|Id▲||Title||Authors||Abstract||Picture||Thematic fields||Recommender||Reviewers||Submission date|
19 Aug 2020
Three points of consideration before testing the effect of patch connectivity on local species richness: patch delineation, scaling and variability of metricsF. Laroche, M. Balbi, T. Grébert, F. Jabot & F. Archaux https://doi.org/10.1101/640995
Good practice guidelines for testing species-isolation relationships in patch-matrix systemsRecommended by Damaris Zurell based on reviews by 3 anonymous reviewers
Conservation biology is strongly rooted in the theory of island biogeography (TIB). In island systems where the ocean constitutes the inhospitable matrix, TIB predicts that species richness increases with island size as extinction rates decrease with island area (the species-area relationship, SAR), and species richness increases with connectivity as colonisation rates decrease with island isolation (the species-isolation relationship, SIR). In conservation biology, patches of habitat (habitat islands) are often regarded as analogous to islands within an unsuitable matrix , and SAR and SIR concepts have received much attention as habitat loss and habitat fragmentation are increasingly threatening biodiversity [3,4].
 MacArthur, R.H. and Wilson, E.O. (1967) The theory of island biogeography. Princeton University Press, Princeton.
|Three points of consideration before testing the effect of patch connectivity on local species richness: patch delineation, scaling and variability of metrics||F. Laroche, M. Balbi, T. Grébert, F. Jabot & F. Archaux||<p>The Theory of Island Biogeography (TIB) promoted the idea that species richness within sites depends on site connectivity, i.e. its connection with surrounding potential sources of immigrants. TIB has been extended to a wide array of fragmented...||Biodiversity, Community ecology, Dispersal & Migration, Landscape ecology, Spatial ecology, Metacommunities & Metapopulations||Damaris Zurell||2019-05-20 16:03:47||View|
06 Jan 2021
Comparing statistical and mechanistic models to identify the drivers of mortality within a rear-edge beech populationCathleen Petit-Cailleux, Hendrik Davi, François Lefevre, Christophe Hurson, Joseph Garrigue, Jean-André Magdalou, Elodie Magnanou and Sylvie Oddou-Muratorio https://doi.org/10.1101/645747
The complexity of predicting mortality in treesRecommended by Lucía DeSoto based on reviews by Lisa Hülsmann and 2 anonymous reviewers
One of the main issues of forest ecosystems is rising tree mortality as a result of extreme weather events (Franklin et al., 1987). Eventually, tree mortality reduces forest biomass (Allen et al., 2010), although its effect on forest ecosystem fluxes seems not lasting too long (Anderegg et al., 2016). This controversy about the negative consequences of tree mortality is joined to the debate about the drivers triggering and the mechanisms accelerating tree decline. For instance, there is still room for discussion about carbon starvation or hydraulic failure determining the decay processes (Sevanto et al., 2014) or about the importance of mortality sources (Reichstein et al., 2013). Therefore, understanding and predicting tree mortality has become one of the challenges for forest ecologists in the last decade, doubling the rate of articles published on the topic (*). Although predicting the responses of ecosystems to environmental change based on the traits of species may seem a simplistic conception of ecosystem functioning (Sutherland et al., 2013), identifying those traits that are involved in the proneness of a tree to die would help to predict how forests will respond to climate threatens.
(*) Number (and percentage) of articles found in Web of Sciences after searching (December the 10th, 2020) “tree mortality”: from 163 (0.006%) in 2010 to 412 (0.013%) in 2020.
