Counting animals in aerial images with a density map estimation model.

Animal abundance estimation is increasingly based on drone or aerial survey photography. Manual postprocessing has been used extensively; however, volumes of such data are increasing, necessitating some level of automation, either for complete counting, or as a labour-saving tool. Any automated processing can be challenging when using such tools on species that nest in close formation such as Pygoscelis penguins. We present here a customized CNN-based density map estimation method for counting of penguins from low-resolution aerial photography. Our model, an indirect regression algorithm, performed significantly better in terms of counting accuracy than standard detection algorithm (Faster-RCNN) when counting small objects from low-resolution images and gave an error rate of only 0.8 percent. Density map estimation methods as demonstrated here can vastly improve our ability to count animals in tight aggregations and demonstrably improve monitoring efforts from aerial imagery.

The call of the emperor penguin: Legal responses to species threatened by climate change.

Species extinction risk is accelerating due to anthropogenic climate change, making it urgent to protect vulnerable species through legal frameworks in order to facilitate conservation actions that help mitigate risk. Here, we discuss fundamental concepts for assessing climate change risks to species using the example of the emperor penguin (Aptenodytes forsteri), currently being considered for protection under the US Endangered Species Act (ESA). This species forms colonies on Antarctic sea ice, which is projected to significantly decline due to ongoing greenhouse gas (GHG) emissions. We project the dynamics of all known emperor penguin colonies under different GHG emission scenarios using a climate-dependent meta-population model including the effects of extreme climate events based on the observational satellite record of colonies. Assessments for listing species under the ESA require information about how species resiliency, redundancy and representation (3Rs) will be affected by threats within the foreseeable future. Our results show that if sea ice declines at the rate projected by climate models under current energy system trends and policies, the 3Rs would be dramatically reduced and almost all colonies would become quasi-extinct by 2100. We conclude that the species should be listed as threatened under the ESA.

Wintertime overlaps between female Antarctic fur seals (Arctocephalus gazella) and the krill fishery at South Georgia, South Atlantic.

The diet of Antarctic fur seals (Arctocephalus gazella) at South Georgia is dominated by Antarctic krill (Euphausia superba). During the breeding season, foraging trips by lactating female fur seals are constrained by their need to return to land to provision their pups. Post-breeding, seals disperse in order to feed and recover condition; estimates indicate c.70% of females remain near to South Georgia, whilst others head west towards the Patagonian Shelf or south to the ice-edge. The krill fishery at South Georgia operates only during the winter, providing the potential for fur seal: fishery interaction during these months. Here we use available winter (May to September) tracking data from Platform Terminal Transmitter (PTT) tags deployed on female fur seals at Bird Island, South Georgia. We develop habitat models describing their distribution during the winters of 1999 and 2003 with the aim of visualising and quantifying the degree of spatial overlap between female fur seals and krill harvesting in South Georgia waters. We show that spatial distribution of fur seals around South Georgia is extensive, and that the krill fishery overlaps with small, highly localised areas of available fur seal habitat. From these findings we discuss the implications for management, and future work.

Tracking of marine predators to protect Southern Ocean ecosystems.

Southern Ocean ecosystems are under pressure from resource exploitation and climate change1,2. Mitigation requires the identification and protection of Areas of Ecological Significance (AESs), which have so far not been determined at the ocean-basin scale. Here, using assemblage-level tracking of marine predators, we identify AESs for this globally important region and assess current threats and protection levels. Integration of more than 4,000 tracks from 17 bird and mammal species reveals AESs around sub-Antarctic islands in the Atlantic and Indian Oceans and over the Antarctic continental shelf. Fishing pressure is disproportionately concentrated inside AESs, and climate change over the next century is predicted to impose pressure on these areas, particularly around the Antarctic continent. At present, 7.1% of the ocean south of 40°S is under formal protection, including 29% of the total AESs. The establishment and regular revision of networks of protection that encompass AESs are needed to provide long-term mitigation of growing pressures on Southern Ocean ecosystems.

