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18 Dec 2019
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Validating morphological condition indices and their relationship with reproductive success in great-tailed grackles

Are condition indices positively related to each other and to fitness?: a test with grackles

Recommended by based on reviews by Javier Seoane and Isabel López-Rull

Reproductive succes, as a surrogate of individual fitness, depends both on extrinsic and intrinsic factors [1]. Among the intrinsic factors, resource level or health are considered important potential drivers of fitness but exceedingly difficult to measure directly. Thus, a host of proxies have been suggested, known as condition indices [2]. The question arises whether all condition indices consistently measure the same "inner state" of individuals and whether all of them similarly correlate to individual fitness. In this preregistration, Berens and colleagues aim to answer this question for two common condition indices, fat score and scaled mass index (Fig. 1), using great-tailed grackles as a model system. Although this question is not new, it has not been satisfactorily solved and both reviewers found merit in the attempt to clarify this matter.

Figure 1. Hypothesized relationships between two condition indices and reproductive success. Single arrow heads indicate causal relationships; double arrow heads indicate only correlation. In a best case scenario, all relationships should be positive and linear.
A problem in adressing this question with grackles is limited population, ergo sample, size and limited possibilites of recapture individuals. Some relationships can be missed due to low statistical power. Unfortunately, existing tools for power analysis fall behind complex designs and the one planned for this study. Thus, any potentially non significant relationship has to be taken cautiously. Nevertheless, even if grackles will not provide a definitive answer (they never meant to do it), this preregistration can inspire broader explorations of matches and mismatches across condition indices and species, as well as uncover non-linear relationships with reproductive success.


[1] Roff, D. A. (2001). Life history evolution. Oxford University Press, Oxford.
[2] Labocha, M. K.; Hayes, J. P. (2012). Morphometric indices of body condition in birds: a review. Journal of Ornithology 153: 1–22. doi: 10.1007/s10336-011-0706-1

Validating morphological condition indices and their relationship with reproductive success in great-tailed gracklesJennifer M. Berens, Corina J. Logan, Melissa Folsom, Luisa Bergeron, Kelsey B. McCuneMorphological variation among individuals has the potential to influence multiple life history characteristics such as dispersal, migration, reproductive fitness, and survival (Wilder, Raubenheimer, and Simpson (2016)). Theoretically, individuals ...Behaviour & Ethology, Conservation biology, Demography, Morphometrics, Preregistrations, ZoologyMarcos Mendez2019-08-05 20:05:56 View
09 Dec 2019
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Niche complementarity among pollinators increases community-level plant reproductive success

Improving our knowledge of species interaction networks

Recommended by based on reviews by Michael Lattorff, Nicolas Deguines and 3 anonymous reviewers

Ecosystems shelter a huge number of species, continuously interacting. Each species interact in various ways, with trophic interactions, but also non-trophic interactions, not mentioning the abiotic and anthropogenic interactions. In particular, pollination, competition, facilitation, parasitism and many other interaction types are simultaneously present at the same place in terrestrial ecosystems [1-2]. For this reason, we need today to improve our understanding of such complex interaction networks to later anticipate their responses. This program is a huge challenge facing ecologists and they today join their forces among experimentalists, theoreticians and modelers. While some of us struggle in theoretical and modeling dimensions [3-4], some others perform brilliant works to observe and/or experiment on the same ecological objects [5-6].
In this nice study [6], Magrach et al. succeed in studying relatively large plant-pollinator interaction networks in the field, in Mediterranean ecosystems. For the first time to my knowledge, they study community-wide interactions instead of traditional and easier accessible pairwise interactions. On the basis of a statistically relevant survey, they focus on plant reproductive success and on the role of pollinator interactions in such a success. A more reductionist approach based on simpler pairwise interactions between plants and pollinators would not be able to highlight the interaction network structure (the topology) possibly impacting its responses [1,5], among which the reproductive success of some (plant) species. Yet, such a network analysis requires a fine control of probable biases, as those linked to size or autocorrelation between data of various sites. Here, Magrach et al. did a nice work in capturing rigorously the structures and trends behind this community-wide functioning.
To grasp possible relationships between plant and pollinator species is a first mandatory step, but the next critical step requires understanding processes hidden behind such relationships. Here, the authors succeed to reach this step too, by starting interpreting the processes at stake in their studied plant-pollinator networks [7]. In particular, the niche complementarity has been demonstrated to play a determinant role in the plant reproductive success, and has a positive impact on it [6].
When will we be able to detect a community-wise process? This is one of my team’s objectives, and we developed new kind of models with this aim. Also, authors focus here on plant-pollinator network, but the next step might be to gather every kind of interactions into a huge ecosystem network which we call the socio-ecosystemic graph [4]. Indeed, why to limit our view to certain interactions only? It will take time to grasp the whole interaction network an ecosystem is sheltering, but this should be our next challenge. And this paper of Magrach et al. [6] is a first fascinating step in this direction.


