|Id||Title||Authors||Abstract||Picture||Thematic fields||Recommender||Reviewers||Submission date|
23 Mar 2020
Intraspecific difference among herbivore lineages and their host-plant specialization drive the strength of trophic cascadesArnaud Sentis, Raphaël Bertram, Nathalie Dardenne, Jean-Christophe Simon, Alexandra Magro, Benoit Pujol, Etienne Danchin and Jean-Louis Hemptinne https://doi.org/10.1101/722140
Tell me what you’ve eaten, I’ll tell you how much you’ll eat (and be eaten)Recommended by Sara Magalhães and Raul Costa-Pereira based on reviews by Bastien Castagneyrol and 1 anonymous reviewer
Tritrophic interactions have a central role in ecological theory and applications [1-3]. Particularly, systems comprised of plants, herbivores and predators have historically received wide attention given their ubiquity and economic importance . Although ecologists have long aimed to understand the forces that govern alternating ecological effects at successive trophic levels , several key open questions remain (at least partially) unanswered . In particular, the analysis of complex food webs has questioned whether ecosystems can be viewed as a series of trophic chains [7,8]. Moreover, whether systems are mostly controlled by top-down (trophic cascades) or bottom-up processes remains an open question .
 Price, P. W., Bouton, C. E., Gross, P., McPheron, B. A., Thompson, J. N., & Weis, A. E. (1980). Interactions among three trophic levels: influence of plants on interactions between insect herbivores and natural enemies. Annual review of Ecology and Systematics, 11(1), 41-65. doi: 10.1146/annurev.es.11.110180.000353
|Intraspecific difference among herbivore lineages and their host-plant specialization drive the strength of trophic cascades||Arnaud Sentis, Raphaël Bertram, Nathalie Dardenne, Jean-Christophe Simon, Alexandra Magro, Benoit Pujol, Etienne Danchin and Jean-Louis Hemptinne||<p>Trophic cascades, the indirect effect of predators on non-adjacent lower trophic levels, are important drivers of the structure and dynamics of ecological communities. However, the influence of intraspecific trait variation on the strength of t...||Community ecology, Eco-evolutionary dynamics, Food webs, Population ecology||Sara Magalhães||2019-08-02 09:11:03||View|
06 Mar 2020
Interplay between the paradox of enrichment and nutrient cycling in food websPierre Quévreux, Sébastien Barot and Élisa Thébault https://doi.org/10.1101/276592
New insights into the role of nutrient cycling in food web dynamicsRecommended by Samraat Pawar based on reviews by Jean-François Arnoldi, Wojciech Uszko and 1 anonymous reviewer
Understanding the factors that govern the relationship between structure, stability and functioning of food webs has been a central problem in ecology for many decades. Historically, apart from microbial and soil food webs, the role of nutrient cycling has largely been ignored in theoretical and empirical food web studies. A prime example of this is the widespread use of Lotka-Volterra type models in theoretical studies; these models per se are not designed to capture the effect of nutrients being released back into the system by interacting populations. Thus overall, we still lack a general understanding of how nutrient cycling affects food web dynamics.
 Quévreux, P., Barot, S. and E. Thébault (2020) Interplay between the paradox of enrichment and nutrient cycling in food webs. bioRxiv, 276592, ver. 7 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/276592
|Interplay between the paradox of enrichment and nutrient cycling in food webs||Pierre Quévreux, Sébastien Barot and Élisa Thébault||<p>Nutrient cycling is fundamental to ecosystem functioning. Despite recent major advances in the understanding of complex food web dynamics, food web models have so far generally ignored nutrient cycling. However, nutrient cycling is expected to ...||Biodiversity, Community ecology, Ecosystem functioning, Food webs, Interaction networks, Theoretical ecology||Samraat Pawar||2018-11-03 21:47:37||View|
06 Mar 2020
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 Kazamia, Francois H. Lallier, Mónica Medina, Ezequiel M. Marzinelli, Teresa Morganti, Laura Núñez Pons, Soizic Pardo, José Pintado Valverde, Mahasweta Saha, Marc-André Selosse, Derek Skillings, Willem Stock, Shinichi Sunagawa, Eve Toulza, Alexey Vorobev, Cat... 10.5281/zenodo.3696771
Marine holobiont in the high throughput sequencing eraRecommended by Sophie Arnaud-Haond and Corinne Vacher 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.
