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of ANODEV tests for the covariates used in the modelling of capture- recapture data for each stream: Winter refers to the winter severity variable (proportion of optimal winter days) modeled on the survival parameter, and Spring to the average April- June temperature, used as predictor of size state transitions
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In organisms such as fish, where body size is considered an important state variable for the study of their population dynamics, size-specific growth and survival rates can be influenced by local variation in both biotic and abiotic factors, but few studies have evaluated the complex relationships between environmental variability and size-dependen...
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... for the ANODEV test revealed that temperature variables explained a higher proportion of the variation in the demographic rates of Orbiandi and Comeya (Table 5). ...Context 2
... particular, r 2 values were the highest for Comeya stream, with more than 99 % of variation in the survival of mature individuals and maturation transitions explained by water temperature variables (Table 5). In Comeya, the slope of the relationship between the proportion of optimal winter days and survival of the largest individuals was positive [beta slope (95 % CI) = 6.215 (3.601; 8.829)]. ...Similar publications
We sampled backwaters in the Grand Valley reach of the Colorado River, CO, to estimate bias and precision of the Interagency Standardized Monitoring Program (ISMP) sampling technique to detect presence and estimate abundance of centrarchid fishes. This was accomplished by sampling backwaters with the relatively low effort ISMP seine-sampling approa...
Dispersal is a central mechanism in ecology and evolution. Dispersal evolution is driven by a trade-off between costs and benefits, which is influenced by inter-individual variability and local environmental conditions (context-dependent dispersal). Many studies have investigated how dispersal decisions may be influenced by environmental factors, i...
Dispersal is a central mechanism in ecology and evolution. Dispersal evolution is driven by a trade-off between costs and benefits, which is influenced by interindividual variability and local environmental conditions (context-dependent dispersal). Many studies have investigated how dispersal decisions may be influenced by environmental factors, in...
Dispersal is a central process in ecology and evolution. At the individual level, the three stages of the dispersal process (i.e. emigration, transience and immigration) are affected by complex interactions between phenotypes and environmental factors. Condition and context‐dependent dispersal have far‐reaching consequences, both for the demography...
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... It is known that different local populations of a species may show differential density trends at each patch, but most studies do not address the demographic processes influencing those differences. Long-term demographic monitoring shows that demographic processes change in each local population, either because the habitat-specific environmental conditions (Doak & Morris 2010;Fernández-Chacón et al. 2015;Frederiksen et al. 2021;Linares & Doak 2010;Murphy 2001;Smith-James et al. 1996;Vincenzi et al. 2016) or because the age-stage-structure of the population (e.g. ages, states) may change between local populations (Lynch et al. 2014;Reichert et al. 2016). ...
... ). In some cases, long-term demographic monitoring at large spatial-temporal scales have shown plasticity in a species for a fast to slow continuum of life histories between different populations subjected to heterogenous environmental conditions and occurrence of local rare events(Fernández-Chacón et al. 2015;Matthews et al. 2013;Vincenzi et al. 2016). That demographic monitoring is crucial to identify extreme responses to rare events, such as those shown by the red coral Corallium rubrum, for which some colonies show extreme shrinkage due to environmental stress(Montero-Serra et al. 2018). ...
While multiple reasons make long-term demographic studies disproportionally valuable, much of their importance comes from the ability to detect and quantify rare events. We argue here that rare events can be critical for understanding important ecological and evolutionary processes. We highlight the additive or interactive nature of anthropogenic rare events with environmental rare events that may cause outsized changes in vital rates and therefore in population dynamics. Rare events may also generate complex responses in populations due to interactions between demographic processes and evolutionary responses. Complex, non-linear dynamics of populations may include threshold, extreme responses such as long transients, tipping points, regime shifts and collapse. When occurring locally, rare events may also exacerbate spatial heterogeneity with consequences for demographic processes. In sum, these effects represent substantial challenges for prediction, especially when considering the increase in the frequency of rare extreme events, and emphasise the need for long-term studies. Our perspective attempts to integrate the occurrence of rare events in variable environments and the consequences for the overall fitness, growth rates, and the spatial-temporal dynamics of populations.
