Latest recommendations
Id | Title | Authors | Abstract▲ | Picture | Thematic fields | Recommender | Reviewers | Submission date | |
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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 Bolker based on reviews by Dana Karelus and Ben AugustineAs 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 Schtickzelle based on reviews by 2 anonymous reviewersProposing 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 | ||
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 MackeEcology 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. Trends in Ecology & Evolution, 30, 766–779. https://doi.org/10.1016/j.tree.2015.09.007 Wisz MS, Pottier J, Kissling WD, Pellissier L, Lenoir J, Damgaard CF, Dormann CF, Forchhammer MC, Grytnes J-A, Guisan A, Heikkinen RK, Høye TT, Kühn I, Luoto M, Maiorano L, Nilsson M-C, Normand S, Öckinger E, Schmidt NM, Termansen M, Timmermann A, Wardle DA, Aastrup P, Svenning J-C (2013) The role of biotic interactions in shaping distributions and realised assemblages of species: implications for species distribution modelling. Biological Reviews, 88, 15–30. https://doi.org/10.1111/j.1469-185X.2012.00235.x | The taxonomic and functional biogeographies of phytoplankton and zooplankton communities across boreal lakes | Nicolas F St-Gelais, Richard J Vogt, Paul A del Giorgio, Beatrix E Beisner | <p>Strong trophic interactions link primary producers (phytoplankton) and consumers (zooplankton) in lakes. 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 | ||
31 May 2023
Conservation networks do not match the ecological requirements of amphibiansMatutini Florence, Jacques Baudry, Marie-Josée Fortin, Guillaume Pain, Joséphine Pithon https://doi.org/10.1101/2022.07.18.500425Amphibians under scrutiny - When human-dominated landscape mosaics are not in full compliance with their ecological requirementsRecommended by Sandrine Charles based on reviews by Peter Vermeiren and 1 anonymous reviewerAmong vertebrates, amphibians are one of the most diverse groups with more than 7,000 known species. Amphibians occupy various ecosystems, including forests, wetlands, and freshwater habitats. Amphibians are known to be highly sensitive to changes in their environment, particularly to water quality and habitat degradation, so that monitoring abundance of amphibian populations can provide early warning signs of ecosystem disturbances that may also affect other organisms including humans (Bishop et al., 2012). Accordingly, efforts in habitat preservation and sustainable land and water management are necessary to safeguard amphibian populations. In this context, Matutini et al. (2023) compared ecological requirements of amphibian species with the quality of agricultural landscape mosaics. Doing so, they identified critical gaps in existing conservation tools that include protected areas, green infrastructures, and inventoried sites. Matutini et al. (2023) focused on nine amphibian species in the Pays-de-la-Loire region where the landscape has been fashioned over the years by human activities. Three of the chosen amphibian species are living in a dense hedgerow mosaic landscape, while five others are more generalists. Matutini et al. (2023) established multi-species habitat suitability maps, together with their levels of confidence, by combining single species maps with a probabilistic stacking method at 500-m resolution. From these maps, habitats were classified in five categories, from not suitable to highly suitable. Then, the circuit theory was used to map the potential connections between each highly suitable patch at the regional scale. Finally, comparing suitability maps with existing conservation tools, Matutini et al. (2023) were able to assess their coverage and efficiency. Whatever their species status (endangered or not), Matutini et al. (2023) highlighted some discrepancies between the ecological requirements of amphibians in terms of habitat quality and the conservation tools of the landscape mosaic within which they are evolving. More specifically, Matutini et al. (2023) found that protected areas and inventoried sites covered only a small proportion of highly suitable habitats, while green infrastructures covered around 50% of the potential habitat for amphibian species. Such a lack of coverage and efficiency of protected areas brings to light that geographical sites with amphibian conservation challenges are known but not protected. Regarding the landscape fragmentation, Matutini et al. (2023) found that