Direct submissions to PCI Ecology from bioRxiv.org are possible using the B2J service
Latest recommendations
Id | Title * | Authors * | Abstract * | Picture * ▲ | Thematic fields * | Recommender | Reviewers | Submission date | |
---|---|---|---|---|---|---|---|---|---|
05 Nov 2019
Crown defoliation decreases reproduction and wood growth in a marginal European beech population.Sylvie Oddou-Muratorio, Cathleen Petit-Cailleux, Valentin Journé, Matthieu Lingrand, Jean-André Magdalou, Christophe Hurson, Joseph Garrigue, Hendrik Davi, Elodie Magnanou. https://doi.org/10.1101/474874Defoliation induces a trade-off between reproduction and growth in a southern population of BeechRecommended by Georges Kunstler based on reviews by 3 anonymous reviewersIndividuals ability to withstand abiotic and biotic stresses is crucial to the maintenance of populations at climate edge of tree species distribution. We start to have a detailed understanding of tree growth response and to a lesser extent mortality response in these populations. In contrast, our understanding of the response of tree fecundity and recruitment remains limited because of the difficulty to monitor it at the individual tree level in the field. Tree recruitment limitation is, however, crucial for tree population dynamics [1-2]. References [1] Clark, J. S. et al. (1999). Interpreting recruitment limitation in forests. American Journal of Botany, 86(1), 1-16. doi: 10.2307/2656950 | Crown defoliation decreases reproduction and wood growth in a marginal European beech population. | Sylvie Oddou-Muratorio, Cathleen Petit-Cailleux, Valentin Journé, Matthieu Lingrand, Jean-André Magdalou, Christophe Hurson, Joseph Garrigue, Hendrik Davi, Elodie Magnanou. | <p>1. Although droughts and heatwaves have been associated to increased crown defoliation, decreased growth and a higher risk of mortality in many forest tree species, their impact on tree reproduction and forest regeneration still remains underst... | Climate change, Eco-evolutionary dynamics, Molecular ecology, Physiology, Population ecology | Georges Kunstler | 2018-11-20 13:29:42 | View | ||
10 Oct 2024
Large-scale spatio-temporal variation in vital rates and population dynamics of an alpine birdChloé R. Nater, Francesco Frassinelli, James A. Martin, Erlend B. Nilsen https://doi.org/10.32942/X2VP6JDo look up: building a comprehensive view of population dynamics from small scale observation through citizen scienceRecommended by Aidan Jonathan Mark Hewison based on reviews by Todd Arnold and 1 anonymous reviewerPopulation ecologists are in the business of decrypting the drivers of variation in the abundance of organisms across space and time (Begon et al. 1986). Comprehensive studies of wild vertebrate populations which provide the necessary information on variations in vital rates in relation to environmental conditions to construct informative models of large-scale population dynamics are rare, ostensibly because of the huge effort required to monitor individuals across ecological contexts and over generations. In this current aim, Nater et al. (2024) are leading the way forward by combining distance sampling data collected through a large-scale citizen science (Fraisl et al. 2022) programme in Norway with state-of-the-art modelling approaches to build a comprehensive overview of the population dynamics of willow ptarmigan. Their work enhances our fundamental understanding of this system and provides evidence-based tools to improve its management (Williams et al. 2002). Even better, they are working for the common good, by providing an open-source workflow that should enable ecologists and managers together to predict what will happen to their favourite model organism when the planet throws its next curve ball. In the case of the ptarmigan, for example, it seems that the impact of climate change on their population dynamics will differ across the species’ distributional range, with a slower pace of life (sensu Stearns 1983) at higher latitudes and altitudes. On a personal note, I have often mused whether citizen science, with its inherent limits and biases, was just another sticking plaster over the ever-deeper cuts in the research budgets to finance long-term ecological research. Here, Nater et al. are doing well to convince me that we would be foolish to ignore such opportunities, particularly when citizens are engaged, motivated, with an inherent capacity for the necessary discipline to employ common protocols in a standardised fashion. A key challenge for us professional ecologists is to inculcate the next generation of citizens with a sense of their opportunity to contribute to a better understanding of the natural world. References Begon, Michael, John L Harper, and Colin R Townsend. 