic spectrum linked to a gradient between conservative and acquisitive plants is now extremely well established [2-3]. Many teams are now working on belowground traits and possible links with the aboveground gradients [4-5]. It seems indeed that there is a root economic spectrum but this spectrum is apparently less pronounced than the leaf economic spectrum. The existence of links between the two spectrums are still controversial and are likely not universal as suggested by discrepant results and after all a plant could have a conservative strategy aboveground and an acquisitive strategy belowground (or vice-versa) because, indeed, constraints are different belowground and aboveground (for example because in given ecosystem/vegetation type light may be abundant but not water or mineral nutrients). The various results obtained also suggest that we do not full understand the diversity of belowground strategies, what is at stake with these strategies, and the links with root characteristics.
Each time I give a conference on the work we are carrying out on African grasses that likely absorb ammonium preferentially because they inhibit nitrification [6-7], somebody asks me a question about the fact that plant essentially absorb nitrate because ammonium is toxic and nitrate more available in the soil. The present article confirms that this is not the case and that, though there are currently some teams working on the subject, we do not really know for the moment whether plants absorb nitrate or ammonium, in which proportion, how plastic this proportion is within individuals and within species. This subject seems to me crucial because it is linked to (1) the capacity of ecosystems to conserve nitrogen [8], because nitrate, much more than ammonium, goes out of ecosystems through leaching and denitrification, (2) to carbon cycling and plant energy budget because absorbing nitrate requires spending mucho more energy than absorbing ammonium because nitrate must be reduced before being incorporated in plant biomass, which is very energy costly. These two issues are naturally very relevant to develop efficient cropping systems in terms of carbon and nitrogen.
Interestingly, the present article, comparing three grass species in different sites, suggests that there is no trade-off between the absorption of nitrate and ammonium: more acquisitive individuals tend to absorb more ammonium and nitrate. This is contrary to hypotheses we made to predict the outcome of competition between plants absorbing nitrate and ammonium in different proportions [9] but should be tested in the future comparing many different types of plants. The results also suggest that more conservative plants absorb relatively more ammonium, which makes sense because this allows them to spare the energy necessary to reduce nitrate. This leads to the question of the effect of these strategies on nitrogen retention within the ecosystem. If nitrification is high (low), absorbing ammonium is not efficient and likely leads to high (low) nitrogen losses. This should be tested in the future. Moreover, the authors have measured the absorption of nitrate and ammonium through measurements at the root scale on cut roots. This should be complemented by measurements at the whole plant scale.

References

[1] Legay, N., Grassein, F., Arnoldi, C., Segura, R., Laîné, P., Lavorel, S. and Clément, J.-C. (2020). Studies of NH4+ and NO3- uptake ability of subalpine plants and resource-use strategy identified by their functional traits. bioRxiv, 372235, ver. 4 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/372235
[2] Shipley, B., Lechowicz, M.J., Wright, I. & Reich, P.B. (2006) Fundamental trade-offs generating the worldwide leaf economics spectrum. Ecology, 87, 535-541. doi: 10.1890/05-1051
[3] Reich, P.B. (2014) The world-wide ‘fast-slow’ plant economics spectrum: a traits manifesto. J. Ecol., 102, 275-301. doi: 10.1111/1365-2745.12211
[4] Maire, V., Gross, N., Pontes, L.D.S., Picon-Cochard, C. & Soussana, J.F. (2009) Trade-off between root nitrogen acquisition and shoot nitrogen utilization across 13 co-occurring pasture grass species. Func. Ecol., 23, 668-679. doi: 10.1111/j.1365-2435.2009.01557.x
[5] Roumet, C., Birouste, M., Picon-Cochard, C., Ghestem, M., Osman, N., Vrignon-Brenas, S., Cao, K.F. & Stokes, A. (2016) Root structure-function relationships in 74 species: evidence of a root economics spectrum related to carbon economy. New. Phytol., 210, 815-826. doi: 10.1111/nph.13828
[6] Lata, J.-C., Degrange, V., Raynaud, X., Maron, P.-A., Lensi, R. & Abbadie, L. (2004) Grass populations control nitrification in savanna soils. Funct. Ecol., 18, 605-611. doi: 10.1111/j.0269-8463.2004.00880.x
[7] Srikanthasamy, T., Leloup, J., N’Dri, A.B., Barot, S., Gervaix, J., Koné, A.W., Koffi, K.F., Le Roux, X., Raynaud, X. & Lata, J.-C. (2018) Contrasting effects of grasses and trees on microbial N-cycling in an African humid savanna. Soil Biol. Biochem., 117, 153-163. doi: 10.1016/j.soilbio.2017.11.016
[8] Boudsocq, S., Lata, J.C., Mathieu, J., Abbadie, L. & Barot, S. (2009) Modelling approach to analyze the effects of nitrification inhibition on primary production. Func. Ecol., 23, 220-230. doi: 10.1111/j.1365-2435.2008.01476.x
[9] Boudsocq, S., Niboyet, A., Lata, J.-C., Raynaud, X., Loeuille, N., Mathieu, J., Blouin, M., Abbadie, L. & Barot, S. (2012) Plant preference for ammonium versus nitrate: a neglected determinant of ecosystem functioning? Am. Nat., 180, 60-69. doi: 10.1086/665997

