Complete tag loss in capture–recapture studies affects abundance estimates: An elephant seal case study

1. In capture–recapture studies, recycled individuals occur when individuals lose all of their tags and are recaptured as though they were new individuals. Typically, the effect of these recycled individuals is assumed negligible.
2. Through a simulation‐based study of double‐tagging experiments, we examined the effect of recycled individuals on parameter estimates in the Jolly–Seber model with tag loss (Cowen & Schwarz, 2006). We validated the simulation framework using long‐term census data of elephant seals.
3. Including recycled individuals did not affect estimates of capture, survival, and tag‐retention probabilities. However, with low tag‐retention rates, high capture rates, and high survival rates, recycled individuals produced overestimates of population size. For the elephant seal case study, we found population size estimates to be between 8% and 53% larger when recycled individuals were ignored.
4. Ignoring the effects of recycled individuals can cause large biases in population size estimates. These results are particularly noticeable in longer studies.

     

Using incidental mark‐encounter data to improve survival estimation

1. Obtaining robust survival estimates is critical, but sample size limitations often result in imprecise estimates or the failure to obtain estimates for population subgroups. Concurrently, data are often recorded on incidental reencounters of marked individuals, but these incidental data are often unused in survival analyses.
2. We evaluated the utility of supplementing a traditional survival dataset with incidental data on marked individuals that were collected ad hoc. We used a continuous time‐to‐event exponential survival model to leverage the matching information contained in both datasets and assessed differences in survival among adult and juvenile and resident and translocated Mojave desert tortoises (Gopherus agassizii).
3. Incorporation of the incidental mark‐encounter data improved precision of all annual survival point estimates, with a 3.4%–37.5% reduction in the spread of the 95% Bayesian credible intervals. We were able to estimate annual survival for three subgroup combinations that were previously inestimable. Point estimates between the radiotelemetry and combined datasets were within |0.029| percentage points of each other, suggesting minimal to no bias induced by the incidental data.
4. Annual survival rates were high (>0.89) for resident adult and juvenile tortoises in both study sites and for translocated adults in the southern site. Annual survival rates for translocated juveniles at both sites and translocated adults in the northern site were between 0.73 and 0.76. At both sites, translocated adults and juveniles had significantly lower survival than resident adults. High mortality in the northern site was driven primarily by a single pulse in mortalities.
5. Using exponential survival models to leverage matching information across traditional survival studies and incidental data on marked individuals may serve as a useful tool to improve the precision and estimability of survival rates. This can improve the efficacy of understanding basic population ecology and population monitoring for imperiled species.

     

Robustness of close‐kin mark–recapture estimators to dispersal limitation and spatially varying sampling probabilities

1. Close‐kin mark–recapture (CKMR) is a method for estimating abundance and vital rates from kinship relationships observed in genetic samples. CKMR inference only requires animals to be sampled once (e.g., lethally), potentially widening the scope of population‐level inference relative to traditional monitoring programs.
2. One assumption of CKMR is that, conditional on individual covariates like age, all animals have an equal probability of being sampled. However, if genetic data are collected opportunistically (e.g., via hunters or fishers), there is potential for spatial variation in sampling probability that can bias CKMR estimators, particularly when genetically related individuals stay in close proximity.
3. We used individual‐based simulation to investigate consequences of dispersal limitation and spatially biased sampling on performance of naive (nonspatial) CKMR estimators of abundance, fecundity, and adult survival. Population dynamics approximated that of a long‐lived mammal species subject to lethal sampling.
4. Naive CKMR abundance estimators were relatively unbiased when dispersal was unconstrained (i.e., complete mixing) or when sampling was random or subject to moderate levels of spatial variation. When dispersal was limited, extreme variation in spatial sampling probabilities negatively biased abundance estimates. Reproductive schedules and survival were well estimated, except for survival when adults could emigrate out of the sampled area. Incomplete mixing was readily detected using Kolmogorov–Smirnov tests.
5. Although CKMR appears promising for estimating abundance and vital rates with opportunistically collected genetic data, care is needed when dispersal limitation is coupled with spatially biased sampling. Fortunately, incomplete mixing is easily detected with adequate sample sizes. In principle, it is possible to devise and fit spatially explicit CKMR models to avoid bias under dispersal limitation, but development of such models necessitates additional complexity (and possibly additional data). We suggest using simulation studies to examine potential bias and precision of proposed modeling approaches prior to implementing a CKMR program.

