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04 Sep 2024
Why we need to clean the Augean stables of ecology – the case of InsectChangeRecommended by Francois Massol based on reviews by Bradley Cardinale and 1 anonymous reviewerAs biodiversity has become a major global concern for a variety of stakeholders, and society in general, assessments of biodiversity trends at all spatial scales have flourished in the past decades. To assess trends, one needs data, and the more precise the data, the more precise the trend. Or, if precision is not perfect, uncertainty in the data must be acknowledged and accounted for. Such considerations have already been raised in ecology, most notably regarding the value of species distribution data to model the current and future distribution of species (Rocchini et al., 2011, Duputié et al., 2014, Tessarolo et al., 2021), leading to serious doubts regarding the value of public databases (Maldonado et al., 2015). And more recently similar issues have been raised regarding databases of species traits (Augustine et al., 2024), emphasizing the importance of good data practice and traceability. Science is by nature a self-correcting human process, with many steps of the scientific activity prone to errors and misinterpretations. Collation of ecological data, sadly, is proof of this. Spurred by the astonishing results of Hallmann et al. (2017) regarding the decline of insect biomass, and to more precisely answer the question of biodiversity trends in insects and settle an ongoing debate (Cardinale et al., 2018), van Klink et al. (2020, 2021) established the InsectChange database. Several perceptive comments have already been made regarding the possible issues in the methods and interpretations of this study (Desquilbet et al., 2020, Jähnig et al., 2021, Duchenne et al., 2022). However, the biggest issue might have been finally unearthed by Gaume & Desquilbet (2024): with poorly curated data, the InsectChange database is unlikely to support most of the initial claims regarding insect biodiversity trends. The compilation of errors and inconsistencies present in InsectChange and evinced by Gaume & Desquilbet (2024) is stunning to say the least, with a mix of field and experimental data combined without regard for experimental manipulation of environmental factors, non-standardised transformations of abundances, the use of non-insect taxa to compute insect trends, and inadequate geographical localizations of samplings. I strongly advise all colleagues interested in the study of biodiversity from global databases to consider the points raised by the authors, as it is quite likely that other databases might suffer from the same ailments as well. Reading this paper is also educating and humbling in its own way, since the publication of the original papers based on InsectChange seems to have proceeded without red flags from reviewers or editors. The need for publishing fast results that will make the next buzz, thus obeying the natural selection of bad science (Smaldino and McElreath, 2016), might be the systemic culprit. However, this might also be the opportunity ecology needs to consider the reviewing and curation of data as a crucial step of science quality assessment. To make final assessments, let us proceed with less haste. References Augustine, S. P., Bailey-Marren, I., Charton, K. T., Kiel, N. G. & Peyton, M. S. (2024) Improper data practices erode the quality of global ecological databases and impede the progress of ecological research. Global Change Biology, 30, e17116. https://doi.org/10.1111/gcb.17116 Cardinale, B. J., Gonzalez, A., Allington, G. R. H. & Loreau, M. (2018) Is local biodiversity declining or not? A summary of the debate over analysis of species richness time trends. Biological Conservation, 219, 175-183. https://doi.org/10.1016/j.biocon.2017.12.021 Desquilbet, M., Gaume, L., Grippa, M., Céréghino, R., Humbert, J.-F., Bonmatin, J.-M., Cornillon, P.-A., Maes, D., Van Dyck, H. & Goulson, D. (2020) Comment on “Meta-analysis reveals declines in terrestrial but increases in freshwater insect abundances”. Science, 370, eabd8947. https://doi.org/10.1126/science.abd8947 Duchenne, F., Porcher, E., Mihoub, J.