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Id | Title * ▲ | Authors * | Abstract * | Picture * | Thematic fields * | Recommender | Reviewers | Submission date | |
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15 Jun 2020
![]() Investigating the rare behavior of male parental care in great-tailed gracklesFolsom MA, MacPherson M, Lukas D, McCune KB, Bergeron L, Bond A, Blackwell A, Rowney C, Logan CJ https://github.com/corinalogan/grackles/blob/master/Files/Preregistrations/gmalecare.RmdStudying a rare behavior in a polygamous bird: male parental care in great-tailed gracklesRecommended by Marie-Jeanne Holveck based on reviews by Matthieu Paquet and André C FerreiraThe Great-tailed grackle (Quiscalus mexicanus) is a polygamous bird species that is originating from Central America and rapidly expanding its geographic range toward the North, and in which females were long thought to be the sole nest builders and caretakers of the young. In their pre-registration [1], Folsom and collaborators report repeated occurrences of male parental care and develop hypotheses aiming at better understanding the occurrence and the fitness consequences of this very rarely observed male behavior. They propose to assess if male parental care correlates with the circulating levels of several relevant hormones, increases offspring survival, is a local adaptation, and is a mating strategy, in surveying three populations located in Arizona (middle of the geographic range expansion), California (northern edge of the geographic range), and in Central America (core of the range). This study is part of a 5-year bigger project. References [1] Folsom MA, MacPherson M, Lukas D, McCune KB, Bergeron L, Bond A, Blackwell A, Rowney C, Logan CJ. 2020. Investigating the rare behavior of male parental care in great-tailed grackles. corinalogan.com/Preregistrations/gmalecare.html In principle acceptance by PCI Ecology of the version on 15 June 2020 corinalogan/grackles/blob/master/Files/Preregistrations/gmalecare.Rmd. | Investigating the rare behavior of male parental care in great-tailed grackles | Folsom MA, MacPherson M, Lukas D, McCune KB, Bergeron L, Bond A, Blackwell A, Rowney C, Logan CJ | This is a PREREGISTRATION submitted for pre-study peer review. Our planned data collection START DATE is May 2020, therefore it would be ideal if the peer review process could be completed before then. Abstract: Great-tailed grackles (Quiscalus... | ![]() | Behaviour & Ethology, Biological invasions, Preregistrations, Zoology | Marie-Jeanne Holveck | 2019-12-05 17:38:47 | View | |
12 Oct 2019
Investigating the use of learning mechanisms in a species that is rapidly expanding its geographic rangeKelsey McCune, Richard McElreath, Corina Logan http://corinalogan.com/Preregistrations/g_sociallearning.htmlHow would variation in environmental predictability affect the use of different learning mechanisms in a social bird?Recommended by Aliza le Roux based on reviews by Matthew Petelle and 1 anonymous reviewerIn their pre-registered paper [1], McCune and colleagues propose a field-based study of social versus individual learning mechanisms in an avian species (great-tailed grackles) that has been expanding its geographic range. The study forms part of a longer-term project that addresses various aspects of this species’ behaviour and biology, and the experience of the team is clear from the preprint. Assessing variation in learning mechanisms in different sections of the grackles’ distribution range, the researchers will investigate how individual learning and social transmission may impact learning about novel challenges in the environment. Considering that this is a social species, the authors expect both individual learning and social transmission to occur, when groups of grackles encounter new challenges/ opportunities in the wild. This in itself is not a very unusual idea to test [2, 3], but the authors are rigorously distinguishing between imitation, emulation, local enhancement, and social enhancement. Such rigour is certainly valuable in studies of cognition in the wild. References [1] McCune, K. B., McElreath, R., and Logan, C. J. (2019). Investigating the use of learning mechanisms in a species that is rapidly expanding its geographic range. In principle recommendation by Peer Community In Ecology. corinalogan.com/Preregistrations/g_sociallearning.html | Investigating the use of learning mechanisms in a species that is rapidly expanding its geographic range | Kelsey McCune, Richard McElreath, Corina Logan | This is one of many studies planned for our long-term research on the role of behavior and learning in rapid geographic range expansions. Project background: Behavioral flexibility, the ability to change behavior when circumstances change based on... | Behaviour & Ethology, Eco-evolutionary dynamics, Foraging, Preregistrations, Social structure, Spatial ecology, Metacommunities & Metapopulations, Zoology | Aliza le Roux | 2019-07-23 18:45:20 | View | ||
26 Mar 2019
Is behavioral flexibility linked with exploration, but not boldness, persistence, or motor diversity?Kelsey McCune, Carolyn Rowney, Luisa Bergeron, Corina Logan http://corinalogan.com/Preregistrations/g_exploration.htmlProbing behaviors correlated with behavioral flexibilityRecommended by Jeremy Van CleveBehavioral plasticity, which is a subset of phenotypic plasticity, is an important component of foraging, defense against predators, mating, and many other behaviors. More specifically, behavioral flexibility, in this study, captures how quickly individuals adapt to new circumstances. In cases where individuals disperse to new environments, which often occurs in range expansions, behavioral flexibility is likely crucial to the chance that individuals can establish in these environments. Thus, it is important to understand how best to measure behavioral flexibility and how measures of such flexibility might vary across individuals and behavioral contexts and with other measures of learning and problem solving. | Is behavioral flexibility linked with exploration, but not boldness, persistence, or motor diversity? | Kelsey McCune, Carolyn Rowney, Luisa Bergeron, Corina Logan | This is a PREREGISTRATION. The DOI was issued by OSF and refers to the whole GitHub repository, which contains multiple files. The specific file we are submitting is g_exploration.Rmd, which is easily accessible at GitHub at https://github.com/cor... | Behaviour & Ethology, Preregistrations, Zoology | Jeremy Van Cleve | 2018-09-27 03:35:12 | View | ||
26 Mar 2019
Is behavioral flexibility manipulatable and, if so, does it improve flexibility and problem solving in a new context?Corina Logan, Carolyn Rowney, Luisa Bergeron, Benjamin Seitz, Aaron Blaisdell, Zoe Johnson-Ulrich, Kelsey McCune http://corinalogan.com/Preregistrations/g_flexmanip.htmlCan context changes improve behavioral flexibility? Towards a better understanding of species adaptability to environmental changesRecommended by Aurélie CoulonBehavioral flexibility is a key for species adaptation to new environments. Predicting species responses to new contexts hence requires knowledge on the amount to and conditions in which behavior can be flexible. This is what Logan and collaborators propose to assess in a series of experiments on the great-tailed grackles, in a context of rapid range expansion. This pre-registration is integrated into this large research project and concerns more specifically the manipulability of the cognitive aspects of behavioral flexibility. Logan and collaborators will use reversal learning tests to test whether (i) behavioral flexibility is manipulatable, (ii) manipulating flexibility improves flexibility and problem solving in a new context, (iii) flexibility is repeatable within individuals, (iv) individuals are faster at problem solving as they progress through serial reversals. The pre-registration carefully details the hypotheses, their associated predictions and alternatives, and the plan of statistical analyses, including power tests. The ambitious program presented in this pre-registration has the potential to provide important pieces to better understand the mechanisms of species adaptability to new environments. | Is behavioral flexibility manipulatable and, if so, does it improve flexibility and problem solving in a new context? | Corina Logan, Carolyn Rowney, Luisa Bergeron, Benjamin Seitz, Aaron Blaisdell, Zoe Johnson-Ulrich, Kelsey McCune | This is one of the first studies planned for our long-term research on the role of behavioral flexibility in rapid geographic range expansions. Behavioral flexibility, the ability to adapt behavior to new circumstances, is thought to play an impor... | Behaviour & Ethology, Preregistrations, Zoology | Aurélie Coulon | 2018-07-03 13:23:10 | View | ||
07 Aug 2019