generalist amphibian species have a more homogeneous distribution of suitable habitats at the regional scale. They also identified two bottlenecks between two areas of suitable habitats, a situation that could prove critical to amphibian movements if amphibians were forced to change habitats to global change. In conclusion, Matutini et al. (2023) bring convincing arguments in support of land-use species-conservation planning based on a better consideration of human-dominated landscape mosaics in full compliance with ecological requirements of the species that inhabit the regions concerned. ReferencesBishop, P.J., Angulo, A., Lewis, J.P., Moore, R.D., Rabb, G.B., Moreno, G., 2012. The Amphibian Extinction Crisis - what will it take to put the action into the Amphibian Conservation Action Plan? Sapiens - Surveys and Perspectives Integrating Environment and Society 5, 1–16. http://journals.openedition.org/sapiens/1406 Matutini, F., Baudry, J., Fortin, M.-J., Pain, G., Pithon, J., 2023. Conservation networks do not match ecological requirements of amphibians. bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2022.07.18.500425 | Conservation networks do not match the ecological requirements of amphibians | Matutini Florence, Jacques Baudry, Marie-Josée Fortin, Guillaume Pain, Joséphine Pithon | <p style="text-align: justify;">1. Amphibians are among the most threatened taxa as they are highly sensitive to habitat degradation and fragmentation. They are considered as model species to evaluate habitats quality in agricultural landscapes. I... | Biodiversity, Biogeography, Human impact, Landscape ecology, Macroecology, Spatial ecology, Metacommunities & Metapopulations, Species distributions, Terrestrial ecology | Sandrine Charles | 2022-09-20 14:40:03 | View | ||
09 Nov 2023
Mark loss can strongly bias estimates of demographic rates in multi-state models: a case study with simulated and empirical datasetsFrédéric Touzalin, Eric J. Petit, Emmanuelle Cam, Claire Stagier, Emma C. Teeling, Sébastien J. Puechmaille https://doi.org/10.1101/2022.03.25.485763Marks lost in action, biased estimationsRecommended by Sylvain Billiard based on reviews by Olivier Gimenez, Devin Johnson and 1 anonymous reviewerCapture-Mark-Recapture (CMR) data are commonly used to estimate ecological variables such as abundance, survival probability, or transition rates from one state to another (e.g. from juvenile to adult, or migration from one site to another). Many studies have shown how estimations can be affected by neglecting one aspect of the population under study (e.g. the heterogeneity in survival between individuals) or one limit of the methodology itself (e.g. the fact that observers might not detect an individual although it is still alive). Strikingly, very few studies have yet assessed the robustness of one fundamental assumption of all CMR-based inferences: marks are supposed definitive and immutable. If they are not, how are estimations affected? Addressing this issue is the main goal of the paper by Touzalin et al. (2023), and they did a very nice work. But, because the answer is not that simple, it also calls for further investigations. When and why would mark loss bias estimation? In at least two situations. First, when estimating survival rates: if an individual loses its mark, it will be considered as dead, hence death rates will be overestimated. Second, more subtly, when estimating transition rates: if one individual loses its mark at the specific moment where its state changes, then a transition will be missed in data. The history of the marked individual would then be split into two independent CMR sequences as if there were two different individuals, including one which died. Touzalin et al. (2023) thoroughly studied these two situations by estimating ecological parameters on 1) well-thought simulated datasets, that cover a large range of possible situations inspired from a nice compilation of hundreds of estimations from fish and bats studies, and 2) on their own bats dataset, for which they had various sources of information about mark losses, i.e. different mark types on the same individuals, including mark based on genotypes, and marks found on the soil in the place where bats lived. Their main findings from the simulated datasets are that there is a general trend for underestimation of survival and transition rates if mark loss is not accounting for in the model, as it would be intuitively expected. However, they also showed from the bats dataset that biases do not show any obvious