The retrospective analysis of Antarctic tracking data project.

The Retrospective Analysis of Antarctic Tracking Data (RAATD) is a Scientific Committee for Antarctic Research project led jointly by the Expert Groups on Birds and Marine Mammals and Antarctic Biodiversity Informatics, and endorsed by the Commission for the Conservation of Antarctic Marine Living Resources. RAATD consolidated tracking data for multiple species of Antarctic meso- and top-predators to identify Areas of Ecological Significance. These datasets and accompanying syntheses provide a greater understanding of fundamental ecosystem processes in the Southern Ocean, support modelling of predator distributions under future climate scenarios and create inputs that can be incorporated into decision making processes by management authorities. In this data paper, we present the compiled tracking data from research groups that have worked in the Antarctic since the 1990s. The data are publicly available through biodiversity.aq and the Ocean Biogeographic Information System. The archive includes tracking data from over 70 contributors across 12 national Antarctic programs, and includes data from 17 predator species, 4060 individual animals, and over 2.9 million observed locations.

Translating Marine Animal Tracking Data into Conservation Policy and Management.

There have been efforts around the globe to track individuals of many marine species and assess their movements and distribution, with the putative goal of supporting their conservation and management. Determining whether, and how, tracking data have been successfully applied to address real-world conservation issues is, however, difficult. Here, we compile a broad range of case studies from diverse marine taxa to show how tracking data have helped inform conservation policy and management, including reductions in fisheries bycatch and vessel strikes, and the design and administration of marine protected areas and important habitats. Using these examples, we highlight pathways through which the past and future investment in collecting animal tracking data might be better used to achieve tangible conservation benefits.

Identification of marine Important Bird and Biodiversity Areas for penguins around the South Shetland Islands and South Orkney Islands.

AIM: To provide a method of analyzing penguin tracking data to identify priority at-sea areas for seabird conservation (marine IBAs), based on pre-existing approaches for flying seabirds but revised according to the specific ecology of Pygoscelis penguin species. LOCATION: Waters around the Antarctic Peninsula, South Shetland, and South Orkney archipelagos (FAO Subareas 48.1 and 48.2). METHODS: We made key improvements to the pre-existing protocol for identifying marine IBAs that include refining the track interpolation method and revision of parameters for the kernel analysis (smoothing factor and utilization distribution) using sensitivity tests. We applied the revised method to 24 datasets of tracking data on penguins (three species, seven colonies, and three different breeding stages-incubation, brood, and crèche). RESULTS: We identified five new marine IBAs for seabirds in the study area, estimated to hold ca. 600,000 adult penguins. MAIN CONCLUSIONS: The results demonstrate the efficacy of a new method for the designation of a network of marine IBAs in Antarctic waters for penguins based on tracking data, which can contribute to an evidence-based, precautionary, management framework for krill fisheries.

Long term movements and activity patterns of an Antarctic marine apex predator: The leopard seal.

Leopard seals are an important Antarctic apex predator that can affect marine ecosystems through local predation. Here we report on the successful use of micro geolocation logging sensor tags to track the movements, and activity, of four leopard seals for trips of between 142-446 days including one individual in two separate years. Whilst the sample size is small the results represent an advance in our limited knowledge of leopard seals. We show the longest periods of tracking of leopard seals' migratory behaviour between the pack ice, close to the Antarctic continent, and the sub-Antarctic island of South Georgia. It appears that these tracked animals migrate in a directed manner towards Bird Island and, during their residency, use this as a central place for foraging trips as well as exploiting the local penguin and seal populations. Movements to the South Orkney Islands were also recorded, similar to those observed in other predators in the region including the krill fishery. Analysis of habitat associations, taking into account location errors, indicated the tracked seals had an affinity for shallow shelf water and regions of sea ice. Wet and dry sensors revealed that seals hauled out for between 22 and 31% of the time with maximum of 74 hours and a median of between 9 and 11 hours. The longest period a seal remained in the water was between 13 and 25 days. Fitting GAMMs showed that haul out rates changed throughout the year with the highest values occurring during the summer which has implications for visual surveys. Peak haul out occurred around midday for the months between October and April but was more evenly spread across the day between May and September. The seals' movements between, and behaviour within, areas important to breeding populations of birds and other seals, coupled with the dynamics of the region's fisheries, shows an understanding of leopard seal ecology is vital in the management of the Southern Ocean resources.

