Len Thomas

Loud anthropogenic underwater noise, such as that associated with sonar operations, pile driving, or seismic surveys, can cause behavioral and physiological disturbance to many animals that may affect their survival or ability to breed. However, no formal framework for assessing the population-level consequences of this disturbance is currently available. We describe an interim version of a framework developed by a working group on the population consequences of disturbance, funded by the US Office of Naval Research through the University of California, that can be used to assess the effects of offshore renewable energy developments on marine mammal populations.

Right whales are vulnerable to many sources of anthropogenic disturbance including ship strikes, entanglement with fishing gear, and anthropogenic noise. The effect of these factors on individual health is unclear. A statistical model using photographic evidence of health was recently built to infer the true or hidden health of individual right whales. However, two important prior assumptions about the role of missing data and unexplained variance on the estimates were not previously assessed. Here we tested these factors by varying prior assumptions and model formulation. We found sensitivity to each assumption and used the output to make guidelines on future model formulation.

Naval exercises using Mid-Frequency Active (MFA) sonar have been implicated in several mass stranding events in which the predominant species were Blainville's (Mesoplodon densirostris) and Cuvier's (Ziphius cavirostris) beaked whales. Beaked whales are known ...

Beaked whales are deep diving elusive animals, difficult to census with conventional visual surveys. Methods are presented for the density estimation of beaked whales, using passive acoustic monitoring data collected at sites in the Gulf of Mexico (GOM) from the period during and following the Deepwater Horizon oil spill (2010-2013). Beaked whale species detected include: Gervais' (Mesoplodon europaeus), Cuvier's (Ziphius cavirostris), Blainville's (Mesoplodon densirostris) and an unknown species of Mesoplodon sp. (designated as Beaked Whale Gulf - BWG). For Gervais' and Cuvier's beaked whales, we estimated weekly animal density using two methods, one based on the number of echolocation clicks, and another based on the detection of animal groups during 5 min time-bins. Density estimates derived from these two methods were in good general agreement. At two sites in the western GOM, Gervais' beaked whales were present throughout the monitoring period, but Cuvier's beaked whales were present only seasonally, with periods of low density during the summer and higher density in the winter. At an eastern GOM site, both Gervais' and Cuvier's beaked whales had a high density throughout the monitoring period.

... by tagging all weaned pups (Mansfield and Beck 1977, Stobo and Zwanenburg 1990) and more recently at longer intervals via aerial photography (Bowen et al. ... Pup production here has been estimated approximately every 4 years from mark-recapture studies (Hammill et al. ...

Automated methods were developed to detect fin whale calls recorded by an array of ocean bottom seismometers (OBSs) deployed off the Portuguese coast between 2007 and 2008. Using recordings collected on a single day in January 2008, a standard seismological method for estimating earthquake location from single instruments, the three-component analysis, was used to estimate the relative azimuth, incidence angle, and horizontal range between each OBS and detected calls. A validation study using airgun shots, performed prior to the call analysis, indicated that the accuracy of the three-component analysis was satisfactory for this preliminary study. Point transect sampling using cue counts, a form of distance sampling, was then used to estimate the average probability of detecting a call via the array during the chosen day. This is a key step to estimating density or abundance of animals using passive acoustic data. The average probability of detection was estimated to be 0.313 (standard error: 0.033). However, fin whale density could not be estimated due to a lack of an appropriate estimate of cue (i.e., vocalization) rate. This study demonstrates the potential for using a sparse array of widely spaced, independently operating acoustic sensors, such as OBSs, for estimating cetacean density.

