Evaluating the coastal environment for marine birds

The marine environment is being increasingly exploited by fisheries and the oil and gas industry. Conservationists urgently need the ability to identify the processes that determine patterns of abundance of marine species. We describe a preliminary Geographic Information System (GIS) in which spatial data on environmental variables (seabird colony locations, sea depth and seabed sediments) are integrated with realistic energy constraints faced by marine birds during the breeding season. A simple foraging model predicts the spatial variation in the quality of given locations as potential feeding sites under different feeding conditions and stages of the breeding cycle. We show how the approach can be used to help managers identify key marine areas and assess the impacts of environmental change or damage.     

Understanding abundance patterns of a declining seabird: implications for monitoring.

The Kittlitz's Murrelet (Brachyramphus brevirostris) is a rare, non-colonial seabird often associated with tidewater glaciers and a recent candidate for listing under the Endangered Species Act. We estimated abundance of Kittlitz's Murrelets across space and time from at-sea surveys along the coast of Alaska (USA) and then used these data to develop spatial models to describe abundance patterns and identify environmental factors affecting abundance. Over a five-week period in the summer of 2005, we recorded 794 Kittlitz's Murrelets, 16 Marbled Murrelets (B. marmoratus), and 70 unidentified murrelets. The overall population estimate (N, mean +/- SE) during the peak period (3-9 July) was 1317 +/- 294 birds, decreasing to 68 +/- 37 by the last survey period (31 July-6 August). Density of Kittlitz's Murrelets was highest in pelagic waters of Taan Fjord (18.6 +/- 7.8 birds/km2, mean +/- SE) during 10-16 July. Spatial models identified consistent "hotspots" of Kittlitz's Murrelets, including several small areas where high densities of murrelets were found throughout the survey period. Of the explanatory variables that we evaluated, tidal current strength influenced murrelet abundance most consistently, with higher abundance associated with strong tidal currents. Simulations based on the empirically derived estimates of variation demonstrated that spatial variation strongly influenced power to detect trend, although power changed little across the threefold difference in the coefficient of variation on detection probability. We include recommendations for monitoring Kittlitz's Murrelets (or other marine species) when there is a high degree of uncertainty about factors affecting abundance, especially spatial variability.     

A Bayesian approach to line-transect analysis for estimating abundance

Line-transect analysis is a widely used method of estimating plant and animal density and abundance. A Bayesian approach to a basic line-transect analysis is developed for a half-normal detection function. We extend the model of Karunamuni and Quinn [Karunamuni, R.J., Quinn II, T.J., 1995. Bayesian estimation of animal abundance for line-transect sampling. Biometrics 51, 1325–1337] by including a binomial likelihood function for the number of objects detected. The method computes a joint posterior distribution on the effective strip width and the density of objects in the sampled area. Analytical and computational methods for binned and unbinned perpendicular distance data are provided. Existing information about effective strip width and density can be brought into the analysis via prior distributions. The Bayesian approach is compared to a standard line-transect analysis using both real and simulated data. Results of the Bayesian and non-Bayesian analyses are similar when there are no prior data on effective strip width or density, but the Bayesian approach performs better when such data are available from previous or related studies. Practical methods for including prior data on effective strip width and density are suggested. A numerical example shows how the Bayesian approach can provide valid estimates when the sample size is too small for the standard approach to work reliably. The proposed Bayesian approach can form the basis for developing more advanced analyses.     

Estimating the abundance of mouse populations of known size: promises and pitfalls of new methods.

Knowledge of animal abundance is fundamental to many ecological studies. Frequently, researchers cannot determine true abundance, and so must estimate it using a method such as mark-recapture or distance sampling. Recent advances in abundance estimation allow one to model heterogeneity with individual covariates or mixture distributions and to derive multimodel abundance estimators that explicitly address uncertainty about which model parameterization best represents truth. Further, it is possible to borrow information on detection probability across several populations when data are sparse. While promising, these methods have not been evaluated using mark-recapture data from populations of known abundance, and thus far have largely been overlooked by ecologists. In this paper, we explored the utility of newly developed mark-recapture methods for estimating the abundance of 12 captive populations of wild house mice (Mus musculus). We found that mark-recapture methods employing individual covariates yielded satisfactory abundance estimates for most populations. In contrast, model sets with heterogeneity formulations consisting solely of mixture distributions did not perform well for several of the populations. We show through simulation that a higher number of trapping occasions would have been necessary to achieve good estimator performance in this case. Finally, we show that simultaneous analysis of data from low abundance populations can yield viable abundance estimates.     

