Modelling harbour seal movements

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Colony-specific differences in decadal longitudinal body composition of a capital-breeding marine top predator

he long‐term studies included in this paper were funded by the Natural Environment Research Council through the grant ‘SMRU Long‐term measurement of marine mammal population structure, dynamics and trophic interactions’, grant reference SMRU1001. PP was in receipt of NERC grant no. NE/G008930/1 and Esmée Fairbairn Foundation funding during the work. SCS was supported as a postdoctoral fellow in an EPSRC award to RK and PP.1. Capital breeding animals such as true seals (Phocidae) rely on accumulated body reserves to rear offspring. A mother's body composition at the start of a breeding episode may depend on recent environmental conditions and sets the resources available for the reproductive episode. 2.  At two grey seal (Halichoerus grypus) breeding colonies with contrasting demographic characteristics, factors influencing individual variation and temporal trends in the body composition (expressed as the lipid‐to‐protein mass ratio) of females were examined. 3.  Maternal reproductive expenditure, and the consequences for mothers and their pups, were investigated. 4.  Individual variation in postpartum maternal body composition was considerable. Mean values of 27% (±5%) lipid and 18% (±1%) protein were estimated by hydrogen isotope dilution. No evidence of age effects was detected. 5.  Mothers with a high lipid‐to‐protein mass ratio expended a higher proportion of lipid resources, conserved protein and returned with more protein the following year. 6.  Average maternal postpartum body composition was similar between the two colonies, but temporal patterns differed at one colony where pup production was decreasing from another where pup production was increasing. Mothers at the declining colony consistently weaned larger pups than mothers at the increasing colony across the range of mother sizes, but measures of maternal body composition did not predict pup weaning masses.PostprintPeer reviewe

Body density and diving gas volume of the northern bottlenose whale (Hyperoodon ampullatus)

Funding for fieldwork and data analysis was provided by the Strategic Environmental Research and Development Program (SERDP), project RC-2337Diving lung volume and tissue density, reflecting lipid store volume, are important physiological parameters that have only been estimated for a few breath-hold diving species. We fitted 12 northern bottlenose whales with data loggers that recorded depth, 3-axis acceleration and speed either with a fly-wheel or from change of depth corrected by pitch angle.We fitted measured values of the change in speed during 5 s descent and ascent glides to a hydrodynamic model of drag and buoyancy forces using a Bayesian estimation framework. The resulting estimate of diving gas volume was 27.4±4.2 (95% credible interval, CI) ml kg−1, closely matching the measured lung capacity of the species. Dive-by-dive variation in gas volume did not correlate with dive depth or duration. Estimated body densities of individuals ranged from 1028.4 to 1033.9 kg m−3 at the sea surface, indicating overall negative tissue buoyancy of this species in seawater. Body density estimates were highly precise with ±95% CI ranging from 0.1to 0.4 kg m−3, which would equate to a precision of <0.5% of lipid content based upon extrapolation from the elephant seal. Six whales tagged near Jan Mayen (Norway, 71°N) had lower body density and were closer to neutral buoyancy than six whales tagged in the Gully (Nova Scotia, Canada, 44°N), a difference that was consistent with the amount of gliding observed during ascent versus descent phases in these animals. Implementation of this approach using longer duration tags could be used to track longitudinal changes in body density and lipid store body condition of free-ranging cetaceans.Publisher PDFPeer reviewe

Fine-scale harbour seal usage for informed marine spatial planning

The work was funded through Scottish Government MSQ0174 contract CR/2014/11; CREEM, University of St Andrews; the National Capability fund from the Natural Environment Research Council to the Sea Mammal Research Unit (grant no. SMRU1001); and MASTS pooling initiative, which is funded by the Scottish Funding Council (grant reference HR09011).High-resolution species distribution maps are required for marine spatial planning, consenting, and licensing to assess interactions between anthropogenic activities and ecosystems. This approach can inform conservation measures for protected species and facilitate commercial developments needed for economic growth. A case study centred on Orkney, UK, is an area where concern for a declining harbour seal population has led to constraints being placed on tidal energy generation developments. Telemetry data from 54 animals tagged between 2003 and 2015 were combined with terrestrial counts from 2008 to 2015 to produce density estimation maps. Predictive habitat models using GAM-GEEs provided robust predictions in areas where telemetry data were absent, and were combined with density estimation maps. Harbour seal usage maps with confidence intervals were produced around Orkney and the North coast of Scotland. The selected habitat model showed that distance from haul out, proportion of sand in seabed sediment, and peak flow of tidal current were important predictors of space-use. Fine-scale usage maps can be used in consenting and licensing of anthropogenic developments to determine local abundance. When quantifying anthropogenic impacts through changes to species distributions, usage maps could be spatially explicitly linked to individual-based models to inform predicted movement and behaviour.Publisher PDFPeer reviewe