[1] Campbell, C., Yang, S., Albert, R., and Shea, K. (2011). A network model for plant–pollinator community assembly. Proceedings of the National Academy of Sciences, 108(1), 197-202. doi: 10.1073/pnas.1008204108
[2] Kéfi, S., Miele, V., Wieters, E. A., Navarrete, S. A., and Berlow, E. L. (2016). How structured is the entangled bank? The surprisingly simple organization of multiplex ecological networks leads to increased persistence and resilience. PLoS biology, 14(8), e1002527. doi: 10.1371/journal.pbio.1002527
[3] Gaucherel, C. (2019). The Languages of Nature. When nature writes to itself. Lulu editions, Paris, France.
[4] Gaucherel, C., and Pommereau, F. Using discrete systems to exhaustively characterize the dynamics of an integrated ecosystem. Methods in Ecology and Evolution, 10(9), 1615-1627. doi: 10.1111/2041-210X.13242
[5] Bennett, J. M. et al. (2018). A review of European studies on pollination networks and pollen limitation, and a case study designed to fill in a gap. AoB Plants, 10(6), ply068. doi: 10.1093/aobpla/ply068
[6] Magrach, A., Molina, F. P., and Bartomeus, I. (2020). Niche complementarity among pollinators increases community-level plant reproductive success. bioRxiv, 629931, ver. 7 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/629931
[7] Bastolla, U., Fortuna, M. A., Pascual-García, A., Ferrera, A., Luque, B., and Bascompte, J. (2009). The architecture of mutualistic networks minimizes competition and increases biodiversity. Nature, 458(7241), 1018-1020. doi: 10.1038/nature07950

Niche complementarity among pollinators increases community-level plant reproductive successAinhoa Magrach, Francisco P. Molina, Ignasi Bartomeus<p>Declines in pollinator diversity and abundance have been reported across different regions, with implications for the reproductive success of plant species. However, research has focused primarily on pairwise plant-pollinator interactions, larg...Ecosystem functioning, Interaction networks, Pollination, Terrestrial ecologyCédric Gaucherel Nicolas Deguines2019-05-07 17:03:23 View
06 Dec 2019
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Does phenology explain plant-pollinator interactions at different latitudes? An assessment of its explanatory power in plant-hoverfly networks in French calcareous grasslands

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

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

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


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

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

Investigate fine scale sex dispersal with spatial and genetic analyses

Recommended by ORCID_LOGO based on reviews by Sylvine Durand and 1 anonymous reviewer

The preregistration "Investigating sex differences in genetic relatedness in great-tailed grackles in Tempe, Arizona to infer potential sex biases in dispersal" [1] presents the analysis plan that will be used to genetically and spatially investigate sex-biased dispersal in great-tailed grackles (Quiscalus mexicanus).
Several hypotheses implying mating systems, intrasexual competition or sex-related handicaps have been proposed to explain the diversity of dispersal patterns between or within species according to their ecological requirements, environmental factors such as seasonality [2], or individual characteristics such as age [3] or sex [4].
In birds, females are classically the dispersing sex, while males remain close to the place they were hatched [5], with potential benefits that males derive from knowing the local environment to establish territories [6].
In great-tailed grackles the males hold territories and the females choose which territory to place their nest in [7]. In this context, the main hypothesis is that females are the dispersing sex in this species. The authors of this preregistration plan to investigate this hypothesis and its 3 alternatives ((i) the males are the dispersing sex, (ii) both sexes disperse or (iii) neither of the two sexes disperse), investigating the spatial distribution of genetic relatives.
The authors plan to measure the genetic relatedness (using SNP markers) and geographic distances among all female dyads and among all male dyads in the fine geographic scale (Tempe campus, Arizona). If females disperse away from relatives, the females will be less likely to be found geographically close to genetic relatives.
This pre-registration shows that the authors are well aware of the possible limitations of their study, particularly in relation to their population of 57 individuals, on a small scale. But they will use methods that should be able to detect a signal. They were very good at incorporating the reviewers' comments and suggestions, which enabled them to produce a satisfactory and interesting version of the manuscript presenting their hypotheses, limitations and the methods they plan to use. Another point I would like to stress is that this pre-registration practice is a very good one that makes it possible to anticipate the challenges and the type of analyses to be carried out, in particular by setting out the working hypotheses and confronting them (as well as the methods envisaged) with peers from this stage. I therefore recommend this manuscript and thank all the contributors (authors and reviewers) for their work. I look forward to seeing the outcomes of this study.