general trend, suggesting complex interactions between different ecological processes and/or with the estimation procedure itself. The results by Touzalin et al. (2023) strongly suggest that mark loss should systematically be included in models estimating parameters from CMR data. In addition to adapt the inferential models, the authors also recommend considering either a double marking, or even a single but ‘permanent’ mark such as one based on the genotypes. However, the potential gain of a double marking or of the use of genotypes is still to be evaluated both in theory and practice, and it seems to be not that obvious at first sight. First because double marking can be costly for experimenters but also for the marked animals, especially as several studies showed that marks can significantly affect survival or recapture rates. Second because multiple sources of errors can affect genotyping, which would result in wrong individual assignations especially in populations with low genetic diversity or high inbreeding, or no individual assignation at all, which would increase the occurrence of missing data in CMR datasets. Touzalin et al. (2023) supposed in their paper that there were no genotyping errors, but one can doubt it to be true in most situations. They have now important and interesting other issues to address. References Frédéric Touzalin, Eric J. Petit, Emmanuelle Cam, Claire Stagier, Emma C. Teeling, Sébastien J. Puechmaille (2023) Mark loss can strongly bias demographic rates in multi-state models: a case study with simulated and empirical datasets. BioRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2022.03.25.485763 | Mark loss can strongly bias estimates of demographic rates in multi-state models: a case study with simulated and empirical datasets | Frédéric Touzalin, Eric J. Petit, Emmanuelle Cam, Claire Stagier, Emma C. Teeling, Sébastien J. Puechmaille | <p style="text-align: justify;">1. The development of methods for individual identification in wild species and the refinement of Capture-Mark-Recapture (CMR) models over the past few decades have greatly improved the assessment of population demo... | Conservation biology, Demography | Sylvain Billiard | 2022-04-12 18:49:34 | View | ||
19 Feb 2020
Soil variation response is mediated by growth trajectories rather than functional traits in a widespread pioneer Neotropical treeSébastien Levionnois, Niklas Tysklind, Eric Nicolini, Bruno Ferry, Valérie Troispoux, Gilles Le Moguedec, Hélène Morel, Clément Stahl, Sabrina Coste, Henri Caron, Patrick Heuret https://doi.org/10.1101/351197Growth trajectories, better than organ-level functional traits, reveal intraspecific response to environmental variationRecommended by François Munoz based on reviews by Georges Kunstler and François MunozFunctional traits are “morpho-physio-phenological traits which impact fitness indirectly via their effects on growth, reproduction and survival” [1]. Most functional traits are defined at organ level, e.g. for leaves, roots and stems, and reflect key aspects of resource acquisition and resource use by organisms for their development and reproduction [2]. More rarely, some functional traits can be related to spatial development, such as vegetative height and lateral spread in plants. References [1] Violle, C., Navas, M. L., Vile, D., Kazakou, E., Fortunel, C., Hummel, I., & Garnier, E. (2007). Let the concept of trait be functional!. Oikos, 116(5), 882-892. doi: 10.1111/j.0030-1299.2007.15559.x | Soil variation response is mediated by growth trajectories rather than functional traits in a widespread pioneer Neotropical tree | Sébastien Levionnois, Niklas Tysklind, Eric Nicolini, Bruno Ferry, Valérie Troispoux, Gilles Le Moguedec, Hélène Morel, Clément Stahl, Sabrina Coste, Henri Caron, Patrick Heuret | <p style="text-align: justify;">1- Trait-environment relationships have been described at the community level across tree species. However, whether interspecific trait-environment relationships are consistent at the intraspecific level is yet unkn... | Botany, Eco-evolutionary dynamics, Habitat selection, Ontogeny, Tropical ecology | François Munoz | 2018-06-21 17:13:17 | View | ||
02 Dec 2021
