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1.
We propose a Bayesian hierarchical modeling approach for estimating the size of a closed population from data obtained by identifying individuals through photographs of natural markings. We assume that noisy measurements of a set of distinctive features are available for each individual present in a photographic catalogue. To estimate the population size from two catalogues obtained during two different sampling occasions, we embed the standard two-stage $M_t$ capture–recapture model for closed population into a multivariate normal data matching model that identifies the common individuals across the catalogues. In addition to estimating the population size while accounting for the matching process uncertainty, this hierarchical modelling approach allows to identify the common individuals by using the information provided by the capture–recapture model. This way, our model also represents a novel and reliable tool able to reduce the amount of effort researchers have to expend in matching individuals. We illustrate and motivate the proposed approach via a real data set of photo-identification of narwhals. Moreover, we compare our method with a set of possible alternative approaches by using both the empirical data set and a simulation study.  相似文献   

2.
A hierarchical model for spatial capture-recapture data   总被引:1,自引:0,他引:1  
Royle JA  Young KV 《Ecology》2008,89(8):2281-2289
Estimating density is a fundamental objective of many animal population studies. Application of methods for estimating population size from ostensibly closed populations is widespread, but ineffective for estimating absolute density because most populations are subject to short-term movements or so-called temporary emigration. This phenomenon invalidates the resulting estimates because the effective sample area is unknown. A number of methods involving the adjustment of estimates based on heuristic considerations are in widespread use. In this paper, a hierarchical model of spatially indexed capture-recapture data is proposed for sampling based on area searches of spatial sample units subject to uniform sampling intensity. The hierarchical model contains explicit models for the distribution of individuals and their movements, in addition to an observation model that is conditional on the location of individuals during sampling. Bayesian analysis of the hierarchical model is achieved by the use of data augmentation, which allows for a straightforward implementation in the freely available software WinBUGS. We present results of a simulation study that was carried out to evaluate the operating characteristics of the Bayesian estimator under variable densities and movement patterns of individuals. An application of the model is presented for survey data on the flat-tailed horned lizard (Phrynosoma mcallii) in Arizona, USA.  相似文献   

3.
We developed a method to estimate population abundance from simultaneous counts of unmarked individuals over multiple sites. We considered that at each sampling occasion, individuals in a population could be detected at 1 of the survey sites or remain undetected and used either multinomial or binomial simultaneous-count models to estimate abundance, the latter being equivalent to an N-mixture model with one site. We tested model performance with simulations over a range of detection probabilities, population sizes, growth rates, number of years, sampling occasions, and sites. We then applied our method to 3 critically endangered vulture species in Cambodia to demonstrate the real-world applicability of the model and to provide the first abundance estimates for these species in Cambodia. Our new approach works best when existing methods are expected to perform poorly (i.e., few sites and large variation in abundance among sites) and if individuals may move among sites between sampling occasions. The approach performed better when there were >8 sampling occasions and net probability of detection was high (>0.5). We believe our approach will be useful in particular for simultaneous surveys at aggregation sites, such as roosts. The method complements existing approaches for estimating abundance of unmarked individuals and is the first method designed specifically for simultaneous counts.  相似文献   

4.
Abstract: The Hihi (Stitchbird, Notiomystis cincta ) is an endemic New Zealand honeyeater that after European colonization survived on only one offshore island. Attempts to reintroduce Hihi to other islands have been unsuccessful, with populations slowly declining. The main hypothesis for these declines was an inadequate year-round supply of carbohydrate food (nectar and fruit) due to human impacts on the forest habitat. When Hihi were reintroduced to Mokoia, another island with regenerating forest, we tested whether survival was limited by carbohydrate food in the year after release. We conducted an "on-off" experiment in which ad libitum sugar water was available to birds for 2 out of every 4 weeks. We compared the masses of individual birds at the end of on and off periods to identify times when birds lost condition with no supplementary food and would be likely to starve. We also used mark-recapture analysis of resighting data to test whether mortality rates were higher when supplementary food was unavailable. The only effect of the supplementary food was that Hihi spent less time foraging for nectar and fruit and more time foraging for invertebrates. There was no time of year when birds lost mass when the food was taken away, and survival rates were not significantly lower when supplementary food was absent. The low (38%) annual survival rate could not be accounted for by shortage of carbohydrate food, and population viability analysis suggests that the population is likely to slowly decline. Our experiment shows that declines of reintroduced Hihi populations may be unrelated to food supply and that alternative hypotheses should be developed and tested. Our results also show the importance of using experimental methods, when possible, to test hypotheses about factors thought to be limiting reintroduced populations.  相似文献   