ABSTRACT Red wood ants are ecologically important members of woodland communities, and some species are of conservation concern. They occur commonly only in certain habitats in Britain, but there is limited knowledge of their numbers and distribution. This study provided baseline information at a key locality (Abernethy Forest, 37 km2) in the central Highlands of Scotland and trialed a new method of surveying red wood ant density and stand type associations: a distance sampling line transect survey of nests. This method is efficient because it allows an observer to quickly survey a large area either side of transect lines, without having to assume that all nests are detected. Instead, data collected on the distance of nests from the line are used to estimate probability of detection and the effective transect width, using the free software "Distance". Surveys took place in August and September 2003 along a total of 71.2 km of parallel, equally-spaced transects. One hundred and forty-four red wood ant nests were located, comprising 89 F. aquilonia (Yarrow, 1955) and 55 F. lugubris (Zetterstedt, 1838) nests. Estimated densities were 1.13 nests per hectare (95% CI 0.74–1.73) for F. aquilonia and 0.83 nests per hectare (95% CI 0.32–2.17) for F. lugubris. These translated to total estimated nest numbers of 4,200 (95% CI 2,700–6,400) and 3,100 (95% CI 1,200–8,100), respectively, for the whole forest. Indices of stand selection indicated that F. aquilonia had some positive association with old-growth and F. lugubris with younger stands (stem exclusion stage). No nests were found in areas that had been clear-felled, and ploughed and planted in the 1970s–1990s. The pattern of stand type association and hence distribution of F. aquilonia and F. lugubris may be due to the differing ability to disperse (F. lugubris is the faster disperser) and compete (F. aquilonia is competitively superior). We recommend using line transect sampling for extensive surveys of ants that construct nest mounds to estimate abundance and stand type association.

... migrants, and other land bird species, the primary source of population information at the ... If the sample design involves stratification, then the average within each stratum should be weighted ... In addition, trends should be weighted by the abundance of individuals at the sample ...

... 4.8 Mountford moving-window estimates of population indices for Carolina Wren between 1966 and 1996 for “without observers” models at four ... I also gratefully acknowledge the help of my supervisory committee, Val LeMay, Jamie Smith, John Smith and Carl Walters, each of ...

... 1992, 1998, Myers et al. 1997) and aerial surveys (Hammill and Stenson 2011). ... These have been monitored intermittently by visual counts or year-class tagging (Hammill et al. 2007). All three regions were surveyed most recently in spring 2010 (Bowen et al. 2011). ...

... LITERATURE CITED Hammill, MO and Stenson, GB 2007. Application of the precautionary approach and conservation reference points to management of Atlantic Seals. ICES Journal of Marine Science. Thomas, L., Hammill, MO and Bowen, WD 2010. ...

ABSTRACT Background/Question/Methods For a given scenario, the PCAD framework developed by the National Research Council Committee on Potential Effects of Ambient Noise in the Ocean on Marine Mammals can be translated into a set of nested, stochastic spatio-temporal models, linking levels of disturbance to changes in individual animal behavior, then to consequent changes in individual survival and reproductive success, and finally to population-level changes in vital rates and hence population growth or decline. Diverse data are often available to help parameterize each level of the hierarchy, although for some important model parameters there is little more than expert opinion. One potential approach to estimate model parameters is to construct a detailed, mechanistic, hierarchical statistical model and attempt to use all available data to simultaneously fit all model parameters: an “integrated” modeling approach. However, because different levels operate at quite different temporal and spatial scales, this is currently infeasible. Further, there is little lost in treating each level separately (or a few together, if convenient), and using the output of one as input to the next. Results/Conclusions The approach we have taken is to construct mechanistic models of individual animal behavior, and fit these using likelihood-based or Bayesian methods. Outputs of these models, such as the estimated distribution of calf survival as a function of different levels of disturbance, are then used as inputs for simulation-based studies of the effects of changes in vital rates on population outcomes, such as growth rate.

ABSTRACT We briefly describe distance sampling, then review recent advances that enhance its usefulness for wildlife and conservation management: • Covariate models for the detection function. • Double-platform methods for when detection on the line or at the point is uncertain. • Spatial distance sampling models. • Indirect distance sampling surveys. • Automated design algorithms. • Adaptive distance sampling designs. The standard software for distance sampling analyses is described, and plans for future versions are outlined. In many distance sampling surveys, the main goal is to estimate trends in abundance over time. We anticipate that wildlife managers will in future wish to embed population dynamics models in these trend estimates, and we outline a state-space framework that allows this.