[1] Sevchik A., Logan C. J., Folsom M., Bergeron L., Blackwell A., Rowney C., and Lukas D. (2019). Investigating sex differences in genetic relatedness in great-tailed grackles in Tempe, Arizona to infer potential sex biases in dispersal. In principle recommendation by Peer Community In Ecology.
[2] Fies, M. L., Puckett, K. M., and Larson-Brogdon, B. (2002). Breeding season movements and dispersal of Northern Bobwhites in fragmented habitats of Virginia. Vol. 5 , Article 35. Available at:
[3] Marvá, M., and San Segundo, F. (2018). Age-structure density-dependent fertility and individuals dispersal in a population model. Mathematical biosciences, 300, 157-167. doi: 10.1016/j.mbs.2018.03.029
[4] Trochet, A., Courtois, E. A., Stevens, V. M., Baguette, M., Chaine, A., Schmeller, D. S., Clobert, J., and Wiens, J. J. (2016). Evolution of sex-biased dispersal. The Quarterly Review of Biology, 91(3), 297-320. doi: 10.1086/688097
[5] Greenwood, P. J., and Harvey, P. H. (1982). The natal and breeding dispersal of birds. Annual review of ecology and systematics, 13(1), 1-21. doi: 10.1146/
[6] Greenwood, P. J. (1980). Mating systems, philopatry and dispersal in birds and mammals. Animal behaviour, 28(4), 1140-1162. doi: 10.1016/S0003-3472(80)80103-5
[7] Johnson, K., DuVal, E., Kielt, M., and Hughes, C. (2000). Male mating strategies and the mating system of great-tailed grackles. Behavioral Ecology, 11(2), 132-141. doi: 10.1093/beheco/11.2.132

Investigating sex differences in genetic relatedness in great-tailed grackles in Tempe, Arizona to infer potential sex biases in dispersalAugust Sevchik, Corina Logan, Melissa Folsom, Luisa Bergeron, Aaron Blackwell, Carolyn Rowney, Dieter LukasIn most bird species, females disperse prior to their first breeding attempt, while males remain close to the place they were hatched for their entire lives (Greenwood and Harvey (1982)). Explanations for such female bias in natal dispersal have f...Behaviour & Ethology, Life history, Preregistrations, Social structure, ZoologySophie Beltran-Bech2019-07-24 12:47:07 View
05 Nov 2019
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Crown defoliation decreases reproduction and wood growth in a marginal European beech population.

Defoliation induces a trade-off between reproduction and growth in a southern population of Beech

Recommended by based on reviews by 3 anonymous reviewers

Individuals ability to withstand abiotic and biotic stresses is crucial to the maintenance of populations at climate edge of tree species distribution. We start to have a detailed understanding of tree growth response and to a lesser extent mortality response in these populations. In contrast, our understanding of the response of tree fecundity and recruitment remains limited because of the difficulty to monitor it at the individual tree level in the field. Tree recruitment limitation is, however, crucial for tree population dynamics [1-2].
In their study Oddou-Muratorio et al. [3] use a new method that they recently developed that jointly estimate male and female effective fecundity in natural populations using naturally established seedlings [4]. Their method uses a spatially explicit Bayesian analysis based on molecular markers and parentage analyses (MEMM program [4]). They apply this method to an unmanaged Beech forest at the southern edge of Beech distribution, where tree defoliation – taken as an integrative indicator of tree abiotic and biotic stress – and growth have been monitored for all adult trees.
This allows the authors to explore alternative hypothesis about tree fecundity response to stress. In one hand, biotic and abiotic stresses are thought to negatively impact tree fecundity. In the other hand, management and studies of orchard fruit tree support the idea that stress could trigger a compensatory increase of fecundity at the cost of other performances such as growth and survival.
They show that both growth and female fecundity are negatively affected by defoliation. There was no evidence that stresses trigger a compensatory increase of fecundity. Yet, they also found that, for large highly defoliated trees, there was a trade-off between growth and female fecundity. Some individuals are able to mitigate stress impact on fecundity by decreasing their growth. It is difficult to understand with available data what is driving such divergent responses between defoliated individuals. This could be related to differences in micro-environmental conditions or genetic background of individual trees. Such individual-level difference in response to stress could be crucial to understand tree populations response to ongoing climate change. This study clearly opens exciting new perspectives to apply such new methods to understand the role of fecundity on tree population dynamics. For instance, could we apply this method across the species distribution to understand how effective fecundity and its response to abiotic stress change between southern edge populations, core populations, and northern edge populations? Using time-series retrieved from such analysis can we disentangle the effect of different climatic drivers? It would also be interesting to see how such results can contribute to analyses covering the full tree life cycle to understand the contribution of fecundity response to population and evolutionary.


[1] Clark, J. S. et al. (1999). Interpreting recruitment limitation in forests. American Journal of Botany, 86(1), 1-16. doi: 10.2307/2656950
[2] Petit, R. J., and Hampe, A. (2006). Some evolutionary consequences of being a tree. Annu. Rev. Ecol. Evol. Syst., 37, 187-214. doi: 10.1146/annurev.ecolsys.37.091305.110215
[3] Oddou-Muratorio, S., Petit, C., Journe, V., Lingrand, M., Magdalou, J. A., Hurson, C., Garrigue, J., Davi, H. and Magnanou, E. (2019). Crown defoliation decreases reproduction and wood growth in a marginal European beech population. bioRxiv, 474874, ver. 4 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/474874
[4] Oddou‐Muratorio, S. and Klein, E. K. (2008). Comparing direct vs. indirect estimates of gene flow within a population of a scattered tree species. Molecular Ecology, 17(11), 2743-2754. doi: 10.1111/j.1365-294X.2008.03783.x