... Capture-mark-recapture (CMR) studies enable the investigation of population dynamics of wildlife species on a long-term scale, and are considered an effective tool in clarifying the impact of diseases on natural populations (e.g., Murray et al. 2009;Phillott et al. 2013). In particular, the multi-event modeling approach, an extension of classical CMR models, allows researchers to test whether and how survival and recapture probability are affected by individual biological states, such as breeding site (Fernández-Chacón et al. 2013), size class (Fernández-Chacón et al. 2015) or infection status (Conn and Cooch 2009;Muths et al. 2020). Previous research that has applied CMR models to the epidemiological study of amphibian populations affected by chytridiomycosis has reported a decrease in the survival probability of infected individuals and populations (e.g., Murray et al. 2009;Pilliod et al. 2010;Phillott et al. 2013;Brannelly et al. 2015;Russell et al. 2019). ...
Chytridiomycosis, the disease caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), has been unambiguously implicated in the decline of amphibian populations worldwide. However, the impact of this devastating infectious disease can be difficult to gauge without empirical data on the population-level effects of Bd. Often, assessments of the amphibian chytridiomycosis panzootic are based primarily on expert opinions; as a result, declines in tropical areas are promptly attributed to Bd while its impact on temperate species not suffering from adult mass mortalities is frequently overlooked. Here, we investigated the survival probability in an amphibian species from a temperate area that until now has not been considered to be severely impacted by the disease. Specifically, we related individual survival to Bd infection status using long-term capture-mark-recapture data of male spiny common toads (Bufo spinosus) in Sierra de Guadarrama National Park in central Spain. Even though the study population has demonstrated potential for adaptation to Bd and die-offs of adult individuals have not been recorded, our results clearly indicated that the probability of survival was lower for Bd-positive individuals. Moreover, the probability of becoming Bd-positive was higher than the probability of clearance, driving the population to a slow but certain decline. These results are consistent with other indicators of a negative population trend and suggest that the impact of Bd on temperate species of less concern may be greater than previously thought.
... In case of Brown Trout, keeping in mind its propensity to invade freshwaters of multiple nations, it is sturdy enough to manage in tough environmental conditions too, and hence the latter factor of physiology would be the key behind its invasiveness. As a strategy to invade, the Brown Trout populations show different growth characteristics and breeding attributes in different environments (Deacon et al., 2011;Fernández-Chacón et al., 2015;Dieterman et al., 2016). This is a sign of phenotypic plasticity, due to local adaptations to the varied environments (Nicola and Almodóvar, 2002). ...
Often regarded as a potential threat to the native fish fauna worldwide, the Brown Trout (Salmo trutta), has successfully established its population in the majority of the Himalayan rivers post its introduction dating back to the eighteenth century. Over the years, the species has gained infamy as a sport fish and is considered a profitable source of income to the locals ensuing a heightened propagule pressure due to lack of appropriate management actions. No comprehensive study has been conducted to date in order to understand the mechanism by which the Brown Trout poses threat to the native fish populations. Through the present study, we could assess its competition with the native Snow Trout (Schizothorax richardsonii) to understand the spatial assemblage of both the species across space in Tirthan, a pristine high-altitude river of the western Himalaya. River Tirthan is one of the major tributaries of River Beas traversing for most of its stretch within the protected boundaries of the Great Himalayan National Park Conservation Area. A total of 108 sampling points were chosen from confluence to origin of rivers/streams, ranging from 989 to 3677msl. A total of 28 explanatory variables were recorded at each point. Overall, the Brown Trout adults were found to be greater in relative abundance (66.1%) than the Snow Trout adults (33.9%). The fingerlings of Snow Trout on the other hand, were distinctively high in relative abundance (61.9%) than those of the invasive Brown Trout (38.1%). Non-native trout showed higher abundance in the higher stream orders i.e. in the main streams while natives mostly restricted themselves to the lower order streams. Redundancy analysis (RDA) for species and environmental covariates resulted in 40.75% of constrained variance with higher eigen values for Redundancy analysis1 and Redundancy analysis2. Ward’s minimum variance clustering of Hellinger transformed data revealed sites agglomerating into six reasonable distinct subgroups with respect to species abundances. Immature individuals of non-native and native trout used similar habitat conditions, but they differed in using habitats at adult stage. Our results show a competitive dominance of Brown Trout in terms of higher abundance and maximum space utilization that highlight an urgent action for preventing its introductions to new areas. We recommend a national policy of ‘The Indian Invasive Species Act’ and management level interventions to control overstocking in the areas of established population.