Identifying fishing grounds from vessel tracks: model-based inference for small scale fisheries

This study (T.M., M.J. and S.S.) was funded by the European Maritime Fisheries Fund ‘Scottish Inshore Fisheries Integrated Data System' (grant reference no. SCO1434). T.P. was supported by a Newton International Fellowship, funded by the Royal Society (grant reference no. NF170682).Recent technological developments facilitate the collection of location data from fishing vessels at an increasing rate. The development of low-cost electronic systems allows tracking of small-scale fishing vessels, a sector of fishing fleets typically characterized by many, relatively small vessels. The imminent production of large spatial datasets for this previously data-poor sector creates a challenge in terms of data analysis. Several methods have been used to infer the spatial distribution of fishing activities from positional data. Here, we compare five approaches using either vessel speed, or speed and turning angle, to infer fishing activity in the Scottish inshore fleet. We assess the performance of each approach using observational records of true vessel activity. Although results are similar across methods, a trip-based Gaussian mixture model provides the best overall performance and highest computational efficiency for our use-case, allowing accurate estimation of the spatial distribution of active fishing (97% of true area captured). When vessel movement data can be validated, we recommend assessing the performance of different methods. These results illustrate the feasibility of designing a monitoring system to efficiently generate information on fishing grounds, fishing intensity, or monitoring of compliance to regulations at a nationwide scale in near-real-time.Publisher PDFPeer reviewe

Habitat partitioning in sympatric delphinids around the Falkland Islands : predicting distributions based on a limited data set

Funding: The field work was funded by the Darwin Initiative UK Overseas Territories Challenge Fund Project “Inshore Cetaceans of the Falkland Islands” (Project Ref: EIDCF019, administered jointly by Falklands Conservation & Mr Grant Munro), and Darwin Plus: Overseas Territories Environment and Climate Fund Project “Dolphins of the kelp: Data priorities for Falkland’s inshore cetaceans” (Project Ref: DPLUS042, administered by SAERI).Spatial modelling based on line transect data is a standard method for characterising marine mammal distributions and habitat preference. However, collecting the data required is costly and may be difficult in remote areas. Models based on habitat variables offer the potential to predict where the species will occur in areas outside the area of a localised survey. This has important implications for spatial management where decisions have to be made that affect wide areas over which comprehensive survey efforts may not be feasible. This study demonstrates that it is possible, using a spatially limited data set, to characterise habitat use and predict the distribution of two poorly known sympatric delphinids around the Falkland (Malvinas) Islands (FI), Commerson’s dolphins (Cephalorhynchus commersonii) and Peale’s dolphins (Lagenorhynchus australis). We used a Hurdle model approach to investigate the relationship between dolphin sightings (from a spatially restricted boat-based line transect survey) and environmental covariates. We then used the modelled relationships to predict the distribution and relative abundance of Commerson’s and Peale’s dolphins over the entire FI inshore waters. We compared the predicted distribution maps to independent sightings from a subsequent island-wide aerial line transect survey, and found a close match between predicted and observed distributions. Commerson’s dolphins preferred nearshore waters with strong tidal mixing and were most numerous close to river mouths and in upper inlets or channels. In contrast, Peale’s dolphins preferred deeper, well-stratified areas further from shore as well as nearshore waters with extensive kelp beds. While the two dolphin species are often considered sympatric, our results indicate fine-scale habitat partitioning based on specific habitat preferences, which is important to consider in further studies and marine spatial planning. We provide several methodological refinements to prepare transect sighting data for spatial analysis and implement Hurdle models more easily using the new “dshm” R-package. We also show the usefulness of such refinements applied to a carefully chosen spatially limited dataset as a cost-effective approach to elucidating species distribution patterns. Our methodology and software implementations can be easily applied to transect survey data of other marine and terrestrial taxa.Publisher PDFPeer reviewe

Compound specific isotope analyses of harp seal teeth : tools for trophic ecology reconstruction

