Expert elicitation of seasonal abundance of North Atlantic right whales Eubalaena glacialis in the mid-Atlantic

This work was supported in part by US Office of Naval Research (ONR) grants to E.F.: N00014-09-1-0896 at University of California, Santa Barbara and N00014-12-1-0274 at University of California, Davis. This work was also supported by ONR grant N000141210286 to the University of St Andrews. In addition, we gratefully acknowledge funding for this work from The Marine Alliance for Science and Technology for Scotland (MASTS). MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions.North Atlantic right whales (Eubalaena glacialis; henceforth right whales) are among the most endangered large whales. Although protected since 1935, their abundance has remained low. Right whales occupy the Atlantic Ocean from southern Greenland and the Gulf of St. Lawrence south to Florida. The highly industrialized mid-Atlantic region is part of the species’ migratory corridor. Gaps in knowledge of the species’ movements through the mid-Atlantic limit informed management of stressors to the species. To contribute to filling of these gaps, we elicited estimates of the relative abundance of adult right whales in the mid-Atlantic during four months, representing each season, from ten experts. We elicited the minimum, maximum, and mode as the number of individuals in a hypothetical population of 100 right whales, and confidence estimates as percentages. For each month-sex combination, we merged the ten experts’ answers into one distribution. The estimated modes of relative abundances of both sexes were highest in January and April (females, 29 and 59; males, 22 and 23) and lowest in July and October (females, five and nine; males, three and five). In some cases, our elicitation results were consistent with the results of studies based on sightings data. However, these studies generally did not adjust for sampling effort, which was low and likely variable. Our results supplement the results of these studies and will increase the accuracy of priors in complementary Bayesian models of right whale abundances and movements through the mid-Atlantic.Publisher PDFPeer reviewe

Quantifying the response of Blainville’s beaked whales to U.S. naval sonar exercises in Hawaii

Funding: US Navy Living Marine Resources Program (Grant Number(s): N39430-17-P-1983).Behavioral responses of beaked whales (family Ziphiidae) to naval use of mid-frequency active sonar (MFAS) have been quantified for some species and regions. We describe the effects of MFAS on the probability of detecting diving groups of Blainville's beaked whales on the U.S. Navy Pacific Missile Range Facility (PMRF) in Hawaii and compare our results to previously published results for the same species at the Atlantic Undersea Test and Evaluation Center (AUTEC) in the Bahamas. We use passive acoustic data collected at bottom-mounted hydrophones before and during six naval training exercises at PMRF along with modelled sonar received levels to describe the effect of training and MFAS on foraging groups of Blainville's beaked whales. We use a multistage generalized additive modeling approach to control for the underlying spatial distribution of vocalizations under baseline conditions. At an MFAS received level of 150 dB re 1 μPa rms the probability of detecting groups of Blainville's beaked whales decreases by 77%, 95% CI [67%, 84%] compared to periods when general training activity was ongoing and by 87%, 95% CI [81%, 91%] compared to baseline conditions. Our results indicate a more pronounced response to naval training and MFAS than has been previously reported.Publisher PDFPeer reviewe

Population abundance and density estimates for Costa Rica’s endemic sea snake, Hydrophis platurus xanthos

Population abundance and density estimates provide key information for conservation assessment and prioritization of efforts and management. However, data are still largely unavailable for many taxa, including sea snakes, which appear to be facing global declines. Here, we present the first quantitative abundance and density estimates for the geographically isolated sea snake Hydrophis platurus xanthos endemic to the inner basin of Golfo Dulce, Costa Rica. Using systematic distance sampling methods, we obtained and analyzed 199 snake detections from 46 transect lines covering the entire known distribution (totaling nine days and 469 km of effort). Our modeling methods accounted for (i) the probability of detecting a snake given it was available to be detected (ii) the average availability of snakes at the water surface during a 24-hr cycle, and (iii) the by-hour variance in the taxon’s activity pattern. The best estimate of population abundance was 29781 individuals (95% CI=20104–44115) with an estimated density of 76 snakes/ km2. Without historical abundance estimates or minimum viable population size, it is unknown whether this number represents a healthy population. However, with all individuals inhabiting a relatively small inlet increasingly exposed to anthropogenic impacts, the long-term persistence of H. p. xanthos may be threatened by ongoing impacts (boat propeller strikes, agricultural runoff, and climate change), as well as unforeseen events in the future

