Geert Aarts

Generalized functional responses for species distributions

Researchers employing resource selection functions (RSFs) and other related methods aim to detect correlates of space-use and mitigate against detrimental environmental change. However, an empirical model fit to data from one place or time is unlikely to capture species responses under different conditions because organisms respond nonlinearly to changes in habitat availability. This phenomenon, known as a functional response in resource selection, has been debated extensively in the RSF literature but continues to be ignored by practitioners for lack of a practical treatment. We therefore extend the RSF approach to enable it to estimate generalized functional responses (GFRs) from spatial data. GFRs employ data from several sampling instances characterized by diverse profiles of habitat availability. By modeling the regression coefficients of the underlying RSF as functions of availability, GFRs can account for environmental change and thus predict population distributions in new environments. We formulate the approach as a mixed-effects model so that it is estimable by readily available statistical software. We illustrate its application using (1) simulation and (2) wolf home-range telemetry. Our results indicate that GFRs can offer considerable improvements in estimation speed and predictive ability over existing mixed-effects approaches.

Marine mammals trace anthropogenic structures at sea

On land, species from all trophic levels have adapted to fill vacant niches in environments heavily modified by humans (e.g. [1]). In the marine environment, ocean infrastructure has led to artificial reefs, resulting in localized increases in fish and crustacean density [2]. Whether marine apex predators exhibit behavioural adaptations to utilise such a scattered potential resource is unknown. Using high resolution GPS data we show how infrastructure, including wind turbines and pipelines, shapes the movements of individuals from two seal species (Phoca vitulina and Halichoerus grypus). Using state-space models, we infer that these animals are using structures to forage. We highlight the ecological consequences of such behaviour, at a time of unprecedented developments in marine infrastructure.

Quantifying the effect of habitat availability on species distributions

1. If animals moved randomly in space, the use of different habitats would be proportional to their availability. Hence, deviations from proportionality between use and availability are considered the tell-tale sign of preference. This principle forms the basis for most habitat selection and species distribution models fitted to use-availability or count data (e.g. MaxEnt and Resource Selection Functions). 2. Yet, once an essential habitat type is sufficiently abundant to meet an individuals needs, increased availability of this habitat type may lead to a decrease in the use/availability ratio. Accordingly, habitat selection functions may estimate negative coefficients when habitats are superabundant, incorrectly suggesting an apparent avoidance. Furthermore, not accounting for the effects of availability on habitat use may lead to poor predictions, particularly when applied to habitats that differ considerably from those for which data have been collected. 3. Using simulations, we show that habitat use varies non-linearly with habitat availability, even when individuals follow simple movement rules to acquire food and avoid risk. The results show that the impact of availability strongly depends on the type of habitat (e.g. whether it is essential or substitutable) and how it interacts with the distribution and availability of other habitats. 4. We demonstrate the utility of a variety of existing and new methods that enable the influence of habitat availability to be explicitly estimated. Models that allow for non-linear effects (using b-spline smoothers) and interactions between environmental covariates defining habitats and measures of their availability were best able to capture simulated patterns of habitat use across a range of environments. 5. An appealing aspect of some of the methods we discuss is that the relative influence of availability is not defined a priori, but directly estimated by the model. This feature is likely to improve model prediction, hint at the mechanism of habitat selection, and may signpost habitats that are critical for the organisms fitness.

Advancing our thinking in presence-only and used-available analysis

1. The problems of analysing used-available data and presence-only data are equivalent, and this paper uses this equivalence as a platform for exploring opportunities for advancing analysis methodology. 2. We suggest some potential methodological advances in used-available analysis, made possible via lessons learnt in the presence-only literature, for example, using modern methods to improve predictive performance. We also consider the converse - potential advances in presence-only analysis inspired by used-available methodology. 3. Notwithstanding these potential advances in methodology, perhaps a greater opportunity is in advancing our thinking about how to apply a given method to a particular data set. 4. It is shown by example that strikingly different results can be achieved for a single data set by applying a given method of analysis in different ways - hence having chosen a method of analysis, the next step of working out how to apply it is critical to performance. 5. We review some key issues to consider in deciding how to apply an analysis method: apply the method in a manner that reflects the study design; consider data properties; and use diagnostic tools to assess how reasonable a given analysis is for the data at hand.