This work resulted from the ARISE project (NE/P006035/1 awarded to CM and RJ, and NE/P00623X/1 awarded to SS), part of the Changing Arctic Ocean programme, funded by the UKRI Natural Environment Research Council (NERC).As sentinels of ecosystem health, high trophic level predators integrate information through all levels of the food web. Their tissues can be used to investigate spatiotemporal variability in foraging behaviour, and with the appropriate analytical methods and tools, archived samples can be used to reconstruct past trophic interactions. Harp seal (Pagophilus groenlandicus) teeth collected in the 1990s from the Northwest Atlantic were analysed for bulk stable carbon and nitrogen isotopes (δ13Cbulk and δ15Nbulk), and compound specific stable nitrogen isotopes of amino acids (δ15NAA) for the first time. We developed a fine-scale, annual growth layer group (GLG) dentine sub-sampling method corresponding to their second and third year of life. In accordance with previous diet studies, while there was individual variability in δ15Nbulk, δ13Cbulk, and δ15NAA measurements, we did not detect significant differences in isotopic niche widths between males and females, or between GLGs. Relative trophic position was calculated as the baseline corrected δ15NAA values using trophic (glutamic acid) and source (phenylalanine and glycine) amino acids. Variability was measured between individuals in their relative trophic position, but within individual variability was low, suggesting that they fed at the same trophic level over these 2 years of life. These novel δ15NAA data may therefore suggest individual, specialist harp seal foraging behaviour in sub-adults. Our findings show that compound specific stable isotope signatures of archived, inert predator tissues can be used as tools for the retrospective reconstruction of trophic interactions on broad spatiotemporal scales.PostprintPeer reviewe

Estimating energetic intake for marine mammal bioenergetic models

This work was primarily funded under an award from Office of Naval Research: N000142012392, and with support from the Marine Mammal Commission project: “A priority setting exercise to identify key unanswered questions in marine mammal bioenergetics”. Funding from the Joint Nature Conservation Committee supported fish energy analyses - award C180241-1285.Bioenergetics is the study of how animals achieve energetic balance. Energetic balance results from the energetic expenditure of an individual and the energy they extract from their environment. Ingested energy depends on several extrinsic (e.g prey species, nutritional value and composition, prey density and availability) and intrinsic factors (e.g. foraging effort, success at catching prey, digestive processes and associated energy losses, and digestive capacity). While the focus in bioenergetic modelling is often on the energetic costs an animal incurs, the robust estimation of an individual’s energy intake is equally critical for producing meaningful predictions. Here, we review the components and processes that affect energy intake from ingested gross energy to biologically useful net energy (NE). The current state of knowledge of each parameter is reviewed, shedding light on research gaps to advance this field. The review highlighted that the foraging behaviour of many marine mammals is relatively well studied via biologging tags, with estimates of success rate typically assumed for most species. However, actual prey capture success rates are often only assumed, although we note studies that provide approaches for its estimation using current techniques. A comprehensive collation of the nutritional content of marine mammal prey species revealed a robust foundation from which prey quality (comprising prey species, size and energy density) can be assessed, though data remain unavailable for many prey species. Empirical information on various energy losses following ingestion of prey was unbalanced among marine mammal species, with considerably more literature available for pinnipeds. An increased understanding and accurate estimate of each of the components that comprise a species NE intake are an integral part of bioenergetics. Such models provide a key tool to investigate the effects of disturbance on marine mammals at an individual and population level and to support effective conservation and management.Publisher PDFPeer reviewe

Patterns of space use in sympatric marine colonial predators reveals scales of spatial partitioning

E.L.J. and D.J.F.R. were funded under Scottish Government grant MMSS001/01. D.J.F.R. was funded by the UK Department of Energy and Climate Change (DECC) as part of their Offshore Energy Strategic Environmental Assessment programme. S.S. was part-funded by the EU MYFISH project.Species distribution maps can provide important information to focus conservation efforts and enable spatial management of human activities. Two sympatric marine predators, grey seals Halichoerus grypus and harbour seals Phoca vitulina have overlapping ranges on land and at sea but contrasting population dynamics around Britain: whilst grey seals have generally increased, harbour seals have shown significant regional declines. We analysed two decades of at-sea movement data and terrestrial count data from these species to produce high resolution, broad-scale maps of distribution and associated uncertainty to inform conservation and management. Our results showed that grey seals use offshore areas connected to their haul-out sites by prominent corridors and harbour seals primarily stay within 50km of the coastline. Both species show fine-scale offshore spatial segregation off the east coast of Britain and broad-scale partitioning off western Scotland. These results illustrate that for broad-scale marine spatial planning, the conservation needs of harbour seals (primarily inshore, the exception being selected offshore usage areas) are different from those of grey seals (up to 100km offshore and corridors connecting these areas to haul-out sites). More generally, our results illustrate the importance of detailed knowledge of marine predator distributions to inform marine spatial planning; for instance, spatial prioritisation is not necessarily the most effective spatial planning strategy even when conserving species with similar taxonomy.Peer reviewe

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe