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Id | Title * | Authors * | Abstract * ▲ | Picture * | Thematic fields * | Recommender | Reviewers | Submission date | |
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14 May 2019
Field assessment of precocious maturation in salmon parr using ultrasound imagingMarie Nevoux, Frédéric Marchand, Guillaume Forget, Dominique Huteau, Julien Tremblay, Jean-Pierre Destouches https://doi.org/10.1101/425561OB-GYN for salmon parrsRecommended by Jean-Olivier IrissonPopulation dynamics and stock assessment models are only as good as the data used to parameterise them. For Atlantic salmon (Salmo salar) populations, a critical parameter may be frequency of precocious maturation. Indeed, the young males (parrs) that mature early, before leaving the river to reach the ocean, can contribute to reproduction but have much lower survival rates afterwards. The authors cite evidence of the potentially major consequences of this alternate reproductive strategy. So, to be parameterised correctly, it needs to be assessed correctly. Cue the ultrasound machine. Through a thorough analysis of data collected on 850 individuals [1], over three years, the authors clearly show that the non-invasive examination of the internal cavity of young fishes to look for gonads, using a portable ultrasound machine, provides reliable and replicable evidence of precocious maturation. They turned into OB-GYN for salmons (albeit for male salmons!) and it worked. While using ultrasounds to detect fish gonads is not a new idea (early attempts for salmonids date back to the 80s [2]), the value here is in the comparison with the classic visual inspection technique (which turns out to be less reliable) and the fact that ultrasounds can now easily be carried out in the field. Beyond the potentially important consequences of this new technique for the correct assessment of salmon population dynamics, the authors also make the case for the acquisition of more reliable individual-level data in ecological studies, which I applaud. References. [1] Nevoux M, Marchand F, Forget G, Huteau D, Tremblay J, and Destouches J-P. (2019). Field assessment of precocious maturation in salmon parr using ultrasound imaging. bioRxiv 425561, ver. 3 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/425561 | Field assessment of precocious maturation in salmon parr using ultrasound imaging | Marie Nevoux, Frédéric Marchand, Guillaume Forget, Dominique Huteau, Julien Tremblay, Jean-Pierre Destouches | <p>Salmonids are characterized by a large diversity of life histories, but their study is often limited by the imperfect observation of the true state of an individual in the wild. Challenged by the need to reduce uncertainty of empirical data, re... | Conservation biology, Demography, Experimental ecology, Freshwater ecology, Life history, Phenotypic plasticity, Population ecology | Jean-Olivier Irisson | 2018-09-25 17:24:59 | View | ||
20 Jun 2019
![]() Sexual segregation in a highly pagophilic and sexually dimorphic marine predatorChristophe Barbraud, Karine Delord, Akiko Kato, Paco Bustamante, Yves Cherel https://doi.org/10.1101/472431Sexual segregation in a sexually dimorphic seabird: a matter of spatial scaleRecommended by Denis Réale based on reviews by Dries Bonte and 1 anonymous reviewerSexual segregation appears in many taxa and can have important ecological, evolutionary and conservation implications. Sexual segregation can take two forms: either the two sexes specialise in different habitats but share the same area (habitat segregation), or they occupy the same habitat but form separate, unisex groups (social segregation) [1,2]. Segregation would have evolved as a way to avoid, or at least, reduce intersexual competition. References [1] Conradt, L. (2005). Definitions, hypotheses, models and measures in the study of animal segregation. In Sexual segregation in vertebrates: ecology of the two sexes (Ruckstuhl K.E. and Neuhaus, P. eds). Cambridge University Press, Cambridge, United Kingdom. Pp:11–34. | Sexual segregation in a highly pagophilic and sexually dimorphic marine predator | Christophe Barbraud, Karine Delord, Akiko Kato, Paco Bustamante, Yves Cherel | <p>Sexual segregation is common in many species and has been attributed to intra-specific competition, sex-specific differences in foraging efficiency or in activity budgets and habitat choice. However, very few studies have simultaneously quantif... | ![]() | Foraging, Marine ecology | Denis Réale | Dries Bonte, Anonymous | 2018-11-19 13:40:59 | 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/10.1101/645747The complexity of predicting mortality in treesRecommended by Lucía DeSoto based on reviews by Lisa Hülsmann and 2 anonymous reviewersOne 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. References 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 | |
26 Mar 2025