-B., Loïs, G. & Fontaine, C. (2022) Controversy over the decline of arthropods: a matter of temporal baseline? Peer Community Journal, 2. https://doi.org/10.24072/pcjournal.131 Duputié, A., Zimmermann, N. E. & Chuine, I. (2014) Where are the wild things? Why we need better data on species distribution. Global Ecology and Biogeography, 23, 457-467. https://doi.org/10.1111/geb.12118 Gaume, L. & Desquilbet, M. (2024) InsectChange: Comment. biorXiv, ver.4 peer-reviewed and recommended by PCI Ecology https://doi.org/10.1101/2023.06.17.545310 Hallmann, C. A., Sorg, M., Jongejans, E., Siepel, H., Hofland, N., Schwan, H., Stenmans, W., Müller, A., Sumser, H., Hörren, T., Goulson, D. & de Kroon, H. (2017) More than 75 percent decline over 27 years in total flying insect biomass in protected areas. PLOS ONE, 12, e0185809. https://doi.org/10.1371/journal.pone.0185809 Jähnig, S. C., Baranov, V., Altermatt, F., Cranston, P., Friedrichs-Manthey, M., Geist, J., He, F., Heino, J., Hering, D., Hölker, F., Jourdan, J., Kalinkat, G., Kiesel, J., Leese, F., Maasri, A., Monaghan, M. T., Schäfer, R. B., Tockner, K., Tonkin, J. D. & Domisch, S. (2021) Revisiting global trends in freshwater insect biodiversity. WIREs Water, 8, e1506. https://doi.org/10.1002/wat2.1506 Maldonado, C., Molina, C. I., Zizka, A., Persson, C., Taylor, C. M., Albán, J., Chilquillo, E., Rønsted, N. & Antonelli, A. (2015) Estimating species diversity and distribution in the era of Big Data: to what extent can we trust public databases? Global Ecology and Biogeography, 24, 973-984. https://doi.org/10.1111/geb.12326 Rocchini, D., Hortal, J., Lengyel, S., Lobo, J. M., Jiménez-Valverde, A., Ricotta, C., Bacaro, G. & Chiarucci, A. (2011) Accounting for uncertainty when mapping species distributions: The need for maps of ignorance. Progress in Physical Geography, 35, 211-226. https://doi.org/10.1177/0309133311399491 Smaldino, P. E. & McElreath, R. (2016) The natural selection of bad science. Royal Society Open Science, 3. https://doi.org/10.1098/rsos.160384 Tessarolo, G., Ladle, R. J., Lobo, J. M., Rangel, T. F. & Hortal, J. (2021) Using maps of biogeographical ignorance to reveal the uncertainty in distributional data hidden in species distribution models. Ecography, 44, 1743-1755. https://doi.org/10.1111/ecog.05793 van Klink, R., Bowler, D. E., Comay, O., Driessen, M. M., Ernest, S. K. M., Gentile, A., Gilbert, F., Gongalsky, K. B., Owen, J., Pe'er, G., Pe'er, I., Resh, V. H., Rochlin, I., Schuch, S., Swengel, A. B., Swengel, S. R., Valone, T. J., Vermeulen, R., Wepprich, T., Wiedmann, J. L. & Chase, J. M. (2021) InsectChange: a global database of temporal changes in insect and arachnid assemblages. Ecology, 102, e03354. https://doi.org/10.1002/ecy.3354 van Klink, R., Bowler, D. E., Gongalsky, K. B., Swengel, A. B., Gentile, A. & Chase, J. M. (2020) Meta-analysis reveals declines in terrestrial but increases in freshwater insect abundances. Science, 368, 417-420. https://doi.org/10.1126/science.aax9931 | InsectChange: Comment | Laurence Gaume, Marion Desquilbet | <p>The InsectChange database (van Klink et al. 2021) underlying the meta-analysis by van Klink et al. (2020a) compiles worldwide time series of the abundance and biomass of invertebrates reported as insects and arachnids, as well as ecological dat... | Biodiversity, Climate change, Freshwater ecology, Landscape ecology, Meta-analyses, Species distributions, Terrestrial ecology, Zoology | Francois Massol | 2024-01-04 18:57:01 | View | ||
10 Aug 2023
Coexistence of many species under a random competition-colonization trade-offZachary R. Miller, Maxime Clenet, Katja Della Libera, François Massol, Stefano Allesina https://doi.org/10.1101/2023.03.23.533867Assembly in metacommunities driven by a competition-colonization tradeoff: more species in, more species outRecommended by Frederik De Laender based on reviews by Canan Karakoç and 1 anonymous reviewerThe output of a community model depends on how you set its parameters. Thus, analyses of specific parameter settings hardwire the results to specific ecological scenarios. Because more general answers are often of interest, one tradition is to give models a statistical treatment: one summarizes how model parameters vary across species, and then predicts how changing the summary, instead of the individual parameters themselves, would change model output. Arguably the best-known example is the work initiated by May, showing that the properties of a community matrix, encoding effects species have on each other near their equilibrium, determine stability (1,2). More recently, this statistical treatment has also been applied to one of community ecology’s more prickly and slippery subjects: community assembly, which deals with the question “Given some regional species pool, which species will be able to persist together at some local ecosystem?”