Crown defoliation decreases reproduction and wood growth in a marginal European beech population.Sylvie Oddou-Muratorio, Cathleen Petit-Cailleux, Valentin Journé, Matthieu Lingrand, Jean-André Magdalou, Christophe Hurson, Joseph Garrigue, Hendrik Davi, Elodie Magnanou.<p>1. Although droughts and heatwaves have been associated to increased crown defoliation, decreased growth and a higher risk of mortality in many forest tree species, their impact on tree reproduction and forest regeneration still remains underst...Climate change, Eco-evolutionary dynamics, Molecular ecology, Physiology, Population ecologyGeorges Kunstler2018-11-20 13:29:42 View
12 Oct 2019
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Investigating the use of learning mechanisms in a species that is rapidly expanding its geographic range

How would variation in environmental predictability affect the use of different learning mechanisms in a social bird?

Recommended by based on reviews by Matthew Petelle and 1 anonymous reviewer

In their pre-registered paper [1], McCune and colleagues propose a field-based study of social versus individual learning mechanisms in an avian species (great-tailed grackles) that has been expanding its geographic range. The study forms part of a longer-term project that addresses various aspects of this species’ behaviour and biology, and the experience of the team is clear from the preprint. Assessing variation in learning mechanisms in different sections of the grackles’ distribution range, the researchers will investigate how individual learning and social transmission may impact learning about novel challenges in the environment. Considering that this is a social species, the authors expect both individual learning and social transmission to occur, when groups of grackles encounter new challenges/ opportunities in the wild. This in itself is not a very unusual idea to test [2, 3], but the authors are rigorously distinguishing between imitation, emulation, local enhancement, and social enhancement. Such rigour is certainly valuable in studies of cognition in the wild.
Further, the authors predict that the contribution of individual versus social learning could vary between populations, as the core may contain fewer unfamiliar/novel stimuli than the edge, where artificial sources of water (for example) may be more common. They make an argument that the core, middle, and edge populations would experience differing levels of environmental predictability. If true, their field experiments could yield very novel results on how changes in environmental predictability affect social/individual learning in a single study species. Their data would then give unusual insights into the ecological value of individual learning and distinct forms of social learning – something that is not easy to test in wild animals. The authors consider a variety of alternative hypotheses that may ultimately explain their findings, and clarify their methods and analyses in fine detail. The authors also set out limitations clearly, and give a thorough account of their approaches and thinking.
The reviewers and I have a still-unanswered question, which is central to the study: what is the predictability or unpredictability of the core versus edge environments? Although the authors have explained similarities and distinctions between the different sections of the grackles’ range, their description feels a bit vague -- it's not as rigorous or well-defined as the rest of the paper. Such a lack of definition may be inevitable in the limitations of a preprint, but ultimately it does suggest that there may be real uncertainty about the qualitative differences between the core, edge, and middle environments. The authors do explain that a lack of variation in individual responses to the field experiments would preclude the testing of further hypothesis, but do not mention how a salient lack of variation in novelty/ predictability between the environments could impact their hypotheses.
An assessment/quantification of the rate at which the different populations of grackles encounter novel stimuli would be a cornerstone of the success of this proposed study. Certainly, the authors cannot address this in much more detail during the preprint stage, but they need to consider how to best assess/describe differences before starting the full study. Such an assessment could take the form of either a GIS desktop study (comparing, for example, rates of dam/canal construction in core versus edge sections of the distribution range), or observational/ movement data contrasting how frequently members of core versus edge populations encounter artificial sources of water/food in a given month/year. Considering the long-term nature of the larger project, it is possible that these data are already available, but I am speculating. I would highly recommend that such an assessment be undertaken, beyond the mere mention of expected differences. This would solidify the central idea that there are concrete differences between the environments.
Despite this concern, the authors attended well to the comments and recommendations of the two reviewers – both experts in cognitive ecology. It is a preprint showing clear thinking and a consideration of most of the challenges that may be encountered during the course of the study. My own opinion and the estimations of the two reviewers all underscore the originality and value of this project – this should be a very valuable and potentially novel study. I look forward to seeing the outcomes of the research.