Allen et al. (2010). A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forests. Forest ecology and management, 259(4), 660-684. doi: https://doi.org/10.1016/j.foreco.2009.09.001
|Comparing statistical and mechanistic models to identify the drivers of mortality within a rear-edge beech population||Cathleen Petit-Cailleux, Hendrik Davi, François Lefevre, Christophe Hurson, Joseph Garrigue, Jean-André Magdalou, Elodie Magnanou and Sylvie Oddou-Muratorio||<p>Since several studies have been reporting an increase in the decline of forests, a major issue in ecology is to better understand and predict tree mortality. The interactions between the different factors and the physiological processes giving ...||Climate change, Physiology, Population ecology||Lucía DeSoto||2019-05-24 11:37:38||View|
07 Oct 2019
Deer slow down litter decomposition by reducing litter quality in a temperate forestSimon Chollet, Morgane Maillard, Juliane Schorghuber, Sue Grayston, Jean-Louis Martin https://doi.org/10.1101/690032
Disentangling effects of large herbivores on litter decompositionRecommended by Sébastien Barot based on reviews by 2 anonymous reviewers
Aboveground – belowground interactions is a fascinating field that has developed in ecology since about 20 years . 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” , 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  tackles this general issue through the prism of the impact of large herbivores on the decomposition of leaf litter.
 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]2.0.co;2
|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 ecology||Sébastien Barot||2019-07-04 14:30:19||View|
12 Oct 2019
Investigating the use of learning mechanisms in a species that is rapidly expanding its geographic rangeKelsey McCune, Richard McElreath, Corina Logan http://corinalogan.com/Preregistrations/g_sociallearning.html
How would variation in environmental predictability affect the use of different learning mechanisms in a social bird?Recommended by Aliza le Roux based on reviews by Matthew Petelle and 1 anonymous reviewer
In their pre-registered paper , 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.
 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. corinalogan.com/Preregistrations/g_sociallearning.html
|Investigating the use of learning mechanisms in a species that is rapidly expanding its geographic range||Kelsey McCune, Richard McElreath, Corina Logan||This 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, Zoology||Aliza le Roux||2019-07-23 18:45:20||View|
29 Nov 2019
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 Lukas http://corinalogan.com/Preregistrations/gdispersal.html
Investigate fine scale sex dispersal with spatial and genetic analysesRecommended by Sophie Beltran-Bech 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"  presents the analysis plan that will be used to genetically and spatially investigate sex-biased dispersal in great-tailed grackles (Quiscalus mexicanus).
 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. corinalogan.com/Preregistrations/gdispersal.html
|Investigating sex differences in genetic relatedness in great-tailed grackles in Tempe, Arizona to infer potential sex biases in dispersal||August Sevchik, Corina Logan, Melissa Folsom, Luisa Bergeron, Aaron Blackwell, Carolyn Rowney, Dieter Lukas||In 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, Zoology||Sophie Beltran-Bech||2019-07-24 12:47:07||View|
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|
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|
18 Dec 2019
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. McCune https://github.com/corinalogan/grackles/blob/master/Files/Preregistrations/gcondition.Rmd
Are condition indices positively related to each other and to fitness?: a test with gracklesRecommended by Marcos Mendez 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 . 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 . 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.
 Roff, D. A. (2001). Life history evolution. Oxford University Press, Oxford.
|Validating morphological condition indices and their relationship with reproductive success in great-tailed grackles||Jennifer M. Berens, Corina J. Logan, Melissa Folsom, Luisa Bergeron, Kelsey B. McCune||Morphological 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, Zoology||Marcos Mendez||2019-08-05 20:05:56||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|
20 Oct 2021
Eco-evolutionary dynamics further weakens mutualistic interaction and coexistence under population declineAvril Weinbach, Nicolas Loeuille, Rudolf P. Rohr https://doi.org/10.1101/570580
Doomed by your partner: when mutualistic interactions are like an evolutionary millstone around a species’ neckRecommended by Sylvain Billiard based on reviews by 2 anonymous reviewers
Mutualistic interactions are the weird uncles of population and community ecology. They are everywhere, from the microbes aiding digestion in animals’ guts to animal-pollination services in ecosystems; They increase productivity through facilitation; They fascinate us when small birds pick the teeth of a big-mouthed crocodile. Yet, mutualistic interactions are far less studied and understood than competition or predation. Possibly because we are naively convinced that there is no mystery here: isn’t it obvious that mutualistic interactions necessarily facilitate species coexistence? Since mutualistic species benefit from one another, if one species evolves, the other should just follow, isn’t that so?