Temporal variation in trophic relationships among three congeneric penguin species breeding in sympatry.

Penguins are a monophyletic group in which many species are found breeding sympatrically, raising questions regarding how these species coexist successfully. Here, the isotopic niche of three sympatric pygoscelid penguin species was investigated at Powell Island, South Orkney Islands, during two breeding seasons (austral summers 2013-2014 and 2015-2016). Measurements of carbon (δ13C) and nitrogen (δ15N) stable isotope ratios were obtained from blood (adults) or feather (chicks) samples collected from Adélie Pygoscelis adeliae, chinstrap P. antarctica, and gentoo P. papua penguins. Isotopic niche regions (a proxy for the realized trophic niches) were computed to provide estimates of the trophic niche width of the studied species during the breeding season. The isotopic niche regions of adults of all three species were similar, but gentoo chicks had noticeably wider isotopic niches than the chicks of the other two species. Moderate to strong overlap in isotopic niche among species was found during each breeding season and for both age groups, suggesting that the potential for competition for shared food sources was similar during the two study years, although the actual level of competition could not be determined owing to the lack of data on resource abundance. Clear interannual shifts in isotopic niche were seen in all three species, though of lower amplitude for adult chinstrap penguins. These shifts were due to variation in carbon, but not nitrogen, isotopic ratios, which could indicate either a change in isotopic signature of their prey or a switch to an alternative food web. The main conclusions of this study are that (1) there is a partial overlap in the isotopic niches of these three congeneric species and that (2) they responded similarly to changes that likely occurred at the base of their food chain between the 2 years of the study.

Linking extreme interannual changes in prey availability to foraging behaviour and breeding investment in a marine predator, the macaroni penguin.

Understanding the mechanisms that link prey availability to predator behaviour and population change is central to projecting how a species may respond to future environmental pressures. We documented the behavioural responses and breeding investment of macaroni penguins Eudyptes chrysolophus across five breeding seasons where local prey density changed by five-fold; from very low to highly abundant. When prey availability was low, foraging trips were significantly longer and extended overnight. Birds also foraged farther from the colony, potentially in order to reach more distant foraging grounds and allow for increased search times. These extended foraging trips were also linked to a marked decrease in fledgling weights, most likely associated with reduced rates of provisioning. Furthermore, by comparing our results with previous work on this population, it appears that lowered first-year survival rates associated, at least partially, with fledging masses were also evident for this cohort. This study integrates a unique set of prey density, predator behaviour and predator breeding investment data to highlight a possible behavioural mechanism linking perturbations in prey availability to population demography.

Sexual and individual foraging segregation in Gentoo penguins Pygoscelis papua from the Southern Ocean during an abnormal winter.