[1] McCune, K. B., McElreath, R., and Logan, C. J. (2019). Investigating the use of learning mechanisms in a species that is rapidly expanding its geographic range. In principle recommendation by Peer Community In Ecology.
[2] Benson-Amram, S. and Holekamp, K. E. (2012). Innovative problem solving by wild spotted hyenas. Proceedings of the Royal Society B: Biological Sciences, 279(1744), 4087–4095. doi: 10.1098/rspb.2012.1450
[3] Federspiel, I. G., Boeckle, M., von Bayern, A. M. P. and Emery, N. J. (2019). Exploring individual and social learning in jackdaws (Corvus monedula). Learning & Behavior, 47(3), 258–270. doi: 10.3758/s13420-019-00383-8

Investigating the use of learning mechanisms in a species that is rapidly expanding its geographic rangeKelsey McCune, Richard McElreath, Corina LoganThis is one of many studies planned for our long-term research on the role of behavior and learning in rapid geographic range expansions. Project background: Behavioral flexibility, the ability to change behavior when circumstances change based on...Behaviour & Ethology, Eco-evolutionary dynamics, Foraging, Preregistrations, Social structure, Spatial ecology, Metacommunities & Metapopulations, ZoologyAliza le Roux2019-07-23 18:45:20 View
07 Oct 2019
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Deer slow down litter decomposition by reducing litter quality in a temperate forest

Disentangling effects of large herbivores on litter decomposition

Recommended by based on reviews by 2 anonymous reviewers

Aboveground – belowground interactions is a fascinating field that has developed in ecology since about 20 years [1]. This field has been very fruitful as measured by the numerous articles published but also by the particular role it has played in the development of soil ecology. While soil ecology has for a long time developed partially independently from “general ecology” [2], the field of aboveground – belowground interactions has shown that all ecological interactions occurring within the soil are likely to impact plant growth and plant physiology because they have their roots within the soil. In turns, this should impact the aerial system of plants (higher or lower biomasses, changes in leaf quality…), which should cascade on the aboveground food web. Conversely, all ecological interactions occurring aboveground likely impact plant growth, which should cascade to their root systems, and thus to the soil functioning and the soil food web (through changes in the emission of exudates or inputs of dead roots…). Basically, plants are linking the belowground and aboveground worlds because, as terrestrial primary producers, they need to have (1) leaves to capture CO2 and exploit light and (2) roots to absorb water and mineral nutrients. The article I presently recommend [3] tackles this general issue through the prism of the impact of large herbivores on the decomposition of leaf litter.
This issue is a relatively old one [4, 5] but still deserves efforts because there have been relatively few studies on the subject and because the issue is relatively complex due to the diversity of mechanisms involved and the difficulty to disentangle them. I recommend this article because the authors have cleverly taken advantage of a ‘‘natural’’ long-term experiment, i.e. three islands with contrasted deer densities, to test whether these large mammals are able to impact leaf litter decomposition and whether they are able to do so through changes in litter quality (because they browse the vegetation) or through changes in soil characteristics (either physical or chemical characteristics or the composition of the decomposer community). They have found that deer decrease litter decomposition, mainly through a decrease in litter quality (increase in its C:N ratio). I particularly appreciate the combination of statistics achieved to test the different hypotheses and the fair and in-depth discussion of the results.
I have to confess that I have two small regrets with this work. First, all replications are implemented within the same three islands, so that it cannot be fully excluded that measured effects should not be attributed to any other possible difference between the three islands. I am fairly sure this is not the case (at least because the three islands have the same environments) but I hope that future studies or meta-analyses will be able analyse independent deer density treatments. Second, as a soil ecologist, I am eager to see results on the decomposer communities, both microorganisms and macrofauna, of the three islands.


[1] Hooper, D. U., Bignell, D. E., Brown, V. K., Brussard, L., Dangerfield, J. M., Wall, D. H. and Wolters, V. (2000). Interactions between Aboveground and Belowground Biodiversity in Terrestrial Ecosystems: Patterns, Mechanisms, and Feedbacks. BioScience, 50(12), 1049-1061. doi: 10.1641/0006-3568(2000)050[1049:ibaabb];2
[2] Barot, S., Blouin, M., Fontaine, S., Jouquet, P., Lata, J.-C., and Mathieu, J. (2007). A Tale of Four Stories: Soil Ecology, Theory, Evolution and the Publication System. PLOS ONE, 2(11), e1248. doi: 10.1371/journal.pone.0001248
[3] Chollet S., Maillard M., Schörghuber J., Grayston S. and Martin J.-L. (2019). Deer slow down litter decomposition by reducing litter quality in a temperate forest. bioRxiv, 690032, ver. 3 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/690032
[4] Wardle, D. A., Barker, G. M., Yeates, G. W., Bonner, K. I., and Ghani, A. (2001). Introduced browsing mammals in New Zealand natural forests: aboveground and belowground consequences. Ecological Monographs, 71(4), 587-614. doi: 10.1890/0012-9615(2001)071[0587:ibminz];2
[5] Bardgett, R. D., and Wardle, D. A. (2003). Herbivore-mediated linkages between aboveground and belowground communities. Ecology, 84(9), 2258-2268. doi: 10.1890/02-0274

Deer slow down litter decomposition by reducing litter quality in a temperate forest Simon Chollet, Morgane Maillard, Juliane Schorghuber, Sue Grayston, Jean-Louis Martin<p>In temperate forest ecosystems, the role of deer in litter decomposition, a key nutrient cycling process, remains debated. Deer may modify the decomposition process by affecting plant cover and thus modifying litter abundance. They can also alt...Community ecology, Ecosystem functioning, Herbivory, Soil ecologySébastien Barot2019-07-04 14:30:19 View
07 Oct 2019
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Which pitfall traps and sampling efforts should be used to evaluate the effects of cropping systems on the taxonomic and functional composition of arthropod communities?

