|Id||Title||Authors||Abstract||Picture||Thematic fields||Recommender||Reviewers||Submission date▲|
10 Oct 2018
Detecting within-host interactions using genotype combination prevalence dataSamuel Alizon, Carmen Lía Murall, Emma Saulnier, Mircea T Sofonea https://doi.org/10.1101/256586
Combining epidemiological models with statistical inference can detect parasite interactionsRecommended by Dustin Brisson based on reviews by Samuel Díaz Muñoz, Erick Gagne and 1 anonymous reviewer
There are several important topics in the study of infectious diseases that have not been well explored due to technical difficulties. One such topic is pursued by Alizon et al. in “Modelling coinfections to detect within-host interactions from genotype combination prevalences” . Both theory and several important examples have demonstrated that interactions among co-infecting strains can have outsized impacts on disease outcomes, transmission dynamics, and epidemiology. Unfortunately, empirical data on pathogen interactions and their outcomes is often correlational making results difficult to decipher.
 Alizon, S., Murall, C.L., Saulnier, E., & Sofonea, M.T. (2018). Detecting within-host interactions using genotype combination prevalence data. bioRxiv, 256586, ver. 3 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/256586
|Detecting within-host interactions using genotype combination prevalence data||Samuel Alizon, Carmen Lía Murall, Emma Saulnier, Mircea T Sofonea||<p>Parasite genetic diversity can provide information on disease transmission dynamics but most methods ignore the exact combinations of genotypes in infections. We introduce and validate a new method that combines explicit epidemiological modelli...||Eco-immunology & Immunity, Epidemiology, Host-parasite interactions, Statistical ecology||Dustin Brisson||Samuel Díaz Muñoz, Erick Gagne||2018-02-01 09:23:26||View|
01 Jun 2018
Data-based, synthesis-driven: setting the agenda for computational ecologyTimothée Poisot, Richard Labrie, Erin Larson, Anastasia Rahlin 10.1101/150128
Some thoughts on computational ecology from people who I’m sure use different passwords for each of their accountsRecommended by Phillip P.A. Staniczenko 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  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.
 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 ecology||Timothée Poisot, Richard Labrie, Erin Larson, Anastasia Rahlin||Computational 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 ecology||Phillip P.A. Staniczenko||2018-02-05 20:51:41||View|
02 Oct 2018
How optimal foragers should respond to habitat changes? On the consequences of habitat conversion.Vincent Calcagno, Frederic Hamelin, Ludovic Mailleret, Frederic Grognard 10.1101/273557
Optimal foraging in a changing world: old questions, new perspectivesRecommended by Francois-Xavier Dechaume-Moncharmont based on reviews by Frederick Adler, Andrew Higginson and 1 anonymous reviewer
Marginal value theorem (MVT) is an archetypal model discussed in every behavioural ecology textbook. Its popularity is largely explained but the fact that it is possible to solve it graphically (at least in its simplest form) with the minimal amount of equations, which is a sensible strategy for an introductory course in behavioural ecology . Apart from this heuristic value, one may be tempted to disregard it as a naive toy model. After a burst of interest in the 70's and the 80's, the once vivid literature about optimal foraging theory (OFT) has lost its momentum . Yet, OFT and MVT have remained an active field of research in the parasitoidologists community, mostly because the sampling strategy of a parasitoid in patches of hosts and its resulting fitness gain are straightforward to evaluate, which eases both experimental and theoretical investigations .
 Fawcett, T. W. & Higginson, A. D. 2012 Heavy use of equations impedes communication among biologists. Proc. Natl. Acad. Sci. 109, 11735–11739. doi: 10.1073/pnas.1205259109
|How optimal foragers should respond to habitat changes? On the consequences of habitat conversion.||Vincent Calcagno, Frederic Hamelin, Ludovic Mailleret, Frederic Grognard||The Marginal Value Theorem (MVT) provides a framework to predict how habitat modifications related to the distribution of resources over patches should impact the realized fitness of individuals and their optimal rate of movement (or patch residen...||Behaviour & Ethology, Dispersal & Migration, Foraging, Landscape ecology, Spatial ecology, Metacommunities & Metapopulations, Theoretical ecology||Francois-Xavier Dechaume-Moncharmont||2018-03-05 10:42:11||View|
20 Sep 2018
When higher carrying capacities lead to faster propagationMarjorie Haond, Thibaut Morel-Journel, Eric Lombaert, Elodie Vercken, Ludovic Mailleret & Lionel Roques https://doi.org/10.1101/307322
When the dispersal of the many outruns the dispersal of the fewRecommended by Matthieu Barbier based on reviews by Yuval Zelnik and 1 anonymous reviewer
Are biological invasions driven by a few pioneers, running ahead of their conspecifics? Or are these pioneers constantly being caught up by, and folded into, the larger flux of propagules from the established populations behind them?