Studies of NH4+ and NO3- uptake ability of subalpine plants and resource-use strategy identified by their functional traitsLegay Nicolas, Grassein Fabrice, Arnoldi Cindy, Segura Raphaël, Laîné Philippe, Lavorel Sandra, Clément Jean-Christophe<p>The leaf economics spectrum (LES) is based on a suite of leaf traits related to plant functioning and ranges from resource-conservative to resource-acquisitive strategies. However, the relationships with root traits, and the associated belowgro...Community ecology, Physiology, Terrestrial ecologySébastien Barot2018-07-19 14:22:28 View
04 Sep 2019
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Gene expression plasticity and frontloading promote thermotolerance in Pocillopora corals

Transcriptomics of thermal stress response in corals

Recommended by based on reviews by Mar Sobral

Climate change presents a challenge to many life forms and the resulting loss of biodiversity will critically depend on the ability of organisms to timely respond to a changing environment. Shifts in ecological parameters have repeatedly been attributed to global warming, with the effectiveness of these responses varying among species [1, 2]. Organisms do not only have to face a global increase in mean temperatures, but a complex interplay with another crucial but largely understudied aspect of climate change: thermal fluctuations. Understanding the mechanisms underlying adaptation to thermal fluctuations is thus a timely and critical challenge.
Coral reefs are among the most threaten ecosystems in the context of current global changes [3]. Brener-Raffalli and colleagues [4] provided a very complete study digging into the physiological, symbiont-based and transcriptomic mechanisms underlying response of corals to temperature changes. They used an experimental approach, following the heat stress response of coral colonies from different species of the genus Pocillopora. While the symbiont community composition did not significantly change facing exposure to warmer temperatures, the authors provided evidence for transcriptomic changes especially linked to stress response genes that may underlie plastic responses to heat stress.
The authors furthermore investigated the thermal stress response of corals originating from two sites differing in their natural thermal regimes, and found that they differ in the extent and nature of plastic response, including the expression of gene regulation factors and the basal expression level of some genes. These two sites also differ in a variety of aspects, including the focal coral species, which precludes from concluding about the role of thermal regime adaptation into the differences observed. However, these results still highlight a very interesting and important direction deserving further investigation [5], and point out the importance of variability in thermal stress response among localities [6] that might potentially mediate global warming consequences on coral reefs.

References

[1] Parmesan, C., & Yohe, G. (2003). A globally coherent fingerprint of climate change impacts across natural systems. Nature, 421(6918), 37–42. doi: 10.1038/nature01286
[2] Menzel, A., Sparks, T. H., Estrella, N., Koch, E., Aasa, A., Ahas, R., … Zust, A. (2006). European phenological response to climate change matches the warming pattern. Global Change Biology, 12(10), 1969–1976. doi: 10.1111/j.1365-2486.2006.01193.x
[3] Bellwood, D. R., Hughes, T. P., Folke, C., & Nyström, M. (2004). Confronting the coral reef crisis. Nature, 429(6994), 827–833. doi: 10.1038/nature02691
[4] Brener-Raffalli, K., Vidal-Dupiol, J., Adjeroud, M., Rey, O., Romans, P., Bonhomme, F., Pratlong, M., Haguenauer, A., Pillot, R., Feuillassier, L., Claereboudt, M., Magalon, H., Gélin, P., Pontarotti, P., Aurelle, D., Mitta, G. and Toulza, E. (2019). Gene expression plasticity and frontloading promote thermotolerance in Pocillopora corals. BioRxiv, 398602, ver 4 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/398602
[5] Kenkel, Carly D., and Matz, M. V. (2017). Gene expression plasticity as a mechanism of coral adaptation to a variable environment. Nature Ecology and Evolution, 1(1), 0014. doi: 10.1038/s41559-016-0014
[6] Kenkel, C. D., Meyer, E., and Matz, M. V. (2013). Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides) from different thermal environments. Molecular Ecology, 22(16), 4322–4334. doi: 10.1111/mec.12390