On the importance of experimental design: pitfall traps and arthropod communities

Recommended by ORCID_LOGO based on reviews by Cécile ALBERT and Matthias Foellmer

Despite the increasing refinement of statistical methods, a robust experimental design is still one of the most important cornerstones to answer ecological and evolutionary questions. However, there is a strong trade-off between a perfect design and its feasibility. A common mantra is that more data is always better, but how much is enough is complex to answer, specially when we want to capture the spatial and temporal variability of a given process. Gardarin and Valantin-Morison [1] make an effort to answer these questions for a practical case: How many pitfalls traps, of which type, and over which extent, do we need to detect shifts in arthropod community composition in agricultural landscapes. There is extense literature on how to approach these challenges using preliminary data in combination with simulation methods [e.g. 2], but practical cases are always welcomed to illustrate the complexity of the decisions to be made. A key challenge in this situation is the nature of simplified and patchy agricultural arthropod communities. In this context, small effect sizes are expected, but those small effects are relevant from an ecological point of view because small increases at low biodiversity may produce large gains in ecosystem functioning [3].
The paper shows that some variables are not important, such as the type of fluid used to fill the pitfall traps. This is good news for potential comparisons among studies using slightly different protocols. However, the bad news are that the sampling effort needed for detecting community changes is larger than the average effort currently implemented. A potential solution is to focus on Community Weighed Mean metrics (CWM; i.e. a functional descriptor of the community body size distribution) rather than on classic metrics such as species richness, as detecting changes on CWM requires a lower sampling effort and it has a clear ecological interpretation linked to ecosystem functioning.
Beyond the scope of the data presented, which is limited to a single region over two years, and hence it is hard to extrapolate to other regions and years, the big message of the paper is the need to incorporate statistical power simulations as a central piece of the ecologist's toolbox. This is challenging, especially when you face questions such as: Should I replicate over space, or over time? The recommended paper is accompanied by the statistical code used, which should facilitate this task to other researchers. Furthermore, we should be aware that some important questions in ecology are highly variable in space and time, and hence, larger sampling effort across space and time is needed to detect patterns. Larger and longer monitoring schemes require a large effort (and funding), but if we want to make relevant ecology, nobody said it would be easy.


[1] Gardarin, A. and Valantin-Morison, M. (2019). Which pitfall traps and sampling efforts should be used to evaluate the effects of cropping systems on the taxonomic and functional composition of arthropod communities? Zenodo, 3468920, ver. 3 peer-reviewed and recommended by PCI Ecology. doi: 10.5281/zenodo.3468920
[2] Johnson, P. C., Barry, S. J., Ferguson, H. M., and Müller, P. (2015). Power analysis for generalized linear mixed models in ecology and evolution. Methods in ecology and evolution, 6(2), 133-142. doi: 10.1111/2041-210X.12306
[3] Cardinale, B. J. et al. (2012). Biodiversity loss and its impact on humanity. Nature, 486(7401), 59-67. doi: 10.1038/nature11148

Which pitfall traps and sampling efforts should be used to evaluate the effects of cropping systems on the taxonomic and functional composition of arthropod communities?Antoine Gardarin and Muriel Valantin-Morison<p>1. Ground dwelling arthropods are affected by agricultural practices, and analyses of their responses to different crop management are required. The sampling efficiency of pitfall traps has been widely studied in natural ecosystems. In arable a...Agroecology, Biodiversity, Biological control, Community ecologyIgnasi Bartomeus2019-01-08 09:40:14 View
16 Sep 2019
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Blood, sweat and tears: a review of non-invasive DNA sampling

Words matter: extensive misapplication of "non-invasive" in describing DNA sampling methods, and proposed clarifying terms