. Summaries of how species grow and interact in this regional pool predict the fraction of survivors and their relative abundances, the kind of dynamics, and various kinds of stability (3,4). One common characteristic of such statistical treatments is the assumption of disorder: if species do not interact in too structured ways, simple and therefore powerful predictions ensue that often stand up to scrutiny in relatively ordered systems. 2. Allesina, S. & Tang, S. (2015). The stability–complexity relationship at age 40: a random matrix perspective. Population Ecology, 57, 63–75. https://doi.org/10.1007/s10144-014-0471-0 3. Bunin, G. (2016). Interaction patterns and diversity in assembled ecological communities. Preprint at http://arxiv.org/abs/1607.04734. 5. Miller, Z. R., Clenet, M., Libera, K. D., Massol, F. & Allesina, S. (2023). Coexistence of many species under a random competition-colonization trade-off. bioRxiv 2023.03.23.533867, ver 3 peer-reviewed and recommended by PCI Ecology. https://doi.org/10.1101/2023.03.23.533867 6. Serván, C. A. & Allesina, S. (2021). Tractable models of ecological assembly. Ecology Letters, 24, 1029–1037. https://doi.org/10.1111/ele.13702 | Coexistence of many species under a random competition-colonization trade-off | Zachary R. Miller, Maxime Clenet, Katja Della Libera, François Massol, Stefano Allesina | <p>The competition-colonization trade-off is a well-studied coexistence mechanism for metacommunities. In this setting, it is believed that coexistence of all species requires their traits to satisfy restrictive conditions limiting their similarit... | Biodiversity, Coexistence, Colonization, Community ecology, Competition, Population ecology, Spatial ecology, Metacommunities & Metapopulations, Theoretical ecology | Frederik De Laender | 2023-03-30 20:42:48 | View | ||
08 Aug 2020
Trophic cascade driven by behavioural fine-tuning as naïve prey rapidly adjust to a novel predatorChris J Jolly, Adam S Smart, John Moreen, Jonathan K Webb, Graeme R Gillespie and Ben L Phillips https://doi.org/10.1101/856997While the quoll’s away, the mice will play… and the seeds will payRecommended by Denis Réale based on reviews by 2 anonymous reviewersA predator can strongly influence the demography of its prey, which can have profound carryover effects on the trophic network; so-called density-mediated indirect interactions (DMII; Werner and Peacor 2003; Schmitz et al. 2004; Trussell et al. 2006). Furthermore, a novel predator can alter the phenotypes of its prey for traits that will change prey foraging efficiency. These trait-mediated indirect interactions may in turn have cascading effects on the demography and features of the basal resources consumed by the intermediate consumer (TMIII; Werner and Peacor 2003; Schmitz et al. 2004; Trussell et al. 2006), but very few studies have looked for these effects (Trusell et al. 2006). The study “Trophic cascade driven by behavioural fine-tuning as naïve prey rapidly adjust to a novel predator”, by Jolly et al. (2020) is therefore a much-needed addition to knowledge in this field. The authors have profited from a rare introduction of Northern quolls (Dasyurus hallucatus) on an Australian island, to examine both the density-mediated and trait-mediated indirect interactions with grassland melomys (Melomys burtoni) and the vegetation of their woodland habitat. References -Bell G, Gonzalez A (2009) Evolutionary rescue can prevent extinction following environmental change. Ecology letters, 12(9), 942-948. https://doi.org/10.1111/j.1461-0248.2009.01350.x | Trophic cascade driven by behavioural fine-tuning as naïve prey rapidly adjust to a novel predator | Chris J Jolly, Adam S Smart, John Moreen, Jonathan K Webb, Graeme R Gillespie and Ben L Phillips | <p>The arrival of novel predators can trigger trophic cascades driven by shifts in prey numbers. Predators also elicit behavioural change in prey populations, via phenotypic plasticity and/or rapid evolution, and such changes may also contribute t... | Behaviour & Ethology, Biological invasions, Evolutionary ecology, Experimental ecology, Foraging, Herbivory, Population ecology, Terrestrial ecology, Tropical ecology | Denis Réale | 2019-11-27 21:39:44 | View | ||
12 Aug 2021