... In these models, however, time-dependent individual covariates, such as weight or body size, cannot be easily accommodated because covariate values are unknown when individuals are not caught (see Bonner and Schwarz 2009). As in Fernández-Chacón et al. (2015), we considered size-classes and accommodated body growth as transitions between classes using a multisite capture-mark-recapture framework (Schwarz et al. 1993). In this case, missing values would not affect the estimate of survival according to size classes. ...
... Finally, to obtain a linear function between survival probability and body size, we considered the observed average body size in size-class j, B j , with j = 1,2, … 5, and constrained the five size-class survivals as: Logit(S r ) = a+b Bj Where S r is the survival of females in size-class r, a and b are the linear predictors of the size-dependent survival (see a similar approach in Fernández- Chacón et al. 2015). Models were built in the program MARK (White and Burnham 1999) and the goodness of fit test was assessed with the program U_CARE (Choquet et al. 2009). ...
In many species with continuous growth, body size is an important driver of life-history tactics and its relative importance is thought to reflect the spatio-temporal variability of selective pressures. We developed a deterministic size-dependent integral projection model (IPM) for three insular neighbouring lizard populations with contrasting adult body sizes to investigate how size-related selective pressures can influence lizard life-history tactics. For each population, we broke down differences in population growth rates into contributions from size-dependent body growth, survival, and fecundity. A life table response experiment (LTRE) was used to compare the population dynamics of the three populations and quantify the contributions of intrinsic demographic coefficients of each population to the population growth rate (λ). Perturbation analyses revealed that the largest adults contributed the most to the population growth rate, but this was not true in the population with the smallest adults and size-independent fertility. Although we were not able to identify a single factor responsible for this difference, the combination of the demographic model on a continuous trait coupled with a life table response experiment analysis revealed how sister populations of the same species follow different life strategies and showed different compensatory mechanisms among survival, individual body growth and fertility. Our results indicate that body size can play a contrasting role even in closely related and closely spaced populations.
... The latter can discern the micro-evolutionary mechanisms acting at early stages of differentiation that determine local adaptation (Grant and Dunham 1990), but also reveal adaptive phenotypic plasticity (Sears and Angilletta 2003) or the strength of selection on traits . At an intra-specific level, in fact, survival varies with several individual and population factors, e.g., sex, age, genetic quality, and/or density-dependent processes (Forslund and Pärt 1995;Clutton-Brock 1991;Tavecchia et al. 2001;Foerster et al. 2003;Lescroël et al. 2009) but also with the habitat, climate, food availability, and with acquired experience (Doherty and Grubb 2002;Gosselink et al. 2007;Coulson et al. 2008;Low et al. 2010;Fernández-Chacón et al. 2015). ...
Elevation represents an important selection agent on self-maintenance traits and correlated life histories in birds, but no study has analysed whether life-history variation along this environmental cline is consistent among and within species. In a sympatric community of passerines, we analysed how the average adult survival of 25 open-habitat species varied with their elevational distribution and how adult survival varied with elevation at the intra-specific level. For such purpose, we estimated intra-specific variation in adult survival in two mountainous species, the Water pipit (Anthus spinoletta) and the Northern wheatear (Oenanthe oenanthe) in NW Spain, by means of capture–recapture analyses. At the inter-specific level, high-elevation species showed higher survival values than low elevation ones, likely because a greater allocation to self-maintenance permits species to persist in alpine environments. At the intra-specific level, the magnitude of survival variation was lower by far. Nevertheless, Water pipit survival slightly decreased at high elevations, while the proportion of transient birds increased. In contrast, no such relationships were found in the Northern wheatear. Intra-specific analyses suggest that living at high elevation may be costly, such as for the Water pipit in our case study. Therefore, it seems that a species can persist with viable populations in uplands, where extrinsic mortality is high, by increasing the investment in self-maintenance and prospecting behaviours.