Methods for estimating peak physiological performance and correlating performance measures

Estimates of animal performance often use the maximum of a small number of laboratory trials, a method which has several statistical disadvantages. Sample maxima always underestimate the true maximum performance, and the degree of the bias depends on sample size. Here, we suggest an alternative approach that involves estimating a specific performance quantile (e.g., the 0.90 quantile). We use the information on within-individual variation in performance to obtain a sampling distribution for the residual performance measures; we use this distribution to estimate a desired performance quantile for each individual. We illustrate our approach using simulations and with data on sprint speed in lizards. The quantile method has several advantages over the sample maximum: it reduces or eliminates bias, it uses all of the data from each individual, and its accuracy is independent of sample size. Additionally, we address the estimation of correlations between two different performance measures, such as sample maxima, quantiles, or means. In particular, because of sampling variability, we propose that the correlation of sample means does a better job estimating the correlation of population maxima than the estimator which is the correlation of sample maxima.     

A multispecies test of source–sink indicators to prioritize habitat for declining populations

For species at risk of decline or extinction in source–sink systems, sources are an obvious target for habitat protection actions. However, the way in which source habitats are identified and prioritized can reduce the effectiveness of conservation actions. Although sources and sinks are conceptually defined using both demographic and movement criteria, simplifications are often required in systems with limited data. To assess the conservation outcomes of alternative source metrics and resulting prioritizations, we simulated population dynamics and extinction risk for 3 endangered species. Using empirically based habitat population models, we linked habitat maps with measured site‐ or habitat‐specific demographic conditions, movement abilities, and behaviors. We calculated source–sink metrics over a range of periods of data collection and prioritized consistently high‐output sources for conservation. We then tested whether prioritized patches identified the habitats that most affected persistence by removing them and measuring the population response. Conservation decisions based on different source–sink metrics and durations of data collection affected species persistence. Shorter time series obscured the ability of metrics to identify influential habitats, particularly in temporally variable and slowly declining populations. Data‐rich source–sink metrics that included both demography and movement information did not always identify the habitats with the greatest influence on extinction risk. In some declining populations, patch abundance better predicted influential habitats for short‐term regional persistence. Because source–sink metrics (i.e., births minus deaths; births and immigrations minus deaths and emigration) describe net population conditions and cancel out gross population counts, they may not adequately identify influential habitats in declining populations. For many nonequilibrium populations, new metrics that maintain the counts of individual births, deaths, and movement may provide additional insight into habitats that most influence persistence.     

Site fidelity and territorial movements of males in a rapidly declining population of yellow-headed blackbirds

We tested several hypotheses to explain low between-year territory fidelity in a breeding population of yellow-headed blackbirds (Xanthocephalus xanthocephalus). During a 5-year study the population of territorial males declined by two-thirds and some of the marshes that supported territories significantly deteriorated. Individual males held territories and bred for an average of 1.9 years. Of males that bred for at least 2 years, 30% skipped owning a territory in the study area during at least 1 year of their breeding lifetimes. Our information suggests that they may have bred outside of the area in those years. Of males with territories in two or more breeding seasons, 60% changed breeding marshes at least once. Males changed territories during 42.9% of between-year opportunities to do so. We found no support for the hypotheses that male yellow-headed blackbirds: (1) are more likely to move when territory density is low; (2) are likely to abandon territories that are deteriorating; or (3) change territories to improve their reproductive success. We suggest three non-mutually exclusive explanations for the yellow-headed blackbird's weak site fidelity: (1) it is a response to habitat deterioration and to other factors that may be causing the population's decline; (2) the males, being migratory, make fresh settlement decisions each year after they arrive on the breeding grounds in the general vicinity of their previous year's breeding; (3) yellow-headed blackbirds may have evolved in, and be adapted to, highly unstable habitats, moving frequently in response to changes in local breeding site conditions. Correspondence to: L.D. Beletsky     

An ecosystem model for estimating potential shellfish culture production in sheltered coastal waters