![]() Code-sharing policies are associated with increased reproducibility potential of ecological findingsAlfredo Sánchez-Tójar, Aya Bezine, Marija Purgar, Antica Culina https://doi.org/10.32942/X21S7HEnsuring reproducible science requires policiesRecommended by Ignasi BartomeusResearchers do not live in a vacuum, and the social context we live in affects how we do science. On one hand, increased competition for scarce funding creates the wrong incentives to do fast analysis, leading sometimes to poorly checked results that accumulate errors (Fraser et al. 2018). On the other hand, the actual challenges the world faces require more than ever robust scientific evidence that can be used to tackle the current rapid human-induced environmental change. Moreover, scientists' credibility is at stake at this moment where the global flow of information can be politically manipulated, and accessing reliable sources of information is paramount for society. At the crossroads of these challenges is scientific reproducibility. Making our results transparent and reproducible ensures that no perverse incentives can compromise our findings, that results can be reliably applied to solve relevant problems, and that we regain societal credibility in the scientific process. Unfortunately, in ecology and evolution, we are still far from publishing open, transparent, and reproducible papers (Maitner et al. 2024). Understanding which factors promote increased use of good practices regarding reproducibility is hence very welcome. Sanchez-Tojar and colleagues (2025) conducted a (reproducible) analysis of code and data-sharing practices (a cornerstone of scientific reproducibility) in journals with and without explicit policies regarding data and code deposition. The gist is that having policies in place increases data and code sharing. Doing science about how we do science (meta-science) is important to understand which actions drive our behavior as scientists. This paper highlights that in the absence of strong societal or personal incentives to share code and data, clear policies can catalyze this process. However, in my opinion, policies are a needed first step to consolidate a more permanent change in researchers' behavior regarding reproducible science, but policies alone will not be enough to fix the problem if we do not change also the cultural values around how we publish science. Appealing to inner values, and recognizing science needs to be reproducible to ensure potential errors are easily spotted and corrected requires a deep cultural change. References Fraser, Hannah, Tim Parker, Shinichi Nakagawa, Ashley Barnett, and Fiona Fidler. "Questionable research practices in ecology and evolution." PloS one 13, no. 7 (2018): e0200303. https://doi.org/10.1371/journal.pone.0200303 Alfredo Sánchez-Tójar, Aya Bezine, Marija Purgar, Antica Culina (2025) Code-sharing policies are associated with increased reproducibility potential of ecological findings. EcoEvoRxiv, ver.4 peer-reviewed and recommended by PCI Ecology. https://doi.org/10.32942/X21S7H | Code-sharing policies are associated with increased reproducibility potential of ecological findings | Alfredo Sánchez-Tójar, Aya Bezine, Marija Purgar, Antica Culina | <p>Software code (e.g., analytical code) is increasingly recognized as an important research output because it improves transparency, collaboration, and research credibility. Many scientific journals have introduced code-sharing policies; however,... | ![]() | Meta-analyses, Preregistrations, Statistical ecology | Ignasi Bartomeus | 2024-12-11 10:33:13 | View | |
04 Apr 2023
![]() Data stochasticity and model parametrisation impact the performance of species distribution models: insights from a simulation studyCharlotte Lambert, Auriane Virgili https://doi.org/10.1101/2023.01.17.524386Species Distribution Models: the delicate balance between signal and noiseRecommended by Timothée PoisotSpecies Distribution Models (SDMs) are one of the most commonly used tools to predict where species are, where they may be in the future, and, at times, what are the variables driving this prediction. As such, applying an SDM to a dataset is akin to making a bet: that the known occurrence data are informative, that the resolution of predictors is adequate vis-à-vis the scale at which their impact is expressed, and that the model will adequately capture the shape of the relationships between predictors and predicted occurrence. In this contribution, Lambert & Virgili (2023) perform a comprehensive assessment of different sources of complications to this process, using replicated simulations of two synthetic species. Their experimental process is interesting, in that both the data generation and the data analysis stick very close to what would happen in "real life". The use of synthetic species is particularly relevant to the assessment of SDM robustness, as they enable the design of species for which the shape of the relationship is given: in short, we know what the model should capture, and can evaluate the model performance against a ground truth that lacks uncertainty. Any simulation study is limited by the assumptions established by the investigators; when it comes to spatial data, the "shape" of the landscape, both in terms of auto-correlation and in where the predictors are available. Lambert & Virgili (2023) nicely circumvent these issues by simulating synthetic species against the empirical distribution of predictors; in other words, the species are synthetic, but the environment for which the prediction is made is real. This is an important step forward when compared to the use of e.g. neutral landscapes (With 1997), which can have statistical properties that are not representative of natural landscapes (see e.g. Halley et al., 2004). A striking point in the study by Lambert & Virgili (2023) is that they reveal a deep, indeed deeper than expected, stochasticity in SDMs; whether this is true in all models remains an open question, but does not invalidate their recommendation to the community: the interpretation of outcomes is a delicate exercise, especially because measures that inform on the goodness of the model fit do not capture the predictive quality of the model outputs. This preprint is both a call to more caution, and a call to more curiosity about the complex behavior of SDMs, while also providing a sensible template to perform future analyses of the potential issues with predictive models.