A study on the role of social information sharing leading to range expansion in songbirds with large vocal repertoires: Enhancing our understanding of the Great-Tailed Grackle (Quiscalus mexicanus) alarm callSamantha Bowser, Maggie MacPherson https://doi.org/10.17605/OSF.IO/2UFJ5Does the active vocabulary in Great-tailed Grackles supports their range expansion? New study will find outRecommended by Jan Oliver Engler ? based on reviews by Guillermo Fandos and 2 anonymous reviewersAlarm calls are an important acoustic signal that can decide the life or death of an individual. Many birds are able to vary their alarm calls to provide more accurate information on e.g. urgency or even the type of a threatening predator. According to the acoustic adaptation hypothesis, the habitat plays an important role too in how acoustic patterns get transmitted. This is of particular interest for range-expanding species that will face new environmental conditions along the leading edge. One could hypothesize that the alarm call repertoire of a species could increase in newly founded ranges to incorporate new habitats and threats individuals might face. Hence selection for a larger active vocabulary might be beneficial for new colonizers. Using the Great-Tailed Grackle (Quiscalus mexicanus) as a model species, Samantha Bowser from Arizona State University and Maggie MacPherson from Louisiana State University want to find out exactly that. The Great-Tailed Grackle is an appropriate species given its high vocal diversity. Also, the species consists of different subspecies that show range expansions along the northern range edge yet to a varying degree. Using vocal experiments and field recordings the researchers have a high potential to understand more about the acoustic adaptation hypothesis within a range dynamic process. Over the course of this assessment, the authors incorporated the comments made by two reviewers into a strong revision of their research plans. With that being said, the few additional comments made by one of the initial reviewers round up the current stage this interesting research project is in. To this end, I can only fully recommend the revised research plan and am much looking forward to the outcomes from the author’s experiments, modeling, and field data. With the suggestions being made at such an early stage I firmly believe that the final outcome will be highly interesting not only to an ornithological readership but to every ecologist and biogeographer interested in drivers of range dynamic processes. References Bowser, S., MacPherson, M. (2021). A study on the role of social information sharing leading to range expansion in songbirds with large vocal repertoires: Enhancing our understanding of the Great-Tailed Grackle (Quiscalus mexicanus) alarm call. In principle recommendation by PCI Ecology. https://doi.org/10.17605/OSF.IO/2UFJ5. Version 3 | A study on the role of social information sharing leading to range expansion in songbirds with large vocal repertoires: Enhancing our understanding of the Great-Tailed Grackle (Quiscalus mexicanus) alarm call | Samantha Bowser, Maggie MacPherson | <p>The acoustic adaptation hypothesis posits that animal sounds are influenced by the habitat properties that shape acoustic constraints (Ey and Fischer 2009, Morton 2015, Sueur and Farina 2015).Alarm calls are expected to signal important habitat... | Biogeography, Biological invasions, Coexistence, Dispersal & Migration, Habitat selection, Landscape ecology | Jan Oliver Engler | Darius Stiels, Anonymous | 2020-12-01 18:11:02 | 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/10.1101/589895On the importance of stoichiometric constraints for understanding global change effects on food web dynamicsRecommended by Elisa Thebault based on reviews by 2 anonymous reviewersThe 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 [1]. Species in ecosystems differ in their elemental composition as well as in their level of elemental homeostasis [2], which can determine the outcome of interactions such as herbivory or decomposition on species coexistence and ecosystem functioning [3, 4]. References [1] 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 | ||
12 May 2020
On the efficacy of restoration in stream networks: comments, critiques, and prospective recommendationsDavid Murray-Stoker https://doi.org/10.1101/611939A stronger statistical test of stream restoration experimentsRecommended by Karl Cottenie based on reviews by Eric Harvey and Mariana Perez RochaThe metacommunity framework acknowledges that local sites are connected to other sites through dispersal, and that these connectivity patterns can influence local dynamics [1]. This framework is slowly moving from a framework that guides fundamental research to being actively applied in for instance a conservation context (e.g. [2]). Swan and Brown [3,4] analyzed the results of a suite of experimental manipulations in headwater and mainstem streams on invertebrate community structure in the context of the metacommunity concept. This was an important contribution to conservation ecology. References [1] Leibold, M. A., Holyoak, M., Mouquet, N. et al. (2004). The metacommunity concept: a framework for multi‐scale community ecology. Ecology letters, 7(7), 601-613. doi: 10.1111/j.1461-0248.2004.00608.x | On the efficacy of restoration in stream networks: comments, critiques, and prospective recommendations | David Murray-Stoker | <p>Swan and Brown (2017) recently addressed the effects of restoration on stream communities under the meta-community framework. Using a combination of headwater and mainstem streams, Swan and Brown (2017) evaluated how position within a stream ne... | Community ecology, Freshwater ecology, Spatial ecology, Metacommunities & Metapopulations | Karl Cottenie | 2019-09-21 22:12:57 | View | ||