A generic ecosystem model has been developed for estimating the potential production of shellfish culture and the effect of that cultivation on the pelagic ecosystem in sheltered coastal waters. The model describes the dynamics of a simple food web, nutrient cycling and growth of shellfish. The design of the model is closely tied to the temporal and spatial scales that are important in determining the sustainable production level for a particular embayment. The pelagic ecosystem, mussel energetics, population dynamics and hydrodynamics are coupled to allow fully dynamic predictions of the effect of the shellfish density. When applied to Beatrix Bay, an intensive culture embayment in the Pelorus Sound of New Zealand, the model successfully captured main features of the observed system behaviour. The hydrodynamic regime of the bay controls mussel growth and production. Although high fluxes of water into the bay suppress nutrient and carbon cycling signals in the system, the model simulations demonstrated that the mussel cultivation can have considerable effects on the ecosystem of the bay including food depletion and nutrient cycling. One of the most obvious effects is nutrient enhancement through mussel excretion at low cultivation densities, which promotes primary production particularly during the N-limitation period in summer. The sensitivity analysis identified uncertainty in some parameters and indicated areas for which experimental studies could lead to model improvement. The modelling exercise has established a primary predictive tool for managing mussel aquaculture of a coastal embayment to estimate relationships between the stock level and the growth rate of mussels, and the potentially achievable harvest and stocking density.     

Spatial methods for plot-based sampling of wildlife populations

Classical sampling methods can be used to estimate the mean of a finite or infinite population. Block kriging also estimates the mean, but of an infinite population in a continuous spatial domain. In this paper, I consider a finite population version of block kriging (FPBK) for plot-based sampling. The data are assumed to come from a spatial stochastic process. Minimizing mean-squared-prediction errors yields best linear unbiased predictions that are a finite population version of block kriging. FPBK has versions comparable to simple random sampling and stratified sampling, and includes the general linear model. This method has been tested for several years for moose surveys in Alaska, and an example is given where results are compared to stratified random sampling. In general, assuming a spatial model gives three main advantages over classical sampling: (1) FPBK is usually more precise than simple or stratified random sampling, (2) FPBK allows small area estimation, and (3) FPBK allows nonrandom sampling designs.     

Transmitter attachment and release methods for short-term shark and stingray tracking on coral reefs

This study details a simple and cost-effective means of attaching acoustic transmitters to coral reef sharks and stingrays, which potentially allows for retrieval and reuse on completion of tracks. Between 2008 and 2011, galvanised timed releases were trialled in both static field tests and on blacktip reef sharks Carcharhinus melanopterus, cowtail Pastinachus atrus, and porcupine Urogymnus asperrimus rays in Coral Bay (?23°08′41″, 113°45′53″), Western Australia. The timed releases remained attached to animals for the duration required for tracking and in four out of five deployments transmitters were recovered after release from the animals. The use of modified Rototags for sharks and stainless steel darts for stingrays allowed rapid and effective attachment to animals, with limited impact on their welfare in the short term. External attachment for short-term tracking of coral reef-associated elasmobranchs should be considered as a complementary option to internal placement of transmitters in animals either by surgery or by ingestion.     

Age determination and growth of the bonnethead shark Sphyrna tiburo: a comparison of two populations

From July 1982 to December 1986, a study of the age and growth of the bonnethead shark Sphyrna tiburo was conducted in Tampa and Florida Bays, Florida, USA. Tetracycline-injected sharks held in captivity and, to a lesser extent, tagged, released and recaptured, were utilized for validating the annual nature of the rings (herein defined as the narrow, translucent regions) appearing on vertebral centra. The technique was validated for all age groups (0 to 6+yr) included in the study. Marginal increment analysis likewise suggested annual ring formation. The rings formed during the winter, when water temperatures were lowest. Using the vertebral ring aging-technique, von Bertalanffy growth curves for males and females from both tampa and Florida Bays were constructed. Growth of sharks born and held in captivity demonstrated that the male and female growth curves diverge after 1 yr and that mean sizes at age are statistically distinct after 2 yr. In both populations, females grew to larger sizes tha males and apparently are longer-lived. Reproductively mature females from Tampa Bay were significantly larger than those from Florida Bay.     

Resampling methods for estimating dispersion indices in random and adaptive designs

In many surveys in environmental and natural phenomena the aim is to evaluate the heterogeneity, and the skewness of the distribution of the number point-objects in the study area opportunely partitioned in sub-regions. For this purpose, in this paper the estimation of dispersion indices is considered by using simple random sampling and adaptive sampling with initial simple random sampling selected with replacement or without replacement. The jackknife and the bootstrap procedures are proposed in both cases for reducing bias. Finally, both a simulation study and a case study on biological population referred to a Oidium tuckeri contamination in a growing vineyard is performed to assess the accuracy of the proposed estimators.     

The use of replicated plot,line and point sampling for estimating species abundance and ecological diversity

The paper deals with the problem of estimating diversity indexes for an ecological community. First the species abundances are unbiasedly and consistently estimated using designs based on n random and independent selections of plots, points or lines over the study area. The problem of sampling elusive populations is also considered. Finally, the diversity index estimates are obtained as functions of the abundance estimates. The resulting estimators turn out to be asymptotically (n large) unbiased, even if a considerable bias may occur for a small n. Accordingly, the method of jackknifing is made use of in order to reduce bias.     