 Levins, R., & Culver, D. (1971). Regional Coexistence of Species and Competition between Rare Species. Proceedings of the National Academy of Sciences, 68(6), 1246–1248. doi: 10.1073/pnas.68.6.1246
|When higher carrying capacities lead to faster propagation||Marjorie Haond, Thibaut Morel-Journel, Eric Lombaert, Elodie Vercken, Ludovic Mailleret & Lionel Roques||<p>This preprint has been reviewed and recommended by Peer Community In Ecology (https://dx.doi.org/10.24072/pci.ecology.100004). Finding general patterns in the expansion of natural populations is a major challenge in ecology and invasion biology...||Biological invasions, Colonization, Dispersal & Migration, Experimental ecology, Population ecology, Spatial ecology, Metacommunities & Metapopulations, Theoretical ecology||Matthieu Barbier||Yuval Zelnik||2018-04-25 10:18:48||View|
29 Dec 2018
The return of the trophic chain: fundamental vs realized interactions in a simple arthropod food webInmaculada Torres-Campos, Sara Magalhães, Jordi Moya-Laraño, Marta Montserrat https://doi.org/10.1101/324178
From deserts to avocado orchards - understanding realized trophic interactions in communitiesRecommended by Francis John Burdon based on reviews by Owen Petchey and 2 anonymous reviewers
The late eminent ecologist Gary Polis once stated that “most catalogued food-webs are oversimplified caricatures of actual communities” and are “grossly incomplete representations of communities in terms of both diversity and trophic connections.” Not content with that damning indictment, he went further by railing that “theorists are trying to explain phenomena that do not exist” . The latter critique might have been push back for Robert May´s ground-breaking but ultimately flawed research on the relationship between food-web complexity and stability . Polis was a brilliant ecologist, and his thinking was clearly influenced by his experiences researching desert food webs. Those food webs possess an uncommon combination of properties, such as frequent omnivory, cannibalism, and looping; high linkage density (L/S); and a nearly complete absence of apex consumers, since few species completely lack predators or parasites . During my PhD studies, I was lucky enough to visit Joshua Tree National Park on the way to a conference in New England, and I could immediately see the problems posed by desert ecosystems. At the time, I was ruminating on the “harsh-benign” hypothesis , which predicts that the relative importance of abiotic and biotic forces should vary with changes in local environmental conditions (from harsh to benign). Specifically, in more “harsh” environments, abiotic factors should determine community composition whilst weakening the influence of biotic interactions. However, in the harsh desert environment I saw first-hand evidence that species interactions were not diminished; if anything, they were strengthened. Teddy-bear chollas possessed murderously sharp defenses to protect precious water, creosote bushes engaged in belowground “chemical warfare” (allelopathy) to deter potential competitors, and rampant cannibalism amongst scorpions drove temporal and spatial ontogenetic niche partitioning. Life in the desert was hard, but you couldn´t expect your competition to go easy on you.