30 Oct 2024
The importance of sampling design for unbiased estimation of survival using joint live-recapture and live resight modelsMaria C. Dzul, Charles B. Yackulic, William L. Kendall https://doi.org/10.48550/arXiv.2312.13414In the quest for estimating true survivalRecommended by Matthieu Paquet based on reviews by Rémi Fay and 1 anonymous reviewerAccurately estimating survival rate and identifying the drivers of its variation is essential for our understanding of population dynamics and life history strategies (Sæther and Bakke 2000), as well as for population management and conservation (Francis et al. 1998, Doherty et al. 2014). Many studies estimate survival from capture–recapture data using the Cormack–Jolly–Seber (CJS) model (Lebreton et al. 1992). However, survival estimates are confounded with permanent emigration from the study area, which can be particularly problematic for mobile species. This is problematic, not only because CJS models under estimate true survival in populations where permanent emigration occurs (i.e. they estimate “apparent” survival), but also because some factors of interest may affect both survival and emigration (e.g., habitat quality, Paquet et al. 2020), leaving the interpretation of results challenging, for example in terms of management decisions. Several methods have been developed to account for permanent emigration when estimating survival, for example by jointly analyzing CMR data with data on individuals’ locations at each capture/resighting site (to estimate their dispersal distances; Schaub and Royle 2013, Badia Boher et al. 2023), with telemetry data (Powel et al. 2000), mark recovery data (Burnham 1993, Fay et al. 2019), or with live-resight data (Barker 1997). The Barker joint live-recapture/live-resight (JLRLR) model can estimate survival when resight data are continuous over a long interval and from a larger area than the capture recapture data. This model becomes particularly promising with the growing collection of data from citizen science, or remote detection tools (Dzul et al. 2023). However, as pointed out by Dzul et al., this model assumes that resight probability is homogeneous across the area where individuals can move, and this assumption is likely violated for example because of non-random movements or because of non-random location of resighting sites. In their manuscript, Dzul et al. performed a thorough simulation study to evaluate the accuracy of survival estimates from JLRLR models under various study designs regarding the location of resight sites (global, random, fixed including the capture site, and fixed excluding the capture site). They simulated data with varying survival and movement values, varying recapture and resight probabilities, and varying sample sizes. Finally, they also developed and fitted a multi state version of the JLRLR model. They show that JLRLR models performed better than CJS models. Survival estimates were still often biased (either positively or negatively) but they were less biased when sesight sites were randomly located (rather than at fixed locations), when recapture sites were included in the resighting design, and when using the multi state JLRLR model they developed. This study highlights (multistate) JLRLR models as an alternative to CJS models one should consider when auxiliary resight data can be collected. Moreover, it shows the importance of evaluating not only model performance, but also the efficiency of alternative sampling designs before choosing one for our studies. Hopefully, this study will help the authors and other researchers making a more informed and efficient choice of model and design to estimate survival in their study populations. References Jaume A. Badia-Boher, Joan Real, Joan Lluís Riera, Frederic Bartumeus, Francesc Parés, Josep Maria Bas, and Antonio Hernández-Matías. Joint estimation of survival and dispersal effectively corrects the permanent emigration bias in mark-recapture