1986. Ecology: individuals, populations and communities. Blackwell Science. Fraisl, Dilek, Gerid Hager, Baptiste Bedessem, Margaret Gold, Pen-Yuan Hsing, Finn Danielsen, Colleen B Hitchcock, et al. 2022. Citizen Science in Environmental and Ecological Sciences. Nature Reviews Methods Primers 2 (1): 64. https://doi.org/10.1038/s43586-022-00144-4 Chloé R. Nater, Francesco Frassinelli, James A. Martin, Erlend B. Nilsen (2024) Large-scale spatio-temporal variation in vital rates and population dynamics of an alpine bird. EcoEvoRxiv, ver.4 peer-reviewed and recommended by PCI Ecology https://doi.org/10.32942/X2VP6J Stearns, S.C. 1983. The influence of size and phylogeny of covariation among life-history traits in the mammals. Oikos, 41, 173–187. https://doi.org/10.2307/3544261 Williams, Byron K, James D Nichols, and Michael J Conroy. 2002. Analysis and Management of Animal Populations. Academic Press. | Large-scale spatio-temporal variation in vital rates and population dynamics of an alpine bird | Chloé R. Nater, Francesco Frassinelli, James A. Martin, Erlend B. Nilsen | <p>Quantifying temporal and spatial variation in animal population size and demography is a central theme in ecological research and important for directing management and policy. However, this requires field sampling at large spatial extents and ... | Biodiversity, Biogeography, Conservation biology, Demography, Euring Conference, Landscape ecology, Life history, Population ecology, Spatial ecology, Metacommunities & Metapopulations, Statistical ecology, Terrestrial ecology | Aidan Jonathan Mark Hewison | 2024-02-02 08:54:06 | View | ||
25 Nov 2022
Positive fitness effects help explain the broad range of Wolbachia prevalences in natural populationsPetteri Karisto, Anne Duplouy, Charlotte de Vries, Hanna Kokko https://doi.org/10.1101/2022.04.11.487824Population dynamics of Wolbachia symbionts playing Dr. Jekyll and Mr. HydeRecommended by Jorge Peña based on reviews by 3 anonymous reviewers"Good and evil are so close as to be chained together in the soul" Maternally inherited symbionts—microorganisms that pass from a female host to her progeny—have two main ways of increasing their own fitness. First, they can increase the fecundity or viability of infected females. This “positive fitness effects” strategy is the one commonly used by mutualistic symbionts, such as Buchnera aphidicola—the bacterial endosymbiont of the pea aphid, Acyrthosiphon pisum [4]. Second, maternally inherited symbionts can manipulate the reproduction of infected females in a way that enhances symbiont transmission at the expense of host fitness. A famous example of this “reproductive parasitism” strategy is the cytoplasmic incompatibility (CI) [3] induced by bacteria of the genus Wolbachia in their arthropod and nematode hosts. CI works as a toxin-antidote system, whereby the sperm of infected males is modified in a lethal way (toxin) that can only be reverted if the egg is also infected (antidote) [1]. As a result, CI imposes a kind of conditional sterility on their hosts: while infected females are compatible with both infected and uninfected males, uninfected females experience high offspring mortality if (and only if) they mate with infected males [7]. These two symbiont strategies (positive fitness effects versus reproductive parasitism) have been traditionally studied separately, both empirically and theoretically. However, it has become clear that the two strategies are not mutually exclusive, and that a reproductive parasite can simultaneously act as a mutualist—an infection type that has been dubbed “Jekyll and Hyde” [6], after the famous novella by Robert Louis Stevenson about kind scientist Dr. Jekyll and his evil alter ego, Mr. Hyde. In important previous work, Zug and Hammerstein [7] analyzed the consequences of positive fitness effects on the dynamics of different kind of infections, including “Jekyll and Hyde” infections characterized by CI and other reproductive parasitism strategies. Building on this and related modeling framework, Karisto