Knowledge about sexual segregation and gender-specific, or indeed individual specialization, in marine organisms has improved considerably in the past decade. In this context, we tested the "Intersexual Competition Hypothesis" for penguins by investigating the feeding ecology of Gentoo penguins during their austral winter non-breeding season. We considered this during unusual environmental conditions (i.e. the year 2009 had observations of high sea surface and air temperatures) in comparison with the long term average at Bird Island, South Georgia. Through conventional (i.e. stomach contents) and stable isotopic values from red blood cells, plasma and feathers of both male and female Gentoo penguins, we showed that there were significant differences between sexes, with males feeding mainly on fish (54% by mass) followed by crustaceans (38%) whereas females fed mainly on crustaceans (89% by mass) followed by fish (4%). Themisto gaudichaudii was the most important crustacean prey for males (64% by mass; 82% by number; 53% by frequency of occurrence) and females (63% by mass; 77% by number; 89% by frequency of occurrence), contrasting with all previous studies that found Antarctic krill Euphausia superba were generally the main prey. Stable isotopic data showed that, in terms of habitat use (based on δ 13C), there were significant differences in short-term carbon signatures between males and females (based on plasma and red blood cells), suggesting that both sexes explored different habitats, with females exploring more offshore pelagic waters and males feeding more in coastal benthic waters. Based on δ 15N, males fed on significantly higher trophic level than females (based on plasma and red blood cells), in agreement with our diet results., Thus, Gentoo penguins behave in a similar manner to other non-breeding penguins species (e.g. king, macaroni and rockhopper penguins), albeit at a smaller spatial scale (as they do not disperse as these other penguins do), in that they have a wider habitat and trophic niche during the Antarctic Winter (in comparison to Summer). We also detected individual specialization in feeding/trophic levels for each gender, with certain males feeding mainly on fish and certain females mainly on crustaceans, which may be driven the prevailing environmental conditions that lead individuals to search for alternative prey, and cause sexual diet segregation. Our results provide further information to help improve understanding about sexual segregation and individual specialization of marine organisms, while contributing valuable information on the winter diet for Antarctic monitoring programs and for modelling Antarctic marine food webs.

Key Questions in Marine Megafauna Movement Ecology.

It is a golden age for animal movement studies and so an opportune time to assess priorities for future work. We assembled 40 experts to identify key questions in this field, focussing on marine megafauna, which include a broad range of birds, mammals, reptiles, and fish. Research on these taxa has both underpinned many of the recent technical developments and led to fundamental discoveries in the field. We show that the questions have broad applicability to other taxa, including terrestrial animals, flying insects, and swimming invertebrates, and, as such, this exercise provides a useful roadmap for targeted deployments and data syntheses that should advance the field of movement ecology.

Too much of a good thing: sea ice extent may have forced emperor penguins into refugia during the last glacial maximum.

The relationship between population structure and demographic history is critical to understanding microevolution and for predicting the resilience of species to environmental change. Using mitochondrial DNA from extant colonies and radiocarbon-dated subfossils, we present the first microevolutionary analysis of emperor penguins (Aptenodytes forsteri) and show their population trends throughout the last glacial maximum (LGM, 19.5-16 kya) and during the subsequent period of warming and sea ice retreat. We found evidence for three mitochondrial clades within emperor penguins, suggesting that they were isolated within three glacial refugia during the LGM. One of these clades has remained largely isolated within the Ross Sea, while the two other clades have intermixed around the coast of Antarctica from Adélie Land to the Weddell Sea. The differentiation of the Ross Sea population has been preserved despite rapid population growth and opportunities for migration. Low effective population sizes during the LGM, followed by a rapid expansion around the beginning of the Holocene, suggest that an optimum set of sea ice conditions exist for emperor penguins, corresponding to available foraging area.

Love thy neighbour or opposites attract? Patterns of spatial segregation and association among crested penguin populations during winter.