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

TAM thanks partial support by Centro de Estatistica e Aplicações, Universidade de Lisboa (funded by FCT—Fundação para a Ciência e a Tecnologia, Portugal, through the project UID/MAT/00006/2013).Various methods for estimating animal density from visual data, including distance sampling (DS) and spatially explicit capture-recapture (SECR), have recently been adapted for estimating call density using passive acoustic monitoring (PAM) data, e.g., recordings of animal calls. Here we summarize three methods available for passive acoustic density estimation: plot sampling, DS, and SECR. The first two require distances from the sensors to calling animals (which are obtained by triangulating calls matched among sensors), but SECR only requires matching (not localizing) calls among sensors. We compare via simulation what biases can arise when assumptions underlying these methods are violated. We use insights gleaned from the simulation to compare the performance of the methods when applied to a case study: bowhead whale call data collected from arrays of directional acoustic sensors at five sites in the Beaufort Sea during the fall migration 2007–2014. Call detections were manually extracted from the recordings by human observers simultaneously scanning spectrograms of recordings from a given site. The large discrepancies between estimates derived using SECR and the other two methods were likely caused primarily by the manual detection procedure leading to non-independent detections among sensors, while errors in estimated distances between detected calls and sensors also contributed to the observed patterns. Our study is among the first to provide a direct comparison of the three methods applied to PAM data and highlights the importance that all assumptions of an analysis method need to be met for correct inference.Publisher PDFPeer reviewe

Low tortoise abundances in pine forest plantations in forest-shrubland transition areas

The Spanish Ministry of Science and European Regional Development Fund funded this work through Projects CGL2012-33536 and CGL2015- 64144; MINECIO/FEDER. Regional Government of the Community of Valencia supported R.R-C. by a postgraduate grant (ACIF/2010/133) and E.G. by a postdoctoral grant (APOSTD/2015/048).In the transition between Mediterranean forest and the arid subtropical shrublands of the southeastern Iberian Peninsula, humans have transformed habitat since ancient times. Understanding the role of the original mosaic landscapes in wildlife species and the effects of the current changes as pine forest plantations, performed even outside the forest ecological boundaries, are important conservation issues. We studied variation in the density of the endangered spur-thighed tortoise (Testudo graeca) in three areas that include the four most common land types within the species’ range (pine forests, natural shrubs, dryland crop fields, and abandoned crop fields). Tortoise densities were estimated using a two-stage modeling approach with line transect distance sampling. Densities in dryland crop fields, abandoned crop fields and natural shrubs were higher (>6 individuals/ha) than in pine forests (1.25 individuals/ha). We also found large variation in density in the pine forests. Recent pine plantations showed higher densities than mature pine forests where shrub and herbaceous cover was taller and thicker. We hypothesize that mature pine forest might constrain tortoise activity by acting as partial barriers to movements. This issue is relevant for management purposes given that large areas in the tortoise’s range have recently been converted to pine plantations.Publisher PDFPeer reviewe

Attributing changes in the distribution of species abundance to weather variables using the example of British breeding birds

The BBS is undertaken by the British Trust for Ornithology (BTO) and jointly funded by the BTO, the Joint Nature Conservation Committee and the Royal Society for the Protection of Birds.1. Modelling spatio-temporal changes in species abundance and attributing those changes to potential drivers such as climate, is an important but difficult problem. The standard approach for incorporating climatic variables into such models is to include each weather variable as a single covariate whose effect is expressed through a low-order polynomial or smoother in an additive model. This, however, confounds the spatial and temporal effects of the covariates. 2. We developed a novel approach to distinguish between three types of change in any particular weather covariate. We decomposed the weather covariate into three new covariates by separating out temporal variation in weather (averaging over space), spatial variation in weather (averaging over years) and a space-time anomaly term (residual variation). These three covariates were each fitted separately in the models. We illustrate the approach using generalized additive models applied to count data for a selection of species from the UK’s Breeding Bird Survey, 1994-2013. The weather covariates considered were the mean temperatures during the preceding winter and temperatures and rainfall during the preceding breeding season. We compare models that include these covariates directly with models including decomposed components of the same covariates, considering both linear and smooth relationships. 3. The lowest QAIC values were always associated with a decomposed weather covariate model. Different relationships between counts and the three new covariates provided strong evidence that the effects of changes in covariate values depended on whether changes took place in space, in time, or in the space-time anomaly. These results promote caution in predicting species distribution and abundance in future climate, based on relationships that are largely determined by environmental variation over space. 4. Our methods estimate the effect of temporal changes in weather, while accounting for spatial effects of long-term climate, improving inference on overall and/or localized effects of climate change. With increasing availability of large-scale data sets, need is growing for appropriate analytical tools. The proposed decomposition of the weather variables represents an important advance by eliminating the confounding issue often inherent in analyses of large-scale data sets.PostprintPeer reviewe

Accuracy and precision of dolphin group size estimates

Estimating the number of dolphins in a group is a challenging task. To assess the accuracy and precision of dolphin group size estimates, observer estimates were compared to counts from large‐format vertical aerial photographs. During 11 research cruises, a total of 2,435 size estimates of 434 groups were made by 59 observers. Observer estimates were modeled as a function of the photo count in a hierarchical Bayesian framework. Accuracy varied widely among observers, and somewhat less widely among dolphin species. Most observers tended to underestimate, and the tendency increased with group size. Groups of 25, 50, 100, and 500 were underestimated by <1%, 16%, 27%, and 47%, respectively, on average. Precision of group size estimates was low, and estimates were highly variable among observers for the same group. Predicted true group size, given an observer estimate, was larger than the observer estimate for groups of more than about 25 dolphins. Predicted group size had low precision, with coefficients of variation ranging from 0.7 to 1.9. Studies which depend on group size estimates will be improved if the tendency to underestimate group size and the high uncertainty of group size estimates are included in the analysis