et al. [2] re-investigate and expand on the interplay between positive fitness effects and reproductive parasitism in Wolbachia infections by focusing on CI in both diplodiploid and haplodiploid populations, and by paying particular attention to the mathematical assumption structure underlying their results. Karisto et al. begin by reviewing classic models of Wolbachia infections in diplodiploid populations that assume a “negative fitness effect” (modeled as a fertility penalty on infected females), characteristic of a pure strategy of reproductive parasitism. Together with the positive frequency-dependent effects due to CI (whereby the fitness benefits to symbionts infecting females increase with the proportion of infected males in the population) this results in population dynamics characterized by two stable equilibria (the Wolbachia-free state and an interior equilibrium with a high frequency of Wolbachia-carrying hosts) separated by an unstable interior equilibrium. Wolbachia can then spread once the initial frequency is above a threshold or an invasion barrier, but is prevented from fixing by a proportion of infections failing to be passed on to offspring. Karisto et al. show that, given the assumption of negative fitness effects, the stable interior equilibrium can never feature a Wolbachia prevalence below one-half. Moreover, they convincingly argue that a prevalence greater than but close to one-half is difficult to maintain in the presence of stochastic fluctuations, as in these cases the high-prevalence stable equilibrium would be too close to the unstable equilibrium signposting the invasion barrier. Karisto et al. then relax the assumption of negative fitness effects and allow for positive fitness effects (modeled as a fertility premium on infected females) in a diplodiploid population. They show that positive fitness effects may result in situations where the original invasion threshold is now absent, the bistable coexistence dynamics are transformed into purely co-existence dynamics, and Wolbachia symbionts can now invade when rare. Karisto et al. conclude that positive fitness effects provide a plausible and potentially testable explanation for the low frequencies of symbiont-carrying hosts that are sometimes observed in nature, which are difficult to reconcile with the assumption of negative fitness effects. Finally, Karisto et al. extend their analysis to haplodiploid host populations (where all fertilized eggs develop as females). Here, they investigate two types of cytoplasmic incompatibility: a female-killing effect, similar to the CI effect studied in diplodiploid populations (the “Leptopilina type” of Vavre et al. [5]) and a masculinization effect, where CI leads to the loss of paternal chromosomes and to the development of the offspring as a male (the “Nasonia type” of Vavre et al. [5]). The models are now two-sex, which precludes a complete analytical treatment, in particular regarding the stability of fixed points. Karisto et al. compensate by conducting large numerical analyses that support their claims. Importantly, all main conclusions regarding the interplay between positive fitness effects and reproductive parasitism continue to hold under haplodiploidy. All in all, the analysis and results by Karisto et al. suggest that it is not necessary to resort to classical (but depending on the situation, unlikely) mechanisms, such as ongoing invasion or source-sink dynamics, to explain arthropod populations featuring low-prevalent Wolbachia infections. Instead, low-frequency equilibria might be simply due to reproductive parasites conferring beneficial fitness effects, or Wolbachia symbionts playing Dr. Jekyll (positive fitness effects) and Mr. Hyde (cytoplasmatic incompatibility). References [1] Beckmann JF, Bonneau M, Chen H, Hochstrasser M, Poinsot D, Merçot H, Weill M, Sicard M, Charlat S (2019) The Toxin–Antidote Model of Cytoplasmic Incompatibility: Genetics and Evolutionary Implications. Trends in Genetics, 35, 175–185. https://doi.org/10.1016/j.tig.2018.12.004 [2] Karisto P, Duplouy A, Vries C de, Kokko H (2022) Positive fitness effects help explain the broad range of Wolbachia prevalences in natural populations. bioRxiv, 2022.04.11.487824, ver. 5 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2022.04.11.487824 [3] Laven H (1956) Cytoplasmic Inheritance in Culex. Nature, 177, 141–142. https://doi.org/10.1038/177141a0 [4] Perreau J, Zhang B, Maeda GP, Kirkpatrick M, Moran NA (2021) Strong within-host selection in a maternally inherited obligate symbiont: Buchnera and aphids. Proceedings of the National Academy of Sciences, 118, e2102467118. https://doi.org/10.1073/pnas.2102467118 [5] Vavre F, Fleury F, Varaldi J, Fouillet P, Bouletreau M (2000) Evidence for Female Mortality in Wolbachia-Mediated Cytoplasmic Incompatibility in Haplodiploid Insects: Epidemiologic and Evolutionary Consequences. Evolution, 54, 191–200. https://doi.org/10.1111/j.0014-3820.2000.tb00019.x [6] Zug R, Hammerstein P (2015) Bad guys turned nice? A critical assessment of Wolbachia mutualisms in arthropod hosts. Biological Reviews, 90, 89–111. https://doi.org/10.1111/brv.12098 [7] Zug R, Hammerstein P (2018) Evolution of reproductive parasites with direct fitness benefits. Heredity, 120, 266–281. https://doi.org/10.1038/s41437-017-0022-5 | Positive fitness effects help explain the broad range of Wolbachia prevalences in natural populations | Petteri Karisto, Anne Duplouy, Charlotte de Vries, Hanna Kokko | <p style="text-align: justify;">The bacterial endosymbiont <em>Wolbachia</em> is best known for its ability to modify its host’s reproduction by inducing cytoplasmic incompatibility (CI) to facilitate its own spread. Classical models predict eithe... | Host-parasite interactions, Population ecology | Jorge Peña | 2022-04-12 12:52:55 | View | ||
30 Oct 2024
The importance of sampling design for unbiased estimation of survival using joint live-recapture and live resight modelsMaria C. Dzul, Charles B. Yackulic, William L. Kendall https://doi.org/10.48550/arXiv.2312.13414In the quest for estimating true survivalRecommended by Matthieu Paquet based on reviews by Rémi Fay and 1 anonymous reviewerAccurately estimating survival rate and identifying the drivers of its variation is essential for our understanding of population dynamics and life history strategies (Sæther and Bakke 2000), as well as for population management and conservation (Francis et al. 1998, Doherty et al. 2014). Many studies estimate survival from capture–recapture data using the Cormack–Jolly–Seber (CJS) model (Lebreton et al. 1992). However, survival estimates are confounded with permanent emigration from the study area, which can be particularly problematic for mobile species. This is problematic, not only because CJS models under estimate true survival in populations where permanent emigration occurs (i.e. they estimate “apparent” survival), but also because some factors of interest may affect both survival and emigration (e.g., habitat quality, Paquet et al. 2020), leaving the interpretation of results challenging, for example in terms of management decisions. Several methods have been developed to account for permanent emigration when estimating survival, for example by jointly analyzing CMR data with data on individuals’ locations at each capture/resighting site (to estimate their dispersal distances; Schaub and Royle 2013, Badia Boher et al. 2023), with telemetry data (Powel et al. 2000), mark recovery data (Burnham 1993, Fay et al. 2019), or with live-resight data (Barker 1997). The Barker joint live-recapture/live-resight (JLRLR) model can estimate survival when resight data are continuous over a long interval and from a larger area than the capture recapture data. This model becomes particularly promising with the growing collection of data from citizen science, or remote detection tools (Dzul et al. 2023). However, as pointed out by Dzul et al., this model assumes that resight probability is homogeneous across the area where individuals can move, and this assumption is likely violated for example because of non-random movements or because of non-random location of resighting sites. In their manuscript, Dzul et al. performed a thorough simulation study to evaluate the accuracy of survival estimates from JLRLR models under various study designs regarding the location of resight sites (global, random, fixed including the capture site, and fixed excluding the capture site). They simulated data with varying survival and movement values, varying recapture and resight probabilities, and varying sample sizes. Finally, they also developed and fitted a multi state version of the JLRLR model. They show that JLRLR models performed better than CJS models. Survival estimates were still often biased (either positively or negatively) but they were less biased when sesight sites were randomly located (rather than at fixed locations), when recapture sites were included in the resighting design, and when using the multi state JLRLR model they developed. This study highlights (multistate) JLRLR models as an alternative to CJS models one should consider when auxiliary resight data can be collected. Moreover, it shows the importance of evaluating not only model performance, but also the efficiency of alternative sampling designs before choosing one for our studies. Hopefully, this study will help the authors and other researchers making a more informed and efficient choice of model and design to estimate survival in their study populations. References Jaume A. Badia-Boher, Joan Real, Joan Lluís Riera, Frederic Bartumeus, Francesc Parés, Josep Maria Bas, and Antonio Hernández-Matías. Joint estimation of survival and dispersal effectively corrects the permanent emigration bias in mark-recapture analyses. (2023) Scientific reports 13, no. 1: 6970. https://doi.org/10.1038/s41598-023-32866-0 Richard J Barker (1997) Joint modeling of live-recapture, tag-resight, and tag-recovery data. Biometrics: 666-677. https://doi.org/10.2307/2533966 Kenneth P. Burnham (1993) Marked Individuals in the Study of Bird Populations (ed. J.D. Lebreton), pp. 199–213. Birkhäuser, Basel Kevin E. Doherty, David E. Naugle, Jason D. Tack, Brett L. Walker, Jon M. Graham, Jeffrey L. Beck (2014) Linking conservation actions to demography: grass height explains variation in greater sage‐grouse nest survival. Wildlife biology 20, no. 6 : 320-325. https://doi.org/10.2981/wlb.00004 Maria C. Dzul, Charles B. Yackulic, William L. Kendall (2023) The importance of sampling design for unbiased estimation of survival using joint live-recapture and live resight models. arXiv, ver.3 peer-reviewed and recommended by PCI Ecology https://doi.org/10.48550/arXiv.2312.13414 Rémi Fay, Stephanie Michler, Jacques Laesser, and Michael Schaub (2019) Integrated population model reveals that kestrels breeding in nest boxes operate as a source population. Ecography 42, no. 12: 2122-2131. https://doi.org/10.1111/ecog.04559 Charles M. Francis, John R. Sauer, Jerome R. Serie (1998) Effect of restrictive harvest regulations on survival and recovery rates of American black ducks. The Journal of Wildlife Management : 1544-1557. https://doi.org/10.2307/3802021 Jean-Dominique Lebreton, Kenneth P. Burnham, Jean Clobert, David R. Anderson (1992) Modeling survival and testing biological hypotheses using marked animals: a unified approach with case studies. Ecological monographs 62.1: 67-118. https://doi.org/10.2307/2937171 Matthieu Paquet, Debora Arlt, Jonas Knape, Matthew Low, Pär Forslund, and Tomas Pärt (2020) Why we should care about movements: Using spatially explicit integrated population models to assess habitat source–sink dynamics. Journal of Animal Ecology 89, no. 12: 2922-2933. https://doi.org/10.1111/1365-2656.13357 Larkin A. Powell, Michael J. Conroy, James E. Hines, James D. Nichols, and David G. Krementz. Simultaneous use of mark-recapture and radiotelemetry to estimate survival, movement, and capture rates. (2000) The Journal of Wildlife Management : 302-313. https://doi.org/10.2307/3803003 Bernt-Erik Sæther, Øyvind Bakke (2000) Avian life history variation and contribution of demographic traits to the population growth rate. Ecology 81.3 : 642-653. https://doi.org/10.1890/0012-9658(2000)081[0642:ALHVAC]2.0.CO;2 Michael Schaub, J. Andrew Royle. Estimating true instead of apparent survival using spatial Cormack–Jolly–Seber models (2014) Methods in Ecology and Evolution 5, no. 12: 1316-1326. https://doi.org/10.1111/2041-210X.12134 | The importance of sampling design for unbiased estimation of survival using joint live-recapture and live resight models | Maria C. Dzul, Charles B. Yackulic, William L. Kendall | <p>Survival is a key life history parameter that can inform management decisions and life history research. Because true survival is often confounded with permanent and temporary emigration from the study area, many studies must estimate apparent ... | Dispersal & Migration, Euring Conference, Population ecology, Statistical ecology | Matthieu Paquet | 2023-12-22 22:31:07 | View |
MANAGING BOARD
Julia Astegiano
Tim Coulson
Anna Eklof
Dominique Gravel
François Massol
Ben Phillips
Cyrille Violle