|A community perspective on the concept of marine holobionts: current status, challenges, and future directions||Simon 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, Symbiosis||Sophie Arnaud-Haond||2019-02-05 17:57:11||View|
06 Mar 2020
The persistence in time of distributional patterns in marine megafauna impacts zonal conservation strategiesCharlotte Lambert, Ghislain Dorémus, Vincent Ridoux https://doi.org/10.1101/790634
The importance of spatio-temporal dynamics on MPA's designRecommended by Sergio Estay based on reviews by Ana S. L. Rodrigues and 1 anonymous reviewer
Marine protected areas (MPA) have arisen as the main approach for conservation of marine species. Fishes, marine mammals and birds can be conservation targets that justify the implementation of these areas. However, MPAs undergo many of the problems faced by their terrestrial equivalent. One of the major concerns is that these conservation areas are spatially constrained, by logistic reasons, and many times these constraints caused that key areas for the species (reproductive sites, refugees, migration) fall outside the limits, making conservation efforts even more difficult. Lambert et al.  evaluate at what point the Bay of Biscay MPA contains key ecological areas for several emblematic species. The evaluation incorporated a spatio-temporal dimension. To evaluate these ideas, authors evaluate two population descriptors: aggregation and persistence of several species of cetaceans and seabirds.
 Lambert, C., Dorémus, G. and V. Ridoux (2020) The persistence in time of distributional patterns in marine megafauna impacts zonal conservation strategies. bioRxiv, 790634, ver. 3 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/790634
|The persistence in time of distributional patterns in marine megafauna impacts zonal conservation strategies||Charlotte Lambert, Ghislain Dorémus, Vincent Ridoux||<p>The main type of zonal conservation approaches corresponds to Marine Protected Areas (MPAs), which are spatially defined and generally static entities aiming at the protection of some target populations by the implementation of a management pla...||Conservation biology, Habitat selection, Species distributions||Sergio Estay||2019-10-03 08:47:17||View|
19 Feb 2020
Soil variation response is mediated by growth trajectories rather than functional traits in a widespread pioneer Neotropical treeSébastien Levionnois, Niklas Tysklind, Eric Nicolini, Bruno Ferry, Valérie Troispoux, Gilles Le Moguedec, Hélène Morel, Clément Stahl, Sabrina Coste, Henri Caron, Patrick Heuret https://doi.org/10.1101/351197
Growth trajectories, better than organ-level functional traits, reveal intraspecific response to environmental variationRecommended by François Munoz based on reviews by Georges Kunstler and François Munoz
Functional traits are “morpho-physio-phenological traits which impact fitness indirectly via their effects on growth, reproduction and survival” . Most functional traits are defined at organ level, e.g. for leaves, roots and stems, and reflect key aspects of resource acquisition and resource use by organisms for their development and reproduction . More rarely, some functional traits can be related to spatial development, such as vegetative height and lateral spread in plants.
 Violle, C., Navas, M. L., Vile, D., Kazakou, E., Fortunel, C., Hummel, I., & Garnier, E. (2007). Let the concept of trait be functional!. Oikos, 116(5), 882-892. doi: 10.1111/j.0030-1299.2007.15559.x
|Soil variation response is mediated by growth trajectories rather than functional traits in a widespread pioneer Neotropical tree||Sébastien Levionnois, Niklas Tysklind, Eric Nicolini, Bruno Ferry, Valérie Troispoux, Gilles Le Moguedec, Hélène Morel, Clément Stahl, Sabrina Coste, Henri Caron, Patrick Heuret||<p style="text-align: justify;">1- Trait-environment relationships have been described at the community level across tree species. However, whether interspecific trait-environment relationships are consistent at the intraspecific level is yet unkn...||Botany, Eco-evolutionary dynamics, Habitat selection, Ontogeny, Tropical ecology||François Munoz||2018-06-21 17:13:17||View|
05 Feb 2020
A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcodingMiriam I Brandt, Blandine Trouche, Laure Quintric, Patrick Wincker, Julie Poulain, Sophie Arnaud-Haond https://doi.org/10.1101/717355
A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcodingRecommended by Stefaniya Kamenova based on reviews by Tiago Pereira and 1 anonymous reviewer
High-throughput sequencing-based techniques such as DNA metabarcoding are increasingly advocated as providing numerous benefits over morphology‐based identifications for biodiversity inventories and ecosystem biomonitoring . These benefits are particularly apparent for highly-diversified and/or hardly accessible aquatic and marine environments, where simple water or sediment samples could already produce acceptably accurate biodiversity estimates based on the environmental DNA present in the samples [2,3]. However, sequence-based characterization of biodiversity comes with its own challenges. A major one resides in the capacity to disentangle true biological diversity (be it taxonomic or genetic) from artefactual diversity generated by sequence-errors accumulation during PCR and sequencing processes, or from the amplification of non-target genes (i.e. pseudo-genes). On one hand, the stringent elimination of sequence variants might lead to biodiversity underestimation through the removal of true species, or the clustering of closely-related ones. On the other hand, a more permissive sequence filtering bears the risks of biodiversity inflation. Recent studies have outlined an excellent methodological framework for addressing this issue by proposing bioinformatic tools that allow the amplicon-specific error-correction as alternative or as complement to the more arbitrary approach of clustering into Molecular Taxonomic Units (MOTUs) based on sequence dissimilarity [4,5]. But to date, the relevance of amplicon-specific error-correction tools has been demonstrated only for a limited set of taxonomic groups and gene markers.
