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1.
Movement models require individually identifiable marks to estimate the movement rates among strata. But they are relatively expensive to apply and monitor. Batch marks can be readily applied, but individual animal movements cannot be identified. We describe a method to estimate population size in a stratified population when movement takes place among strata and animals are marked with a combination of batch and individually identifiable tags. A hierarchical model with Bayesian inference is developed that pools information across segments on the detection efficiency based on radio‐tagged fish and also uses the movement of the radio‐tagged fish to impute the movement of the batch‐marked fish to provide estimates of the population size on a segment and river level. The batch marks provide important information to help estimate the movement rates, but contribute little to the overall estimate of the population size. In this case, the approximate equal catchability among strata in either sample obviates the need for stratification. 相似文献
2.
R. M. Hillary 《Biometrics》2011,67(1):76-85
Summary The vast majority of population models work using age or stage not length but there are many cases where animals cannot be aged sensibly or accurately. For these cases length‐based models form the logical alternative but there has been little work done to develop and compare different methods of estimating growth transition matrices to be used in such models. This article demonstrates how a consistent Bayesian framework for estimating growth parameters and a novel method for constructing length transition matrices accounts for variation in growth in a clear and consistent manner and avoids potential subjective choices required using more established methods. The inclusion of the resultant growth uncertainty in population assessment models and the potential impact on management decisions is also addressed. 相似文献
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Discrete state‐space models are used in ecology to describe the dynamics of wild animal populations, with parameters, such as the probability of survival, being of ecological interest. For a particular parametrization of a model it is not always clear which parameters can be estimated. This inability to estimate all parameters is known as parameter redundancy or a model is described as nonidentifiable. In this paper we develop methods that can be used to detect parameter redundancy in discrete state‐space models. An exhaustive summary is a combination of parameters that fully specify a model. To use general methods for detecting parameter redundancy a suitable exhaustive summary is required. This paper proposes two methods for the derivation of an exhaustive summary for discrete state‐space models using discrete analogues of methods for continuous state‐space models. We also demonstrate that combining multiple data sets, through the use of an integrated population model, may result in a model in which all parameters are estimable, even though models fitted to the separate data sets may be parameter redundant. 相似文献
5.
If animals are independently detected during surveys, many methods exist for estimating animal abundance despite detection probabilities <1. Common estimators include double‐observer models, distance sampling models and combined double‐observer and distance sampling models (known as mark‐recapture‐distance‐sampling models; MRDS). When animals reside in groups, however, the assumption of independent detection is violated. In this case, the standard approach is to account for imperfect detection of groups, while assuming that individuals within groups are detected perfectly. However, this assumption is often unsupported. We introduce an abundance estimator for grouped animals when detection of groups is imperfect and group size may be under‐counted, but not over‐counted. The estimator combines an MRDS model with an N‐mixture model to account for imperfect detection of individuals. The new MRDS‐Nmix model requires the same data as an MRDS model (independent detection histories, an estimate of distance to transect, and an estimate of group size), plus a second estimate of group size provided by the second observer. We extend the model to situations in which detection of individuals within groups declines with distance. We simulated 12 data sets and used Bayesian methods to compare the performance of the new MRDS‐Nmix model to an MRDS model. Abundance estimates generated by the MRDS‐Nmix model exhibited minimal bias and nominal coverage levels. In contrast, MRDS abundance estimates were biased low and exhibited poor coverage. Many species of conservation interest reside in groups and could benefit from an estimator that better accounts for imperfect detection. Furthermore, the ability to relax the assumption of perfect detection of individuals within detected groups may allow surveyors to re‐allocate resources toward detection of new groups instead of extensive surveys of known groups. We believe the proposed estimator is feasible because the only additional field data required are a second estimate of group size. 相似文献
6.