Is behavioral flexibility related to foraging and social behavior in a rapidly expanding species?Corina Logan, Luisa Bergeron, Carolyn Rowney, Kelsey McCune, Dieter Lukas http://corinalogan.com/Preregistrations/g_flexforaging.htmlUnderstanding geographic range expansions in human-dominated landscapes: does behavioral flexibility modulate flexibility in foraging and social behavior?Recommended by Julia AstegianoWhich biological traits modulate species distribution has historically been and still is one of the core questions of the macroecology and biogeography agenda [1, 2]. As most of the Earth surface has been modified by human activities [3] understanding the strategies that allow species to inhabit human-dominated landscapes will be key to explain species geographic distribution in the Anthropocene. In this vein, Logan et al. [4] are working on a long-term and integrative project aimed to investigate how great-tailed grackles rapidly expanded their geographic range into North America [4]. Particularly, they want to determine which is the role of behavioral flexibility, i.e. an individual’s ability to modify its behavior when circumstances change based on learning from previous experience [5], in rapid geographic range expansions. The authors are already working in a set of complementary questions described in pre-registrations that have already been recommended at PCI Ecology: (1) Do individuals with greater behavioral flexibility rely more on causal cognition [6]? (2) Which are the mechanisms that lead to behavioral flexibility [7]? (3) Does the manipulation of behavioral flexibility affect exploration, but not boldness, persistence, or motor diversity [8]? (4) Can context changes improve behavioral flexibility [9]? References [1] Gaston K. J. (2003) The structure and dynamics of geographic ranges. Oxford series in Ecology and Evolution. Oxford University Press, New York. | Is behavioral flexibility related to foraging and social behavior in a rapidly expanding species? | Corina Logan, Luisa Bergeron, Carolyn Rowney, Kelsey McCune, Dieter Lukas | This is one of the first studies planned for our long-term research on the role of behavioral flexibility in rapid geographic range expansions. Project background: Behavioral flexibility, the ability to change behavior when circumstances change ba... | Behaviour & Ethology, Preregistrations, Zoology | Julia Astegiano | 2018-10-23 00:47:03 | View | ||
27 Apr 2021
![]() Joint species distributions reveal the combined effects of host plants, abiotic factors and species competition as drivers of species abundances in fruit fliesBenoit Facon, Abir Hafsi, Maud Charlery de la Masselière, Stéphane Robin, François Massol, Maxime Dubart, Julien Chiquet, Enric Frago, Frédéric Chiroleu, Pierre-François Duyck & Virginie Ravigné https://doi.org/10.1101/2020.12.07.414326Understanding the interplay between host-specificity, environmental conditions and competition through the sound application of Joint Species Distribution ModelsRecommended by Joaquín HortalUnderstanding why and how species coexist in local communities is one of the central questions in ecology. There is general agreement that species distribution and coexistence are determined by a number of key mechanisms, including the environmental requirements of species, dispersal, evolutionary constraints, resource availability and selection, metapopulation dynamics, and biotic interactions (e.g. Soberón & Nakamura 2009; Colwell & Rangel 2009; Ricklefs 2015). These factors are however intricately intertwined in a scale-structured fashion (Hortal et al. 2010; D’Amen et al. 2017), making it particularly difficult to tease apart the effects of each one of them. This could be addressed by the novel field of Joint Species Distribution Modelling (JSDM; Okasvainen & Abrego 2020), as it allows assessing the effects of several sets of factors and the co-occurrence and/or covariation in abundances of potentially interacting species at the same time (Pollock et al. 2014; Ovaskainen et al. 2016; Dormann et al. 2018). However, the development of JSDM has been hampered by the general lack of good-quality detailed data on species co-occurrences and abundances (see Hortal et al. 2015). Facon et al. (2021) use a particularly large compilation of field surveys to study the abundance and co-occurrence of Tephritidae fruit flies in c. 400 orchards, gardens and natural areas throughout the island of Réunion. Further, they combine such information with lab data on their host-selection fundamental niche (i.e. in the absence of competitors), codifying traits of female choice and larval performances in 21 host species. They use Poisson Log-Normal models, a type of mixed model that allows one to jointly model the random effects associated with all species, and retrieve the covariations in abundance that are not explained by environmental conditions or differences in sampling effort. Then, they use a series of models to evaluate the effects on these matrices of ecological covariates (date, elevation, habitat, climate and host plant), species interactions (by comparing with a constrained residual variance-covariance matrix) and the species’ host-selection fundamental niches (through separate models for each fly species). The eight Tephritidae species inhabiting Réunion include