analyses. (2023) Scientific reports 13, no. 1: 6970. https://doi.org/10.1038/s41598-023-32866-0 Richard J Barker (1997) Joint modeling of live-recapture, tag-resight, and tag-recovery data. Biometrics: 666-677. https://doi.org/10.2307/2533966 Kenneth P. Burnham (1993) Marked Individuals in the Study of Bird Populations (ed. J.D. Lebreton), pp. 199–213. Birkhäuser, Basel Kevin E. Doherty, David E. Naugle, Jason D. Tack, Brett L. Walker, Jon M. Graham, Jeffrey L. Beck (2014) Linking conservation actions to demography: grass height explains variation in greater sage‐grouse nest survival. Wildlife biology 20, no. 6 : 320-325. https://doi.org/10.2981/wlb.00004 Maria C. Dzul, Charles B. Yackulic, William L. Kendall (2023) The importance of sampling design for unbiased estimation of survival using joint live-recapture and live resight models. arXiv, ver.3 peer-reviewed and recommended by PCI Ecology https://doi.org/10.48550/arXiv.2312.13414 Rémi Fay, Stephanie Michler, Jacques Laesser, and Michael Schaub (2019) Integrated population model reveals that kestrels breeding in nest boxes operate as a source population. Ecography 42, no. 12: 2122-2131. https://doi.org/10.1111/ecog.04559 Charles M. Francis, John R. Sauer, Jerome R. Serie (1998) Effect of restrictive harvest regulations on survival and recovery rates of American black ducks. The Journal of Wildlife Management : 1544-1557. https://doi.org/10.2307/3802021 Jean-Dominique Lebreton, Kenneth P. Burnham, Jean Clobert, David R. Anderson (1992) Modeling survival and testing biological hypotheses using marked animals: a unified approach with case studies. Ecological monographs 62.1: 67-118. https://doi.org/10.2307/2937171 Matthieu Paquet, Debora Arlt, Jonas Knape, Matthew Low, Pär Forslund, and Tomas Pärt (2020) Why we should care about movements: Using spatially explicit integrated population models to assess habitat source–sink dynamics. Journal of Animal Ecology 89, no. 12: 2922-2933. https://doi.org/10.1111/1365-2656.13357 Larkin A. Powell, Michael J. Conroy, James E. Hines, James D. Nichols, and David G. Krementz. Simultaneous use of mark-recapture and radiotelemetry to estimate survival, movement, and capture rates. (2000) The Journal of Wildlife Management : 302-313. https://doi.org/10.2307/3803003 Bernt-Erik Sæther, Øyvind Bakke (2000) Avian life history variation and contribution of demographic traits to the population growth rate. Ecology 81.3 : 642-653. https://doi.org/10.1890/0012-9658(2000)081[0642:ALHVAC]2.0.CO;2 Michael Schaub, J. Andrew Royle. Estimating true instead of apparent survival using spatial Cormack–Jolly–Seber models (2014) Methods in Ecology and Evolution 5, no. 12: 1316-1326. https://doi.org/10.1111/2041-210X.12134 | The importance of sampling design for unbiased estimation of survival using joint live-recapture and live resight models | Maria C. Dzul, Charles B. Yackulic, William L. Kendall | <p>Survival is a key life history parameter that can inform management decisions and life history research. Because true survival is often confounded with permanent and temporary emigration from the study area, many studies must estimate apparent ... | Dispersal & Migration, Euring Conference, Population ecology, Statistical ecology | Matthieu Paquet | 2023-12-22 22:31:07 | View | ||
11 Mar 2022
Comment on “Information arms race explains plant-herbivore chemical communication in ecological communities”Ethan Bass, André Kessler https://doi.org/10.32942/osf.io/xsbtmDoes information theory inform chemical arms race communication?Recommended by Rodrigo Medel based on reviews by Claudio Ramirez and 2 anonymous reviewersOne of the long-standing questions in evolutionary ecology is on the mechanisms involved in arms race coevolution. One way to address this question is to understand the conditions under which one species evolves traits in response to the presence of a second species and so on. However, specialized pairwise interactions are by far less common in nature than interactions involving a higher number of interacting species (Bascompte, Jordano 2013). While interactions between large sets of species are the norm rather than the exception in mutualistic (pollination, seed dispersal), and antagonist (herbivory, parasitism) relationships, few is known on the way species identify, process, and respond to information provided by other interacting species under field conditions (Schaefer, Ruxton 2011). Zu et al. (2020) addressed this general question by developing an interesting information theory-based approach that hypothesized conditional entropy in chemical communication plays a role as proxy of fitness in