AIM: Competition for food among populations of closely related species and conspecifics that occur in both sympatry and parapatry can be reduced by interspecific and intraspecific spatial segregation. According to predictions of niche partitioning, segregation is expected to occur at habitat boundaries among congeners and within habitats among conspecifics, while negative relationships in the density of species or populations will occur in areas of overlap. We tested these predictions by modelling the winter distributions of two crested penguin species from three colonies in the south-western Atlantic. LOCATION: Penguins were tracked from two large colonies on the Falkland Islands and one in South Georgia, from where they dispersed through the South Atlantic, Southern Ocean and south-eastern Pacific. METHODS: Forty macaroni penguins (Eudyptes chrysolophus) from South Georgia and 82 southern rockhopper penguins (Eudyptes chrysocome chrysocome) from two colonies in the Falkland Islands were equipped with global location sensors which log time and light, allowing positions to be estimated twice-daily, from April to August in 2011. Positions were gridded and converted into maps of penguin density. Metrics of overlap were calculated and density was related to remote-sensed oceanographic variables and competitor density using generalized additive models. RESULTS: Macaroni penguins from western South Georgia and southern rockhopper penguins from Steeple Jason Island, Falkland Islands, were spatially segregated by differences in their habitat preferences thus supporting our first prediction regarding interspecific segregation. However, southern rockhopper penguins from Beauchêne Island showed a marked spatial overlap with macaroni penguins as the two had similar habitat preferences and strong mutual associations when controlling for habitat. Contrary to our predictions relating to intraspecific segregation, southern rockhopper penguins from Beauchêne Island and Steeple Jason Island were segregated by differences in habitat selection. MAIN CONCLUSIONS: Morphological differentiation probably allows macaroni penguins from South Georgia and southern rockhopper penguins from Beauchêne Island to coexist in areas of spatial overlap, whereas segregation of the two Falkland rockhopper penguin populations may have arisen from two distinct lineages retaining cultural fidelity to ancestral wintering areas.

The South Georgia and the South Sandwich Islands MPA: protecting a biodiverse oceanic island chain situated in the flow of the antarctic circumpolar current.

South Georgia and the South Sandwich Islands (SGSSI) are surrounded by oceans that are species-rich, have high levels of biodiversity, important endemism and which also support large aggregations of charismatic upper trophic level species. Spatial management around these islands is complex, particularly in the context of commercial fisheries that exploit some of these living resources. Furthermore, management is especially complicated as local productivity relies fundamentally upon biological production transported from outside the area. The MPA uses practical management boundaries, allowing access for the current legal fisheries for Patagonian toothfish, mackerel icefish and Antarctic krill. Management measures developed as part of the planning process designated the whole SGSSI Maritime Zone as an IUCN Category VI reserve, within which a number of IUCN Category I reserves were identified. Multiple-use zones and temporal closures were also designated. A key multiple-use principle was to identify whether the ecological impacts of a particular fishery threatened either the pelagic or benthic domain.

The roles of sex, mass and individual specialisation in partitioning foraging-depth niches of a pursuit-diving predator.

Intra-specific foraging niche partitioning can arise due to gender differences or individual specialisation in behaviour or prey selection. These may in turn be related to sexual size dimorphism or individual variation in body size through allometry. These variables are often inter-related and challenging to separate statistically. We present a case study in which the effects of sex, body mass and individual specialisation on the dive depths of the South Georgia shag on Bird Island, South Georgia are investigated simultaneously using a linear mixed model. The nested random effects of trip within individual explained a highly significant amount of the variance. The effects of sex and body mass were both significant independently but could not be separated statistically owing to them being strongly interrelated. Variance components analysis revealed that 45.5% of the variation occurred among individuals, 22.6% among trips and 31.8% among Dives, while R(2) approximations showed gender explained 31.4% and body mass 55.9% of the variation among individuals. Male dive depths were more variable than those of females at the levels of individual, trip and dive. The effect of body mass on individual dive depths was only marginally significant within sexes. The percentage of individual variation in dive depths explained by mass was trivial in males (0.8%) but substantial in females (24.1%), suggesting that differences in dive depths among males was largely due to them adopting different behavioural strategies whereas in females allometry played an additional role. Niche partitioning in the study population therefore appears to be achieved through the interactive effects of individual specialisation and gender upon vertical foraging patch selection, and has the potential to interact in complex ways with other axes of the niche hypervolume such as foraging locations, timing of foraging and diet.

Ecosystem services of the Southern Ocean: trade-offs in decision-making.

Ecosystem services are the benefits that mankind obtains from natural ecosystems. Here we identify the key services provided by the Southern Ocean. These include provisioning of fishery products, nutrient cycling, climate regulation and the maintenance of biodiversity, with associated cultural and aesthetic benefits. Potential catch limits for Antarctic krill (Euphausia superba Dana) alone are equivalent to 11% of current global marine fisheries landings. We also examine the extent to which decision-making within the Antarctic Treaty System (ATS) considers trade-offs between ecosystem services, using the management of the Antarctic krill fishery as a case study. Management of this fishery considers a three-way trade-off between fisheries performance, the status of the krill stock and that of predator populations. However, there is a paucity of information on how well these components represent other ecosystem services that might be degraded as a result of fishing. There is also a lack of information on how beneficiaries value these ecosystem services. A formal ecosystem assessment would help to address these knowledge gaps. It could also help to harmonize decision-making across the ATS and promote global recognition of Southern Ocean ecosystem services by providing a standard inventory of the relevant ecosystem services and their value to beneficiaries.

A space oddity: geographic and specific modulation of migration in Eudyptes penguins.

Post-breeding migration in land-based marine animals is thought to offset seasonal deterioration in foraging or other important environmental conditions at the breeding site. However the inter-breeding distribution of such animals may reflect not only their optimal habitat, but more subtle influences on an individual's migration path, including such factors as the intrinsic influence of each locality's paleoenvironment, thereby influencing animals' wintering distribution. In this study we investigated the influence of the regional marine environment on the migration patterns of a poorly known, but important seabird group. We studied the inter-breeding migration patterns in three species of Eudyptes penguins (E. chrysolophus, E. filholi and E. moseleyi), the main marine prey consumers amongst the World's seabirds. Using ultra-miniaturized logging devices (light-based geolocators) and satellite tags, we tracked 87 migrating individuals originating from 4 sites in the southern Indian Ocean (Marion, Crozet, Kerguelen and Amsterdam Islands) and modelled their wintering habitat using the MADIFA niche modelling technique. For each site, sympatric species followed a similar compass bearing during migration with consistent species-specific latitudinal shifts. Within each species, individuals breeding on different islands showed contrasting migration patterns but similar winter habitat preferences driven by sea-surface temperatures. Our results show that inter-breeding migration patterns in sibling penguin species depend primarily on the site of origin and secondly on the species. Such site-specific migration bearings, together with similar wintering habitat used by parapatrics, support the hypothesis that migration behaviour is affected by the intrinsic characteristics of each site. The paleo-oceanographic conditions (primarily, sea-surface temperatures) when the populations first colonized each of these sites may have been an important determinant of subsequent migration patterns. Based on previous chronological schemes of taxonomic radiation and geographical expansion of the genus Eudyptes, we propose a simple scenario to depict the chronological onset of contrasting migration patterns within this penguin group.

Heart rate and estimated energy expenditure of flapping and gliding in black-browed albatrosses.

Albatrosses are known to expend only a small amount of energy during flight. The low energy cost of albatross flight has been attributed to energy-efficient gliding (soaring) with sporadic flapping, although little is known about how much time and energy albatrosses expend in flapping versus gliding during cruising flight. Here, we examined the heart rates (used as an instantaneous index of energy expenditure) and flapping activities of free-ranging black-browed albatrosses (Thalassarche melanophrys) to estimate the energy cost of flapping as well as time spent in flapping activities. The heart rate of albatrosses during flight (144 beats min(-1)) was similar to that while sitting on the water (150 beats min(-1)). In contrast, heart rate was much higher during takeoff and landing (ca. 200 beats min(-1)). Heart rate during cruising flight was linearly correlated with the number of wing flaps per minute, suggesting an extra energy burden of flapping. Albatrosses spend only 4.6±1.4% of their time flapping during cruising flight, which was significantly lower than during and shortly after takeoff (9.8±3.5%). Flapping activity, which amounted to just 4.6% of the time in flight, accounted for 13.3% of the total energy expenditure during cruising flight. These results support the idea that albatrosses achieve energy-efficient flight by reducing the time spent in flapping activity, which is associated with high energy expenditure.