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Animal tracking data are indispensable for understanding the ecology, behaviour and physiology of mobile or cryptic species. Meaningful signals in these data can be obscured by noise due to imperfect measurement technologies, requiring rigorous quality control as part of any comprehensive analysis. State–space models are powerful tools that separate signal from noise. These tools are ideal for quality control of error-prone location data and for inferring where animals are and what they are doing when they record or transmit other information. However, these statistical models can be challenging and time-consuming to fit to diverse animal tracking data sets. The R package aniMotum eases the tasks of conducting quality control on and inference of changes in movement from animal tracking data. This is achieved via: (1) a simple but extensible workflow that accommodates both novice and experienced users; (2) automated processes that alleviate complexity from data processing and model specification/fitting steps; (3) simple movement models coupled with a powerful numerical optimization approach for rapid and reliable model fitting. We highlight aniMotum's capabilities through three applications to real animal tracking data. Full R code for these and additional applications is included as Supporting Information, so users can gain a deeper understanding of how to use aniMotum for their own analyses.

Coastal polynyas are key regions of Dense Shelf Water (DSW) formation that ultimately contributes to the ventilation of the ocean abyss. However, not all polynyas form DSW. In this study, we analyse the main drivers of DSW formation in four East Antarctic polynyas: Mackenzie, Barrier, Shackelton and Vincennes Bay from west to east. Mackenzie and Barrier (in lesser extent) were the only two polynyas where DSW formation was observed while it is absent in Shackelton and Vincennes Bay in the particular years when they were best sampled. We analysed the role of Bathymetry, water-mass distribution and transformation, stratification of the water column, sea-ice production rate and associated salt advection. We found that sea ice production was highest in Mackenzie, particularly in early winter, which likely contributed to reach higher salinity than the other polynyas at the beginning of the sea ice formation season. From April to September, the total salinity change in Mackenzie polynya was lower than in the other polynyas, and the strong contribution of the brine rejection was partly offset by freshwater advection. Overall, the preconditioning in early winter in Mackenzie polynya, likely due to strong SIP in February and March was the main driver determining DSW formation in MAckenzie in contrast with the other East Antarctic polynyas.

Antarctic polynyas are persistent open water areas which enable early and large seasonal phytoplankton blooms. This high primary productivity, boosted by iron supply from coastal glaciers, attracts organisms from all trophic levels to form a rich and diverse community. How the ecological benefit of polynya productivity is translated to the highest trophic levels remains poorly resolved. We studied 119 southern elephant seals feeding over the Antarctic shelf and demonstrated that: (i) 96% of seals foraging here used polynyas, with individuals spending on average 62% of their time there; (ii) the seals exhibited more area-restricted search behaviour when in polynyas; and (iii) these seals gained more energy (indicated by increased buoyancy from greater fat stores) when inside polynyas. This higher-quality foraging existed even when ice was not present in the study area, indicating that these are important and predictable foraging grounds year-round. Despite these energetic advantages from using polynyas, not all the seals used them extensively. Factors other than food supply may influence an individual's choice in their use of feeding grounds, such as exposure to predation or the probability of being able to return to distant sub-Antarctic breeding sites.

This study addresses the consequences of repeated human handling on the survival of an endangered phocid, the southern elephant seal and the implications for wildlife research. Southern elephant seal pups were repeatedly handled during the first six weeks of their lives. The possibility that such anthropogenic research may have altered the very parameters that were being investigated is a topical and relevant study area that we address here. Our results show that there were no measurable effects on pups that were repeatedly handled and subjected to invasive research methods with respect to survivorship in the short term (the 24-day nursing period) nor in the long term (the first year of life and beyond) and hence fitness one year after handling. In support of this conclusion we were unable to detect any significant differences in the survival rates of the most intensively handled seals and the least intensively handled seals.

Marine mammals help gather information on some of the harshest environments on the planet, through the use of miniaturized ocean sensors glued on their fur. Since 2004, hundreds of diving marine animals, mainly Antarctic and Arctic seals, have been fitted with a new generation of Argos tags developed by the Sea Mammal Research Unit of the University of St Andrews in Scotland, UK. These tags investigate the at-sea ecology of these animals while simultaneously collecting valuable oceanographic data. Some of the study species travel thousands of kilometres continuously diving to great depths (up to 2100 m). The resulting data are now freely available to the global scientific community at http://www.meop.net. Despite great progress in their reliability and data accuracy, the current generation of loggers while approaching standard ARGO quality specifications have yet to match them. Yet, improvements are underway; they involve updating the technology, implementing a more systematic phase of calibration and taking benefit of the recently acquired knowledge on the dynamical response of sensors. Together these efforts are rapidly transforming animal tagging into one of the most important sources of oceanographic data in polar regions and in many coastal areas. Publisher PDF Non