Nina Luisa Santostasi Paolo Ciucci Romolo Caniglia Elena Fabbri Luigi Molinari Willy Reggioni Olivier Gimenez 《Ecology and evolution》2019,9(2):744-755
Estimating the relative abundance (prevalence) of different population segments is a key step in addressing fundamental research questions in ecology, evolution, and conservation. The raw percentage of individuals in the sample (naive prevalence) is generally used for this purpose, but it is likely to be subject to two main sources of bias. First, the detectability of individuals is ignored; second, classification errors may occur due to some inherent limits of the diagnostic methods. We developed a hidden Markov (also known as multievent) capture–recapture model to estimate prevalence in free‐ranging populations accounting for imperfect detectability and uncertainty in individual's classification. We carried out a simulation study to compare naive and model‐based estimates of prevalence and assess the performance of our model under different sampling scenarios. We then illustrate our method with a real‐world case study of estimating the prevalence of wolf (Canis lupus) and dog (Canis lupus familiaris) hybrids in a wolf population in northern Italy. We showed that the prevalence of hybrids could be estimated while accounting for both detectability and classification uncertainty. Model‐based prevalence consistently had better performance than naive prevalence in the presence of differential detectability and assignment probability and was unbiased for sampling scenarios with high detectability. We also showed that ignoring detectability and uncertainty in the wolf case study would lead to underestimating the prevalence of hybrids. Our results underline the importance of a model‐based approach to obtain unbiased estimates of prevalence of different population segments. Our model can be adapted to any taxa, and it can be used to estimate absolute abundance and prevalence in a variety of cases involving imperfect detection and uncertainty in classification of individuals (e.g., sex ratio, proportion of breeders, and prevalence of infected individuals). 相似文献
7.
Guillaume Péron Jean‐Michel Gaillard Christophe Barbraud Christophe Bonenfant Anne Charmantier Rémi Choquet Tim Coulson Vladimir Grosbois Anne Loison Gilbert Marzolin Norman Owen‐Smith Déborah Pardo Floriane Plard Roger Pradel Carole Toïgo Olivier Gimenez 《Evolution; international journal of organic evolution》2016,70(12):2909-2914
The canalization hypothesis postulates that the rate at which trait variation generates variation in the average individual fitness in a population determines how buffered traits are against environmental and genetic factors. The ranking of a species on the slow‐fast continuum – the covariation among life‐history traits describing species‐specific life cycles along a gradient going from a long life, slow maturity, and low annual reproductive output, to a short life, fast maturity, and high annual reproductive output – strongly correlates with the relative fitness impact of a given amount of variation in adult survival. Under the canalization hypothesis, long‐lived species are thus expected to display less individual heterogeneity in survival at the onset of adulthood, when reproductive values peak, than short‐lived species. We tested this life‐history prediction by analysing long‐term time series of individual‐based data in nine species of birds and mammals using capture‐recapture models. We found that individual heterogeneity in survival was higher in species with short‐generation time (< 3 years) than in species with long generation time (> 4 years). Our findings provide the first piece of empirical evidence for the canalization hypothesis at the individual level from the wild. 相似文献
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Understanding how climatic variation affects animal populations and communities is essential for addressing threats posed by climate change, especially in systems where impacts are projected to be high. We evaluated abundance dynamics of five common species of diurnal lizards over 25 years in a Sonoran Desert transition zone where precipitation decreased and temperature increased across time, and assessed hypotheses for the influence of climatic flux on spatiotemporal variation in abundances. We repeatedly surveyed lizards in spring and summer of each year at up to 32 sites, and used hierarchical mixture models to estimate detection probabilities, abundances, and population growth rates. Among terrestrial species, abundances of a short‐lived, winter–spring breeder increased markedly by an estimated 237%–285% across time, while two larger spring–summer breeders with higher thermal preferences declined by up to 64%. Abundances of two arboreal species that occupy shaded and thus sheltered microhabitats fluctuated but did not decline