Recommended by based on reviews by 2 anonymous reviewers

The ability to successfully sequence trace quantities of environmental DNA (eDNA) has provided unprecedented opportunities to use genetic analyses to elucidate animal ecology, behavior, and population structure without affecting the behavior, fitness, or welfare of the animal sampled. Hair associated with an animal track in the snow, the shed exoskeleton of an insect, or a swab of animal scat are all examples of non-invasive methods to collect eDNA. Despite the seemingly uncomplicated definition of "non-invasive" as proposed by Taberlet et al. [1], Lefort et al. [2] highlight that its appropriate application to sampling methods in practice is not so straightforward. For example, collecting scat left behind on the forest floor by a mammal could be invasive if feces is used by that species to mark territorial boundaries. Other collection strategies such as baited DNA traps to collect hair, capturing and handling an individual to swab or stimulate emission of a body fluid, or removal of a presumed non essential body part like a feather, fish scale, or even a leg from an insect are often described as "non-invasive" sampling methods. However, such methods cannot be considered truly non-invasive. At a minimum, attracting or capturing and handling an animal to obtain a DNA sample interrupts its normal behavioral routine, but additionally can cause both acute and long-lasting physiological and behavioral stress responses and other effects. Even invertebrates exhibit long-term hypersensitization after an injury, which manifests as heightened vigilance and enhanced escape responses [3-5].
Through an extensive analysis of 380 papers published from 2013-2018, Lefort et al. [2] document the widespread misapplication of the term "non-invasive" to methods used to sample DNA. An astonishing 58% of these papers employed the term incorrectly. A big part of the problem is that "non-invasive" is usually used by authors in the medical or veterinary sense of not breaking the skin or entering the body [6], rather than in the broader, ecological sense of Taberlet et al. [1]. The authors argue that correct use of the term matters, because it may lead naive readers – one can imagine students, policy makers, and the general public – to incorrectly assume a particular method is safe to use in a situation where disturbing the animal could affect experimental results or raise animal welfare concerns. Such assumptions can affect experimental design, as well as interpretations of one's own or others' data.
The importance of the Lefort et al. [2] paper lies in part on the authors' call for the research community to be much more careful when applying the term "non-invasive" to methods of DNA sampling. This call cannot be shrugged off as a minor problem in a few papers – as their literature review demonstrates, "non-invasive" is being applied incorrectly more often than not. The authors recognize that not all DNA sampling must be non-invasive to be useful or ethical. Examples include taking samples for DNA extraction from museum specimens, or opportunistically from carcasses of animals hunted either legally or seized by authorities from poachers. In many cases, there may be no viable non-invasive method to obtain DNA, but a researcher strives to collect samples using methods that, although they may involve taking a sample directly from the animal's body, do not disrupt, or only slightly disrupt behavior, fitness, or welfare of the animal. Thus, the other important contribution by Lefort et al. [2] is to propose the terms "non-disruptive" and "minimally-disruptive" to describe such sampling methods, which are not strictly non-invasive. While gray areas undoubtedly remain, as acknowledged by the authors, answering the call for correct use of "non-invasive" and applying the proposed new terms for certain types of invasive sampling with a focus on level of disruption, will go a long way in limiting misconceptions and misinterpretations caused by the current confusion in terminology.


[1] Taberlet P., Waits L. P. and Luikart G. 1999. Noninvasive genetic sampling: look before you leap. Trends Ecol. Evol. 14: 323-327. doi: 10.1016/S0169-5347(99)01637-7
[2] Lefort M.-C., Cruickshank R. H., Descovich K., Adams N. J., Barun A., Emami-Khoyi A., Ridden J., Smith V. R., Sprague R., Waterhouse B. R. and Boyer S. 2019. Blood, sweat and tears: a review of non-invasive DNA sampling. bioRxiv, 385120, ver. 4 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/385120
[3] Khuong T. M., Wang Q.-P., Manion J., Oyston L. J., Lau M.-T., Towler H., Lin Y. Q. and Neely G. G. 2019. Nerve injury drives a heightened state of vigilance and neuropathic sensitization in Drosophila. Science Advances 5: eaaw4099. doi: 10.1126/sciadv.aaw4099
[4] Crook, R. J., Hanlon, R. T. and Walters, E. T. 2013. Squid have nociceptors that display widespread long-term sensitization and spontaneous activity after bodily injury. Journal of Neuroscience, 33(24), 10021-10026. doi: 10.1523/JNEUROSCI.0646-13.2013
[5] Walters E. T. 2018. Nociceptive biology of molluscs and arthropods: evolutionary clues about functions and mechanisms potentially related to pain. Frontiers in Physiololgy 9: doi: 10.3389/fphys.2018.01049
[6] Garshelis, D. L. 2006. On the allure of noninvasive genetic sampling-putting a face to the name. Ursus 17: 109-123. doi: 10.2192/1537-6176(2006)17[109:OTAONG]2.0.CO;2

Blood, sweat and tears: a review of non-invasive DNA samplingMarie-Caroline Lefort, Robert H Cruickshank, Kris Descovich, Nigel J Adams, Arijana Barun, Arsalan Emami-Khoyi, Johnaton Ridden, Victoria R Smith, Rowan Sprague, Benjamin Waterhouse, Stephane Boyer<p>The use of DNA data is ubiquitous across animal sciences. DNA may be obtained from an organism for a myriad of reasons including identification and distinction between cryptic species, sex identification, comparisons of different morphocryptic ...Behaviour & Ethology, Conservation biology, Molecular ecology, ZoologyThomas Wilson Sappington2018-11-30 13:33:31 View
06 Sep 2019
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Assessing metacommunity processes through signatures in spatiotemporal turnover of community composition

On the importance of temporal meta-community dynamics for our understanding of assembly processes