Metabarcoding faecal samples to investigate spatiotemporal variation in the diet of the endangered Westland petrel (Procellaria westlandica)Marina Querejeta, Marie-Caroline Lefort, Vincent Bretagnolle, Stéphane Boyer https://doi.org/10.1101/2020.10.30.360289The promise and limits of DNA based approach to infer diet flexibility in endangered top predatorsRecommended by Sophie Arnaud-Haond based on reviews by Francis John Burdon and Babett GüntherThere is growing evidence of worldwide decline of populations of top predators, including marine ones (Heithaus et al, 2008, Mc Cauley et al., 2015), with cascading effects expected at the ecosystem level, due to global change and human activities, including habitat loss or fragmentation, the collapse or the range shifts of their preys. On a global scale, seabirds are among the most threatened group of birds, about one-third of them being considered as threatened or endangered (Votier& Sherley, 2017). The large consequences of the decrease of the populations of preys they feed on (Cury et al, 2011) points diet flexibility as one important element to understand for effective management (McInnes et al, 2017). Nevertheless, morphological inventory of preys requires intrusive protocols, and the differential digestion rate of distinct taxa may lead to a large bias in morphological-based diet assessments. The use of DNA metabarcoding on feces (or diet DNA, dDNA) now allows non-invasive approaches facilitating the recollection of samples and the detection of multiple preys independently of their digestion rates (Deagle et al., 2019). Although no gold standard exists yet to avoid bias associated with metabarcoding (primer bias, gaps in reference databases, inability to differentiate primary from secondary predation…), the use of these recent techniques has already improved the knowledge of the foraging behaviour and diet of many animals (Ando et al., 2020). Both promise and shortcomings of this approach are illustrated in the article “Metabarcoding faecal samples to investigate spatiotemporal variation in the diet of the endangered Westland petrel (Procellaria westlandica)” by Quereteja et al. (2021). In this work, the authors assessed the nature and spatio-temporal flexibility of the foraging behaviour and consequent diet of the endangered petrel Procellaria westlandica from New-Zealand through metabarcoding of faeces samples. The results of this dDNA, non-invasive approach, identify some expected and also unexpected prey items, some of which require further investigation likely due to large gaps in the reference databases. They also reveal the temporal (before and after hatching) and spatial (across colonies only 1.5km apart) flexibility of the foraging behaviour, additionally suggesting a possible influence of fisheries activities in the surroundings of the colonies. This study thus both underlines the power of the non-invasive metabarcoding approach on faeces, and the important results such analysis can deliver for conservation, pointing a potential for diet flexibility that may be essential for the resilience of this iconic yet endangered species. References Ando H, Mukai H, Komura T, Dewi T, Ando M, Isagi Y (2020) Methodological trends and perspectives of animal dietary studies by noninvasive fecal DNA metabarcoding. Environmental DNA, 2, 391–406. https://doi.org/10.1002/edn3.117 Cury PM, Boyd IL, Bonhommeau S, Anker-Nilssen T, Crawford RJM, Furness RW, Mills JA, Murphy EJ, Österblom H, Paleczny M, Piatt JF, Roux J-P, Shannon L, Sydeman WJ (2011) Global Seabird Response to Forage Fish Depletion—One-Third for the Birds. Science, 334, 1703–1706. https://doi.org/10.1126/science.1212928 Deagle BE, Thomas AC, McInnes JC, Clarke LJ, Vesterinen EJ, Clare EL, Kartzinel TR, Eveson JP (2019) Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data? Molecular Ecology, 28, 391–406. https://doi.org/10.1111/mec.14734 Heithaus MR, Frid A, Wirsing AJ, Worm B (2008) Predicting ecological consequences of marine top predator declines. Trends in Ecology & Evolution, 23, 202–210. https://doi.org/10.1016/j.tree.2008.01.003 McCauley DJ, Pinsky ML, Palumbi SR, Estes JA, Joyce FH, Warner RR (2015) Marine defaunation: Animal loss in the global ocean. Science, 347, 1255641. https://doi.org/10.1126/science.1255641 McInnes JC, Jarman SN, Lea M-A, Raymond B, Deagle BE, Phillips RA, Catry P, Stanworth A, Weimerskirch H, Kusch A, Gras M, Cherel Y, Maschette D, Alderman R (2017) DNA Metabarcoding as a Marine Conservation and Management Tool: A Circumpolar Examination of Fishery Discards in the Diet of Threatened Albatrosses. Frontiers in Marine Science, 4, 277. https://doi.org/10.3389/fmars.2017.00277 Querejeta M, Lefort M-C, Bretagnolle V, Boyer S (2021) Metabarcoding faecal samples to investigate spatiotemporal variation in the diet of the endangered Westland petrel (Procellaria westlandica). bioRxiv, 2020.10.30.360289, ver. 4 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2020.10.30.360289 Votier SC, Sherley RB (2017) Seabirds. Current Biology, 27, R448–R450. https://doi.org/10.1016/j.cub.2017.01.042 | Metabarcoding faecal samples to investigate spatiotemporal variation in the diet of the endangered Westland petrel (Procellaria westlandica) | Marina Querejeta, Marie-Caroline Lefort, Vincent Bretagnolle, Stéphane Boyer | <p style="text-align: justify;">As top predators, seabirds can be indirectly impacted by climate variability and commercial fishing activities through changes in marine communities. However, high mobility and foraging behaviour enables seabirds to... | Conservation biology, Food webs, Marine ecology, Molecular ecology | Sophie Arnaud-Haond | 2020-10-30 20:14:50 | View | ||
22 Apr 2021
The hidden side of the Allee effect: correlated demographic traits and extinction risk in experimental populationsVercken Elodie, Groussier Géraldine, Lamy Laurent, Mailleret Ludovic https://hal.archives-ouvertes.fr/hal-02570868Allee effects under the magnifying glassRecommended by David Alonso based on reviews by Tom Van Dooren, Dani Oro and 1 anonymous reviewerFor decades, the effect of population density on individual performance has been studied by ecologists using both theoretical, observational, and experimental approaches. The generally accepted definition of the Allee effect is a positive correlation between population density and average individual fitness that occurs at low population densities, while individual fitness is typically decreased through intraspecific competition for resources at high population densities. Allee effects are very relevant in conservation biology because species at low population densities would then be subjected to much higher extinction risks. However, due to all kinds of stochasticity, low population numbers are always more vulnerable to extinction than larger population sizes. This effect by itself cannot be necessarily ascribed to lower individual performance at low densities, i.e, Allee effects. Vercken and colleagues (2021) address this challenging question and measure the extent to which average individual fitness is affected by population density analyzing 30 experimental populations. As a model system, they use populations of parasitoid wasps of the genus Trichogramma. They report Allee effect in 8 out 30 experimental populations. Vercken and colleagues's work has several strengths. First of all, it is nice to see that they put theory at work. This is a very productive way of using theory in ecology. As a starting point, they look at what simple theoretical population models say about Allee effects (Lewis and Kareiva 1993; Amarasekare 1998; Boukal and Berec 2002). These models invariably predict a one-humped relation between population-density and per-capita growth rate. It is important to remark that pure logistic growth, the paradigm of density-dependence, would never predict such qualitative behavior. It is only when there is a depression of per-capita growth rates at low densities that true Allee effects arise. Second, these authors manage to not only experimentally test this main prediction but also report additional demographic traits that are consistently affected by population density. In these wasps, individual performance can be measured in terms of the average number of individuals every adult is able to put into the next generation ---the lambda parameter in their analysis. The first panel in figure 3 shows that the per-capita growth rates are lower in populations presenting Allee effects, the ones showing a one-humped behavior in the relation between per-capita growth rates and population densities (see figure 2). Also other population traits, such maximum population size and exitinction probability, change in a correlated and consistent manner. In sum, Vercken and colleagues's results are experimentally solid and based on theory expectations. However, they are very intriguing. They find the signature of Allee effects in only 8 out 30 populations, all from the same genus Trichogramma, and some populations belonging to the same species (from different sampling sites) do not show consistently Allee effects. Where does this population variability comes from? What are the reasons underlying this within- and between-species variability? What are the individual mechanisms driving Allee effects in these populations? Good enough, this piece of work generates more intriguing questions than the question is able to