systematically. Abundances of all species increased with precipitation at short lag times (1–1.5 years) likely due to enhanced food availability, but often declined after periods of high precipitation at longer lag times (2–4 years) likely due to predation and other biotic pressures. Although rising maximum daily temperatures (Tmax) are expected to drive global declines of lizards, associations with Tmax were variable and weak for most species. Instead, abundances of all species declined with rising daily minimum temperatures, suggesting degradation of cool refugia imposed widespread metabolic or other costs. Our results suggest climate warming and drying are having major impacts on lizard communities by driving declines in species with traits that augment exposure to abiotic extremes and by modifying species interactions. The complexity of patterns we report indicates that evaluating and responding to the influence of climate change on biodiversity must consider a broad array of ecological processes. 相似文献
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In capture–recapture models, survival and capture probabilities can be modelled as functions of time‐varying covariates, such as temperature or rainfall. The Cormack–Jolly–Seber (CJS) model allows for flexible modelling of these covariates; however, the functional relationship may not be linear. We extend the CJS model by semi‐parametrically modelling capture and survival probabilities using a frequentist approach via P‐splines techniques. We investigate the performance of the estimators by conducting simulation studies. We also apply and compare these models with known semi‐parametric Bayesian approaches on simulated and real data sets. 相似文献
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Filipe Alves Ana Dinis Cátia Nicolau Cláudia Ribeiro Manfred Kaufmann Caterina Fortuna Luís Freitas 《Marine Mammal Science》2015,31(1):106-121
Estimates of population parameters for the short‐finned pilot whale, Globicephala macrorhynchus, are scarce in literature, contributing to an International Union for Conservation of Nature (IUCN) status of Data Deficient. In this study, photo‐identification data collected over 7 yr from Madeira were used to estimate for the first time survivorship, capture probability, and abundance in this species using mark‐recapture methodology. The Cormack‐Jolly‐Seber model estimated that the adult island‐associated (i.e., resident and regular visitor) whales had a constant survival rate of 0.960 (95% CI: 0.853–0.990) and an annual capture probability varying between 0.372 (CI: 0.178–0.619) and 0.843 (CI: 0.619–0.947). A parameterization of the Jolly‐Seber model estimated that 140 island‐associated whales (CI: 131–151) used the area throughout the course of the study. Based on a closed population model, the most precise (lower CV) annual estimate of the total number of pilot whales using the southern and eastern waters of Madeira (~900 km2) in a 3 mo period covering summer/autumn was 334 animals (CI: 260–437). No trend was observed. Despite including biases, the approach used in this study provided plausible estimates of population parameters, which can contribute to the regional conservation strategies. 相似文献
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Mauricio Cantor Leonardo L. Wedekin Fábio G. Daura‐Jorge Marcos R. Rossi‐Santos Paulo C. Simões‐Lopes 《Marine Mammal Science》2012,28(1):63-83
This study represents the first attempt to study the population dynamics of Guiana dolphins (Sotalia guianensis), by evaluating a set of demographic parameters. The population of the Caravelas River estuary, eastern Brazil, was systematically monitored through a long‐term mark‐recapture experiment (2002–2009). Abundance estimates revealed a small population (57–124 dolphins), comprised of resident dolphins and individuals that temporarily leave or pass through the study area. Temporary emigration from the estuary to adjacencies (γ″= 0.33 ± 0.07 SE) and return rate (1 ?γ′= 0 .67) were moderate and constant, indicating that some dolphins use larger areas. Survival rate (?= 0.88 ± 0.07 SE) and abundance were constant throughout the study period. Power analysis showed that the current monitoring effort has high probability of detecting abrupt population declines (1 ?β= 0.9). Although the monitoring is not yet sensitive to subtle population trends, sufficient time to identify them is feasible (additional 3 yr). Despite such apparent stability, this population, as many others, inhabits waters exposed to multiple human‐related threats. Open and closed population modeling applied to photo‐identification data provide a robust baseline for estimating several demographic parameters and can be applied to other populations to allow further comparisons. Such synergistic efforts will allow a reliable definition of conservation status of this species. 相似文献
13.