5.
The mean and variance of lifetime reproductive success, ELRS and VLRS, influence the ratio of effective to census population size, Ne/Nc. Because the complete data needed to calculate ELRS and VLRS are seldom available, we provide alternatives for estimating Ne/Nc from incomplete data. These estimates should be useful to conservation biologists trying to compute the effective size of a censused population. An analytical approach makes assumptions regarding the process influencing offspring survival. We provide a method for examining the validity of those assumptions and show that particular violations can result in either over- or underestimates. When the assumptions are violated or when more data are available, we suggest estimating Ne/Nc using computer simulations of models based on individuals. We examine how such simulations can be used to estimate Ne/Nc using an individual-based model for Lesser Snow Geese ( Anser caerulescens ). We demonstrate that such estimates can be biased unless the simulations are based on complete cohorts and samples of known age. We show that because the estimate of Ne/Nc depends on the stage of the reproductive cycle used as a point of reference in the model, the census population size Nc must be based on the same stage to provide unbiased estimates of Ne.  相似文献   

6.
A number of models have been proposed to provide adaptive explanations of sex-ratio variation in mammals. Two models have been applied commonly to primates and ungulates with varying success—the Trivers-Willard (TW) hypothesis, and the local resource competition (LRC) hypothesis. For polygynous, sexually dimorphic mammals, where males are larger and disperse more readily, these models predict opposite outcomes of sex-ratio adjustment within the same environmental context (high-resource years: TW—more sons; LRC—more daughters). However, many of the predictions of these two models can vary depending on factors influencing resource availability, such as environmental stochasticity, resource predictability, and population density. The New Zealand fur seal (Arctocephalus forsteri) is a polygynous mammal showing marked sexual dimorphism (larger males), with higher variation in male reproductive success expected. We provide clear evidence of male-biased sex ratios from a large sample of A. forsteri pups captured around South Island, New Zealand during 1996/1998, even after accounting for a sex bias in capture probability. The extent of the bias depended upon year and, in 1998, strong climatic perturbations (El Niño/Southern Oscillation, ENSO) probably reduced food availability. Significant male-biased sex ratios were found in all years; however, there was a significant decline in the male bias in 1998. There was no relationship between sex ratio and population density. We suggest that the sex-ratio bias resulted from the production of relatively more male pups. Under the density-independent scenario, the strong male bias in A. forsteri sex ratios is support for the TW model within an environment of high resource predictability. We suggest that some plasticity in the determination of pup sex among years is a mechanism by which A. forsteri females in New Zealand, and perhaps other otariid seals, can maximise fitness benefits when living in regions of high, yet apparently predictable, environmental variability. We also suggest that much of the inconsistency in the reported sex ratios for otariid seals results from the complex interaction of population density and environmental stochasticity influencing relative food availability over time.  相似文献   

7.
The estimation of population density animal population parameters, such as capture probability, population size, or population density, is an important issue in many ecological applications. Capture–recapture data may be considered as repeated observations that are often correlated over time. If these correlations are not taken into account then parameter estimates may be biased, possibly producing misleading results. We propose a generalized estimating equations (GEE) approach to account for correlation over time instead of assuming independence as in the traditional closed population capture–recapture studies. We also account for heterogeneity among observed individuals and over-dispersion, modelling capture probabilities as a function of covariates. The GEE versions of all closed population capture–recapture models and their corresponding estimating equations are proposed. We evaluate the effect of accounting for correlation structures on capture–recapture model selection based on the quasi-likelihood information criterion (QIC). An example is used for an illustrative application and for comparison to currently used methodology. A Horvitz–Thompson-like estimator is used to obtain estimates of population size based on conditional arguments. A simulation study is conducted to evaluate the performance of the GEE approach in capture-recapture studies. The GEE approach performs well for estimating population parameters, particularly when capture probabilities are high. The simulation results also reveal that estimated population size varies on the nature of the existing correlation among capture occasions.  相似文献   

