Bayesian Estimation of Animal Movement from Archival and Satellite Tags

The reliable estimation of animal location, and its associated error is fundamental to animal ecology. There are many existing techniques for handling location error, but these are often ad hoc or are used in isolation from each other. In this study we present a Bayesian framework for determining location that uses all the data available, is flexible to all tagging techniques, and provides location estimates with built-in measures of uncertainty. Bayesian methods allow the contributions of multiple data sources to be decomposed into manageable components. We illustrate with two examples for two different location methods: satellite tracking and light level geo-location. We show that many of the problems with uncertainty involved are reduced and quantified by our approach. This approach can use any available information, such as existing knowledge of the animal's potential range, light levels or direct location estimates, auxiliary data, and movement models. The approach provides a substantial contribution to the handling uncertainty in archival tag and satellite tracking data using readily available tools

Phocid Seal Leptin: Tertiary Structure and Hydrophobic Receptor Binding Site Preservation during Distinct Leptin Gene Evolution

The cytokine hormone leptin is a key signalling molecule in many pathways that control physiological functions. Although leptin demonstrates structural conservation in mammals, there is evidence of positive selection in primates, lagomorphs and chiropterans. We previously reported that the leptin genes of the grey and harbour seals (phocids) have significantly diverged from other mammals. Therefore we further investigated the diversification of leptin in phocids, other marine mammals and terrestrial taxa by sequencing the leptin genes of representative species. Phylogenetic reconstruction revealed that leptin diversification was pronounced within the phocid seals with a high dN/dS ratio of 2.8, indicating positive selection. We found significant evidence of positive selection along the branch leading to the phocids, within the phocid clade, but not over the dataset as a whole. Structural predictions indicate that the individual residues under selection are away from the leptin receptor (LEPR) binding site. Predictions of the surface electrostatic potential indicate that phocid seal leptin is notably different to other mammalian leptins, including the otariids. Cloning the grey seal leptin binding domain of LEPR confirmed that this was structurally conserved. These data, viewed in toto, support a hypothesis that phocid leptin divergence is unlikely to have arisen by random mutation. Based upon these phylogenetic and structural assessments, and considering the comparative physiology and varying life histories among species, we postulate that the unique phocid diving behaviour has produced this selection pressure. The Phocidae includes some of the deepest diving species, yet have the least modified lung structure to cope with pressure and volume changes experienced at depth. Therefore, greater surfactant production is required to facilitate rapid lung re-inflation upon surfacing, while maintaining patent airways. We suggest that this additional surfactant requirement is met by the leptin pulmonary surfactant production pathway which normally appears only to function in the mammalian foetus

Shearwater Foraging in the Southern Ocean: The Roles of Prey Availability and Winds

Background Sooty (Puffinus griseus) and short-tailed (P. tenuirostris) shearwaters are abundant seabirds that range widely across global oceans. Understanding the foraging ecology of these species in the Southern Ocean is important for monitoring and ecosystem conservation and management. Methodology/Principal Findings Tracking data from sooty and short-tailed shearwaters from three regions of New Zealand and Australia were combined with at-sea observations of shearwaters in the Southern Ocean, physical oceanography, near-surface copepod distributions, pelagic trawl data, and synoptic near-surface winds. Shearwaters from all three regions foraged in the Polar Front zone, and showed particular overlap in the region around 140°E. Short-tailed shearwaters from South Australia also foraged in Antarctic waters south of the Polar Front. The spatial distribution of shearwater foraging effort in the Polar Front zone was matched by patterns in large-scale upwelling, primary production, and abundances of copepods and myctophid fish. Oceanic winds were found to be broad determinants of foraging distribution, and of the flight paths taken by the birds on long foraging trips to Antarctic waters. Conclusions/Significance The shearwaters displayed foraging site fidelity and overlap of foraging habitat between species and populations that may enhance their utility as indicators of Southern Ocean ecosystems. The results highlight the importance of upwellings due to interactions of the Antarctic Circumpolar Current with large-scale bottom topography, and the corresponding localised increases in the productivity of the Polar Front ecosystem

Investigating annual diving behaviour by Hooded seals (Cystophora cristata) within the Northwest Atlantic Ocean