Gene expression plasticity and frontloading promote thermotolerance in Pocillopora coralsK. Brener-Raffalli, J. Vidal-Dupiol, M. Adjeroud, O. Rey, P. Romans, F. Bonhomme, M. Pratlong, A. Haguenauer, R. Pillot, L. Feuillassier, M. Claereboudt, H. Magalon, P. Gélin, P. Pontarotti, D. Aurelle, G. Mitta, E. Toulza<p>Ecosystems worldwide are suffering from climate change. Coral reef ecosystems are globally threatened by increasing sea surface temperatures. However, gene expression plasticity provides the potential for organisms to respond rapidly and effect...Climate change, Evolutionary ecology, Marine ecology, Molecular ecology, Phenotypic plasticity, SymbiosisStaffan Jacob2018-08-29 10:46:55 View
03 Jan 2024
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Efficient sampling designs to assess biodiversity spatial autocorrelation : should we go fractal?

Spatial patterns and autocorrelation challenges in ecological conservation

Recommended by ORCID_LOGO based on reviews by Nigel Yoccoz and Charles J Marsh

Pattern, like beauty, is to some extent in the eye of the beholder” (Grant 1977 in Wiens, 1989)

Ecologists are immersed in unraveling the complex spatial patterns that govern species diversity, driven by both practical and theoretical imperatives (Rahbek, 2005; Wang et al., 2019). This dual focus necessitates a practical imperative for strategic biodiversity conservation, requiring a nuanced understanding of locations with peak species richness and dynamic shifts in species assemblages (Chase et al., 2020). Simultaneously, there is a theoretical interest in using diversity patterns as empirical testing grounds for theories explaining factors influencing diversity disparities and the associated increase in species turnover correlated with inter-site distance (Condit et al., 2002).
 
McGill (2010), in his paper "Matters of Scale", highlights the scale-dependent nature of ecology, aligning with the recognition that spatial autocorrelation is inherent in biogeographical data and often correlated with sample size (Rahbek, 2005). Spatial autocorrelation, often underestimated in ecological studies (Dormann, 2007), occurs when proximate locations exhibit similarities in ecological attributes (Tobler, 1970; Getis, 2010), introducing a latent bias that compromises the robustness of ecological findings (Dormann, 2007; Dormann et al., 2007). This phenomenon serves as both an asset, providing valuable information for inferring processes from patterns (Palma et al. 1999), and a challenge, imposing limitations on hypothesis testing and prediction (Dormann et al., 2007 and references therein). Various factors contribute to spatial autocorrelation, with three primary contributors (Dormann et al., 2007; Legendre, 1993; Legendre and Fortin, 1989; Legendre and Legendre, 2012): (i) distance-related effects in biological processes, (ii) misrepresentation of non-linear relationships between the environment and species as linear and (iii) the oversight of a crucial spatially structured environmental determinant in the statistical model, leading to spatial structuring in the response (Dormann et al., 2007).
 
Recognising the pivotal role of spatial heterogeneity in ecological theories (Wang et al., 2019), it becomes imperative to discern and address the limitations introduced by spatial autocorrelation (Legendre, 1993). McGill (2011) emphasises that the ultimate goal of biodiversity pattern studies should be to develop a quantitative predictive theory useful for conservation. The spatial dimension's importance in study planning, determining the system's scale, appropriate quadrat size, and spacing between sampling stations, is paramount (Fortin, 1999a,b). Responses to these considerations are intricately linked with study objectives and insights from pre-sampling campaigns, underscoring the need for a nuanced and rigorous approach (Delmelle, 2021).
 