... Because here we were interested in the proportions of deaths associated with different fishing practices, the state DF was eventually divided in three gear-based states, all representing the different sources of fishing mortality existing in our system: dead by hand line (DH), dead by fixed gear (gill nets and fyke nets; DG), and dead by other gear types (trawl and longlines; DT). In addition, because information on body length was also included in the events, size classes were implemented as biological states in the model (for a similar approach see Fernández-Chacón et al. 2015a, 2015b. To accommodate encounters of fish of different sizes, alive and newly dead states were combined with legal (big) and sublegal (small) size states (i.e., L big , L small , DH big , DH small , etc.). ...
Knowledge on mortality causes is key for an effective management of animal populations and can help to restore depleted fish stocks. Here we investigated the mortality dynamics of coastal Atlantic cod in Skagerrak, south Norway, by analyzing local mark-recapture and recovery data collected from 2005 to 2013 (N = 9360 fish, mean length = 41 cm, range = 16-93 cm). By applying multi-event models to the data, we could link field observations to multiple “dead states” and estimate the proportion of deaths associated with different fishing gears while controlling for unobserved mortality and detection errors. Deaths due to hand lines and fixed gear types were dominant compared to other causes, especially in legal-sized cod (≥40 cm). Gear-specific mortality changed over time and between size classes but annual survival remained low and stable (~0.3). Assuming fully additive mortality, we predicted annual survival of cod to be above 0.5 if only one or both of the dominant gear types were removed, providing insights as to the relative impact of diverse harvesting practices on local population dynamics.
... For instance, identified differences in mortality patterns between a Spanish and a Danish population. Spatial variations were also identified among close populations (e.g., variations in competition strength and survival within a watershed; Fernández-Chacón et al. 2015). A major source of inconsistency among studies of brown trout population dynamics lies in the identification of density-dependent mortality. ...
Managing brown trout (Salmo trutta fario) populations is of high concerns for many stakeholders (e.g. angling associations or hydropower companies). However, building trout life cycle models remains challenging. Here, we describe a general hierarchical Bayesian model of brown trout population dynamics that combines global (e.g. an average value of age-class annual survival) and local parameters (e.g. shelter availability influencing local carrying capacity). To fit the model, we used annual fish samplings (i.e., two-pass electrofishing followed by density estimation) conducted at 40 reaches. Reaches were located in natural (n=21) or bypassed (i.e. downstream dam; n=19) stream sections across France, thus offering different habitat characteristics. Habitat characteristics were measured at each reach, including daily flow, daily hydraulics conditions, daily temperature and shelter availability. This study (1) allowed us to understand between-reach differences in survival processes, (2) was consistent with previous studies and explained spatial variations in resident brown trout population dynamics and (3) offers a promising framework for future developments.
Chaque année des dizaines de millions d'oiseaux migrateurs voyagent entre leurs aires de reproduction et leurs aires d'hivernage. Ce voyage de plusieurs milliers de kilomètres implique des contraintes météorologiques et énergétiques qui conduisent les oiseaux à effectuer des haltes migratoires. Les contraintes énergétiques forcent alors les oiseaux à refaire leurs réserves d'énergie durant ces haltes pour pouvoir effectuer de nouveau un vol de plusieurs centaines de kilomètres. En conséquence de cela, plus de 80% du temps total de migration est passé sur les sites de halte. Mieux comprendre les déterminants du départ d'un site de halte migratoire est donc crucial pour mieux appréhender le phénomène de la migration dans sa globalité ainsi que les variations de fitness d'une espèce. C'est pourquoi cette thèse, à l'interface entre modélisation et écologie de la migration, vise à obtenir une meilleure compréhension des décisions d'oiseaux migrateurs lors de leurs haltes à partir de données de capture-marquage-recapture récoltées parfois depuis des dizaines d'années et sur différents sites. En plus de cela, les potentielles implications en termes de gestion d'un site de halte seront abordées. La thèse s'articule sous la forme de 4 parties principales. La première vise à mesurer la part relative des conditions environnementales et du temps depuis l'arrivée dans la décision de départ d'un passereau migrateur. Elle a démontré que le temps depuis l'arrivée était alors plus important que les conditions