plant-herbivore communities. More specifically, plant fitness was assumed to be related to the efficiency to code signals by plant species, and herbivore fitness to the capacity to decode plant signals. In this way, from the plant perspective, the elaboration of plant signals that elude decoding by herbivores is expected to be favored, as herbivores are expected to attack plants with simple chemical signals. The empirical observation upon which the model was tested was the redundancy in volatile organic compounds (VOC) found across plant species in a plant-herbivore community. Interestingly, Zu et al.’s model predicted successfully that VOC redundancy in the plant community associates with increased conditional entropy, which conveys herbivore confusion and plant protection against herbivory. In this way, plant species that evolve VOCs already present in the community might be benefitted, ultimately leading to the patterns of VOC redundancy commonly observed in nature. Bass & Kessler performed a series of interesting observations on Zu et al. (2020), that can be organized along three lines of reasoning. First, from an evolutionary perspective, Bass & Kessler note the important point that accepting that conditional information entropy, estimated from the contribution of every plant species to volatile redundancy implies that average plant fitness seems to depend on community-level properties (i.e., what the other species in the community are doing) rather than on population-level characteristics (I.e., what the individuals belonging a population are doing). While the level at which selection acts upon is a longstanding debate (e.g., Goodnight, 1990; Williams, 1992), the model seems to contradict one of the basic tenets of Darwinian evolution. The extent to which this important observation invalidates the contribution of Zu et al. (2020) is open to scrutiny. However, one can indulge the evolutionary criticism by arguing that every theoretical model performs a number of assumptions to preserve the simplicity of analyses. Furthermore, even accepting the criticism, the overall information-based framework is valuable as it provides a fresh perspective to the way coding and decoding chemical information in plant-herbivore interactions may result in arm race coevolution. The question to be assessed by members of the scientific community is how strong the evolutionary assumptions are to be acceptable. A second line of reasoning involves consideration of additional routes of chemical information transfer. If chemical volatiles are involved in another ecological function unrelated to arm race (as they are) such as toxicity, crypsis, aposematism, etc., the conditional information indices considered as proxy to plant and herbivore fitness may be only secondarily related to arms race. This is an interesting observation, which suggests that VOC production may have more than one ecological function, as it often happens in “pleiotropic” traits (Strauss, Irwin 2004). This is an exciting avenue for future research. Finally, a third category of comments involves the relationship between conditional information entropy and plant and herbivore fitness. Bass & Kessler developed a Bayesian treatment of the community-level information developed by Zu et al. (2020) that permitted to estimate fitness on a species rather than community level. Their results revealed that community conditional entropies fail to align with species-level indices, suggesting that conclusions of Strauss & Irwin (2004) are not commensurate with fitness at the species level, where the analysis seems to be pertinent. In general, I strongly recommend Bass & Kessler’s contribution as it provides a series of observations and new perspectives to Zu et al. (2020). Rather than restricting their manuscript to blind criticisms, Bass & Kessler provides new interesting perspectives, which is always welcome as it improves the value and scope of the original work. References Bascompte J, Jordano P (2013) Mutualistic Networks. Princeton University Press. https://doi.org/10.23943/princeton/9780691131269.001.0001 Bass E, Kessler A (2022) Comment on “Information arms race explains plant-herbivore chemical communication in ecological communities.” EcoEvoRxiv, ver. 8 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.32942/osf.io/xsbtm Goodnight CJ (1990) Experimental Studies of Community Evolution I: The Response to Selection at the Community Level. Evolution, 44, 1614–1624. https://doi.org/10.1111/j.1558-5646.1990.tb03850.x Schaefer HM, Ruxton GD (2011) Plant-Animal Communication. Oxford University