Understanding statistical techniques and nested sampling designs is crucial to answering fundamental ecological questions (Dormann et al., 2007; McDonald, 2012). In addressing spatial autocorrelation challenges, ecologists must recognize the limitations of many standard statistical methods in ecological studies (Dale and Fortin, 2002; Legendre and Fortin, 1989; Steel et al., 2013). In the initial phases of description or hypothesis generation, ecologists should proactively acknowledge the spatial structure in their data and conduct tests for spatial autocorrelation (for a comprehensive description, see Legendre and Fortin, 1989): various tools, including correlograms, spectral analysis, the Mantel test, and clustering methods, facilitate the assessment and description of spatial structures. The partial Mantel test enables the study of causal models with space as an explanatory variable. Techniques for mapping ecological variables, such as interpolation, trend surface analysis, and constrained clustering, yield maps providing valuable insights into the spatial dynamics of ecological systems.
 
This refined consideration of spatial autocorrelation emerges as an imperative in ecological research, fostering a deeper and more precise understanding of the intricate interplay between species diversity, spatial patterns, and the inherent limitations imposed by spatial autocorrelation (Legendre et al., 2002). This not only contributes significantly to the scientific discourse in ecology but also aligns with McGill's vision of developing predictive theories for effective conservation (Bacaro et al., 2016; McGill, 2011).
 
In this study by Fabien Laroche (2023), titled “Efficient sampling designs to assess biodiversity spatial autocorrelation: should we go fractal?” the primary focus was on addressing the challenges associated with estimating the autocorrelation range of species distribution across spatial scales. The study aimed to explore alternative sampling designs, with a particular focus on the application of fractal designs—self-similar designs with well-identified scales. The overarching goal was to evaluate whether fractal designs could offer a more efficient compromise compared to traditional hybrid designs, which involve mixing random sampling points with a systematic grid.
 
Virtual ecology provides a way to test whether sampling designs can accurately detect or quantify effects of interest before implementing them in the field. Beyond the question of assessing the power of empirical designs, a virtual ecology analysis contributes to clearly formulating the set of questions associated with a design. However, only a few virtual studies have focused on efficient designs to accurately estimate the autocorrelation range of biodiversity variables. In this study, the statistical framework of optimal design of experiments was employed—a methodology often used in building and comparing designs of temporal or spatiotemporal biodiversity surveys but rarely applied to the specific problem of quantifying spatial autocorrelation.
 
Key findings from the study shed light on optimal sampling strategies, with a notable dependence on the feasible grid mesh size over the study area in relation to expected autocorrelation range values. The results demonstrated that the efficiency of designs varied based on the specific effect under study. Fractal designs, however, exhibited superior performance, particularly when assessing the effect of a monotonic environmental gradient across space.
 
In conclusion, the study provides valuable insights into the potential benefits of incorporating fractal designs in biodiversity studies, offering a nuanced and efficient approach to estimate spatial autocorrelation. These findings contribute significantly to the ongoing scientific discourse in ecology, providing practical considerations for improving sampling designs in biodiversity assessments.
 
References
 
Bacaro, G., Altobelli, A., Cameletti, M., Ciccarelli, D., Martellos, S., Palmer, M.W., Ricotta, C., Rocchini, D., Scheiner, S.M., Tordoni, E., Chiarucci, A., 2016. Incorporating spatial autocorrelation in rarefaction methods: Implications for ecologists and conservation biologists. Ecological Indicators 69, 233-238. https://doi.org/10.1016/j.ecolind.2016.04.026
 
Chase, J.M., Jeliazkov, A., Ladouceur, E., Viana, D.S., 2020. Biodiversity conservation through the lens of metacommunity ecology. Annals of the New York Academy of Sciences 1469, 86-104. https://doi.org/10.1111/nyas.14378
 
Condit, R., Pitman, N., Leigh, E.G., Chave, J., Terborgh, J., Foster, R.B., Núñez, P., Aguilar, S., Valencia, R., Villa, G., Muller-Landau, H.C., Losos, E., Hubbell, S.P., 2002. Beta-Diversity in Tropical Forest Trees. Science 295, 666-669. https://doi.org/10.1126/science.1066854
 
Dale, M.R.T., Fortin, M.-J., 2002. Spatial autocorrelation and statistical tests in ecology. Écoscience 9, 162-167. https://doi.org/10.1080/11956860.2002.11682702
 
Delmelle, E.M., 2021. Spatial Sampling, in: Fischer, M.M., Nijkamp, P. (Eds.), Handbook of Regional Science. Springer Berlin Heidelberg, Berlin, Heidelberg, pp. 1829-1844.
 
