Tom Hart's research while affiliated with University of Oxford and other places

Publications (59)

Technical Report
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Since the beginning of 2022, the increasing intensity of highly pathogenic avian influenza (HPAI) H5N1 outbreaks has resulted in the death of hundreds of thousands of seabirds in the Northern Hemisphere, around the Atlantic and Pacific Oceans and southern Africa. The SCAR Antarctic Wildlife Health Working Group (AWHWG) is highly concerned about the...
Article
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Penguins lost the ability to fly more than 60 million years ago, subsequently evolving a hyper-specialized marine body plan. Within the framework of a genome-scale, fossil-inclusive phylogeny, we identify key geological events that shaped penguin diversification and genomic signatures consistent with widespread refugia/recolonization during major c...
Preprint
Animal-borne telemetry devices provide essential insights into the life-history strategies of far-ranging species and allow us to understand how they interact with their environment. Many species in the seabird family Alcidae undergo a synchronous moult of all primary flight feathers during the non-breeding season, making them flightless and more s...
Article
Advances in artificial intelligence for computer vision hold great promise for increasing the scales at which ecological systems can be studied. The distribution and behavior of individuals is central to ecology, and computer vision using deep neural networks can learn to detect individual objects in imagery. However, developing supervised models f...
Article
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The South Sandwich Islands are an isolated, oceanic, volcanically formed archipelago in the Atlantic sector of the Southern Ocean. The complex bathymetry, coupled with the location in the marginal sea-ice zone and the relationship with the ACC makes the region both productive and biodiverse. Although remote, the region is not pristine and has been...
Article
If not carefully managed, harvesting of krill risks disturbing the ecological balance of many Antarctic and sub-Antarctic sites where krill-dependent predators feed. One of the least disturbed sites anywhere within the Southern Ocean and one where krill fishing has so far been virtually non-existent is the South Sandwich Islands volcanic archipelag...
Article
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Penguins (Sphenisciformes) are an iconic order of flightless, diving seabirds distributed across a large latitudinal range in the Southern Hemisphere. The extensive area over which penguins are endemic is likely to have fostered variation in pathogen pressure, which in turn will have imposed differential selective pressures on the penguin immune sy...
Preprint
Full-text available
Advances in artificial intelligence for image processing hold great promise for increasing the scales at which ecological systems can be studied. The distribution and behavior of individuals is central to ecology, and computer vision using deep neural networks can learn to detect individual objects in imagery. However, developing computer vision fo...
Article
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Many remote islands present barriers to effective wildlife monitoring in terms of challenging terrain and frequency of visits. The sub-Antarctic islands of South Georgia and the South Sandwich Islands are home to globally significant populations of seabirds and marine mammals. South Georgia hosts the largest breeding populations of Antarctic fur se...
Article
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Though climate change is widely known to negatively affect the distribution and abundance of many species, few studies have focused on species that may benefit. Gentoo Penguin (Pygoscelis papua) populations have grown along the Western Antarctic Peninsula (WAP), a region accounting for ~ 30% of their global population. These trends of population gr...
Article
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Using satellite imagery, drone imagery, and ground counts, we have assembled the first comprehensive global population assessment of Chinstrap penguins (Pygoscelis antarctica) at 3.42 (95th-percentile CI: [2.98, 4.00]) million breeding pairs across 375 extant colonies. Twenty-three previously known Chinstrap penguin colonies are found to be absent...
Article
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There is growing interest in uncovering the viral diversity present in wild animal species. The remote Antarctic region is home to a wealth of uncovered microbial diversity, some of which is associated with its megafauna, including penguin species, the dominant avian biota. Penguins interface with a number of other biota in their roles as marine me...
Article
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Abstract Changes in the physical environment along the Antarctic Peninsula have been among the most rapid anywhere on the planet. In concert with environmental change, the potential for direct human disturbance resulting from tourism, scientific programs, and commercial fisheries continues to rise in the region. While seabirds, such as the gentoo p...