     

Intraspecific genetic variation of a Fagus sylvatica population in a temperate forest derived from airborne imaging spectroscopy time series

1. The growing pace of environmental change has increased the need for large‐scale monitoring of biodiversity. Declining intraspecific genetic variation is likely a critical factor in biodiversity loss, but is especially difficult to monitor: assessments of genetic variation are commonly based on measuring allele pools, which requires sampling of individuals and extensive sample processing, limiting spatial coverage. Alternatively, imaging spectroscopy data from remote platforms may hold the potential to reveal genetic structure of populations. In this study, we investigated how differences detected in an airborne imaging spectroscopy time series correspond to genetic variation within a population of Fagus sylvatica under natural conditions.
2. We used multi‐annual APEX (Airborne Prism Experiment) imaging spectrometer data from a temperate forest located in the Swiss midlands (Laegern, 47°28'N, 8°21'E), along with microsatellite data from F. sylvatica individuals collected at the site. We identified variation in foliar reflectance independent of annual and seasonal changes which we hypothesize is more likely to correspond to stable genetic differences. We established a direct connection between the spectroscopy and genetics data by using partial least squares (PLS) regression to predict the probability of belonging to a genetic cluster from spectral data.
3. We achieved the best genetic structure prediction by using derivatives of reflectance and a subset of wavebands rather than full‐analyzed spectra. Our model indicates that spectral regions related to leaf water content, phenols, pigments, and wax composition contribute most to the ability of this approach to predict genetic structure of F. sylvatica population in natural conditions.
4. This study advances the use of airborne imaging spectroscopy to assess tree genetic diversity at canopy level under natural conditions, which could overcome current spatiotemporal limitations on monitoring, understanding, and preventing genetic biodiversity loss imposed by requirements for extensive in situ sampling.

     

The relative importance of reproduction and survival for the conservation of two dolphin populations

It has been proposed that in slow‐growing vertebrate populations survival generally has a greater influence on population growth than reproduction. Despite many studies cautioning against such generalizations for conservation, wildlife management for slow‐growing populations still often focuses on perturbing survival without careful evaluation as to whether those changes are likely or feasible. Here, we evaluate the relative importance of reproduction and survival for the conservation of two bottlenose dolphin (Tursiops cf aduncus) populations: a large, apparently stable population and a smaller one that is forecast to decline. We also assessed the feasibility and effectiveness of wildlife management objectives aimed at boosting either reproduction or survival. Consistent with other analytically based elasticity studies, survival had the greatest effect on population trajectories when altering vital rates by equal proportions. However, the findings of our alternative analytical approaches are in stark contrast to commonly used proportional sensitivity analyses and suggest that reproduction is considerably more important. We show that

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Distribution,status, and recent population dynamics of Alpine ibex Capra ibex in Europe