Distribution and abundance of choanoflagellates (Acanthoecidae) in the coastal cold ocean of Newfoundland, Canada

Water samples from six bays were taken over a 5-year period (1988 to 1992) to determine the distribution and abundance of loricate choanoflagellates in coastal Newfoundland, and to assess the impact that these organisms might have on this cold ocean food web. Scanning electron microscopy was used to study the morphology of these flagellates, allowing us to identify 11 species of loricate choanoflagellates. Parvicorbicula socialis (Meunier) Deflandre was the most abundant species (80 × 10³ cells l⁻¹), particularly during the spring diatom bloom. Single-cell species, such as Bicosta spini fera (Throndsen) Leadbeater and Calliacantha natans (Grontved) Leadbeater, were found more commonly after the spring diatom bloom in the summer months. Many of the single-cell choanoflagellates were attached to bacteria-rich microaggregates and debris in the water column and in unpoisoned sediment traps. The P. socialis cell flux was calculated to be 5.3 × 10⁶ cells m⁻² d⁻¹ in late May sediment traps. P. socialis in the upper 100 m of the water column was removing 0.3% of the standing crop of bacteria each day (April/May), and the equivalent of 7.4% of the daily bacterial production over the water column. Diel studies of P. socialis in Conception Bay suggest that the sharp decline in population numbers observed in midnight samples may be related to the high number of grazing zooplankton observed during the same period. Pelagic tunicate and zooplankton fecal pellets were found to contain large numbers of choanoflagellate costae, thus providing a direct link from the microbial loop to the macrozooplankton. Received: 17 March 1997 / Accepted: 9 May 1997     

Tracing impacts of partner abundance in facultative pollination mutualisms: from individuals to populations

Partner abundance affects costs and benefits in obligate mutualisms, but its role in facultative partnerships is less clear. We address this gap in a pollination web consisting of two clovers (Trifolium) that differ in specialization on a bumble bee pollinator Bombus balteatus. We examine how pollination niche breadth affects plant responses to pollinator abundance, comparing early-flowering (specialized) and late-flowering (generalized) cohorts of T. parryi and early T. parryi to T. dasyphyllum, a pollination generalist. Co-pollinators disrupt the link between B. halteatus visitation and pollination rate for both clovers. Only for early-flowering T. parryi do visitation, pollination, and seed set increase with density of B. balteatus. Bumble bee density also alters timing of seed germination in T. parryi, with seeds from plants receiving augmented B. balteatus germinating sooner than seeds of open-pollinated counterparts. Benefits saturate at intermediate bumble bee densities. Despite strong effects of B. balteatus density on individual plant fitness components, population models suggest little impact of B. balteatus density on lamda in T. parryi or T. dasyphyllum. Findings show that functional redundancy in a pollinator guild mediates host-plant responses to partner density. Unexpected effects of pollinator density on life history schedule have implications for recruitment under pollinator decline.     

Use made in marine ecology of methods for estimating demographic parameters from size/frequency data

Macdonald and Pitcher's method of decomposing a sizefrequency histogram into cohorts (mathematical optimization of the fit of the distribution function to the histogram) has been used to estimate the composition of random samples drawn from populations with known cohort structure. The large-sample behaviour of the method is in accordance with the results of asymptotic theory. With sample sizes typical of those used in many ecological studies, good estimates often could not be obtained without imposing constraints upon the estimation procedure, even when the number of age classes in the population was known. If the number of age classes was not known, it was frequently difficult to determine from small samples. When unconstrained solutions were obtainable, confidence limits about estimates were often very wide. Our results and information in the theoretical literature indicate that if the Petersen method (whereby several modes on a size-frequency histogram are taken to represent single age classes and all age classes to be present) does not work, accurate estimates of demographic parameters are unlikely to be obtainable using more rigorous methods. In view of these difficulties, we recommend that an iptimization method, such as that described by Macdonald and Pitcher, be used to estimate demographic parameters. Standard errors of estimates should be reported. Optimization methods give an indication when the data is inadequate to obtain accurate parameter estimates, either by failing to converge or by placing large standard errors about the estimates. Graphical methods do not give a clear warning of this, and should be avoided except where the modes on the size-frequency histogram are very well separated and sample sizes are large. Often, assumptions must be made about population parameters to enable their estimation. This may involve constraining some parameters to particular values, assuming a fixed relationship between cohort mean sizes and their standard deviations, or by assuming that individuals grow according to a von Bertalanffy curve. Any such assumptions need detailed justification in each case.     