clearly answer. Science is not a collection of final answers but instead good questions are the ones that make science progress. References Amarasekare P (1998) Allee Effects in Metapopulation Dynamics. The American Naturalist, 152, 298–302. https://doi.org/10.1086/286169 Boukal DS, Berec L (2002) Single-species Models of the Allee Effect: Extinction Boundaries, Sex Ratios and Mate Encounters. Journal of Theoretical Biology, 218, 375–394. https://doi.org/10.1006/jtbi.2002.3084 Lewis MA, Kareiva P (1993) Allee Dynamics and the Spread of Invading Organisms. Theoretical Population Biology, 43, 141–158. https://doi.org/10.1006/tpbi.1993.1007 Vercken E, Groussier G, Lamy L, Mailleret L (2021) The hidden side of the Allee effect: correlated demographic traits and extinction risk in experimental populations. HAL, hal-02570868, ver. 4 peer-reviewed and recommended by Peer community in Ecology. https://hal.archives-ouvertes.fr/hal-02570868 | The hidden side of the Allee effect: correlated demographic traits and extinction risk in experimental populations | Vercken Elodie, Groussier Géraldine, Lamy Laurent, Mailleret Ludovic | <p style="text-align: justify;">Because Allee effects (i.e., the presence of positive density-dependence at low population size or density) have major impacts on the dynamics of small populations, they are routinely included in demographic models ... | Demography, Experimental ecology, Population ecology | David Alonso | 2020-09-30 16:38:29 | View | ||
04 May 2021
Are the more flexible great-tailed grackles also better at behavioral inhibition?Logan CJ, McCune KB, MacPherson M, Johnson-Ulrich Z, Rowney C, Seitz B, Blaisdell AP, Deffner D, Wascher CAF https://doi.org/10.31234/osf.io/vpc39Great-tailed grackle research reveals need for researchers to consider their own flexibility and test limitations in cognitive test batteries.Recommended by Aliza le Roux based on reviews by Pizza Ka Yee Chow and Alex DeCasianIn the article, "Are the more flexible great-tailed grackles also better at behavioral inhibition?", Logan and colleagues (2021) are setting an excellent standard for cognitive research on wild-caught animals. Using a decent sample (N=18) of wild-caught birds, they set out to test the ambiguous link between behavioral flexibility and behavioral inhibition, which is supported by some studies but rejected by others. Where this study is more thorough and therefore also more revealing than most extant research, the authors ran a battery of tests, examining both flexibility (reversal learning and solution switching) and inhibition (go/no go task; detour task; delay of gratification) through multiple different test series. They also -- somewhat accidentally -- performed their experiments and analyses with and without different criteria for correctness (85%, 100%). Their mistakes, assumptions and amendments of plans made during preregistration are clearly stated and this demonstrates the thought-process of the researchers very clearly. Logan et al. (2021) show that inhibition in great-tailed grackles is a multi-faceted construct, and demonstrate that the traditional go/no go task likely tests a very different aspect of inhibition than the detour task, which was never linked to any of their flexibility measures. Their comprehensive Bayesian analyses held up the results of some of the frequentist statistics, indicating a consistent relationship between flexibility and inhibition, with more flexible individuals also showing better inhibition (in the go/no go task). This same model, combined with inconsistencies in the GLM analyses (depending on the inclusion or exclusion of an outlier), led them to recommend caution in the creation of arbitrary thresholds for "success" in any cognitive tasks. Their accidental longer-term data collection also hinted at patterns of behaviour that shorter-term data collection did not. Of course, researchers have to decide on success criteria in order to conduct experiments, but in the same way that frequentist statistics are acknowledged to have flaws, the setting of success criteria must be acknowledged as inherently arbitrary. Where possible, researchers could reveal novel, biologically salient patterns by continuing beyond the point where a convenient success criterion has been reached. This research also underscores that tests may not be examining the features we expected them to measure, and are highly sensitive to biological and ecological variation between species as well as individual variation within populations. To me, this