1. Despite its recent successful and well-documented reintroduction history, a comprehensive and current update of the distribution and status of the Alpine ibex Capra ibex is lacking. As some concerns persist about its conservation, a status update appears essential for future conservation and management strategies on a large scale.
2. We provide an exhaustive update of the geographic range of the species, alongside estimates of its current abundance and population trends from 2004 to 2015.
3. We gathered census and distribution data for all the Alpine ibex colonies from management authorities and research groups that monitor them in different countries, and from the literature and publicly available reports. We produced a distribution map, reported the number of individuals observed in the most recent censuses, and estimated global, national, and local population trends using Bayesian hierarchical models.
4. Our model estimated that there were a total of 55297 Alpine ibex in the Alps in 2015 (lower 95% credible interval [CrI]: 51157; upper 95% CrI: 62710). The total number of individuals appears to have increased slightly over the last 10 years from the 47000-51000 estimated in previous reports. Positive population trends were observed in Switzerland and Italy, while no trend was apparent in France. For Austria, Germany, and Slovenia, there were insufficient data to estimate a trend. The slopes of the colonies’ trends were positively correlated with the year of colony foundation.
5. The geographic range of the Alpine ibex does not seem to have increased in size in recent years, although the accuracy of the spatial data varies among countries.
6. The periodic and standardised collection of census data for all colonies and a common policy of data sharing at a European level appear essential for monitoring the global trend of this species and for planning balanced conservation and management actions.

     

Estimating population density of insectivorous bats based on stationary acoustic detectors: A case study

1. Automated recording units are commonly used by consultants to assess environmental impacts and to monitor animal populations. Although estimating population density of bats using stationary acoustic detectors is key for evaluating environmental impacts, estimating densities from call activity data is only possible through recently developed numerical methods, as the recognition of calling individuals is impossible.
2. We tested the applicability of generalized random encounter models (gREMs) for determining population densities of three bat species (Common pipistrelle Pipistrellus pipistrellus, Northern bat Eptesicus nilssonii, and Natterer's bat Myotis nattereri) based on passively collected acoustical data. To validate the results, we compared them to (a) density estimates from the literature and to (b) Royle–Nichols (RN) models of detection/nondetection data.
3. Our estimates for M. nattereri matched both the published data and RN‐model results. For E. nilssonii, the gREM yielded similar estimates to the RN‐models, but the published estimates were more than twice as high. This discrepancy might be because the high‐altitude flight of E. nilssonii is not accounted for in gREMs. Results of gREMs for P. pipistrellus were supported by published data but were ~10 times higher than those of RN‐models. RN‐models use detection/nondetection data, and this loss of information probably affected population estimates of very active species like P. pipistrellus.
4. gREM models provided realistic estimates of bat population densities based on automatically recorded call activity data. However, the average flight altitude of species should be accounted for in future analyses. We suggest including flight altitude in the calculation of the detection range to assess the detection sphere more accurately and to obtain more precise density estimates.

     

Long‐term mark‐and‐recapture study of a freshwater mussel reveals patterns of habitat use and an association between survival and river discharge

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Movement and early survival of age‐0 brown trout

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Combining data‐derived priors with postrelease monitoring data to predict persistence of reintroduced populations

Monitoring is an essential part of reintroduction programs, but many years of data may be needed to obtain reliable population projections. This duration can potentially be reduced by incorporating prior information on expected vital rates (survival and fecundity) when making inferences from monitoring data. The prior distributions for these parameters can be derived from data for previous reintroductions, but it is important to account for site‐to‐site variation. We evaluated whether such informative priors improved our ability to estimate the finite rate of increase (λ) of the North Island robin (Petroica longipes) population reintroduced to Tawharanui Regional Park, New Zealand. We assessed how precision improved with each year of postrelease data added, comparing models that used informative or uninformative priors. The population grew from about 22 to 80 individuals from 2007 to 2016, with λ estimated to be 1.23 if density dependence was included in the model and 1.13 otherwise. Under either model, 7 years of data were required before the lower 95% credible limit for λ was > 1, giving confidence that the population would persist. The informative priors did not reduce this requirement. Data‐derived priors are useful before reintroduction because they allow λ to be estimated in advance. However, in the case examined here, the value of the priors was overwhelmed once site‐specific monitoring data became available. The Bayesian method presented is logical for reintroduced populations. It allows prior information (used to inform prerelease decisions) to be integrated with postrelease monitoring. This makes full use of the data for ongoing management decisions. However, if the priors properly account for site‐to‐site variation, they may have little predictive value compared with the site‐specific data. This value will depend on the degree of site‐to‐site variation as well as the quality of the data.     