Recommended by based on reviews by Joaquín Hortal and 2 anonymous reviewers

The processes that trigger community assembly are still in the centre of ecological interest. While prior work mostly focused on spatial patterns of co-occurrence within a meta-community framework [reviewed in 1, 2] recent studies also include temporal patterns of community composition [e.g. 3, 4, 5, 6]. In this preprint [7], Franck Jabot and co-workers extend they prior approaches to quasi neutral community assembly [8, 9, 10] and develop an analytical framework of spatial and temporal diversity turnover. A simple and heuristic path model for beta diversity and an extended ecological drift model serve as starting points. The model can be seen as a counterpart to Ulrich et al. [5]. These authors implemented competitive hierarchies into their neutral meta-community model while the present paper focuses on environmental filtering. Most important, the model and parameterization of four empirical data sets on aquatic plant and animal meta-communities used by Jabot et al. returned a consistent high influence of environmental stochasticity on species turnover. Of course, this major result does not come to a surprise. As typical for this kind of models it depends also to a good deal on the initial model settings. It nevertheless makes a strong conceptual point for the importance of environmental variability over dispersal and richness effects. One interesting side effect regards the impact of richness differences (ΔS). Jabot et al. interpret this as a ‘nuisance variable’ as they do not have a stringent explanation. Of course, it might be a pure statistical bias introduced by the Soerensen metric of turnover that is normalized by richness. However, I suspect that there is more behind the ΔS effect. Richness differences are generally associated with respective differences in total abundances and introduce source – sink dynamics that inevitably shape subsequent colonization – extinction processes. It would be interesting to see whether ΔS alone is able to trigger observed patterns of community assembly and community composition. Such an analysis would require partitioning of species turnover into richness and nestedness effects [11]. I encourage Jabot et al. to undertake such an effort.
The present paper is also another call to include temporal population variability into metapopulation models for a better understanding of the dynamics and triggering of community assembly. In a next step, competitive interactions should be included into the model to infer the relative importance of both factors.


[1] Götzenberger, L. et al. (2012). Ecological assembly rules in plant communities—approaches, patterns and prospects. Biological reviews, 87(1), 111-127. doi: 10.1111/j.1469-185X.2011.00187.x
[2] Ulrich, W., & Gotelli, N. J. (2013). Pattern detection in null model analysis. Oikos, 122(1), 2-18. doi: 10.1111/j.1600-0706.2012.20325.x
[3] Grilli, J., Barabás, G., Michalska-Smith, M. J., & Allesina, S. (2017). Higher-order interactions stabilize dynamics in competitive network models. Nature, 548(7666), 210. doi: 10.1038/nature23273
[4] Nuvoloni, F. M., Feres, R. J. F., & Gilbert, B. (2016). Species turnover through time: colonization and extinction dynamics across metacommunities. The American Naturalist, 187(6), 786-796. doi: 10.1086/686150
[5] Ulrich, W., Jabot, F., & Gotelli, N. J. (2017). Competitive interactions change the pattern of species co‐occurrences under neutral dispersal. Oikos, 126(1), 91-100. doi: 10.1111/oik.03392
[6] Dobramysl, U., Mobilia, M., Pleimling, M., & Täuber, U. C. (2018). Stochastic population dynamics in spatially extended predator–prey systems. Journal of Physics A: Mathematical and Theoretical, 51(6), 063001. doi: 10.1088/1751-8121/aa95c7
[7] Jabot, F., Laroche, F., Massol, F., Arthaud, F., Crabot, J., Dubart, M., Blanchet, S., Munoz, F., David, P., and Datry, T. (2019). Assessing metacommunity processes through signatures in spatiotemporal turnover of community composition. bioRxiv, 480335, ver. 3 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/480335
[8] Jabot, F., & Chave, J. (2011). Analyzing tropical forest tree species abundance distributions using a nonneutral model and through approximate Bayesian inference. The American Naturalist, 178(2), E37-E47. doi: 10.1086/660829
[9] Jabot, F., & Lohier, T. (2016). Non‐random correlation of species dynamics in tropical tree communities. Oikos, 125(12), 1733-1742. doi: 10.1111/oik.03103
[10] Datry, T., Bonada, N., & Heino, J. (2016). Towards understanding the organisation of metacommunities in highly dynamic ecological systems. Oikos, 125(2), 149-159. doi: 10.1111/oik.02922
[11] Baselga, A. (2010). Partitioning the turnover and nestedness components of beta diversity. Global ecology and biogeography, 19(1), 134-143. doi: 10.1111/j.1466-8238.2009.00490.x

Assessing metacommunity processes through signatures in spatiotemporal turnover of community compositionFranck Jabot, Fabien Laroche, Francois Massol, Florent Arthaud, Julie Crabot, Maxime Dubart, Simon Blanchet, Francois Munoz, Patrice David, Thibault Datry<p>Although metacommunity ecology has been a major field of research in the last decades, with both conceptual and empirical outputs, the analysis of the temporal dynamics of metacommunities has only emerged recently and still consists mostly of r...Biodiversity, Coexistence, Community ecology, Spatial ecology, Metacommunities & MetapopulationsWerner Ulrich2018-11-29 14:58:54 View