Dormann, C.F., 2007. Effects of incorporating spatial autocorrelation into the analysis of species distribution data. Global Ecology & Biogeography 16, 129-128. https://doi.org/10.1111/j.1466-8238.2006.00279.x
 
Dormann, C.F., McPherson, J.M., Araújo, M.B., Bivand, R., Bolliger, J., Carl, G., Davies, R.G., Hirzel, A., Jetz, W., Kissling, W.D., Kühn, I., Ohlemüler, R., Peres-Neto, P.R., Reineking, B., Schröder, B., Schurr, F.M., Wilson, R., 2007. Methods to account for spatial autocorrelation in the analysis of species distributional data: a review. Ecography 33, 609-628. https://doi.org/10.1111/j.2007.0906-7590.05171.x
 
Fortin, M.-J., 1999a. Effects of quadrat size and data measurement on the detection of boundaries. Journal of Vegetation Science 10, 43-50. https://doi.org/10.2307/3237159
 
Fortin, M.-J., 1999b. Effects of sampling unit resolution on the estimation of spatial autocorrelation. Écoscience 6, 636-641. https://doi.org/10.1080/11956860.1999.11682547
 
Getis, A., 2010. Spatial Autocorrelation, in: Fischer, M.M., Getis, A. (Eds.), Handbook of Applied Spatial Analysis: Software Tools, Methods and Applications. Springer Berlin Heidelberg, Berlin, Heidelberg, pp. 255-278.
 
Laroche, F., 2023. Efficient sampling designs to assess biodiversity spatial autocorrelation: should we go fractal? bioRxiv, 2022.07.29.501974, ver. 4 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2022.07.29.501974
 
Legendre, P., 1993. Spatial Autocorrelation: Trouble or New Paradigm? Ecology 74, 1659-1673. https://doi.org/10.2307/1939924
 
Legendre, P., Dale, M.R.T., Fortin, M.-J., Gurevitch, J., Hohn, M., Myers, D., 2002. The consequences of spatial structure for the design and analysis of ecological field surveys. Ecography 25, 601-615. https://doi.org/10.1034/j.1600-0587.2002.250508.x
 
Legendre, P., Fortin, M.J., 1989. Spatial pattern and ecological analysis. Vegetatio 80, 107-138. https://doi.org/10.1007/BF00048036
 
Legendre, P., Legendre, L., 2012. Numerical Ecology, Third Edition ed. Elsevier, The Netherlands.
 
McDonald, T., 2012. Spatial sampling designs for long-term ecological monitoring, in: Cooper, A.B., Gitzen, R.A., Licht, D.S., Millspaugh, J.J. (Eds.), Design and Analysis of Long-term Ecological Monitoring Studies. Cambridge University Press, Cambridge, pp. 101-125.
 
McGill, B.J., 2010. Matters of Scale. Science 328, 575-576. https://doi.org/10.1126/science.1188528
 
McGill, B.J., 2011. Linking biodiversity patterns by autocorrelated random sampling. American Journal of Botany 98, 481-502. https://doi.org/10.3732/ajb.1000509
 
Rahbek, C., 2005. The role of spatial scale and the perception of large-scale species-richness patterns. Ecology Letters 8, 224-239. https://doi.org/10.1111/j.1461-0248.2004.00701.x
 
Steel, E.A., Kennedy, M.C., Cunningham, P.G., Stanovick, J.S., 2013. Applied statistics in ecology: common pitfalls and simple solutions. Ecosphere 4, art115. https://doi.org/10.1890/ES13-00160.1
 
Tobler, W.R., 1970. A Computer Movie Simulating Urban Growth in the Detroit Region. Economic Geography 46, 234-240. https://doi.org/10.2307/143141
 
Wang, S., Lamy, T., Hallett, L.M., Loreau, M., 2019. Stability and synchrony across ecological hierarchies in heterogeneous metacommunities: linking theory to data. Ecography 42, 1200-1211. https://doi.org/10.1111/ecog.04290
 
Wiens, J.A., 1989. The ecology of bird communities. Cambridge University Press.
Efficient sampling designs to assess biodiversity spatial autocorrelation : should we go fractal?Fabien Laroche<p>Quantifying the autocorrelation range of species distribution in space is necessary for applied ecological questions, like implementing protected area networks or monitoring programs. However, the power of spatial sampling designs to estimate t...Biodiversity, Landscape ecology, Spatial ecology, Metacommunities & Metapopulations, Statistical ecologyEric Goberville2023-04-21 10:54:29 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.

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