environnementales pour un passereau migrateur transsaharien quand il s'agissait de décider de partir d'un site de halte. La seconde consiste à évaluer comment différents trajets de migration influencent les décisions de départ sur différents sites de halte d'une même espèce de limicole. Elle a de son côté démontré que la durée moyenne de halte était plus longue pour les oiseaux se préparant à un vol au-dessus de l'océan mais que les conditions environnementales choisies pour le départ convergeaient entre les deux sites. La troisième a pour but le développement d'un modèle multi-espèces pour explorer la synchronie dans la décision de départ d'un site de halte entre plusieurs espèces de passereaux migrateurs transsahariens. Elle a révélé que les variations quotidiennes de probabilités de départ étaient fortement synchrones entre les différentes espèces et que ce résultat était réplicable entre différents sites. De plus, dans la continuité de la partie 1, elle a révélé que le temps depuis l'arrivée était l'élément qui tendait à synchroniser les variations de probabilités de départ entre les espèces. La quatrième porte sur le pourquoi et comment utiliser la durée de halte estimée par les modèles de capture-recapture comme un outil de gestion des zones de halte migratoire. Elle passe en revue les différents aspects utiles de cette métrique pour des problématiques de gestion et de conservation des oiseaux migrateurs. Dans l'ensemble, ces travaux permettent d'affiner nos connaissances sur les décisions de départ d'un site de halte migratoire et des outils d'analyses associés pouvant à la fois être utiles pour découvrir de nouvelles facettes de la migration ainsi que pour la gestion et la conservation des oiseaux migrateurs et de leurs zones de halte.
Survival analyses are a key tool for demographers, ecologists, and evolutionary biologists. This chapter presents the most common methods and illustrates their use for species across the Tree of Life. It discusses the challenges associated with various types of survival data, how to model species with a complex life cycle, and includes the impact of environmental factors and individual heterogeneity. It covers the analysis of ‘known-fate’ data collected in lab conditions, using the Kaplan–Meier estimator and Cox’s proportional hazard regression analysis. Alternatively, survival data collected on free-ranging populations usually involve individuals missing at certain monitoring occasions and unknown time at death. The chapter provides an overview of capture–mark–recapture (CMR) models, from single-state to multi-state and multi-event models, and their use in animal and plant demography to estimate demographic parameters while correcting for imperfect detection of individuals. It discusses various inference frameworks available to implement CMR models using a frequentist or Bayesian approach. Only humans are an exception among free-ranging populations, with the existence of several consequent databases with perfect knowledge of age and cause of death for all individuals. The chapter presents an overview of the most common models used to describe mortality patterns over age and time using human mortality data. Throughout, focus is placed on eight case studies, which involve lab organisms, free-ranging animal populations, plant populations, and human populations. Each example includes data and codes, together with step-by-step guidance to run the survival analysis.
Recently isolated populations offer a good biological model to infer the evolutionary forces responsible for the current divergences across populations. We coupled genetic, morphometric, ecological, and demographic analyses from three island populations of the endemic Balearic Wall Lizard, Podarcis lilfordi, (Balearic archipelago, Spain) to infer the mechanisms underlying the observed differences in body size. For each population, we described plant community structure, derived a biotic capacity index, and used individual-based data on 1369 lizards captured and released during 6 yr (2009–2015) to estimate population density and body growth patterns. We used genetic data collected on 80 individuals (∼27 for each population) to infer genetic divergences across islets and population history. Body size divergences cannot be explained by the ecological or population characteristics. Individual growth was slower in the smallest island, where lizards reached the largest average body size. In addition to having the highest density, results suggested that resource availability does not constrain asymptotic body size, but the speed at which individuals reach it does. The Approximate Bayesian Computation used to infer population history from genetic data supported the occurrence of two bottlenecks in the islet with the highest anthropogenic footprint. We emphasize the need to integrate ecological and genetic data and the importance of considering the effects of past human disturbance as an additional force in being able to model present island fauna.