Seasonal abundance, philopatry and demographic structure of Caribbean reef shark (Carcharhinus perezi) assemblages in the north-east Exuma Sound, The Bahamas

The Caribbean reef shark (Carcharhinus perezi), an abundant coral-reef-associated apex predator, is one of the most economically and ecologically important, yet least studied species of large shark in the greater Caribbean region. The relative abundance and population structure of C. perezi off Cape Eleuthera, The Bahamas, was surveyed by standardised longline surveys from May 2008 to October 2011, which resulted in the capture of 331 sharks. Abundance peaked in the summer and was lowest during the winter. Females were 1.6 times more abundant than males and the assemblage was dominated by immature female sharks (45.5 %). The abundance of mature male and female sharks peaked a month apart in June and August, respectively. All 331 sharks were tagged and released with 15.4 % being recaptured after periods at liberty between 5 and 1,159 days (Mean = 333.4 ± 42.7 SE). The mean distance between tagging and recapture was 1.77 km for recaptures in excess of 6 months, indicating seasonally stratified philopatry in this species. C. perezi inhabiting Bahamian waters have developed complex habitat use patterns that are both spatiotemporally and demographically segregated, most probably in response to the large and diverse habitat mosaic available on the Bahamas Banks compared to contemporary study sites. This study represents an important step in understanding the spatiotemporal population structure of C. perezi and illustrates the potential for studies examining behavioural plasticity in response to environmental variation and anthropogenic disturbance.     

Variation in populations of the coastal dune building grassLeymus arenarius in Iceland revealed by endospermal prolamins

Variation in the endospermal protein patterns of seeds amongst and between inland and coastal populations of the dune building grassLeymus arenarius was examined in Iceland. Seeds were collected from six coastal populations and five inland populations in Iceland. Endospermal proteins (prolamins) of seeds were extracted with Tris-buffered 2-propanol (50%) and β-mercaptoethanol (0.5% v/v). We used 8% and 12% sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) to separate the prolamin protein bands, which were stained with Coomassie Brilliant Blue R. Coastal populations were differentiated from inland populations on the basis of high frequency of high molar weight (HMW) (110–150 kg mol⁻¹) prolamins. Coastal populations had significantly higher proportions of their seed with more than two HMW prolamins, than those of inland populations. Subtle differences were found among the HMW prolamins of coastal and inland populations indicating limited intrapopulation variation. The dynamic environment of sand dunes probably influences the genetic composition of these populations. The results suggest that seeds of the inland and coastal populations should be treated separately in sand dune reclamation and restoration works     

A comparison of three methods for estimating call densities of migrating bowhead whales using passive acoustic monitoring

Environmental and Ecological Statistics - Various methods for estimating animal density from visual data, including distance sampling (DS) and spatially explicit capture-recapture (SECR), have...     

Vertical profiles of bacterial abundance,productivity and growth rates in coastal sediments of the central Great Barrier Reef lagoon

Vertical patterns of bacterial densities, productivity and specific growth rates in coastal muds, quartz sands and muddy sands of the central Great Barrier Reef lagoon were examined in summer (February) and autumn (May) 1988. Variations in these parameters with station location, sediment depth and season were complex, exhibiting significant main and interaction effects in most instances. Some trends were apparent despite the large and complex variations. Bacterial densities did not vary seasonally, ranging from 2.9 to 38.1×10⁹ cells g^-1 dry wt, averaged over sediment depth (0 to 20 cm) and seasons. Trend analysis revealed that densities decreased with increasing sediment depth. Bacterial production (tritiated thymidine incorporation into DNA) was high, ranging from 0.4 to 5.7 gCm^-2 d^-1 (integrated over 10 cm depth), as were specific growth rates (grand mean, =0.25 d^-1; range=0.004 to 1.3 d^-1). Both were generally higher in summer than in autumn. Vertical profiles of productivity and specific growth rates revealed actively growing bacterial assemblages down to 20 cm depth. Factors which may account for these very abundant and productive communities are: (1) subsurface accumulations of detritus exported from adjacent mangrove forests, and (2) physical disturbance from tidal scouring and severe climate (e.g. cyclones, wet-season floods). Disturbance events occur frequently enough to inhibit the development of highly sulphidic conditions, but stimulate production of bacterial types (aerobes, fermenters) capable of incorporating labelled thymidine into their DNA.