 Porter, T. M., and Hajibabaei, M. (2018). Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis. Molecular Ecology, 27(2), 313–338. doi: 10.1111/mec.14478
|A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcoding||Miriam I Brandt, Blandine Trouche, Laure Quintric, Patrick Wincker, Julie Poulain, Sophie Arnaud-Haond||<p>Environmental metabarcoding is an increasingly popular tool for studying biodiversity in marine and terrestrial biomes. With sequencing costs decreasing, multiple-marker metabarcoding, spanning several branches of the tree of life, is becoming ...||Biodiversity, Community ecology, Marine ecology, Molecular ecology||Stefaniya Kamenova||2019-08-02 20:52:45||View|
01 Feb 2020
Evidence of tool use in a seabird?Benjamin G. Farrar 10.31234/osf.io/463hk
Touchy matter: the delicate balance between Morgan’s canon and open-minded description of advanced cognitive skills in the animalRecommended by Francois-Xavier Dechaume-Moncharmont based on reviews by Valérie Dufour and Alex Taylor
In a recent paper published in PNAS, Fayet et al.  reported scarce field observations of two Atlantic puffins (four years apart) apparently scratching their bodies using sticks, which was interpreted by the authors as evidence of tool use in this species. In a short response, Benjamin Farrar  raises serious concerns about this interpretation and proposes simpler, more parsimonious, mechanisms explaining the observed behaviour: a textbook case of Morgan's canon.
 Fayet, A. L., Hansen, E. S., and Biro, D. (2020). Evidence of tool use in a seabird. Proceedings of the National Academy of Sciences, 117(3), 1277–1279. doi: 10.1073/pnas.1918060117
|Evidence of tool use in a seabird?||Benjamin G. Farrar||Fayet, Hansen and Biro (1) provide two observations of Atlantic puffins, *Fratercula arctica*, performing self-directed actions while holding a stick in their beaks. The authors interpret this as evidence of tool use as they suggest that the stick...||Behaviour & Ethology||Francois-Xavier Dechaume-Moncharmont||2020-01-22 11:55:27||View|
30 Jan 2020
Diapause is not selected as a bet-hedging strategy in insects: a meta-analysis of reaction norm shapesJens Joschinski and Dries Bonte 10.1101/752881
When to diapause or not to diapause? Winter predictability is not the answerRecommended by Bastien Castagneyrol 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 . But climate changes, temperatures rise and become more variable from year to year, which imposes strong pressure upon insect phenology . How can insects adapt to changes in the mean and variance of winter onset?
 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
|Diapause is not selected as a bet-hedging strategy in insects: a meta-analysis of reaction norm shapes||Jens Joschinski and Dries Bonte||Many 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 ecology||Bastien Castagneyrol||2019-09-20 11:47:47||View|
29 Jan 2020
Stoichiometric constraints modulate the effects of temperature and nutrients on biomass distribution and community stabilityArnaud Sentis, Bart Haegeman, and José M. Montoya https://doi.org/10.1101/589895
On the importance of stoichiometric constraints for understanding global change effects on food web dynamicsRecommended by Elisa Thebault based on reviews by 2 anonymous reviewers
The constraints associated with the mass balance of chemical elements (i.e. stoichiometric constraints) are critical to our understanding of ecological interactions, as outlined by the ecological stoichiometry theory . Species in ecosystems differ in their elemental composition as well as in their level of elemental homeostasis , which can determine the outcome of interactions such as herbivory or decomposition on species coexistence and ecosystem functioning [3, 4].
 Sterner, R. W. and Elser, J. J. (2017). Ecological Stoichiometry, The Biology of Elements from Molecules to the Biosphere. doi: 10.1515/9781400885695
|Stoichiometric constraints modulate the effects of temperature and nutrients on biomass distribution and community stability||Arnaud Sentis, Bart Haegeman, and José M. Montoya||<p>Temperature and nutrients are two of the most important drivers of global change. Both can modify the elemental composition (i.e. stoichiometry) of primary producers and consumers. Yet their combined effect on the stoichiometry, dynamics, and s...||Climate change, Community ecology, Food webs, Theoretical ecology, Thermal ecology||Elisa Thebault||2019-08-08 12:20:08||View|
08 Jan 2020
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 https://doi.org/10.1101/372235
Nitrate or not nitrate. That is the questionRecommended by Sébastien Barot based on reviews by Vincent Maire and 1 anonymous reviewer
The article by Legay et al.  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.
 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
|Studies of NH4+ and NO3- uptake ability of subalpine plants and resource-use strategy identified by their functional traits||Legay 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 ecology||Sébastien Barot||2018-07-19 14:22:28||View|