 Polis, G. A. (1991). Complex trophic interactions in deserts: an empirical critique of food-web theory. The American Naturalist, 138(1), 123-155. doi: 10.1086/285208
|The return of the trophic chain: fundamental vs realized interactions in a simple arthropod food web||Inmaculada Torres-Campos, Sara Magalhães, Jordi Moya-Laraño, Marta Montserrat||<p>The mathematical theory describing small assemblages of interacting species (community modules or motifs) has proved to be essential in understanding the emergent properties of ecological communities. These models use differential equations to ...||Community ecology, Experimental ecology||Francis John Burdon||2018-05-16 19:34:10||View|
01 Mar 2019
Parasite intensity is driven by temperature in a wild birdAdèle Mennerat, Anne Charmantier, Sylvie Hurtrez-Boussès, Philippe Perret, Marcel M Lambrechts https://doi.org/10.1101/323311
The global change of species interactionsRecommended by Jan Hrcek based on reviews by 2 anonymous reviewers
What kinds of studies are most needed to understand the effects of global change on nature? Two deficiencies stand out: lack of long-term studies  and lack of data on species interactions . The paper by Mennerat and colleagues  is particularly valuable because it addresses both of these shortcomings. The first one is obvious. Our understanding of the impact of climate on biota improves with longer times series of observations. Mennerat et al.  analysed an impressive 18-year series from multiple sites to search for trends in parasitism rates across a range of temperatures. The second deficiency (lack of species interaction data) is perhaps not yet fully appreciated, despite studies pointing this out ten years ago [2,4]. The focus is often on species range limits and how taking species interactions into account changes species range predictions based on climate alone (climate envelope models; ). But range limits are not everything, as the function of a species (or community, network, etc.) ultimately depends on the strengths of species interactions and not only on the presence or absence of a given species [2,4]. Mennerat et al.  show that in the case of birds and their nest parasites, it is the strength of the interaction that has changed, while the species involved stayed the same. Mennerat et al.  found nest parasitism to increase with temperature at the nestling stage. They have also searched for trends of parasitism dynamics dependence on the host, but did not find any, probably because the nest parasites are generalists and attack other bird species within the study sites. This study thus draws attention to wider networks of interacting species, and we urgently need more data to predict how interaction networks will rewire with progressing environmental change [6,7].
 Lindenmayer, D.B., Likens, G.E., Andersen, A., Bowman, D., Bull, C.M., Burns, E., et al. (2012). Value of long-term ecological studies. Austral Ecology, 37(7), 745–57. doi: 10.1111/j.1442-9993.2011.02351.x
|Parasite intensity is driven by temperature in a wild bird||Adèle Mennerat, Anne Charmantier, Sylvie Hurtrez-Boussès, Philippe Perret, Marcel M Lambrechts||<p>Increasing awareness that parasitism is an essential component of nearly all aspects of ecosystem functioning, as well as a driver of biodiversity, has led to rising interest in the consequences of climate change in terms of parasitism and dise...||Climate change, Evolutionary ecology, Host-parasite interactions, Parasitology, Zoology||Jan Hrcek||2018-05-17 14:37:14||View|
10 Jun 2018
A reply to “Ranging Behavior Drives Parasite Richness: A More Parsimonious Hypothesis”Charpentier MJE, Kappeler PM https://arxiv.org/abs/1805.08151v3
Does elevated parasite richness in the environment affect daily path length of animals or is it the converse? An answer bringing some new elements of discussionRecommended by Cédric Sueur based on reviews by 2 anonymous reviewers
In 2015, Brockmeyer et al.  suggested that mandrills (Mandrillus sphinx) may accept additional ranging costs to avoid heavily parasitized areas. Following this paper, Bicca-Marques and Calegaro-Marques  questioned this interpretation and presented other hypotheses. To summarize, whilst Brockmeyer et al.  proposed that elevated daily path length may be a consequence of elevated parasite richness, Bicca-Marques and Calegaro-Marques  viewed it as a cause. In this current paper, Charpentier and Kappeler  respond to some of the criticisms by Bicca-Marques and Calegaro-Marques and discuss the putative parsimony of the two competing scenarios. The manuscript is interesting and focuses on an important question concerning the discussion about the social organization and home range use in wild mandrills. This answer helps to move this debate forward and should stimulate more empirical studies of the role of environmentally-transmitted parasites in shaping ranging and movement patterns of wild vertebrates. Given the elements this paper brings to the topics, it should have been published in American Journal of Primatology, the journal that published the two previous articles.