Article
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Circoviruses infect a variety of animal species and have small (~1.8–2.2 kb) circular single-stranded DNA genomes. Recently a penguin circovirus (PenCV) was identified associated with an Adélie Penguin (Pygoscelis adeliae) with feather disorder and in the cloacal swabs of three asymptomatic Adélie Penguins at Cape Crozier, Antarctica. A total of 75...
Article
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Time-lapse cameras facilitate remote and high-resolution monitoring of wild animal and plant communities, but the image data produced require further processing to be useful. Here we publish pipelines to process raw time-lapse imagery, resulting in count data (number of penguins per image) and ‘nearest neighbour distance’ measurements. The latter p...
Article
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Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities...
Article
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Over evolutionary time, pathogen challenge shapes the immune phenotype of the host to better respond to an incipient threat. The extent and direction of this selection pressure depends on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local...
Article
Climate shifts are key drivers of ecosystem change. Despite the critical importance of Antarctica and the Southern Ocean for global climate, the extent of climate-driven ecological change in this region remains controversial. In particular, the biological effects of changing sea ice conditions are poorly understood. We hypothesize that rapid postgl...
Article
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Significance We reveal species-specific changes in penguin trophic responses to historic shifts in krill availability over the last century by applying new molecular isotope techniques to historic penguin museum specimens. Generalist foraging gentoo penguins, whose population increased 6-fold in the last 40 y, showed adaptive shifts in trophic posi...
Article
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An amendment to this paper has been published and can be accessed via a link at the top of the paper
Article
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Background: Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving...
Article
In this article, we analyze the impacts of climate change on Antarctic marine ecosystems. Observations demonstrate large-scale changes in the physical variables and circulation of the Southern Ocean driven by warming, stratospheric ozone depletion, and a positive Southern Annular Mode. Alterations in the physical environment are driving change thro...
Article
The emergence of islands has been linked to spectacular radiations of diverse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically young islands. Islands may thus have been crucial to the evolutionary diversification of penguins. We test thi...
Article
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The mechanisms that determine patterns of species dispersal are important factors in the production and maintenance of biodiversity. Understanding these mechanisms helps to forecast the responses of species to environmental change. Here we used a comparative framework and genome‐wide data obtained through RAD‐seq to compare the patterns of connecti...
Article
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Variation in the phenology of avian taxa has long been studied to understand how a species reacts to environmental changes over both space and time. Penguins (Sphenicidae) serve as an important example of how biotic and abiotic factors influence certain stages of seabird phenology because of their large ranges and the extreme, dynamic conditions pr...
Article
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Automated time-lapse cameras can facilitate reliable and consistent monitoring of wild animal populations. In this report, data from 73,802 images taken by 15 different Penguin Watch cameras are presented, capturing the dynamics of penguin (Spheniscidae; Pygoscelis spp.) breeding colonies across the Antarctic Peninsula, South Shetland Islands and S...
Article
The South Sandwich Islands are a relatively pristine volcanic archipelago in the Southern Ocean that experience high levels of natural disturbance. The archipelago spans the biological transition between the sub-Antarctic and maritime Antarctic. They host the southern boundary for some sub-Antarctic communities and the northern boundary for some ma...
Article
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Collecting spatially extensive data on phenology and reproductive success is important for seabird conservation and management, but can be logistically challenging in remote regions. Autonomous time‐lapse camera systems offer an opportunity to provide such coverage. We describe a method to estimate nest‐level breeding phenology and reproductive suc...
Article
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Long-term monitoring of seabird breeding cycles and breeding success is essential for conservation and a valuable indicator of ecological change, but is logistically expensive and time consuming. We describe the annual cycle and year-round colony attendance patterns for Gentoo Penguins Pygoscelis papua at Martillo Island, Beagle Channel, by analyzi...