Halley, J. M., et al. (2004) “Uses and Abuses of Fractal Methodology in Ecology: Fractal Methodology in Ecology.” Ecology Letters, vol. 7, no. 3, pp. 254–71. https://doi.org/10.1111/j.1461-0248.2004.00568.x. Lambert, Charlotte, and Auriane Virgili (2023). Data Stochasticity and Model Parametrisation Impact the Performance of Species Distribution Models: Insights from a Simulation Study. bioRxiv, ver. 2 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2023.01.17.524386 With, Kimberly A. (1997) “The Application of Neutral Landscape Models in Conservation Biology. Aplicacion de Modelos de Paisaje Neutros En La Biologia de La Conservacion.” Conservation Biology, vol. 11, no. 5, pp. 1069–80. https://doi.org/10.1046/j.1523-1739.1997.96210.x. | Data stochasticity and model parametrisation impact the performance of species distribution models: insights from a simulation study | Charlotte Lambert, Auriane Virgili | <p>Species distribution models (SDM) are widely used to describe and explain how species relate to their environment, and predict their spatial distributions. As such, they are the cornerstone of most of spatial planning efforts worldwide. SDM can... | ![]() | Biogeography, Habitat selection, Macroecology, Marine ecology, Spatial ecology, Metacommunities & Metapopulations, Species distributions, Statistical ecology | Timothée Poisot | 2023-01-20 09:43:51 | View | |
30 Sep 2020
How citizen science could improve Species Distribution Models and their independent assessmentFlorence Matutini, Jacques Baudry, Guillaume Pain, Morgane Sineau, Josephine Pithon https://doi.org/10.1101/2020.06.02.129536Citizen science contributes to SDM validationRecommended by Francisco Lloret based on reviews by Maria Angeles Perez-Navarro and 1 anonymous reviewerCitizen science is becoming an important piece for the acquisition of scientific knowledge in the fields of natural sciences, and particularly in the inventory and monitoring of biodiversity (McKinley et al. 2017). The information generated with the collaboration of citizens has an evident importance in conservation, by providing information on the state of populations and habitats, helping in mitigation and restoration actions, and very importantly contributing to involve society in conservation (Brown and Williams 2019).