8.
Accurate estimates of demographic parameters are key for understanding and predicting population dynamics and for providing insights for effective wildlife management. Up until recently, no suitable methodology has been available to estimate survival probabilities of species with asynchronous reproduction and a high level of individual variation in capture probabilities. The present work develops a capture-mark-recapture model for cheetahs in the Serengeti National Park, Tanzania, which (a) deals with continuous reproduction, (b) takes into account the high level of individual heterogeneity in capture probabilities and (c) is spatially explicit. Results show that (1) our approach, which is an extensive modification of the Cormack-Jolly-Seber model, provides a lower female adult survival estimate and a higher male adolescent survival estimate than previous approaches to estimate cheetah survival in the area, (2) using sighting location alone is not sufficient to capture the individual variation in resighting probabilities for both sexes, and (3) precision in estimated survival probabilities is generally increased. Species which are individually recognizable, wide-ranging and/or where individuals differ substantially in sightability are particularly appropriate to our modelling approach, and our methodology would thus be appropriate for a wide number of species to provide more accurate estimates of survival.  相似文献   

9.
Diet quality is a key determinant of population dynamics. If a higher trophic level, more fish-based diet is of higher quality for marine predators, then individuals with a higher trophic level diet should have a greater body mass than those feeding at a lower trophic level. We examined this hypothesis using stable isotope analysis to infer dietary trophic level and foraging habitat over three years in eastern rockhopper penguins Eudyptes chrysocome filholi on sub-Antarctic Campbell Island, New Zealand. Rockhopper penguins are ‘Vulnerable’ to extinction because of widespread and dramatic population declines, perhaps related to nutritional stress caused by a climate-induced shift to a lower trophic level, lower quality diet. We related the stable nitrogen (δ15N) and carbon (δ13C) isotope values of blood from 70 chicks, 55 adult females, and 55 adult males to their body masses in the 2010, 2011, and 2012 breeding seasons and examined year, stage, age, and sex differences. Opposite to predictions, heavier males consumed a lower trophic level diet during incubation in 2011, and average chick mass was heavier in 2011 when chicks were fed a more zooplankton-based, pelagic/offshore diet than in 2012. Contrary to the suggested importance of a fish-based diet, our results support the alternative hypothesis that rockhopper penguin populations are likely to be most successful when abundant zooplankton prey are available. We caution that historic shifts to lower trophic level prey should not be assumed to reflect nutritional stress and a cause of population declines.  相似文献   

10.
In societies characterized by a high degree of fission-fusion dynamics, individuals adjust their grouping patterns according to the shifting balance of costs and benefits associated with grouping. This study examines influences on fission-fusion dynamics for dusky dolphins (Lagenorhynchus obscurus) in Admiralty Bay, New Zealand. This area is an important foraging habitat for dusky dolphins during the winter and spring. Admiralty Bay has little predation risk, but nearshore mussel farms may infringe on available habitat. I used generalized estimating equations to determine the influences of coordinated foraging, predation risk, and presence of mussel farms on party size, rate of fission-fusion, and behavioral state. I conducted 168 boat-based group focal follows totaling 168 h. The proportion of individuals observed foraging was positively related to party size and rate of party fusion. Resting had no effect on party size and did not vary according to location. Near mussel farms, traveling decreased, and rate of party fission decreased. I conclude that (1) coordinated foraging strategies are a primary influence on fission-fusion dynamics within this population, (2) dolphins may respond to decreased predation risk by not adjusting party size or location during resting, and (3) areas near mussel farms are not used for traveling.  相似文献   