Summary Estimation of abundance is important in both open and closed population capture–recapture analysis, but unmodeled heterogeneity of capture probability leads to negative bias in abundance estimates. This article defines and develops a suite of open population capture–recapture models using finite mixtures to model heterogeneity of capture and survival probabilities. Model comparisons and parameter estimation use likelihood‐based methods. A real example is analyzed, and simulations are used to check the main features of the heterogeneous models, especially the quality of estimation of abundance, survival, recruitment, and turnover. The two major advances in this article are the provision of realistic abundance estimates that take account of heterogenetiy of capture, and an appraisal of the amount of overestimation of survival arising from conditioning on the first capture when heterogeneity of survival is present. 相似文献
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Yoichiro Kanno Benjamin H. Letcher Nathaniel P. Hitt David A. Boughton John E. B. Wofford Elise F. Zipkin 《Global Change Biology》2015,21(5):1856-1870
Climate change affects seasonal weather patterns, but little is known about the relative importance of seasonal weather patterns on animal population vital rates. Even when such information exists, data are typically only available from intensive fieldwork (e.g., mark–recapture studies) at a limited spatial extent. Here, we investigated effects of seasonal air temperature and precipitation (fall, winter, and spring) on survival and recruitment of brook trout (Salvelinus fontinalis) at a broad spatial scale using a novel stage‐structured population model. The data were a 15‐year record of brook trout abundance from 72 sites distributed across a 170‐km‐long mountain range in Shenandoah National Park, Virginia, USA. Population vital rates responded differently to weather and site‐specific conditions. Specifically, young‐of‐year survival was most strongly affected by spring temperature, adult survival by elevation and per‐capita recruitment by winter precipitation. Low fall precipitation and high winter precipitation, the latter of which is predicted to increase under climate change for the study region, had the strongest negative effects on trout populations. Simulations show that trout abundance could be greatly reduced under constant high winter precipitation, consistent with the expected effects of gravel‐scouring flows on eggs and newly hatched individuals. However, high‐elevation sites would be less vulnerable to local extinction because they supported higher adult survival. Furthermore, the majority of brook trout populations are projected to persist if high winter precipitation occurs only intermittently (≤3 of 5 years) due to density‐dependent recruitment. Variable drivers of vital rates should be commonly found in animal populations characterized by ontogenetic changes in habitat, and such stage‐structured effects may increase population persistence to changing climate by not affecting all life stages simultaneously. Yet, our results also demonstrate that weather patterns during seemingly less consequential seasons (e.g., winter precipitation) can have major impacts on animal population dynamics. 相似文献
15.
Graziella V. DiRenzo Christian Che‐Castaldo Sarah P. Saunders Evan H. Campbell Grant Elise F. Zipkin 《Ecology and evolution》2019,9(2):899-909
Obtaining inferences on disease dynamics (e.g., host population size, pathogen prevalence, transmission rate, host survival probability) typically requires marking and tracking individuals over time. While multistate mark–recapture models can produce high‐quality inference, these techniques are difficult to employ at large spatial and long temporal scales or in small remnant host populations decimated by virulent pathogens, where low recapture rates may preclude the use of mark–recapture techniques. Recently developed N‐mixture models offer a statistical framework for estimating wildlife disease dynamics from count data. N‐mixture models are a type of state‐space model in which observation error is attributed to failing to detect some individuals when they are present (i.e., false negatives). The analysis approach uses repeated surveys of sites over a period of population closure to estimate detection probability. We review the challenges of modeling disease dynamics and describe how N‐mixture models can be used to estimate common metrics, including pathogen prevalence, transmission, and recovery rates while accounting for imperfect host and pathogen detection. We also offer a perspective on future research directions at the intersection of quantitative and disease ecology, including the estimation of false positives in pathogen presence, spatially explicit disease‐structured N‐mixture models, and the integration of other data types with count data to inform disease dynamics. Managers rely on accurate and precise estimates of disease dynamics to develop strategies to mitigate pathogen impacts on host populations. At a time when pathogens pose one of the greatest threats to biodiversity, statistical methods that lead to robust inferences on host populations are critically needed for rapid, rather than incremental, assessments of the impacts of emerging infectious diseases. 相似文献
16.