This work was funded through the Atlantic Seal Research Programme, International Governance Programme (DFO), the Greenland Institute of Natural Resources, and a CFI grant to YFW. The authors also acknowledge the support of the Marine Alliance for Science and Technology for Scotland (MASTS) pooling initiative in the completion of this study. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.With the exception of relatively brief periods when they reproduce and moult, hooded seals, Cystophora cristata, spend most of the year in the open ocean where they undergo feeding migrations to either recover or prepare for the next fasting period. Valuable insights into habitat use and diving behaviour during these periods have been obtained by attaching Satellite Relay Data Loggers (SRDLs) to 51 Northwest (NW) Atlantic hooded seals (33 females and 18 males) during ice-bound fasting periods (2004−2008). Using General Additive Models (GAMs) we describe habitat use in terms of First Passage Time (FPT) and analyse how bathymetry, seasonality and FPT influence the hooded seals’ diving behaviour described by maximum dive depth, dive duration and surface duration. Adult NW Atlantic hooded seals exhibit a change in diving activity in areas where they spend >20 h by increasing maximum dive depth, dive duration and surface duration, indicating a restricted search behaviour. We found that male and female hooded seals are spatially segregated and that diving behaviour varies between sexes in relation to habitat properties and seasonality. Migration periods are described by increased dive duration for both sexes with a peak in May, October and January. Males demonstrated an increase in dive depth and dive duration towards May (post-breeding/pre-moult) and August–October (post-moult/pre-breeding) but did not show any pronounced increase in surface duration. Females dived deepest and had the highest surface duration between December and January (post-moult/pre-breeding). Our results suggest that the smaller females may have a greater need to recover from dives than that of the larger males. Horizontal segregation could have evolved as a result of a resource partitioning strategy to avoid sexual competition or that the energy requirements of males and females are different due to different energy expenditure during fasting periods.Publisher PDFPeer reviewe

Seagrass and epiphytic algae support nutrition of a fisheries species, Sillago schomburgkii, in adjacent intertidal habitats

The importance of organic matter produced in seagrass meadows (seagrass and epiphytic algae) to the nutrition of a valuable fisheries species (yellowfin whiting Sillago schomburgkii Peters) occurring over unvegetated mudflats was measured using the isotopic composition (d13C, d15N) of fish, their polychaete prey, and available autotrophic sources at several locations in southern Australia during 2 periods (summer, winter). Values for d13C and d15N for autotrophs and fishes varied little between seasons. Sources could be separated into 3 groups based on d13C: seagrass and epiphytes (mean d13C = -10.5马 benthic microalgae and macroalgae (-19.5马 and saltmarsh and mangroves (-26.5驮 Values of d15N for the sources were 2 to 5鮠Values of d13C for fish (-13.3驠corresponded with those of their polychaete prey (-12.5驠and ultimately with those of seagrass and epiphytes. Values of d15N were 5 to 6頭ore enriched than sources. Modelling of feasible source mixtures showed that seagrass and epiphytes were the most important contributors to the nutrition of fish, but their relative importance varied between seasons. The median contribution by other sources was <10%. Spatial analyses showed that saltmarsh plants contributed significantly to the variability in S. schomburgkii nutrition among locations, while macroalgae contributed in summer. The similarity in d13C values of polychaetes and S. schomburgkii is consistent with source material from a subtidal habitat being incorporated into food webs supporting a fisheries species in adjacent intertidal habitats via a largely sedentary intermediary.Griffith Sciences, Griffith School of EnvironmentFull Tex

Fine-scale variability in elemental composition of estuarine water and otoliths: developing environmental markers for determining larval fish dispersal histories within estuaries

Otolith chemistry has been widely used as a natural tag for determining environmental histories of fish that migrate across large distances and environmental gradients. However, it is not as well established as to whether otolith chemistry can be a useful tool for determining fine-scale movement and dispersal patterns of fish, particularly larvae, within estuaries. In this study, we collected water samples and otoliths from larvae of black bream, Acanthopagrus butcheri, an estuarine resident fish, and analyzed each for a suite of trace elements to determine the degree of spatio-temporal variability in elemental composition and which elements were incorporated into otoliths in relation to their associated water chemistry. We found that there were three distinct water layer signatures based on their Me : Cawater (Me = each element): a freshwater signature, a halocline signature, and a marine signature. There were also significant spatio-temporal patterns in Me : Caotolith, most notably for Li : Ca, K : Ca, and Mn : Ca. This study provides encouraging evidence for the utility of intra-estuary otolith chemistry to reconstruct environmental histories during larval development. This application will enable a better understanding of the abundance, timing, and duration of residency in particular water masses and locations that are important larval nursery habitats for species that develop within estuaries