Methodological bias in the seed bank flora holds significant implications for understanding seed bank community functions

• Persistent seed banks are a key plant regeneration strategy, buffering environmental variation to allow population and species persistence. Understanding seed bank functioning within herb layer dynamics is therefore important. However, rather than assessing emergence from the seed bank in herb layer gaps, most studies evaluate the seed bank functioning via a greenhouse census. We hypothesise that greenhouse data may not reflect seed bank‐driven emergence in disturbance gaps due to methodological differences. Failure in detecting (specialist) species may then introduce methodological bias into the ecological interpretation of seed bank functions using greenhouse data.
• The persistent seed bank was surveyed in 40 semi‐natural grassland plots across a fragmented landscape, quantifying seedling emergence in both the greenhouse and in disturbance gaps. Given the suspected interpretational bias, we tested whether each census uncovers similar seed bank responses to fragmentation.
• Seed bank characteristics were similar between censuses. Census type affected seed bank composition, with >25% of species retrieved better by either census type, dependent on functional traits including seed longevity, production and size. Habitat specialists emerged more in disturbance gaps than in the greenhouse, while the opposite was true for ruderal species. Both censuses uncovered fragmentation‐induced seed bank patterns.
• Low surface area sampling, larger depth of sampling and germination conditions cause underrepresentation of the habitat‐specialised part of the persistent seed bank flora during greenhouse censuses. Methodological bias introduced in the recorded seed bank data may consequently have significant implications for the ecological interpretation of seed bank community functions based on greenhouse data.

     

Beyond ecological opportunity: Prey diversity rather than abundance shapes predator niche variation

1. Ecological opportunity (i.e. the diversity of available resources) has a pivotal role in shaping niche variation and trophic specialisation of animals. However, ecological opportunity can be described with regard to both diversity and abundance of resources. The degree to which these two components contribute to niche variation remains unexplored.
2. To address this, we used an extensive dataset on fish diet and benthic invertebrate diversity and density from 73 sampling events in three Norwegian rivers in order to explore realised trophic niches and the response of dietary niche variation along gradients of resource diversity (potential trophic niches), resource density (as a proxy of resource abundance) and fish density (as a proxy of inter‐ and intra‐specific competition) in a freshwater top predator (the brown trout, Salmo trutta L.).
3. Linear models indicated that individual and population niche variation increased with increasing ecological opportunity in terms of prey diversity. However, no simple cause‐and‐effect associations between niche indices and prey abundance were found. Our multiple regression analyses indicated that the abundance of certain resources (e.g. Chironomidae) can interact with prey diversity to determine individual and population realised trophic niches. Niche variation (within‐individual component and inter‐individual diet variation) decreased with increasing inter‐ and intra‐specific competition.
4. This study extends prevailing trophic ecology theory by identifying diversity, rather than density, of available prey resources as a primary driver of niche variation in fish of temperate riverine systems with no extensive resource limitation. The study also shows that ecological opportunity may mask the direction of the effect (compression or expansion) of competition on niche variation when food resources are diverse.
5. Our study provides novel empirical insight to the driving forces behind niche variation and reveals that diversity, rather than density, of available prey resources may be a primary driver of niche variation in freshwater fish. Our study supports the view that a broader potential trophic niche promotes broader realised trophic niche variation by individuals, which leads to individual niche diversification by opening access to alternatives resources, resulting in a concomitant rise in the realised trophic niche width of the population.

     

Estimating population size using single‐nucleotide polymorphism‐based pedigree data

Reliable population estimates are an important aspect of sustainable wildlife management and conservation but can be difficult to obtain for rare and elusive species. Here, we test a new census method based on pedigree reconstruction recently developed by Creel and Rosenblatt (2013). Using a panel of 96 single‐nucleotide polymorphisms (SNPs), we genotyped fecal samples from two Swedish brown bear populations for pedigree reconstruction. Based on 433 genotypes from central Sweden (CS) and 265 from northern Sweden (NS), the population estimates (N = 630 for CS, N = 408 for NS) fell within the 95% CI of the official estimates. The precision and accuracy improved with increasing sampling intensity. Like genetic capture–mark–recapture methods, this method can be applied to data from a single sampling session. Pedigree reconstruction combined with noninvasive genetic sampling may thus augment population estimates, particularly for rare and elusive species for which sampling may be challenging.     