11.
The formulation of conservation policy for species that are rare and migratory requires broad cooperation to ensure that adequate levels of standardized data collection are achieved and that the results of local analyses are comparable. Estimates of apparent survival rate, relative change in abundance, and proportions of newly marked and returning individuals can inform local management decisions while highlighting corresponding changes at other linked research stations. We have applied computer-assisted photo-identification and mark-recapture population modeling to whale sharks Rhincodon typus at Ningaloo Marine Park (NMP), Western Australia, to create a baseline trend for comparison with other regional aggregations of the species. We estimate several ecological parameters of interest, including an average apparent survival rate of 0.55 yr(-1) for sharks newly marked (new) and 0.83 yr(-1) for sharks captured in multiple seasons (philopatric). The average proportion of philopatric sharks is found to be 0.65 of the total population, and we derive an average population growth rate of 1.12 yr(-1) for them. Our analysis uncovered significant heterogeneity in capture and survival probabilities in this study population; our chosen model structures and data analysis account for these influences and demonstrate a good overall fit to the time-series data. The results show good correspondence between capture probability and an available measure of recapture effort, suggesting that unmodeled systematic effects contribute insignificantly to the model fits. We find no evidence of a decline in the whale shark population at NMP, and our results provide metrics of value to their future management. Overall, our study suggests an effective approach to analyzing and modeling mark-recapture data for a rare species using computer-assisted photo-identification and opportunistic data collection from ecotourism to ensure the quality and volume of data required for population analysis.  相似文献   

12.
Five polymorphic microsatellite loci were developed and then used to assess the population genetic structure of a commercially harvested merobenthic octopus species (Octopus maorum) in south-east Australian and New Zealand (NZ) waters. Beak and stylet morphometrics were also used to assess population differentiation in conjunction with the genetic data. Genetic variation across all loci and all sampled populations was very high (mean number alleles = 15, mean expected heterozygosity = 0.85). Microsatellites revealed significant genetic structuring (overall F ST = 0.024, p < 0.001), which did not fit an isolation-by-distance model of population differentiation. Divergence was observed between Australian and NZ populations, between South Australia and north-east Tasmania, and between two relatively proximate Tasmanian sites. South Australian and southern Tasmanian populations were genetically homogeneous, indicating a level of connectivity on a scale of 1,500 km. Morphometric data also indicated significant differences between Australian and NZ populations. The patterns of population structuring identified can be explained largely in relation to regional oceanographic features.  相似文献   

13.
Estimating the age of individuals in wild populations can be of fundamental importance for answering ecological questions, modeling population demographics, and managing exploited or threatened species. Significant effort has been devoted to determining age through the use of growth annuli, secondary physical characteristics related to age, and growth models. Many species, however, either do not exhibit physical characteristics useful for independent age validation or are too rare to justify sacrificing a large number of individuals to establish the relationship between size and age. Length-at-age models are well represented in the fisheries and other wildlife management literature. Many of these models overlook variation in growth rates of individuals and consider growth parameters as population parameters. More recent models have taken advantage of hierarchical structuring of parameters and Bayesian inference methods to allow for variation among individuals as functions of environmental covariates or individual-specific random effects. Here, we describe hierarchical models in which growth curves vary as individual-specific stochastic processes, and we show how these models can be fit using capture-recapture data for animals of unknown age along with data for animals of known age. We combine these independent data sources in a Bayesian analysis, distinguishing natural variation (among and within individuals) from measurement error. We illustrate using data for African dwarf crocodiles, comparing von Bertalanffy and logistic growth models. The analysis provides the means of predicting crocodile age, given a single measurement of head length. The von Bertalanffy was much better supported than the logistic growth model and predicted that dwarf crocodiles grow from 19.4 cm total length at birth to 32.9 cm in the first year and 45.3 cm by the end of their second year. Based on the minimum size of females observed with hatchlings, reproductive maturity was estimated to be at nine years. These size benchmarks are believed to represent thresholds for important demographic parameters; improved estimates of age, therefore, will increase the precision of population projection models. The modeling approach that we present can be applied to other species and offers significant advantages when multiple sources of data are available and traditional aging techniques are not practical.  相似文献   