An obvious advantage of these initiatives is the ability to mobilize human resources on a large territorial scale and in the medium term, which would otherwise be difficult to finance. The resulting increasing information then can be processed with advanced computational techniques (Hochachka et al 2012; Kelling et al. 2015), thus improving our interpretation of the distribution of species. Specifically, the ability to obtain information on a large territorial scale can be integrated into studies based on Species Distribution Models SDMs. One of the common problems with SDMs is that they often work from species occurrences that have been opportunistically recorded, either by professionals or amateurs. A great challenge for data obtained from non-professional citizens, however, remains to ensure its standardization and quality (Kosmala et al. 2016). This requires a clear and effective design, solid volunteer training, and a high level of coordination that turns out to be complex (Brown and Williams 2019). Finally, it is essential to perform a quality validation following scientifically recognized standards, since they are often conditioned by errors and biases in obtaining information (Bird et al. 2014). There are two basic approaches to obtain the necessary data for this validation: getting it from an external source (external validation), or allocating a part of the database itself (internal validation or cross-validation) to this function. References [1] Bird TJ et al. (2014) Statistical solutions for error and bias in global citizen science datasets. Biological Conservation 173: 144-154. doi: 10.1016/j.biocon.2013.07.037 | How citizen science could improve Species Distribution Models and their independent assessment | Florence Matutini, Jacques Baudry, Guillaume Pain, Morgane Sineau, Josephine Pithon | <p>Species distribution models (SDM) have been increasingly developed in recent years but their validity is questioned. Their assessment can be improved by the use of independent data but this can be difficult to obtain and prohibitive to collect.... | Biodiversity, Biogeography, Conservation biology, Habitat selection, Spatial ecology, Metacommunities & Metapopulations, Species distributions, Statistical ecology | Francisco Lloret | 2020-06-03 09:36:34 | View | ||
02 Jan 2024
![]() Mt or not Mt: Temporal variation in detection probability in spatial capture-recapture and occupancy modelsRahel Sollmann https://doi.org/10.1101/2023.08.08.552394Useful clarity on the value of considering temporal variability in detection probabilityRecommended by Benjamin BolkerAs so often quoted, "all models are wrong; more specifically, we always neglect potentially important factors in our models of ecological systems. We may neglect these factors because no-one has built a computational framework to include them; because including them would be computationally infeasible; or because we don't have enough data. When considering whether to include a particular process or form of heterogeneity, the gold standard is to fit models both with and without the component, and then see whether we needed the component in the first place -- that is, whether including that component leads to an important difference in our conclusions. However, this approach is both tedious and endless, because there are an infinite number of components that we could consider adding to any given model. Therefore, thoughtful exercises that evaluate the importance of particular complications under a realistic range of simulations and a representative set of case studies are extremely valuable for the field. While they cannot provide ironclad guarantees, they give researchers a general sense of when they can (probably) safely ignore some factors in their analyses. This paper by Sollmann (2024) shows that for a very wide range of scenarios, temporal and spatiotemporal variability in the probability of detection have little effect on the conclusions of spatial capture-recapture and occupancy models. The author is thoughtful about when such variability may be important, e.g. when variation in detection and density is correlated and thus confounded, or when variation is driven by animals' behavioural responses to being captured. | Mt or not Mt: Temporal variation in detection probability in spatial capture-recapture and occupancy models | Rahel Sollmann | <p>State variables such as abundance and occurrence of species are central to many questions in ecology and conservation, but our ability to detect and enumerate species is imperfect and often varies across space and time. Accounting for imperfect... | ![]() | Euring Conference, Statistical ecology | Benjamin Bolker | Dana Karelus, Ben Augustine, Ben Augustine | 2023-08-10 09:18:56 | View |
03 Oct 2023