Ecosystem-based management objectives for the North Sea:Riding the forage fish rollercoaster

The North Sea provides a useful model for considering forage fish (FF) within ecosystem-based management as it has a complex assemblage of FF species. This paper is designed to encourage further debate and dialogue between stakeholders about management objectives. Changing the management of fisheries on FF will have economic consequences for all fleets in the North Sea. The predators that are vulnerable to the depletion of FF are Sandwich terns, great skua and common guillemots, and to a lesser extent, marine mammals. Comparative evaluations of management strategies are required to consider whether maintaining the reserves of prey biomass or a more integral approach of monitoring mortality rates across the trophic system is more robust under the ecosystem approach. In terms of trophic energy transfer, stability, and resilience of the ecosystem, FF should be considered as both a sized-based pool of biomass and as species components of the system by managers and modellers. Policy developers should not consider the knowledge base robust enough to embark on major projects of ecosystem engineering. Management plans appear able to maintain sustainable exploitation in the short term. Changes in the productivity of FF populations are inevitable so management should remain responsive and adaptive.

The Influence of Topographic and Dynamic Cyclic Variables on the Distribution of Small Cetaceans in a Shallow Coastal System

The influence of topographic and temporal variables on cetacean distribution at a fine-scale is still poorly understood. To study the spatial and temporal distribution of harbour porpoise Phocoena phocoena and the poorly known Risso’s dolphin Grampus griseus we carried out land-based observations from Bardsey Island (Wales, UK) in summer (2001–2007). Using Kernel analysis and Generalized Additive Models it was shown that porpoises and Risso’s appeared to be linked to topographic and dynamic cyclic variables with both species using different core areas (dolphins to the West and porpoises to the East off Bardsey). Depth, slope and aspect and a low variation in current speed (for Risso’s) were important in explaining the patchy distributions for both species. The prime temporal conditions in these shallow coastal systems were related to the tidal cycle (Low Water Slack and the flood phase), lunar cycle (a few days following the neap tidal phase), diel cycle (afternoons) and seasonal cycle (peaking in August) but differed between species on a temporary but predictable basis. The measure of tidal stratification was shown to be important. Coastal waters generally show a stronger stratification particularly during neap tides upon which the phytoplankton biomass at the surface rises reaching its maximum about 2–3 days after neap tide. It appeared that porpoises occurred in those areas where stratification is maximised and Risso’s preferred more mixed waters. This fine-scale study provided a temporal insight into spatial distribution of two species that single studies conducted over broader scales (tens or hundreds of kilometers) do not achieve. Understanding which topographic and cyclic variables drive the patchy distribution of porpoises and Risso’s in a Headland/Island system may form the initial basis for identifying potentially critical habitats for these species.

Feeding ecology of harbour porpoises: stable isotope analysis of carbon and nitrogen in muscle and bone

Abstract Harbour porpoises are the most common small cetaceans in the North Sea and Dutch coastal waters. To study their trophic level and feeding location, stable carbon and nitrogen isotope ratios (δ13C and δ15N) were analysed in muscle and bone samples collected from 157 porpoises stranded along the Dutch coast (2006–2008). In addition, samples from 30 prey species were analysed. Prey samples showed high δ15N values in species of higher trophic level. In addition, geographic differences in isotopic composition were found, with higher δ15N and δ13C values in prey from more southern, coastal and estuarine areas. Based on muscle δ15N values, we found neonatal enrichment and that larger porpoises, in particular males, seem to feed on lower trophic level species, compared to smaller individuals. Also bone δ15N values show that larger animals had fed on lower trophic levels in distant times. Porpoises from the Eastern Scheldt reveal distinct δ13C values in muscle, but not in bone. This shows that these animals had foraged in the Eastern Scheldt for a longer time period but were not born there. Seasonal variation in bone δ15N and δ13C values revealed two distinct groups of porpoises along the Dutch coast, a winter group (mainly males) that migrated from neighbouring regions and a Dutch subpopulation in summer. These results furthered our insight about shifts in trophic level and feeding location of harbour porpoises from the southern North Sea over time.

