Hidden Markov Models

Hidden Markov Models (HMMs), although known for decades, have made a big career nowadays and are still in state of development. This book presents theoretical issues and a variety of HMMs applications in speech recognition and synthesis, medicine, neurosciences, computational biology, bioinformatics, seismology, environment protection and engineering. I hope that the reader will find this book useful and helpful for their own research

Behavioral response of mule deer to natural gas development in the Piceance Basin

2015 Spring.Includes bibliographical references.To view the abstract, please see the full text of the document

Fine scale foraging behavior of gray whales in relation to prey fields and vessel disturbance along the Oregon Coast

The desire to understand the spatial and temporal drivers of animal behavior and distribution relative to scale is central to movement ecology. Optimal foraging theory states that a predator should continue exploiting a patch until it is no longer profitable to do so. As human developments increasingly encroach on the marine environment, understanding how anthropogenic interactions affect predator searching and foraging behaviors is key to minimizing disturbance. In 2015 and 2016, two studies were conducted to assess how gray whale behavior state changes (1) relative to static and dynamic environmental cues, and (2) relative to vessel interactions. The first study was addressed through the non-invasive documentation of gray whale movements (n = 76 tracks) using shore-based theodolites for eight weeks from July-August 2016, in Port Orford, Oregon, USA. When conditions allowed, a research kayak was concurrently navigated to 18 sampling stations in two comparative study sites (Mill Rocks and Tichenor Cove) within the study area. Go-Pro cameras were used to record zooplankton relative density in the water column (n=198 casts), and zooplankton net tows (n=107) were used to assess community structure. Video stills were scored for quality and relative density of zooplankton, and averaged through the water column to provide a daily density estimate of zooplankton density for each station. Whale behaviors were categorized into search, forage, and transit using the Residence in Space and Time (RST) method; behavior state was then assessed relative to static and dynamic variables at multiple scales. Despite being only one kilometer apart, there were significant spatio-temporal differences in the community assemblages of zooplankton between the two study areas, and whales demonstrated scale-dependent habitat selection relative to predictable static features (kelp) and dynamic prey availability. In Tichenor Cove, mysids (Holmesimysis sculpta), a known regional gray whale prey item, dominated the community, yet whales spent little time foraging here. Whales preferentially foraged in Mill Rocks where a combination of mysids and gammarid amphipods, previously undocumented as gray whale prey in Oregon, were prevalent. The second study occurred in the summer of 2015, and tracked whales and vessels using non-invasive, shore based theodolite and photo ID techniques. Two sites with differing levels of vessel traffic, Boiler Bay and Port Orford, were monitored for 4 weeks each. Whale focal follows were again analyzed with RST to assess behavior state changes relative to location, individual, and vessel presence, type, and distance to whale. There were significant differences in population level gray whale activity budgets between control and impact conditions, and between study sites. No significant difference in individual response to vessels disturbance was found. Taken together, the results of these two studies show that gray whales maximize energy gain through predictable, successful foraging. In the absence of vessels, foraging gray whales use information from a static feature and prey availability at a fine scale (<0.5 km) and larger regional scale (1-2 km), but searching behavior may be influenced by these features in a scale-dependent manner. When a vessel is present, disturbance appears to be tolerated as long as the foraging is profitable. Multi-faceted studies such as these advance the knowledge of which factors inform fine scale predator decision making in an increasingly anthropogenically impacted environment and have the potential to inform local management and conservation efforts.Keywords: Eschrichtius robustus, vessel interactions, Oregon, gray whales, foraging ecology, ecotouris

Uniting models and otoliths to explore migration, connectivity and space use in marine fishes

Movements of animals en masse are impressive phenomena that continue to fascinate scientists of all persuasions. Fishes display some of the most striking examples, and an extensive literature has explored the subject in marine species with long histories of commercial harvest, and/or strong, enduring cultural values. Yet, as recognition of the cognitive capacity of fishes grows, and strong inter-individual variability in behavioural traits among sympatric conspecifics is revealed as the norm, fundamental questions on the drivers underpinning both large-scale migrations, and the spatial outcomes of such moves require reexamination. This thesis comprises five papers that focus broadly on understanding the factors that shape movement decisions, distribution patterns and connectivity in schooling marine fishes. Using Atlantic herring (Clupea harengus L.) in Iceland, and striped red mullet (Mullus surmuletus L.) in the North Sea and Eastern English Channel for illustration, the work combines new Bayesian modelling approaches with analyses of otolith (ear stone) chemistry to test the role of intrinsic (i.e. collective behaviour, demographic traits, ontogeny) and extrinsic (i.e. the environment, fishing pressure, prey availability) factors in influencing the spatial dynamics of these commercially-important species. The outcomes highlight the natural synergy between model-based and empirical approaches in addressing questions on the movements of group-living fishes, and demonstrate how these can be integrated to guide fishery-management decisions, both under present conditions, and under future scenarios of environmental change.Hreyfingar og hjarðhegðun dýra er heillandi og áhrifamikil sjónarspil sem hefur verið uppspretta ýmissa rannsókna. Fiskar eru meðal þeirra dýra sem sýna hvað mest sláandi dæmi um hjarðhegðun og margar heimildir eru til um slíkt atferli hjá nytjastofnum sem og öðrum lífverum sjávar. Eftir því sem meiri vitneskja safnast um vitsmunalega getu fiska, sem og um breytileika á meðal einstaklinga innan sömu tegundar, vakna spurningar um hvaða þættir hafa mest áhrif á hegðun þeirra. Þessi ritgerð samanstendur af fimm vísindagreinum þar sem notuð eru líkön til að lýsa útbreiðslu fiska í sjó með sérstakri áherslu á að skýra þætti sem hafa áhrif á úbreiðslu íslenskrar sumargotssíldar (Clupea harengus L.) við Ísland og rauðröndungs (Mullus surmuletus L.) í Norðursjó og Ermasundi. Notaðar eru nýjar Bayesian aðferðir í líkanagerð sem eru samtvinnaðar við greiningar á efnainnihaldi kvarna til að skoða innri þætti (s.s. samhæft atferli, lýðfræðilega eiginleika, einstaklingsþroska) og ytri þætti (s.s. umhverfisþætti, veiðiálag, fæðuframboð) sem áhrif hafa á dreifingu þessarra mikilvægu nytjastofna. Niðurstöðurnar sýna að með því að tengja saman innri og ytri þætti þá má betur lýsa göngum torfufiska. Þá er einnig sýnt fram á hvernig nýta má niðurstöðurnar við fiskveiðistjórnun, bæði við núverandi umhverfisaðstæður og einnig ef umhverfisaðstæður breytast

Population genetics and behavioural ecology of North Atlantic minke whales (Balaenoptera acutorostrata)

Regional habitat use by a species, dictated by the spatial and temporal availability of resources, influences its distribution patterns and ultimately population genetic structure. Seasonal migrations between geographically separated breeding and feeding areas, as occur in many baleen whales, can complicate these relationships. Here I try to integrate the population structure of minke whales over the whole North Atlantic with regional habitat use and behavioural adaptations to a particular summer feeding ground, the Hebrides off West Scotland. Whereas no genetic differentiation could be found between separate feeding areas as far apart as Canada, the UK and Svalbard, using microsatellites and mtDNA, the presence of two cryptic breeding populations was detected, which form mixed assemblages on feeding grounds across the North Atlantic. This implies fidelity to at least two breeding grounds irrespective of proximity to feeding areas, i.e. extensive seasonal migrations (over half the North Atlantic or more), which may require a re-assessment of current management stocks. These findings were consistent with the mobility and flexibility in habitat use and behaviour observed within the Hebrides. Results from Generalized Additive Models indicated that minke whale distribution was dependent largely on temporally variable parameters (temperature in spring, chlorophyll concentration in autumn), besides depth and, to a lesser extent, topography. However, fine-scale foraging behaviour was dictated primarily by the strength and direction of tidal currents. Distribution patterns according to environmental parameters changed through the season, but were largely consistent between the entire Hebrides (cell resolution of 4min) and a smaller core study area (2min), and over a time period of 15 years. Significantly higher sighting rates in areas of likely sandeel presence in spring, but not during the rest of the season, combined with prey samples from the core study area consisting almost entirely of sprat in August/September, indicate a switch in diet between early and late season and are consistent with the changes in habitat use. Site fidelity within the core study area was high only during periods of high feeding activity, but low at other times and between years, so that individual specializations to fine-scale feeding areas, as observed off Washington State, seem unlikely. Significant interannual changes in minke sighting rates between 2003-07, both within the core study area and over the entire Hebrides, were paralleled by changes in phytoplankton concentration, local sprat landings by the fishing fleet, and seabird breeding success and numbers counted at sea, particularly common guillemots. Auks were also the seabird guild that minke whales were most likely to associate with during foraging, taking advantage of tight bait-balls concentrated by them. The significant relationships with primary productivity make bottom-up control the most likely scenario for dictating concentrations of whale and seabird prey species in West Scotland. The ability to switch between different prey according to their availability through the season, and a distribution influenced by temporally variable parameters (temperature and chlorophyll concentration), combined with adjustments in foraging activity dependent on variable conditions at fine spatial scales (tides), enable minke whales to optimise exploitation of patchy prey concentrations

Foraging and Nutritional Ecology of Eastern Australian White Sharks (Carcharodon carcharias)

Understanding and predicting foraging requires considering animals’ intrinsic (physiological) state, extrinsic (environmental/ecological) context, and the reciprocal interplays between these that shape feeding and behaviour. In particular, interactions between nutritional requirements (macronutrient balance) and ecological context are key determinants of foraging. Understanding these dynamics is especially critical in trophic keystone species, like marine top predators. Yet challenges in spatiotemporal observation and insufficient information on marine prey nutritional variability have limited knowledge of marine predator nutritional ecology so far. Here I explore the intrinsic and extrinsic drivers and outcomes of foraging in the white shark (Carcharodon carcharias), an ecologically important, threatened top predator that epitomizes the research challenges above. Using stomach contents, I provide the first diet assessment for white sharks in eastern Australia, identifying differences in prey use from other populations (South Africa) and size-based nutritional niche variation. I develop and apply a new framework leveraging stable isotopes to establish time-integrated nutritional niches and reveal how individual white sharks may specialise on functionally different (benthic or pelagic) but nutritionally complementary prey mixes to achieve similar nutritional goals. Using biologging I identify new functional bases for fine-scale white shark behaviour and recovery following capture and release, offering critical information for conservation and management. Finally, I quantify interspecific and spatiotemporal variation in prey proximate compositions to examine the nutritional landscape of eastern Australian white sharks and suggest new links to prey preference and movement. My thesis advances our understanding of the nutritional and ecological aspects of white shark foraging and develops new adaptable frameworks to enhance field studies in nutritional ecology generally

The application of ocean front metrics for understanding habitat selection by marine predators

Marine predators such as seabirds, cetaceans, turtles, pinnipeds, sharks and large teleost fish are essential components of healthy, biologically diverse marine ecosystems. However, intense anthropogenic pressure on the global ocean is causing rapid and widespread change, and many predator populations are in decline. Conservation solutions are urgently required, yet only recently have we begun to comprehend how these animals interact with the vast and dynamic oceans that they inhabit. A better understanding of the mechanisms that underlie habitat selection at sea is critical to our knowledge of marine ecosystem functioning, and to ecologically-sensitive marine spatial planning. The collection of studies presented in this thesis aims to elucidate the influence of biophysical coupling at oceanographic fronts – physical interfaces at the transitions between water masses – on habitat selection by marine predators. High-resolution composite front mapping via Earth Observation remote sensing is used to provide oceanographic context to several biologging datasets describing the movements and behaviours of animals at sea. A series of species-habitat models reveal the influence of mesoscale (10s to 100s of kilometres) thermal and chlorophyll-a fronts on habitat selection by taxonomically diverse species inhabiting contrasting ocean regions; northern gannets (Morus bassanus; Celtic Sea), basking sharks (Cetorhinus maximus; north-east Atlantic), loggerhead turtles (Caretta caretta; Canary Current), and grey-headed albatrosses (Thalassarche chrysostoma; Southern Ocean). Original aspects of this work include an exploration of quantitative approaches to understanding habitat selection using remotely-sensed front metrics; and explicit investigation of how the biophysical properties of fronts and species-specific foraging ecology interact to influence associations. Main findings indicate that front metrics, particularly seasonal indices, are useful predictors of habitat preference across taxa. Moreover, frontal persistence and spatiotemporal predictability appear to mediate the use of front-associated foraging habitats, both in shelf seas and in the open oceans. These findings have implications for marine spatial planning and the design of protected area networks, and may prove useful in the development of tools supporting spatially dynamic ocean management

Statistical modelling of collective animal movement: with an application to reindeer movement in northern Sweden

The ways in which animals move are a complex phenomena, from small scale interactions to larger migratory movement. Internal and external stimuli govern a variety of behavioural patterns whose processes are vital for species survival. Analysing these movement and behavioural processes can have significant applications for conservation and management. Although there are many statistical tools readily available for investigating animal movement, they are largely directed towards individual-level cases and do not consider the group movement present in collective species such as ungulates. This thesis aims to redress the shortcomings of statistical literature by providing a modelling framework for collective animal movement in continuous time. Our modelling approach builds upon general themes of group movement originally put forward by Langrock et al. (2014), where each individual in the group is at times attracted to an unobserved leading point. However, the behaviour of each individual can switch between ‘following the group’ and ‘moving independently’, modelled as an Ornstein Uhlenbeck process and Brownian motion respectively. The movement of the leading point is also modelled as an Ornstein-Uhlenbeck process or, if we forgo the leader’s drift term, as Brownian motion. An inhomogeneous Kalman filter Markov chain Monte Carlo algorithm is used to estimate the diffusion and switching parameters and the behavioural states of each individual at a given time point. We assess the model’s performance in a variety of simulated settings before providing a real world application using the location data of semi-domesticated reindeer (rangifer tarandus). We extend this methodology by allowing switching to depend explicitly on covariate information. We define a general auxiliary model for the inclusion of covariate data which accounts for a wide range of environmental heterogeneity. We give a simulated illustration where the animals switch behaviour sinusoidally depending on the time of day. Then, we revisit the reindeer application by including covariate data on insect harassment, which is thought to influence reindeer movement