![]() Integrating biodiversity assessments into local conservation planning: the importance of assessing suitable data sourcesThibaut Ferraille, Christian Kerbiriou, Charlotte Bigard, Fabien Claireau, John D. Thompson https://doi.org/10.1101/2023.05.09.539999Biodiversity databases are ever more numerous, but can they be used reliably for Species Distribution Modelling?Recommended by Nicolas SchtickzelleProposing efficient guidelines for biodiversity conservation often requires the use of forecasting tools. Species Distribution Models (SDM) are more and more used to predict how the distribution of a species will react to environmental change, including any large-scale management actions that could be implemented. Their use is also boosted by the increase of publicly available biodiversity databases[1]. The now famous aphorism by George Box "All models are wrong but some are useful"[2] very well summarizes that the outcome of a model must be adjusted to, and will depend on, the data that are used to parameterize it. The question of the reliability of using biodiversity databases to parameterize biodiversity models such as SDM –but the question would also apply to other kinds of biodiversity models, e.g. Population Viability Analysis models[3]– is key to determine the confidence that can be placed in model predictions. This point is often overlooked by some categories of biodiversity conservation stakeholders, in particular the fact that some data were collected using controlled protocols while others are opportunistic. In this study[4], the authors use a collection of databases covering a range of species as well as of geographic scales in France and using different data collection and validation approaches as a case study to evaluate the impact of data quality when performing Strategic Environmental Assessment (SEA). Among their conclusions, the fact that a large-scale database (what they call the “country” level) is necessary to reliably parameterize SDM. Besides this and other conclusions of their study, which are likely to be in part specific to their case study –unfortunately for its conservation, biodiversity is complex and varies a lot–, the merit of this work lies in the approach used to test the impact of data on model predictions. References 1. Feng, X. et al. A review of the heterogeneous landscape of biodiversity databases: Opportunities and challenges for a synthesized biodiversity knowledge base. Global Ecology and Biogeography 31, 1242–1260 (2022). https://doi.org/10.1111/geb.13497 2. Box, G. E. P. Robustness in the Strategy of Scientific Model Building. in Robustness in Statistics (eds. Launer, R. L. & Wilkinson, G. N.) 201–236 (Academic Press, 1979). https://doi.org/10.1016/B978-0-12-438150-6.50018-2. 3. Beissinger, S. R. & McCullough, D. R. Population Viability Analysis. (The University of Chicago Press, 2002). 4. Ferraille, T., Kerbiriou, C., Bigard, C., Claireau, F. & Thompson, J. D. (2023) Integrating biodiversity assessments into local conservation planning: the importance of assessing suitable data sources. bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2023.05.09.539999 | Integrating biodiversity assessments into local conservation planning: the importance of assessing suitable data sources | Thibaut Ferraille, Christian Kerbiriou, Charlotte Bigard, Fabien Claireau, John D. Thompson | <p>Strategic Environmental Assessment (SEA) of land-use planning is a fundamental tool to minimize environmental impacts of artificialization. In this context, Systematic Conservation Planning (SCP) tools based on Species Distribution Models (SDM)... | ![]() | Biodiversity, Conservation biology, Species distributions, Terrestrial ecology | Nicolas Schtickzelle | 2023-05-11 09:41:05 | View | |
14 Apr 2025
Behavioral flexibility is related to exploration, but not boldness, persistence or motor diversityKelsey B. McCune, Dieter Lukas, Maggie MacPherson, Corina J. Logan https://doi.org/10.32942/X2H33FExploring exploration and behavioral flexibility in grackles: how to handle issues of "jingle-jangle" and repeatabilityRecommended by Jeremy Van CleveAnimal behavior, like other kinds of phenotypic plasticity, is crucial for survival and reproduction in environments that vary over space and time. Behaviors themselves may need to be flexible when the distributions of environmental conditions themselves change; for example, short-term weather patterns and long-term climate conditions are changing due to human activity, and behavioral flexibility will likely be key to some population persisting during these changes and others going extinct. Thus, measuring this flexibility is key to understanding which species may be resilient to climate change. Measuring behavioral flexibility is tricky as different studies may define and measure it differently and yet other studies may measure similar kinds of flexibility yet call them different things. This so-called "jingle-jangle" issue suggests that studies can more robustly measure a behavioral trait when they use multiple behavioral tests. An additional issue is that measuring behavioral traits that vary between individuals due to genetic or development effects, often referred to as "personality" traits, requires that those trait differences be repeatable across time and between individuals. With these issues in mind, McCune et al. (2019) presented a preregistration for experiments using a population of great-tailed grackles to investigate how behavioral flexibility relates to other important traits that are known to vary across individuals including exploratory behavior, boldness, and persistence and motor diversity in accessing a new food source. Behavioral flexibility is measured by the rate of learning a color associated with reward after first learning an association with a different color. That preregistration was recommended by PCI Ecology (Van Cleve, 2019). Now, McCune et al. (2025) present results from this study and find that only exploration of a novel environment and persistence were statistically repeatable behaviors. Both behaviors were not significantly correlated with behavioral