both generalists and specialists in Solanaceae and Cucurbitaceae with a known history of interspecific competition. Facon et al. (2021) use a comprehensive JSDM approach to assess the effects of different factors separately and altogether. This allows them to identify large effects of plant hosts and the fundamental host-selection niche on species co-occurrence, but also to show that ecological covariates and weak –though not negligible– species interactions are necessary to account for all residual variance in the matrix of joint species abundances per site. Further, they also find evidence that the fitness per host measured in the lab has a strong influence on the abundances in each host plant in the field for specialist species, but not for generalists. Indeed, the stronger effects of competitive exclusion were found in pairs of Cucurbitaceae specialist species. However, these analyses fail to provide solid grounds to assess why generalists are rarely found in Cucurbitaceae and Solanaceae. Although they argue that this may be due to Connell’s (1980) ghost of competition past (past competition that led to current niche differentiation), further data on the evolutionary history of these fruit flies is needed to assess this hypothesis. Finding evidence for the effects of competitive interactions on species’ occurrences and spatial distributions is often difficult, perhaps because these effects occur over longer time scales than the ones usually studied by ecologists (Yackulic 2017). The work by Facon and colleagues shows that weak effects of competition can be detected also at the short ecological timescales that determine coexistence in local communities, under the virtuous combination of good-quality data and sound analytical designs that account for several aspects of species’ niches, their biotopes and their joint population responses. This adds a new dimension to the application of Hutchinson’s (1978) niche framework to understand the spatial dynamics of species and communities (see also Colwell & Rangel 2009), although further advances to incorporate dispersal-driven metacommunity dynamics (see, e.g., Ovaskainen et al. 2016; Leibold et al. 2017) are certainly needed. Nonetheless, this work shows the potential value of in-depth analyses of species coexistence based on combining good-quality field data with well-thought out JSDM applications. If many studies like this are conducted, it is likely that the uprising field of Joint Species Distribution Modelling will improve our understanding of the hierarchical relationships between the different factors affecting species coexistence in ecological communities in the near future.
References Colwell RK, Rangel TF (2009) Hutchinson’s duality: The once and future niche. Proceedings of the National Academy of Sciences, 106, 19651–19658. https://doi.org/10.1073/pnas.0901650106 Connell JH (1980) Diversity and the Coevolution of Competitors, or the Ghost of Competition Past. Oikos, 35, 131–138. https://doi.org/10.2307/3544421 D’Amen M, Rahbek C, Zimmermann NE, Guisan A (2017) Spatial predictions at the community level: from current approaches to future frameworks. Biological Reviews, 92, 169–187. https://doi.org/10.1111/brv.12222 Dormann CF, Bobrowski M, Dehling DM, Harris DJ, Hartig F, Lischke H, Moretti MD, Pagel J, Pinkert S, Schleuning M, Schmidt SI, Sheppard CS, Steinbauer MJ, Zeuss D, Kraan C (2018) Biotic interactions in species distribution modelling: 10 questions to guide interpretation and avoid false conclusions. Global Ecology and Biogeography, 27, 1004–1016. https://doi.org/10.1111/geb.12759 Facon B, Hafsi A, Masselière MC de la, Robin S, Massol F, Dubart M, Chiquet J, Frago E, Chiroleu F, Duyck P-F, Ravigné V (2021) Joint species distributions reveal the combined effects of host plants, abiotic factors and species competition as drivers of community structure in fruit flies. bioRxiv, 2020.12.07.414326. ver. 4 peer-reviewed and recommended by Peer community in Ecology. https://doi.org/10.1101/2020.12.07.414326 Hortal J, de Bello F, Diniz-Filho JAF, Lewinsohn TM, Lobo JM, Ladle RJ (2015) Seven Shortfalls that Beset Large-Scale Knowledge of Biodiversity. Annual Review of Ecology, Evolution, and Systematics, 46, 523–549. https://doi.org/10.1146/annurev-ecolsys-112414-054400 Hortal J, Roura‐Pascual N, Sanders NJ, Rahbek C (2010) Understanding (insect) species distributions across spatial scales. Ecography, 33, 51–53. https://doi.org/10.1111/j.1600-0587.2009.06428.x Hutchinson, G.E. (1978) An introduction to population biology. Yale University Press, New Haven, CT. Leibold MA, Chase JM, Ernest SKM (2017) Community assembly and the functioning of ecosystems: how metacommunity processes alter