 Brockmeyer, T., Kappeler, P. M., Willaume, E., Benoit, L., Mboumba, S., & Charpentier, M. J. E. (2015). Social organization and space use of a wild mandrill (Mandrillus sphinx) group. American Journal of Primatology, 77(10), 1036–1048. doi: 10.1002/ajp.22439
|A reply to “Ranging Behavior Drives Parasite Richness: A More Parsimonious Hypothesis”||Charpentier MJE, Kappeler PM||In a recent article, Bicca-Marques and Calegaro-Marques  discussed the putative assumptions related to an interpretation we provided regarding an observed positive relationship between weekly averaged parasite richness of a group of mandrill...||Behaviour & Ethology, Evolutionary ecology, Foraging, Host-parasite interactions, Spatial ecology, Metacommunities & Metapopulations, Zoology||Cédric Sueur||2018-05-22 10:59:33||View|
16 Oct 2018
Impact of group management and transfer on individual sociality in Highland cattle (Bos Taurus)Sebastian Sosa, Marie Pelé, Elise Debergue, Cedric Kuntz, Blandine Keller, Florian Robic, Flora Siegwalt-Baudin, Camille Richer, Amandine Ramos, Cédric Sueur https://arxiv.org/abs/1805.11553v4
How empirical sciences may improve livestock welfare and help their managementRecommended by Marie Charpentier based on reviews by Alecia CARTER and 1 anonymous reviewer
Understanding how livestock management is a source of social stress and disturbances for cattle is an important question with potential applications for animal welfare programs and sustainable development. In their article, Sosa and colleagues  first propose to evaluate the effects of individual characteristics on dyadic social relationships and on the social dynamics of four groups of cattle. Using network analyses, the authors provide an interesting and complete picture of dyadic interactions among groupmates. Although shown elsewhere, the authors demonstrate that individuals that are close in age and close in rank form stronger dyadic associations than other pairs. Second, the authors take advantage of some transfers of animals between groups -for management purposes- to assess how these transfers affect the social dynamics of groupmates. Their central finding is that the identity of transferred animals is a key-point. In particular, removing offspring strongly destabilizes the social relationships of mothers while adding a bull into a group also profoundly impacts female-female social relationships, as social networks before and after transfer of these key-animals are completely different. In addition, individuals, especially the young ones, that are transferred without familiar conspecifics take more time to socialize with their new group members than individuals transferred with familiar groupmates, generating a potential source of stress. Interestingly, the authors end up their article with some thoughts on the implications of their findings for animal welfare and ethics. This study provides additional evidence that empirical science has a major role to play in providing recommendations regarding societal questions such as livestock management and animal wellbeing.
 Sosa, S., Pelé, M., Debergue, E., Kuntz, C., Keller, B., Robic, F., Siegwalt-Baudin, F., Richer, C., Ramos, A., & Sueur C. (2018). Impact of group management and transfer on individual sociality in Highland cattle (Bos Taurus). arXiv:1805.11553v4 [q-bio.PE] peer-reviewed and recommended by PCI Ecol. https://arxiv.org/abs/1805.11553v4
|Impact of group management and transfer on individual sociality in Highland cattle (Bos Taurus)||Sebastian Sosa, Marie Pelé, Elise Debergue, Cedric Kuntz, Blandine Keller, Florian Robic, Flora Siegwalt-Baudin, Camille Richer, Amandine Ramos, Cédric Sueur||The sociality of cattle facilitates the maintenance of herd cohesion and synchronisation, making these species the ideal choice for domestication as livestock for humans. However, livestock populations are not self-regulated, and farmers transfer ...||Behaviour & Ethology, Social structure||Marie Charpentier||2018-05-30 14:05:39||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|
14 Dec 2018
Recommendations to address uncertainties in environmental risk assessment using toxicokinetics-toxicodynamics modelsVirgile Baudrot and Sandrine Charles https://doi.org/10.1101/356469
Addressing uncertainty in Environmental Risk Assessment using mechanistic toxicological models coupled with Bayesian inferenceRecommended by Luis Schiesari based on reviews by Andreas Focks and 2 anonymous reviewers
Environmental Risk Assessment (ERA) is a strategic conceptual framework to characterize the nature and magnitude of risks, to humans and biodiversity, of the release of chemical contaminants in the environment. Several measures have been suggested to enhance the science and application of ERA, including the identification and acknowledgment of uncertainties that potentially influence the outcome of risk assessments, and the appropriate consideration of temporal scale and its linkage to assessment endpoints .
 Dale, V. H., Biddinger, G. R., Newman, M. C., Oris, J. T., Suter, G. W., Thompson, T., ... & Chapman, P. M. (2008). Enhancing the ecological risk assessment process. Integrated environmental assessment and management, 4(3), 306-313. doi: 10.1897/IEAM_2007-066.1
|Recommendations to address uncertainties in environmental risk assessment using toxicokinetics-toxicodynamics models||Virgile Baudrot and Sandrine Charles||<p>Providing reliable environmental quality standards (EQS) is a challenging issue for environmental risk assessment (ERA). These EQS are derived from toxicity endpoints estimated from dose-response models to identify and characterize the environm...||Chemical ecology, Ecotoxicology, Experimental ecology, Statistical ecology||Luis Schiesari||2018-06-27 21:33:30||View|