Impact of Spatial and Temporal Variation in Calf Survival on the Growth of Elk Populations

Abstract: The realized impact of a vital rate on population growth (λ) is determined by both the relative influence of the vital rate on λ (elasticity) and its magnitude of variability. We estimated mean survival and reproductive rates in elk (Cervus elaphus) and spatial and temporal variation in these rates from 37 sources located primarily across the Rocky Mountain region and northwestern United States. We removed sampling variance from estimates of process variance both within and across vital-rate data sets using the variance discounting method developed by White (2000). Deterministic elasticities calculated from a population matrix model parameterized with these mean vital rates ranked adult female survival (e_Scow = 0.869) much higher than calf survival (e_Scalf = 0.131). However, process variance in calf survival was >11 times greater than process variance in female survival across data sets and 10 times greater on average within studies. We conducted Life-Stage Simulation Analysis to incorporate both vital-rate elasticity patterns and empirical estimates of variability to identify those vital rates most influential in elk population dynamics. The overwhelming magnitude of variation in calf survival explained 75% of the variation in the population growth rates generated from 1,000 matrix replicates, compared to just 16% of the variation in λ explained by variation in female survival. Variation in calf survival greatly impacts elk population growth and calls into question the utility of classical elasticity analysis alone for guiding elk management. These results also suggest that the majority of interannual variability that wildlife managers document in late-winter and spring elk surveys is attributable to variation in calf survival over the previous year and less influenced by variation in the harvest of females during the preceding autumn. To meet elk population size objectives, managers should consider the inherent variation in calf survival, and its apparent sensitivity to management, in addition to female harvest.     

Population ecology and the management of whale watching operations on a data‐deficient dolphin population

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Nondetection sampling bias in marked presence‐only data

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The population decline of the New Zealand sea lion Phocarctos hookeri: a review of possible causes

• 1 The New Zealand (NZ) sea lion Phocarctos hookeri is NZ's only endemic pinniped and is listed as ‘nationally critical’. The species breeds in the NZ sub‐Antarctic: 71% of the population at the Auckland Islands (2010 pup production: 1814 ± 39) and the remaining 29% on Campbell Island (726 pups in 2010).
• 2 Pup production at the Auckland Islands has declined by 40% since 1998 (1998: 3021 pups produced): only 1501 pups were born in 2009. This decline is directly linked to philopatric females not returning to breeding areas. While the Auckland Island population has declined, the Campbell Island population appears to be increasing slowly.
• 3 Potential reasons for the decline in the Auckland Island population, but not in the Campbell Island population, include non‐anthropogenic factors: (i) disease epizootics, (ii) predation, (iii) permanent dispersal or migration, (iv) environmental change; and anthropogenic impacts: (v) population ‘overshoot’, (vi) genetic effects, (vii) effects of contaminants, (viii) indirect effects of fisheries (i.e. resource competition) and (ix) direct effects of fisheries (i.e. by‐catch deaths). Of the nine potential reasons examined here, six can be discounted (ii–vii). Bacterial epizootics (i) occur in the NZ sea lion population, but their impact has predominantly increased pup mortality, which is unlikely to cause the severe decline observed, as pup mortality throughout the species is naturally high and variable.
• 4 The most plausible hypotheses, based on available evidence, are that the observed decline, in particular, the decreasing number of breeding females in the Auckland Island population, is caused by (viii) fisheries‐induced resource competition and (ix) fisheries‐related by‐catch. By‐catch is the main known anthropogenic cause of mortality in the species. Competition with fisheries resulting in resource competition, nutrient stress and decreased reproductive ability in NZ sea lions should be a priority area for future research.