14.
Waples RS  Do C  Chopelet J 《Ecology》2011,92(7):1513-1522
The concept of effective population size (Ne) was developed under a discrete-generation model, but most species have overlapping generations. In the early 1970s, J. Felsenstein and W. G. Hill independently developed methods for calculating Ne in age-structured populations; the two approaches produce the same answer under certain conditions and have contrasting advantages and disadvantages. Here, we describe a hybrid approach that combines useful features of both. Like Felsenstein's model, the new method is based on age-specific survival and fertility rates and therefore can be directly applied to any species for which life table data are available. Like Hill, we relax the restrictive assumption in Felsenstein's model regarding random variance in reproductive success, which allows more general application. The basic principle underlying the new method is that age structure stratifies a population into winners and losers in the game of life: individuals that live longer have more opportunities to reproduce and therefore have a higher mean lifetime reproductive success. This creates different classes of individuals within the population, and grouping individuals by age at death provides a simple means of calculating lifetime variance in reproductive success of a newborn cohort. The new method has the following features: (1) it can accommodate unequal sex ratio and sex-specific vital rates and overdispersed variance in reproductive success; (2) it can calculate effective size in species that change sex during their lifetime; (3) it can calculate Ne and the ratio Ne/N based on various ways of defining N; (4) it allows one to explore the relationship between Ne and the effective number of breeders per year (Nb), which is a quantity that genetic estimators of contemporary Ne commonly provide information about; and (5) it is implemented in freely available software (AgeNe).  相似文献   

15.
A method to reconstruct anguilliform fishes from partially digested items   总被引:1,自引:0,他引:1  
Estimating the amounts of resources consumed by individuals is important in many studies. For predators, allometric relationships can be used to extrapolate the size of preys from undigested remains found in the stomach and in the faeces. However, such equations are available for a limited number of species. Based on a large sample size gathered in New Caledonia on both predators (sea kraits) and their preys (anguilliform fishes), we provide the first allometric relationships that allow estimating accurately the mass and the size of various anguilliform fish species.  相似文献   

16.
The spread of invasive species is a major ecological and economic problem. Dynamic spread modelling is a potentially valuable tool to assist regional and central government authorities to monitor and control invasive species. To date a lack of suitable data has meant that most broad scale dispersal models have not been validated with independent datasets, and so their predictive ability and reliability has remained unscrutinised. A dynamic, stochastic dispersal model of the widely invasive plant Buddleja davidii was calibrated on European spread data and then used to project the temporal progression of B. davidii's distribution in New Zealand, starting from several different historical distributions. To assess the model's performance, we constructed an occupancy map based on the average number of simulation realisations that have a population present. The application of Receiver Operating Characteristic (ROC) curves to occupancy maps is introduced, but with specificity substituted by the proportion of available area used in a realisation. A derivative measure, the partial area under these curves when assessed through time (pAUC), is introduced and used to assess overall performance of the spread model. The model was able to attain a high level of model sensitivity, encompassing all of the known locations within the occupancy envelope. However, attempting to simulate the spread of this invasive species beyond a decade had very low model specificity. This is due to several factors, including the exponential process of spread (the further a population spreads the more sites exist from which it can spread stochastically), and the Markovian chain property of the stochastic system whereby differences between realisations compound through time. These features are seen in many reports of spread models, without being explicitly acknowledged. Our measure of pAUC through time allows a model's temporal performance and its specificity to be simultaneously assessed. While the rapid deterioration in model performance limits the utility of this type of modelling for forecasting long-term broad-scale strategic management of biological invasions, it does not necessarily limit its attractiveness for informing smaller scale and shorter term invasion management activities such as surveillance, containment and local eradication.  相似文献   

17.
Over the past 1000 years New Zealand has lost 40–50% of its bird species, and over half of these extinctions are attributable to predation by introduced mammals. Populations of many extant forest bird species continue to be depredated by mammals, especially rats, possums, and mustelids. The management history of New Zealand's forests over the past 50 years presents a unique opportunity because a varied program of mammalian predator control has created a replicated management experiment. We conducted a meta-analysis of population-level responses of forest birds to different levels of mammal control recorded across New Zealand. We collected data from 32 uniquely treated sites and 20 extant bird species representing a total of 247 population responses to 3 intensities of invasive mammal control (zero, low, and high). The treatments varied from eradication of invasive mammals via ground-based techniques to periodic suppression of mammals via aerially sown toxin. We modeled population-level responses of birds according to key life history attributes to determine the biological processes that influence species’ responses to management. Large endemic species, such as the Kaka (Nestor meridionalis) and New Zealand Pigeon (Hemiphaga novaeseelandiae), responded positively at the population level to mammal control in 61 of 77 cases for species ≥20 g compared with 31 positive responses from 78 cases for species <20 g. The Fantail (Rhipidura fuliginosa) and Grey Warbler (Gerygone igata), both shallow endemic species, and 4 nonendemic species (Blackbird [Turdus merula], Chaffinch [Fringilla coelebs], Dunnock [Prunella modularis], and Silvereye [Zosterops lateralis]) that arrived in New Zealand in the last 200 years tended to have slight negative or neutral responses to mammal control (59 of 77 cases). Our results suggest that large, deeply endemic forest birds, especially cavity nesters, are most at risk of further decline in the absence of mammal control and, conversely suggest that 6 species apparently tolerate the presence of invasive mammals and may be sensitive to competition from larger endemic birds.  相似文献   