flexibility. However, grackles that were trained to perform better in the color reversal learning task were more exploratory. This association between behavioral flexibility and exploratory tendencies may have evolved in grackles to help them survive in new environments, which they have proven very capable of doing as they have expanded their range in North American over the last 140 years (Wehtje, 2003). There are a few key features of McCune et al. (2025) to merit recommendation. First, the authors are intent on demonstrating careful behavioral research practices including, as evidenced above, preregistering their hypotheses and predictions and making available both the preregistered and final analysis code. Second, the study demonstrates a thorough attempt to address two aspects that bedevil behavioral research, namely the "jingle-jangle" issue and repeatability of traits across individuals. Even after measuring multiple features of boldness, exploratory, persistence, McCune et al. (2025) find that only a subset of the measured behaviors are repeatable and only a subset of those are associated with behavioral flexibility. This suggests that only thorough studies like McCune et al. (2025) can start to probe difficult to measure behavioral associations that may be key to understanding how species will respond to our changing world. References McCune K, Lukas D, MacPherson M, Logan CJ (2025) Behavioral flexibility is related to exploration, but not boldness, persistence or motor diversity. EcoEvoRxiv, ver.2 peer-reviewed and recommended by PCI Ecology https://doi.org/10.32942/X2H33F Van Cleve, J. (2019) Probing behaviors correlated with behavioral flexibility. PCI Ecology, 100020. https://doi.org/10.24072/pci.ecology.100020 McCune K, Rowney C, Bergeron L, Logan CJ. (2019) Is behavioral flexibility linked with exploration, but not boldness, persistence, or motor diversity? (http://corinalogan.com/Preregistrations/g_exploration.html) In principle acceptance by PCI Ecology of the version on 27 Mar 2019 Wehtje, W. (2003) The range expansion of the great-tailed grackle (Quiscalus mexicanus Gmelin) in North America since 1880. Journal of Biogeography 30:1593–1607 https://doi.org/10.1046/j.1365-2699.2003.00970.x. | Behavioral flexibility is related to exploration, but not boldness, persistence or motor diversity | Kelsey B. McCune, Dieter Lukas, Maggie MacPherson, Corina J. Logan | <p><strong><em>This is REVISION 1 for the post-study manuscript of the preregistration that was pre-study peer reviewed and received an In Principle Recommendation on 27 March 2019 by Jeremy Van Cleve.</em></strong><br>Behavioral flexibility, the ... | Behaviour & Ethology, Biological invasions | Jeremy Van Cleve | 2024-11-11 15:29:20 | View | ||
25 Oct 2021
![]() The taxonomic and functional biogeographies of phytoplankton and zooplankton communities across boreal lakesNicolas F St-Gelais, Richard J Vogt, Paul A del Giorgio, Beatrix E Beisner https://doi.org/10.1101/373332The difficult interpretation of species co-distributionRecommended by Dominique Gravel based on reviews by Anthony Maire and Emilie Macke ?Ecology is the study of the distribution of organisms in space and time and their interactions. As such, there is a tradition of studies relating abiotic environmental conditions to species distribution, while another one is concerned by the effects of consumers on the abundance of their resources. Interestingly, joining the dots appears more difficult than it would suggest: eluding the effect of species interactions on distribution remains one of the greatest challenges to elucidate nowadays (Kissling et al. 2012). Theory suggests that yes, species interactions such as predation and competition should influence range limits (Godsoe et al. 2017), but the common intuition among many biogeographers remains that over large areas such as regions and continents, environmental drivers like temperature and precipitation overwhelm their local effects. Answering this question is of primary importance in the context where species are moving around with climate warming. Inconsistencies in food web structure may arise with asynchronized movements of consumers and their resources, leading to a major disruption in regulation and potentially ecosystem functioning. Solving this problem, however, remains very challenging because we have to rely on observational data since experiments are hard to perform at the biogeographical scale. The study of St-Gelais is an interesting step forward to solve this problem. Their main objective was to assess the strength of the association between phytoplankton and zooplankton communities at a large spatial scale, looking at the spatial covariation of both taxonomic and functional composition. To do so, they undertook a massive survey of more than 100 lakes across three regions of the boreal region of Québec. Species and functional composition were recorded, along with a set of abiotic variables. Classic community ecology at this point. The difficulty they faced was to disentangle the multiple causal relationships involved in the distribution of both trophic levels. Teasing apart bottom-up and top-down forces driving the assembly of plankton communities using observational data is not an easy task. On the one hand, both trophic levels could respond to variations in temperature, nutrient availability and dissolved organic carbon. The interpretation is fairly straightforward