ecosystems attributes. Ecology, 98, 909–919. https://doi.org/10.1002/ecy.1697 Ovaskainen O, Abrego N (2020) Joint Species Distribution Modelling: With Applications in R. Cambridge University Press, Cambridge. https://doi.org/10.1017/9781108591720 Ovaskainen O, Roy DB, Fox R, Anderson BJ (2016) Uncovering hidden spatial structure in species communities with spatially explicit joint species distribution models. Methods in Ecology and Evolution, 7, 428–436. https://doi.org/10.1111/2041-210X.12502 Pollock LJ, Tingley R, Morris WK, Golding N, O’Hara RB, Parris KM, Vesk PA, McCarthy MA (2014) Understanding co-occurrence by modelling species simultaneously with a Joint Species Distribution Model (JSDM). Methods in Ecology and Evolution, 5, 397–406. https://doi.org/10.1111/2041-210X.12180 Ricklefs RE (2015) Intrinsic dynamics of the regional community. Ecology Letters, 18, 497–503. https://doi.org/10.1111/ele.12431 Soberón J, Nakamura M (2009) Niches and distributional areas: Concepts, methods, and assumptions. Proceedings of the National Academy of Sciences, 106, 19644–19650. https://doi.org/10.1073/pnas.0901637106 Yackulic CB (2017) Competitive exclusion over broad spatial extents is a slow process: evidence and implications for species distribution modeling. Ecography, 40, 305–313. https://doi.org/10.1111/ecog.02836 | Joint species distributions reveal the combined effects of host plants, abiotic factors and species competition as drivers of species abundances in fruit flies | Benoit Facon, Abir Hafsi, Maud Charlery de la Masselière, Stéphane Robin, François Massol, Maxime Dubart, Julien Chiquet, Enric Frago, Frédéric Chiroleu, Pierre-François Duyck & Virginie Ravigné | <p style="text-align: justify;">The relative importance of ecological factors and species interactions for phytophagous insect species distributions has long been a controversial issue. Using field abundances of eight sympatric Tephritid fruit fli... | ![]() | Biodiversity, Coexistence, Community ecology, Competition, Herbivory, Interaction networks, Species distributions | Joaquín Hortal | Carsten Dormann, Joaquín Calatayud | 2020-12-08 06:44:25 | View |
05 Apr 2022
![]() Late-acting self-incompatible system, preferential allogamy and delayed selfing in the heterostylous invasive populations of Ludwigia grandiflora subsp. hexapetalaLuis O. Portillo Lemus, Maryline Harang, Michel Bozec, Jacques Haury, Solenn Stoeckel, Dominique Barloy https://doi.org/10.1101/2021.07.15.452457Water primerose (Ludwigia grandiflora subsp. hexapetala) auto- and allogamy: an ecological perspectiveRecommended by Antoine VernayInvasive plant species are widely studied by the ecologist community, especially in wetlands. Indeed, alien plants are considered one of the major threats to wetland biodiversity (Reid et al., 2019). Ludwigia grandiflora subsp. hexapetala (Hook. & Arn.) G.L.Nesom & Kartesz, 2000 (Lgh) is one of them and has received particular attention for a long time (Hieda et al., 2020; Thouvenot, Haury, & Thiebaut, 2013). The ecology of this invasive species and its effect on its biotic and abiotic environment has been studied in previous works. Different processes were demonstrated to explain their invasibility such as allelopathic interference (Dandelot et al., 2008), resource competition (Gérard et al., 2014), and high phenotypic plasticity (Thouvenot, Haury, & Thiébaut, 2013), to cite a few of them. However, although vegetative reproduction is a well-known invasive process for alien plants like Lgh (Glover et al., 2015), the sexual reproduction of this species is still unclear and may help to understand the Lgh population dynamics. Portillo Lemus et al. (2021) showed that two floral morphs of Lgh co-exist in natura, involving self-compatibility for short-styled phenotype and self-incompatibility for long-styled phenotype processes. This new article (Portillo Lemus et al., 2022) goes further and details the underlying mechanisms of the sexual reproduction of the two floral morphs. Complementing their previous study, the authors have described a late self-incompatible process associated with the long-styled morph, which authorized a small proportion of autogamy. Although this represents a small fraction of the L-morph reproduction, it may have a considerable impact on the L-morph population dynamics. Indeed, authors report that “floral morphs are mostly found in allopatric monomorphic populations (i.e., exclusively S-morph or exclusively L-morph populations)” with a large proportion of L-morph populations compared to S-morph populations in the field. It may seem counterintuitive as L-morph mainly relies on cross-fecundation. Results show that L-morph autogamy mainly occurs in the fall, late in the reproduction season. Therefore, the reproduction may be ensured if no exogenous pollen reaches the stigma of L-morph individuals. It partly explains the large proportion of L-morph populations in the field. Beyond the description of late-acting self-incompatibility, which makes the Onagraceae a third family of Myrtales with this reproductive adaptation, the study raises several ecological questions linked to the results presented in the article. First, it seems that even if autogamy is possible, Lgh would favour allogamy, even in S-morph, through the faster development of pollen tubes from other individuals. This may confer an adaptative and evolutive advantage for the Lgh, increasing its invasive potential. The article shows this faster pollen tube development in S-morph but does not test the evolutive consequences. It is an interesting perspective for future research. It would also be interesting to describe cellular processes which recognize and then influence the speed of the pollen tube. Second, the importance of sexual reproduction vs vegetative reproduction would also provide information on the benefits of sexual dimorphism within populations. For instance, how fruit production increases the dispersal potential of Lgh would help to understand Lgh population dynamics and to propose adapted management practices (Delbart et al., 2013; Meisler, 2009). To conclude, the study proposes a morphological, reproductive and physiological description of the Lgh sexual reproduction process. However, underlying ecological questions are well included in the article and the ecophysiological results enlighten some questions about the role of sexual reproduction in the invasiveness of Lgh. I advise the reader to pay attention to the reviewers’ comments; the debates were very constructive and, thanks to the great collaboration with the authorship, lead to an interesting paper about Lgh reproduction and with promising perspectives in ecology and invasion ecology. References Dandelot S, Robles C, Pech N, Cazaubon A, Verlaque R (2008) Allelopathic potential of two invasive alien Ludwigia spp. Aquatic Botany, 88, 311–316. https://doi.org/10.1016/j.aquabot.2007.12.004 Delbart E, Mahy G, Monty A (2013) Efficacité des méthodes de lutte contre le développement de cinq espèces de plantes invasives amphibies : Crassula helmsii, Hydrocotyle ranunculoides, Ludwigia grandiflora, Ludwigia peploides et Myriophyllum aquaticum (synthèse bibliographique). BASE, 17, 87–102. https://popups.uliege.be/1780-4507/index.php?id=9586 Gérard J, Brion N, Triest L (2014) Effect of water column phosphorus reduction on competitive outcome and traits of Ludwigia grandiflora and L. peploides, invasive species in Europe. Aquatic Invasions, 9, 157–166. https://doi.org/10.3391/ai.2014.9.2.04 Glover R, Drenovsky RE, Futrell CJ, Grewell BJ (2015) Clonal integration in Ludwigia hexapetala under different light regimes. Aquatic Botany, 122, 40–46. https://doi.org/10.1016/j.aquabot.2015.01.004 Hieda S, Kaneko Y, Nakagawa M, Noma N (2020) Ludwigia grandiflora (Michx.) Greuter & Burdet subsp. hexapetala (Hook. & Arn.) G. L. Nesom & Kartesz, an Invasive Aquatic Plant in Lake Biwa, the Largest Lake in Japan. Acta Phytotaxonomica et Geobotanica, 71, 65–71. https://doi.org/10.18942/apg.201911 Meisler J (2009) Controlling Ludwigia hexaplata in Northern California. Wetland Science and Practice, 26, 15–19. https://doi.org/10.1672/055.026.0404 Portillo Lemus LO, Harang M, Bozec M, Haury J, Stoeckel S, Barloy D (2022) Late-acting self-incompatible system, preferential allogamy and delayed selfing in the heteromorphic invasive populations of Ludwigia grandiflora subsp. hexapetala. bioRxiv, 2021.07.15.452457, ver. 4 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2021.07.15.452457 Portillo Lemus LO, Bozec M, Harang M, Coudreuse J, Haury J, Stoeckel S, Barloy D (2021) Self-incompatibility limits sexual reproduction rather than environmental conditions in an invasive water primrose. Plant-Environment Interactions, 2, 74–86. https://doi.org/10.1002/pei3.10042 Reid AJ, Carlson AK, Creed IF, Eliason EJ, Gell PA, Johnson PTJ, Kidd KA, MacCormack TJ, Olden JD, Ormerod SJ, Smol JP, Taylor WW, Tockner K, Vermaire JC, Dudgeon D, Cooke SJ (2019) Emerging threats and persistent conservation challenges for freshwater biodiversity. Biological Reviews, 94, 849–873. https://doi.org/10.1111/brv.12480 Thouvenot L, Haury J, Thiebaut G (2013) A success story: water primroses, aquatic plant pests. Aquatic Conservation: Marine and Freshwater Ecosystems, 23, 790–803. https://doi.org/10.1002/aqc.2387 Thouvenot L, Haury J, Thiébaut G (2013) Seasonal plasticity of Ludwigia grandiflora under light and water depth gradients: An outdoor mesocosm experiment. Flora - Morphology, Distribution, Functional Ecology of Plants, 208, 430–437. https://doi.org/10.1016/j.flora.2013.07.004 | Late-acting self-incompatible system, preferential allogamy and delayed selfing in the heterostylous invasive populations of Ludwigia grandiflora subsp. hexapetala | Luis O. Portillo Lemus, Maryline Harang, Michel Bozec, Jacques Haury, Solenn Stoeckel, Dominique Barloy | <p style="text-align: justify;">Breeding system influences local population genetic structure, effective size, offspring fitness and functional variation. Determining the respective importance of self- and cross-fertilization in hermaphroditic flo... | ![]() | Biological invasions, Botany, Freshwater ecology, Pollination | Antoine Vernay | 2021-07-16 09:53:50 | View | |
12 Sep 2023
Linking intrinsic scales of ecological processes to characteristic scales of biodiversity and functioning patternsYuval R. Zelnik, Matthieu Barbier, David W. Shanafelt, Michel Loreau, Rachel M. Germain https://doi.org/10.1101/2021.10.11.463913The impact of process at different scales on diversity and ecosystem functioning: a huge challengeRecommended by David AlonsoScale is a big topic in ecology [1]. Environmental variation happens at particular scales. The typical scale at which organisms disperse is species-specific, but, as a first approximation, an ensemble of similar species, for instance, trees, could be considered to share a typical dispersal scale. Finally, characteristic spatial scales of species interactions are, in general, different from the typical scales of dispersal and environmental variation. Therefore, conceptually, we can distinguish these three characteristic spatial scales associated with three different processes: species selection for a given environment (E), dispersal (D), and species interactions (I), respectively. From the famous species-area relation to the spatial distribution of biomass and species richness, the different macro-ecological patterns we usually study emerge from an interplay between dispersal and local interactions in a physical environment that constrains species establishment and persistence in every location. To make things even more complicated, local environments are often modified by the species that thrive in them, which establishes feedback loops. It is usually assumed that local interactions are short-range in comparison with species dispersal, and dispersal scales are typically smaller than the scales at which the environment varies (I < D < E, see [2]), but this should not always be the case. The authors of this paper [2] relax this typical assumption and develop a theoretical framework to study how diversity and ecosystem functioning are affected by different relations between the typical scales governing interactions, dispersal, and environmental variation. This is a huge challenge. First, diversity and ecosystem functioning across space and time have been empirically characterized through a wide variety of macro-ecological patterns. Second, accommodating local interactions, dispersal and environmental variation and species environmental preferences to model spatiotemporal dynamics of full ecological communities can be done also in a lot of different ways. One can ask if the particular approach suggested by the authors is the best choice in the sense of producing robust results, this is, results that would be predicted by alternative modeling approaches and mathematical analyses [3]. The recommendation here is to read through and judge by yourself. The main unusual assumption underlying the model suggested by the authors is non-local species interactions. They introduce interaction kernels to weigh the strength of the ecological interaction with distance, which gives rise to a system of coupled integro-differential equations. This kernel is the key component that allows for control and varies the scale of ecological interactions. Although this is not new in ecology [4], and certainly has a long tradition in physics ---think about the electric or the gravity field, this approach has been widely overlooked in the development of the set of theoretical frameworks we have been using over and over again in community ecology, such as the Lotka-Volterra equations or, more recently, the metacommunity concept [5]. In Physics, classic fields have been revised to account for the fact that information cannot travel faster than light. In an analogous way, a focal individual cannot feel the presence of distant neighbors instantaneously. Therefore, non-local interactions do not exist in ecological communities. As the authors of this paper point out, they emerge in an effective way as a result of non-random movements, for instance, when individuals go regularly back and forth between environments (see [6], for an application to infectious diseases), or even migrate between regions. And, on top of this type of movement, species also tend to disperse and colonize close (or far) environments. Individual mobility and dispersal are then two types of movements, characterized by different spatial-temporal scales in general. Species dispersal, on the one hand, and individual directed movements underlying species interactions, on the other, are themselves diverse across species, but it is clear that they exist and belong to two distinct categories. In spite of the long and rich exchange between the authors' team and the reviewers, it was not finally clear (at least, to me and to one of the reviewers) whether the model for the spatio-temporal dynamics of the ecological community (see Eq (1) in [2]) is only presented as a coupled system of integro-differential equations on a continuous landscape for pedagogical reasons, but then modeled on a discrete regular grid for computational convenience. In the latter case, the system represents a regular network of local communities, becomes a system of coupled ODEs, and can be numerically integrated through the use of standard algorithms. By contrast, in the former case, the system is meant to truly represent a community that develops on continuous time and space, as in reaction-diffusion systems. In that case, one should keep in mind that numerical instabilities can arise as an artifact when integrating both local and non-local spatio-temporal systems. Spatial patterns could be then transient or simply result from these instabilities. Therefore, when analyzing spatiotemporal integro-differential equations, special attention should be paid to the use of the right numerical algorithms. The authors share all their code at https://zenodo.org/record/5543191, and all this can be checked out. In any case, the whole discussion between the authors and the reviewers has inherent value in itself, because it touches on several limitations and/or strengths of the author's approach, and I highly recommend checking it out and reading it through. Beyond these methodological issues, extensive model explorations for the different parameter combinations are presented. Several results are reported, but, in practice, what is then the main conclusion we could highlight here among all of them? The authors suggest that "it will be difficult to manage landscapes to preserve biodiversity and ecosystem functioning simultaneously, despite their causative relationship", because, first, "increasing dispersal and interaction scales had opposing References [1] Levin, S. A. 1992. The problem of pattern and scale in ecology. Ecology 73:1943–1967. https://doi.org/10.2307/1941447 [2] Yuval R. Zelnik, Matthieu Barbier, David W. Shanafelt, Michel Loreau, Rachel M. Germain. 2023. Linking intrinsic scales of ecological processes to characteristic scales of biodiversity and functioning patterns. bioRxiv, ver. 2 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2021.10.11.463913 [3] Baron, J. W. and Galla, T. 2020. Dispersal-induced instability in complex ecosystems. Nature Communications 11, 6032. https://doi.org/10.1038/s41467-020-19824-4 [4] Cushing, J. M. 1977. Integrodifferential equations and delay models in population dynamics [5] M. A. Leibold, M. Holyoak, N. Mouquet, P. Amarasekare, J. M. Chase, M. F. Hoopes, R. D. Holt, J. B. Shurin, R. Law, D. Tilman, M. Loreau, A. Gonzalez. 2004. The metacommunity concept: a framework for multi-scale community ecology. Ecology Letters, 7(7): 601-613. https://doi.org/10.1111/j.1461-0248.2004.00608.x [6] M. Pardo-Araujo, D. García-García, D. Alonso, and F. Bartumeus. 2023. Epidemic thresholds and human mobility. Scientific reports 13 (1), 11409. https://doi.org/10.1038/s41598-023-38395-0 | Linking intrinsic scales of ecological processes to characteristic scales of biodiversity and functioning patterns | Yuval R. Zelnik, Matthieu Barbier, David W. Shanafelt, Michel Loreau, Rachel M. Germain | <p style="text-align: justify;">Ecology is a science of scale, which guides our description of both ecological processes and patterns, but we lack a systematic understanding of how process scale and pattern scale are connected. Recent calls for a ... | Biodiversity, Community ecology, Dispersal & Migration, Ecosystem functioning, Landscape ecology, Theoretical ecology | David Alonso | 2021-10-13 23:24:45 | 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 BilliardCapture-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 | ||
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 |
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