18.
Estimation of population size has traditionally been viewed from a finite population sampling perspective. Typically, the objective is to obtain an estimate of the total population count of individuals within some region. Often, some stratification scheme is used to estimate counts on subregions, whereby the total count is obtained by aggregation with weights, say, proportional to the areas of the subregions. We offer an alternative to the finite population sampling approach for estimating population size. The method does not require that the subregions on which counts are available form a complete partition of the region of interest. In fact, we envision counts coming from areal units that are small relative to the entire study region and that the total area sampled is a very small proportion of the total study area. In extrapolating to the entire region, we might benefit from assuming that there is spatial structure to the counts. We implement this by modeling the intensity surface as a realization from a spatially correlated random process. In the case of multiple population or species counts, we use the linear model of coregionalization to specify a multivariate process which provides associated intensity surfaces hence association between counts within and across areal units. We illustrate the method of population size estimation with simulated data and with tree counts from a Southwestern pinyon-juniper woodland data set.  相似文献   

19.
Eradication of introduced mammalian predators from islands has become increasingly common, with over 800 successful projects around the world. Historically, introduced predators extirpated or reduced the size of many seabird populations, changing the dynamics of entire island ecosystems. Although the primary outcome of many eradication projects is the restoration of affected seabird populations, natural population responses are rarely documented and mechanisms are poorly understood. We used a generic model of seabird colony growth to identify key predictor variables relevant to recovery or recolonization. We used generalized linear mixed models to test the importance of these variables in driving seabird population responses after predator eradication on islands around New Zealand. The most influential variable affecting recolonization of seabirds around New Zealand was the distance to a source population, with few cases of recolonization without a source population ≤25 km away. Colony growth was most affected by metapopulation status; there was little colony growth in species with a declining status. These characteristics may facilitate the prioritization of newly predator‐free islands for active management. Although we found some evidence documenting natural recovery, generally this topic was understudied. Our results suggest that in order to guide management strategies, more effort should be allocated to monitoring wildlife response after eradication. Conductores de la Recuperación de Poblaciones de Aves Marinas en Islas de Nueva Zelanda después de la Erradicación de Depredadores  相似文献   

20.
Because of increasing transport and trade there is a growing threat of marine invasive species being introduced into regions where they do not presently occur. So that the impacts of such species can be mitigated, it is important to predict how individuals, particularly passive dispersers are transported and dispersed in the ocean as well as in coastal regions so that new incursions of potential invasive species are rapidly detected and origins identified. Such predictions also support strategic monitoring, containment and/or eradication programs. To determine factors influencing a passive disperser, around coastal New Zealand, data from the genus Physalia (Cnidaria: Siphonophora) were used. Oceanographic data on wave height and wind direction and records of occurrences of Physalia on swimming beaches throughout the summer season were used to create models using artificial neural networks (ANNs) and Na?ve Bayesian Classifier (NBC). First, however, redundant and irrelevant data were removed using feature selection of a subset of variables. Two methods for feature selection were compared, one based on the multilayer perceptron and another based on an evolutionary algorithm. The models indicated that New Zealand appears to have two independent systems driven by currents and oceanographic variables that are responsible for the redistribution of Physalia from north of New Zealand and from the Tasman Sea to their subsequent presence in coastal waters. One system is centred in the east coast of northern New Zealand and the other involves a dynamic system that encompasses four other regions on both coasts of the country. Interestingly, the models confirm, molecular data obtained from Physalia in a previous study that identified a similar distribution of systems around New Zealand coastal waters. Additionally, this study demonstrates that the modelling methods used could generate valid hypotheses from noisy and complicated data in a system about which there is little previous knowledge.  相似文献   

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