if the two levels respond to different factors, but the situation is much more complicated when they do respond similarly. There are potentially three possible underlying scenarios. First, the phyto and zooplankton communities may share the same environmental requirements, thereby generating a joint distribution over gradients such as temperature and nutrient availability. Second, the abiotic environment could drive the distribution of the phytoplankton community, which would then propagate up and influence the distribution of the zooplankton community. Alternatively, the abiotic environment could constrain the distribution of the zooplankton, which could then affect the one of phytoplankton. In addition to all of these factors, St-Gelais et al also consider that dispersal may limit the distribution, well aware of previous studies documenting stronger dispersal limitations for zooplankton communities. Unfortunately, there is not a single statistical approach that could be taken from the shelf and used to elucidate drivers of co-distribution. Joint species distribution was once envisioned as a major step forward in this direction (Warton et al. 2015), but there are several limits preventing the direct interpretation that co-occurrence is linked to interactions (Blanchet et al. 2020). Rather, St-Gelais used a variety of multivariate statistics to reveal the structure in their observational data. First, using a Procrustes analysis (a method testing if the spatial variation of one community is correlated to the structure of another community), they found a significant correlation between phytoplankton and zooplankton communities, indicating a taxonomic coupling between the groups. Interestingly, this observation was maintained for functional composition only when interaction-related traits were considered. At this point, these results strongly suggest that interactions are involved in the correlation, but it's hard to decipher between bottom-up and top-down perspectives. A complementary analysis performed with a constrained ordination, per trophic level, provided complementary pieces of information. First observation was that only functional variation was found to be related to the different environmental variables, not taxonomic variation. Despite that trophic levels responded to water quality variables, spatial autocorrelation was more important for zooplankton communities and the two layers appear to respond to different variables. It is impossible with those results to formulate a strong conclusion about whether grazing influence the co-distribution of phytoplankton and zooplankton communities. That's the mere nature of observational data. While there is a strong spatial association between them, there are also diverging responses to the different environmental variables considered. But the contrast between taxonomic and functional composition is nonetheless informative and it seems that beyond the idiosyncrasies of species composition, trait distribution may be more informative and general. Perhaps the most original contribution of this study is the hierarchical approach to analyze the data, combined with the simultaneous analysis of taxonomic and functional distributions. Having access to a vast catalog of multivariate statistical techniques, a careful selection of analyses helps revealing key features in the data, rejecting some hypotheses and accepting others. Hopefully, we will see more and more of such multi-trophic approaches to distribution because it is now clear that the factors driving distribution are much more complicated than anticipated in more traditional analyses of community data. Biodiversity is more than a species list, it is also all of the interactions between them, influencing their distribution and abundance (Jordano 2016). References Blanchet FG, Cazelles K, Gravel D (2020) Co-occurrence is not evidence of ecological interactions. Ecology Letters, 23, 1050–1063. https://doi.org/10.1111/ele.13525 Godsoe W, Jankowski J, Holt RD, Gravel D (2017) Integrating Biogeography with Contemporary Niche Theory. Trends in Ecology & Evolution, 32, 488–499. https://doi.org/10.1016/j.tree.2017.03.008 Jordano P (2016) Chasing Ecological Interactions. PLOS Biology, 14, e1002559. https://doi.org/10.1371/journal.pbio.1002559 Kissling WD, Dormann CF, Groeneveld J, Hickler T, Kühn I, McInerny GJ, Montoya JM, Römermann C, Schiffers K, Schurr FM, Singer A, Svenning J-C, Zimmermann NE, O’Hara RB (2012) Towards novel approaches to modelling biotic interactions in multispecies assemblages at large spatial extents. Journal of Biogeography, 39, 2163–2178. https://doi.org/10.1111/j.1365-2699.2011.02663.x St-Gelais NF, Vogt RJ, Giorgio PA del, Beisner BE (2021) The taxonomic and functional biogeographies of phytoplankton and zooplankton communities across boreal lakes. bioRxiv, 373332, ver. 4 peer-reviewed and recommended by Peer community in Ecology. https://doi.org/10.1101/373332 Warton DI, Blanchet FG, O’Hara RB, Ovaskainen O, Taskinen S, Walker SC, Hui FKC (2015) So Many Variables: Joint Modeling in Community Ecology. 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However, the influence of such interactions on the biogeographical distribution of the taxa and functional traits of planktonic organ... | ![]() | Biogeography, Community ecology, Species distributions | Dominique Gravel | 2018-07-24 15:01:51 | View |
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