Press, Oxford. https://doi.org/10.1093/acprof:osobl/9780199563609.001.0001 Strauss SY, Irwin RE (2004) Ecological and Evolutionary Consequences of Multispecies Plant-Animal Interactions. Annual Review of Ecology, Evolution, and Systematics, 35, 435–466. https://doi.org/10.1146/annurev.ecolsys.35.112202.130215 Williams GC (1992) Natural Selection: Domains, Levels, and Challenges. Oxford University Press, Oxford, New York. Zu P, Boege K, del-Val E, Schuman MC, Stevenson PC, Zaldivar-Riverón A, Saavedra S (2020) Information arms race explains plant-herbivore chemical communication in ecological communities. Science, 368, 1377–1381. https://doi.org/10.1126/science.aba2965 | Comment on “Information arms race explains plant-herbivore chemical communication in ecological communities” | Ethan Bass, André Kessler | <p style="text-align: justify;">Zu et al (Science, 19 Jun 2020, p. 1377) propose that an ‘information arms-race’ between plants and herbivores explains plant-herbivore communication at the community level. However, the analysis presented here show... | Chemical ecology, Community ecology, Eco-evolutionary dynamics, Evolutionary ecology, Herbivory, Interaction networks, Theoretical ecology | Rodrigo Medel | 2021-10-02 06:06:07 | 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/10.1101/570580Doomed by your partner: when mutualistic interactions are like an evolutionary millstone around a species’ neckRecommended by Sylvain Billiard based on reviews by 2 anonymous reviewersMutualistic 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. References 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 | ||
01 Mar 2024
Cities as parasitic amplifiers? Malaria prevalence and diversity in great tits along an urbanization gradientAude E. Caizergues, Benjamin Robira, Charles Perrier, Melanie Jeanneau, Arnaud Berthomieu, Samuel Perret, Sylvain Gandon, Anne Charmantier https://doi.org/10.1101/2023.05.03.539263Exploring the Impact of Urbanization on Avian Malaria Dynamics in Great Tits: Insights from a Study Across Urban and Non-Urban EnvironmentsRecommended by Adrian Diaz based on reviews by Ana Paula Mansilla and 2 anonymous reviewersAcross the temporal expanse of history, the impact of human activities on global landscapes has manifested as a complex interplay of ecological alterations. From the advent of early agricultural practices to the successive waves of industrialization characterizing the 18th and 19th centuries, anthropogenic forces have exerted profound and enduring transformations upon Earth's ecosystems. Indeed, by 2017, more than 80% of the terrestrial biosphere was transformed by human populations and land use, and just 19% remains as wildlands (Ellis et al. 2021). Caizergues AE, Robira B, Perrier C, Jeanneau M, Berthomieu A, Perret S, Gandon S, Charmantier A (2023) Cities as parasitic amplifiers? Malaria prevalence and diversity in great tits along an urbanization gradient. bioRxiv, 2023.05.03.539263, ver. 3 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2023.05.03.539263 Ellis EC, Gauthier N, Klein Goldewijk K, Bliege Bird R, Boivin N, Díaz S, Fuller DQ, Gill JL, Kaplan JO, Kingston N, Locke H, McMichael CNH, Ranco D, Rick TC, Shaw MR, Stephens L, Svenning JC, Watson JEM. People have shaped most of terrestrial nature for at least 12,000 years. Proc Natl Acad Sci U S A. 2021 Apr 27;118(17):e2023483118. https://doi.org/10.1073/pnas.2023483118. Faeth SH, Bang C, Saari S (2011) Urban biodiversity: Patterns and mechanisms. Ann N Y Acad Sci 1223:69–81. https://doi.org/10.1111/j.1749-6632.2010.05925.x Faeth SH, Bang C, Saari S (2011) Urban biodiversity: Patterns and mechanisms. Ann N Y Acad Sci 1223:69–81. https://doi.org/10.1111/j.1749-6632.2010.05925.x Reyes R, Ahn R, Thurber K, Burke TF (2013) Urbanization and Infectious Diseases: General Principles, Historical Perspectives, and Contemporary Challenges. Challenges Infect Dis 123. https://doi.org/10.1007/978-1-4614-4496-1_4 | Cities as parasitic amplifiers? Malaria prevalence and diversity in great tits along an urbanization gradient | Aude E. Caizergues, Benjamin Robira, Charles Perrier, Melanie Jeanneau, Arnaud Berthomieu, Samuel Perret, Sylvain Gandon, Anne Charmantier | <p style="text-align: justify;">Urbanization is a worldwide phenomenon that modifies the environment. By affecting the reservoirs of pathogens and the body and immune conditions of hosts, urbanization alters the epidemiological dynamics and divers... | Epidemiology, Host-parasite interactions, Human impact | Adrian Diaz | Anonymous, Gauthier Dobigny, Ana Paula Mansilla | 2023-09-11 20:24:44 | View |
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