     

Spatial distribution,sampling efficiency and Taylor's power law. 2. Interpreting density-dependent sampling efficiency

1. The intimate relationship between sampling efficiency and Taylor's power law (TPL) was investigated with gypsy moth sample data. The data were used to compute sampling efficiency directly and indirectly by TPL.
2. Comparison of TPLs and efficiency plots of male and female pupae confirmed the identities linking TPL with sampling efficiency. Divergence of sex-specific TPL plots indicated local scale density-dependent sex ratio.
3. Egg mass sample data confirmed the sampling efficiency and TPL identities provided the same variance and mean vectors were used to compute TPLs. Small differences in sample numbers destroy the identities but approximate efficiency estimates are still obtainable from the TPLs. Sampling efficiency of timed walks, fixed area and variable area surveys were estimated and ranked.
4. Rescaling moth catches per trap to number per unit volume changes slope, intercept and correlation coefficient while stretching the pattern of data points. Comparison of absolute density estimates over two different time intervals showed density-dependent variation declining with increasing sample interval.
5. Fitting power laws by ordinary dependent regression is less efficient than fitting by geometric mean regression and produces biased regression parameters. The significance of this for the analysis and interpretation of ecological sample data generally is discussed.

     

A method for estimating natural survival rate and mean fecundity of an adult insect population by dissecting the female reproductive organs

Several problems were discussed in relation toMacDonald' s method (MacDonald , 1957) for estimating the survival rate of a natural population of adults with varying survival rates and unstable age structure.

1. Random samplings with a fixed sampling ratio and an appropriate census interval is pre-requisite during the occurrence of the adults.
2. At each sampling, female adults are dissected to know the ratio, p_i, of nulliparous females in ith sample (i=0, 1, 2, 3, …,). The Σn_ip_i/Σn_i gives an estimate of the ratio, Fα/F, of nulliparous females in the population where n_i refers to the population size on ith census date. If a constant daily survival rate is assumed, the daily survival rate is estimated from equation (4′). When the survival rate is not constant over the period of adult occurrence, e. g. before and after the initiation of oviposition, the survival rate during pre-ovipositional period is estimated by equation (4″).
3. Decision of an economic census interval to obtain a reliable estimate of the ratio, Fα/F, is depending on the form of emergence curve, particularly on its duration and the length of pre-ovipositional period. If the normal distribution can be assumed for the emergence curve, an interval less than one third of the emergence period is recommended. Concerning with insects having a long pre-ovipositional period, a census interval which exceeds one third of the emergence period still gives a good estimate of Fα/F.
4. The mean realized fecundity of some kind of insects can be estimated by equation (5′ or 5″) using the estimates obtained by the present method.

     

Estimates of vital rates and predictions of population dynamics change along a long-term monitoring program

Despite the widespread recognition of the importance of monitoring, only a few studies have explored how estimates of vital rates and predictions of population dynamics change with additional data collected along the monitoring program. We investigate how estimates of survival and individual growth, along with predictions about future population size, change with additional years of monitoring and data collected, using as a model system freshwater populations of marble (Salmo marmoratus), rainbow (Oncorhynchus mykiss), and brown trout (Salmo trutta L.) living in Western Slovenian streams. Fish were sampled twice a year between 2004 and 2015. We found that in 3 out of 4 populations, a few years of data (3 or 4 sampling occasions, between 300 and 500 tagged individuals for survival, 100–200 for growth) provided the same estimates of average survival and growth as those obtained with data from more than 15 sampling occasions, while the estimation of the range of survival (i.e., the difference, over all sampling occasions considered, between maximum and minimum survival estimated in a sampling occasion) required more sampling occasions (up to 22 for marble trout), with little reduction of uncertainty around the point estimates. Predictions of mean density and variation in density over time did not change with more data collected after the first 5 years (i.e., 10 sampling occasions) and overall were within 10% of the observed mean and variation in density over the whole monitoring program.