Luca Scrucca 《Biometrical journal. Biometrische Zeitschrift》2019,61(4):873-888
Finite mixture of Gaussian distributions provide a flexible semiparametric methodology for density estimation when the continuous variables under investigation have no boundaries. However, in practical applications, variables may be partially bounded (e.g., taking nonnegative values) or completely bounded (e.g., taking values in the unit interval). In this case, the standard Gaussian finite mixture model assigns nonzero densities to any possible values, even to those outside the ranges where the variables are defined, hence resulting in potentially severe bias. In this paper, we propose a transformation‐based approach for Gaussian mixture modeling in case of bounded variables. The basic idea is to carry out density estimation not on the original data but on appropriately transformed data. Then, the density for the original data can be obtained by a change of variables. Both the transformation parameters and the parameters of the Gaussian mixture are jointly estimated by the expectation‐maximization (EM) algorithm. The methodology for partially and completely bounded data is illustrated using both simulated data and real data applications. 相似文献
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Summary Variable selection for clustering is an important and challenging problem in high‐dimensional data analysis. Existing variable selection methods for model‐based clustering select informative variables in a “one‐in‐all‐out” manner; that is, a variable is selected if at least one pair of clusters is separable by this variable and removed if it cannot separate any of the clusters. In many applications, however, it is of interest to further establish exactly which clusters are separable by each informative variable. To address this question, we propose a pairwise variable selection method for high‐dimensional model‐based clustering. The method is based on a new pairwise penalty. Results on simulated and real data show that the new method performs better than alternative approaches that use ?1 and ?∞ penalties and offers better interpretation. 相似文献
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Vasco Manuel Nobre de Carvalho da Silva Vieira Rui Orlando Pimenta Santos 《Journal of phycology》2010,46(6):1128-1137
Studies investigating the demographic traits that drive the patterns of phase dominance (the ploidy ratio) in isomorphic biphasic life cycles have not found an integrative solution. Either fertility or survival has been suggested independently as the main driver. Here, we provide a global theoretical framework on how demographic mechanisms determine the ploidy ratio, unifying previous numerical and observational attempts at this question. The analytical solutions of both the ploidy ratio and its elasticities to model parameters of a stage/size‐structured model patterned after the life cycle of a marine alga were derived and analyzed. A complex interaction among vital rates determines the patterns of phase dominance of biphasic life cycles. Three co‐occurring processes—growth, fertility, and looping—may dominate the dynamics of the population, determining both its growth rate and ploidy ratio. Our analyses show that in species where fertility is low, the ploidy ratio is highly elastic to looping transitions (survival, breakage, and clonal growth). Consequently, the subtle morphological, ecophysiological, and biochemistry phase differences that have been reported in isomorphic life cycles as not explaining the observed ploidy ratios, may, in fact, explain them if they translate into slight phase differences in looping transitions. In species where fertility is low, the looping dissimilarities between phases cannot be too high favoring simultaneously one phase, as the population structure would be completely dominated by that phase. In the case of ecological similarity between phases (equal looping and growth rates between phases), a ploidy ratio different from one can only be set by strong phase differences in fertility. 相似文献
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Fábio G. Daura‐Jorge Simon N. Ingram Paulo C. Simões‐Lopes 《Marine Mammal Science》2013,29(2):293-311
A subgroup of a population of Tursiops truncatus in southern Brazil is known for a cooperative behavior with artisanal fishermen whereby the dolphins shoal fish towards net‐casting fishermen. Combining photo‐identification data collected between September 2007 and 2009 with mark‐recapture and Pollock's robust design models, we assessed abundance within seasons and survival and temporary emigration rates of dolphins between seasons. We also reanalyzed a previous data set collected during 1989–1991, and Cormack‐Jolly‐Seber models were applied to estimate survival rates for each of the study periods. The abundance of marked “cooperative” dolphins varied between seasons from 18 (CI: 17–24) to 21 (CI: 20–24). The total abundance varied from 59 in the winter of 2008 (CI: 49–72) to 50 in the autumn of 2009 (CI: 40–62). The annual adult survival was estimated to be 0.917 (CI: 0.876–0.961), close to that estimated from data collected in the 1990s (0.941; CI: 0.888–0.998). The emigration probability was low (0.031; CI: 0.011–0.084) and different capture probabilities between the “cooperative” and “noncooperative” dolphins indicated a degree of behavioral segregation. The precision of our estimates is likely to provide sufficient power to detect population change, but we recommend a precautionary management approach to protect this vulnerable dolphin community and its unique cooperative feeding tradition. 相似文献