Roaring and repetition : how bowhead whales adjust their call density and source level (Lombard effect) in the presence of natural and seismic airgun survey noise

Over 500 000 automated and manual acoustic localizations, measured over seven years between 2008 and 2014, were used to examine how natural wind-driven noise and anthropogenic seismic airgun survey noise influence bowhead whale call densities (calls/km2/min) and source levels during their fall migration in the Alaskan Beaufort Sea. Noise masking effects, which confound measurements of behavioral changes, were removed using a modified point transect theory. The authors found that mean call densities generally rose with increasing continuous wind-driven noise levels. The occurrence of weak airgun pulse sounds also prompted an increase in call density equivalent to a 10–15 dB change in natural noise level, but call density then dropped substantially with increasing cumulative sound exposure level (cSEL) from received airgun pulses. At low in-band noise levels the mean source level of the acoustically-active population changed to nearly perfectly compensate for noise increases, but as noise levels increased further the mean source level failed to keep pace, reducing the population's communication space. An increase of >40 dB cSEL from seismic airgun activity led to an increase in source levels of just a few decibels. These results have implications for bowhead acoustic density estimation, and evaluations of the masking impacts of anthropogenic noise.Publisher PDFPeer reviewe

Quantifying the response of Blainville’s beaked whales to U.S. naval sonar exercises in Hawaii

Behavioral responses of beaked whales (family Ziphiidae) to naval use of mid-frequency active sonar (MFAS) have been quantified for some species and regions. We describe the effects of MFAS on the probability of detecting diving groups of Blainville's beaked whales on the U.S. Navy Pacific Missile Range Facility (PMRF) in Hawaii and compare our results to previously published results for the same species at the Atlantic Undersea Test and Evaluation Center (AUTEC) in the Bahamas. We use passive acoustic data collected at bottom-mounted hydrophones before and during six naval training exercises at PMRF along with modelled sonar received levels to describe the effect of training and MFAS on foraging groups of Blainville's beaked whales. We use a multistage generalized additive modeling approach to control for the underlying spatial distribution of vocalizations under baseline conditions. At an MFAS received level of 150 dB re 1 μPa rms the probability of detecting groups of Blainville's beaked whales decreases by 77%, 95% CI [67%, 84%] compared to periods when general training activity was ongoing and by 87%, 95% CI [81%, 91%] compared to baseline conditions. Our results indicate a more pronounced response to naval training and MFAS than has been previously reported

Roaring and repetition: How bowhead whales adjust their call density and source level (Lombard effect) in the presence of natural and seismic airgun survey noise

Over 500 000 automated and manual acoustic localizations, measured over seven years between 2008 and 2014,were used to examine how natural wind-driven noise and anthropogenic seismic airgun survey noise influence bowheadwhale call densities (calls/km2/min) and source levels during their fall migration in the Alaskan Beaufort Sea.Noise masking effects, which confound measurements of behavioral changes, were removed using a modified pointtransect theory. The authors found that mean call densities generally rose with increasing continuous wind-drivennoise levels. The occurrence of weak airgun pulse sounds also prompted an increase in call density equivalent to a10–15 dB change in natural noise level, but call density then dropped substantially with increasing cumulative soundexposure level (cSEL) from received airgun pulses. At low in-band noise levels the mean source level of theacoustically-active population changed to nearly perfectly compensate for noise increases, but as noise levelsincreased further the mean source level failed to keep pace, reducing the population’s communication space. Anincrease of >40 dB cSEL from seismic airgun activity led to an increase in source levels of just a few decibels.These resultsOver 500 000 automated and manual acoustic localizations, measured over seven years between 2008 and 2014,were used to examine how natural wind-driven noise and anthropogenic seismic airgun survey noise influence bowheadwhale call densities (calls/km2/min) and source levels during their fall migration in the Alaskan Beaufort Sea.Noise masking effects, which confound measurements of behavioral changes, were removed using a modified pointtransect theory. The authors found that mean call densities generally rose with increasing continuous wind-drivennoise levels. The occurrence of weak airgun pulse sounds also prompted an increase in call density equivalent to a10–15 dB change in natural noise level, but call density then dropped substantially with increasing cumulative soundexposure level (cSEL) from received airgun pulses. At low in-band noise levels the mean source level of theacoustically-active population changed to nearly perfectly compensate for noise increases, but as noise levelsincreased further the mean source level failed to keep pace, reducing the population’s communication space. Anincrease of >40 dB cSEL from seismic airgun activity led to an increase in source levels of just a few decibels.These results have implications for bowhead acoustic density estimation, and evaluations of the masking impacts ofdanthropogenic noisehave implications for bowhead acoustic density estimation, and evaluations of the masking impacts ofanthropogenic nois