study is an excellent argument for pre-registration of research (registered as Logan et al. 2019 and accepted by Vogel 2019), as the authors did not end up cherry-picking only those results or methods that worked. The fact that some of the tests did not "work", but was still examined, added much value to the study. The current paper is a bit densely written because of the comprehensiveness of the research. Some editorial polishing would likely make for more elegant writing. However, the arguments are clear, the results novel, and the questions thoroughly examined. The results are important not only for cognitive research on birds, but are potentially valuable to any cognitive scientist. I recommend this article as excellent food for thought. References Logan CJ, McCune K, Johnson-Ulrich Z, Bergeron L, Seitz B, Blaisdell AP, Wascher CAF. (2019) Are the more flexible individuals also better at inhibition? http://corinalogan.com/Preregistrations/g_inhibition.html In principle acceptance by PCI Ecology of the version on 6 Mar 2019 Logan CJ, McCune KB, MacPherson M, Johnson-Ulrich Z, Rowney C, Seitz B, Blaisdell AP, Deffner D, Wascher CAF (2021) Are the more flexible great-tailed grackles also better at behavioral inhibition? PsyArXiv, ver. 7 peer-reviewed and recommended by Peer community in Ecology. https://doi.org/10.31234/osf.io/vpc39 Vogel E (2019) Adapting to a changing environment: advancing our understanding of the mechanisms that lead to behavioral flexibility. Peer Community in Ecology, 100016. https://doi.org/10.24072/pci.ecology.100016 | Are the more flexible great-tailed grackles also better at behavioral inhibition? | Logan CJ, McCune KB, MacPherson M, Johnson-Ulrich Z, Rowney C, Seitz B, Blaisdell AP, Deffner D, Wascher CAF | <p style="text-align: justify;">Behavioral flexibility (hereafter, flexibility) should theoretically be positively related to behavioral inhibition (hereafter, inhibition) because one should need to inhibit a previously learned behavior to change ... | Preregistrations | Aliza le Roux | 2020-12-04 13:57:07 | View | ||
15 May 2023
Behavioral flexibility is manipulable and it improves flexibility and innovativeness in a new contextLogan CJ, Lukas D, Blaisdell AP, Johnson-Ulrich Z, MacPherson M, Seitz BM, Sevchik A, McCune KB https://doi.org/10.32942/osf.io/5z8xsAn experiment to improve our understanding of the link between behavioral flexibility and innovativenessRecommended by Aurélie Coulon based on reviews by Maxime Dahirel, Andrea Griffin, Aliza le Roux and 1 anonymous reviewerWhether individuals are able to cope with new environmental conditions, and whether this ability can be improved, is certainly of great interest in our changing world. One way to cope with new conditions is through behavioral flexibility, which can be defined as “the ability to adapt behavior to new circumstances through packaging information and making it available to other cognitive processes” (Logan et al. 2023). Flexibility is predicted to be positively correlated with innovativeness, the ability to create a new behavior or use an existing behavior in a few situations (Griffin & Guez 2014). Coulon A (2019) Can context changes improve behavioral flexibility? Towards a better understanding of species adaptability to environmental changes. Peer Community in Ecology, 100019. https://doi.org/10.24072/pci.ecology.100019 Griffin, A. S., & Guez, D. (2014). Innovation and problem solving: A review of common mechanisms. Behavioural Processes, 109, 121–134. https://doi.org/10.1016/j.beproc.2014.08.027 Logan C, Rowney C, Bergeron L, Seitz B, Blaisdell A, Johnson-Ulrich Z, McCune K (2019) Logan CJ, Lukas D, Blaisdell AP, Johnson-Ulrich Z, MacPherson M, Seitz B, Sevchik A, McCune KB (2023) Behavioral flexibility is manipulable and it improves flexibility and innovativeness in a new context. EcoEcoRxiv, version 5 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.32942/osf.io/5z8xs | Behavioral flexibility is manipulable and it improves flexibility and innovativeness in a new context | Logan CJ, Lukas D, Blaisdell AP, Johnson-Ulrich Z, MacPherson M, Seitz BM, Sevchik A, McCune KB | <p style="text-align: justify;">Behavioral flexibility, the ability to adapt behavior to new circumstances, is thought to play an important role in a species’ ability to successfully adapt to new environments and expand its geographic range. Howev... | Behaviour & Ethology, Preregistrations, Zoology | Aurélie Coulon | 2022-01-13 19:08:52 | View |
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