Assessing the Impact of Underwater Clearance of Unexploded Ordnance on Harbour Porpoises (Phocoena phocoena) in the Southern North Sea

(UXO) are still present in the North Sea. UXO are frequently accidentally encountered by fishermen and dredging vessels. Out of concern for human safety and to avoid damage to equipment and infrastructure from uncontrolled explosions, most reported UXO found in the Dutch Continental Shelf (DCS) are detonated in a controlled way. These underwater detonations produce high amplitude shock waves that may adversely affect marine mammals. The most abundant marine mammal in the DCS is the harbour porpoise (Phocoena phocoena), a species demonstrated to be highly sensitive to sound. Therefore, an assessment of potential impacts of underwater explosions on harbour porpoises was undertaken. Information regarding UXO cleared in the DCS provided by the Netherlands Ministry of Defence was used in a propagation model to produce sound exposure maps. These were combined with estimates of exposure levels predicted to cause hearing loss in harbour porpoises and survey-based models of harbour porpoise seasonal distribution on the DCS. It was estimated that in a 1-y period, the 88 explosions that occurred in the DCS very likely caused 1,280, and possibly up to 5,450, permanent hearing loss events (i.e., instances of a harbour porpoise predicted to have received sufficient sound exposure to cause permanent hearing loss). This study is the first to address the impacts of underwater explosions on the population scale of a marine mammal species. The methodology is applicable to other studies on the effects of underwater explosions on the marine environment.

Mapping underwater sound in the dutch part of the North Sea

The European Union requires member states to achieve or maintain good environmental status for their marine territorial waters and explicitly mentions potentially adverse effects of underwater sound. In this study, we focused on producing maps of underwater sound from various natural and anthropogenic origins in the Dutch North Sea. The source properties and sound propagation are simulated by mathematical methods. These maps could be used to assess and predict large-scale effects on behavior and distribution of underwater marine life and therefore become a valuable tool in assessing and managing the impact of underwater sound on marine life.

Estimating the spatial position of marine mammals based on digital camera recordings

Estimating the spatial position of organisms is essential to quantify interactions between the organism and the characteristics of its surroundings, for example, predator–prey interactions, habitat selection, and social associations. Because marine mammals spend most of their time under water and may appear at the surface only briefly, determining their exact geographic location can be challenging. Here, we developed a photogrammetric method to accurately estimate the spatial position of marine mammals or birds at the sea surface. Digital recordings containing landscape features with known geographic coordinates can be used to estimate the distance and bearing of each sighting relative to the observation point. The method can correct for frame rotation, estimates pixel size based on the reference points, and can be applied to scenarios with and without a visible horizon. A set of R functions was written to process the images and obtain accurate geographic coordinates for each sighting. The method is applied to estimate the spatiotemporal fine-scale distribution of harbour porpoises in a tidal inlet. Video recordings of harbour porpoises were made from land, using a standard digital single-lens reflex (DSLR) camera, positioned at a height of 9.59 m above mean sea level. Porpoises were detected up to a distance of ∽3136 m (mean 596 m), with a mean location error of 12 m. The method presented here allows for multiple detections of different individuals within a single video frame and for tracking movements of individuals based on repeated sightings. In comparison with traditional methods, this method only requires a digital camera to provide accurate location estimates. It especially has great potential in regions with ample data on local (a)biotic conditions, to help resolve functional mechanisms underlying habitat selection and other behaviors in marine mammals in coastal areas.