It is not as simple as that, for several reasons. First, because simple mutualistic Lotka-Volterra models showed that most of the time mutualistic systems should drift to infinity and be unstable (e.g. Goh 1979). This is not what happens in natural populations, so something is missing in simple models. At a larger scale, that of communities, this is even worse, since we are still far from understanding the link between the topology of mutualistic networks and the stability of a community. Second, interactions are context-dependent: mutualistic species exchange resources, and thus from the point of view of one species the interaction is either beneficial or not, depending on the net gain of energy (e.g. Holland and DeAngelis 2010). In other words, considering interactions as mutualistic per se is too caricatural. Third, since evolution is blind, the evolutionary response of a species to an environmental change can have any effect on its mutualistic partner, and not necessarily a neutral or positive effect. This latter reason is particularly highlighted by the paper by A. Weinbach et al. (2021).
Weinbach et al. considered a simple two-species mutualistic Lotka-Volterra model and analyzed the evolutionary dynamics of a trait controlling for the rate of interaction between the two species by using the classical Adaptive Dynamics framework. They showed that, depending on the form of the trade-off between this interaction trait and its effect on the intrinsic growth rate, several situations can occur at evolutionary equilibrium: species can stably coexist and maintain their interaction, or the interaction traits can evolve to zero where species can coexist without any interactions.
Weinbach et al. then investigated the fate of the two-species system if a partner species is strongly affected by environmental change, for instance, a large decrease of its growth rate. Because of the supposed trade-off between the interaction trait and the growth rate, the interaction trait in the focal species tends to decrease as an evolutionary response to the decline of the partner species. If environmental change is too large, the interaction trait can evolve to zero and can lead the partner species to extinction. An “evolutionary murder”.
Even though Weinbach et al. interpreted the results of their model through the lens of plant-pollinators systems, their model is not specific to this case. On the contrary, it is very general, which has advantages and caveats. By its generality, the model is informative because it is a proof of concept that the evolution of mutualistic interactions can have unexpected effects on any category of mutualistic systems. Yet, since the model lacks many specificities of plant-pollinator interactions, it is hard to evaluate how their result would apply to plant-pollinators communities.
I wanted to recommend this paper as a reminder that it is certainly worth studying the evolution of mutualistic interactions, because i) some unexpected phenomenons can occur, ii) we are certainly too naive about the evolution and ecology of mutualistic interactions, and iii) one can wonder to what extent we will be able to explain the stability of mutualistic communities without accounting for the co-evolutionary dynamics of mutualistic species.
Goh BS (1979) Stability in Models of Mutualism. The American Naturalist, 113, 261–275. http://www.jstor.org/stable/2460204.
Holland JN, DeAngelis DL (2010) A consumer–resource approach to the density-dependent population dynamics of mutualism. Ecology, 91, 1286–1295. https://doi.org/10.1890/09-1163.1
Weinbach A, Loeuille N, Rohr RP (2021) Eco-evolutionary dynamics further weakens mutualistic interaction and coexistence under population decline. bioRxiv, 570580, ver. 5 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/570580
|Eco-evolutionary dynamics further weakens mutualistic interaction and coexistence under population decline||Avril Weinbach, Nicolas Loeuille, Rudolf P. Rohr||<p style="text-align: justify;">With current environmental changes, evolution can rescue declining populations, but what happens to their interacting species? Mutualistic interactions can help species sustain each other when their environment wors...||Coexistence, Eco-evolutionary dynamics, Evolutionary ecology, Interaction networks, Pollination, Theoretical ecology||Sylvain Billiard||2019-09-05 11:29:45||View|