Data
Raw data used during analyses of Adélie penguin (Pygoscelis adeliae) abundance at the Yalour Islands from 2012–2014 in.csv format. (CSV)
Article
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Polar seabirds adopt different over-wintering strategies to survive and build condition during the critical winter period. Penguin species either reside at the colony during the winter months or migrate long distances. Tracking studies and survey methods have revealed differences in winter migration routes among penguin species and colonies, depend...
Data
Adélie penguin (Pygoscelis adeliae) abundance at median photoperiod (aka. daylight hours) and temperature (°C) for each of the three sea ice types observed: open water, pack, and compact. (TIFF)
Article
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Despite concerted international effort to track and interpret shifts in the abundance and distribution of Adélie penguins, large populations continue to be identified. Here we report on a major hotspot of Adélie penguin abundance identified in the Danger Islands off the northern tip of the Antarctic Peninsula (AP). We present the first complete cen...
Article
Identifying the at-sea distribution of wide-ranging marine predators is critical to understanding their ecology. Advances in electronic tracking devices and intrinsic biogeochemical markers have greatly improved our ability to track animal movements on ocean-wide scales. Here, we show that, in combination with direct tracking, stable carbon isotope...
Article
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When monitoring species with extensive ranges in harsh climates, comprehensive studies across a species' range are both logistically and technically challenging and therefore rare. Such scarcity in data collection is particularly true in the polar regions where sea ice and weather constraints prevent widespread access to sites for much of the year,...
Article
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Understanding the boundaries of breeding populations is of great importance for conservation efforts and estimates of extinction risk for threatened species. However, determining these boundaries can be difficult when population structure is subtle. Emperor penguins are highly reliant on sea ice, and some populations may be in jeopardy as climate c...
Article
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Past research during the breeding season in the Antarctic Peninsula region indicates that gentoo penguins (Pygoscelis papua) are generalist foragers whereas Adélie (P. adeliae) and chinstrap (P. antarcticus) penguins tend to specialize on Antarctic krill (Euphausia superba). However, little is known about the degree of temporal consistency in the d...
Article
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Background Seabirds are important components of marine ecosystems, both as predators and as indicators of ecological change, being conspicuous and sensitive to changes in prey abundance. To determine whether fluctuations in population sizes are localised or indicative of large-scale ecosystem change, we must first understand population structure an...
Article
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Climate change, fisheries' pressure on penguin prey, and direct human disturbance of wildlife have all been implicated in causing large shifts in the abundance and distribution of penguins in the Southern Ocean. Without mark-recapture studies, understanding how colonies form and, by extension, how ranges shift is challenging. Genetic studies, parti...
Article
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Aggregations of young animals are common in a range of endothermic and ectothermic species, yet the adaptive behavior may depend on social circumstance and local conditions. In penguins, many species form aggregations (aka. crèches) for a variety of purposes, whilst others have never been observed exhibiting this behavior. Those that do form aggreg...
Data
Complete data set of gentoo (Pygoscelis papua) chick aggregations and environmental variables at four sites. (CSV)
Article
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Long-term monitoring of seabird numbers around Antarctica has revealed that the chinstrap penguin (Pygoscelis antarctica) is largely declining throughout its range in the Scotia Arc. Whether archipelagos across this large area remain connected via dispersal or represent genetically isolated groups has not yet been established. The purpose of this s...
Article
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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 forste...
Article
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Climate change is a major threat to global biodiversity. Antarctic ecosystems are no exception. Investigating past species responses to climatic events can distinguish natural from anthropogenic impacts. Climate change produces 'winners', species that benefit from these events and 'losers', species that decline or become extinct. Using molecular te...
Article
We examined sexual dimorphism in bill size in adult Adélie Penguins Pygoscelis adeliae, adult Chinstrap Penguins P. antarctica and adult and juvenile Gentoo Penguins P. papua at King George Island, Antarctica, using a DNA-based molecular sexing technique. Bill length and depth were the most consistent dimorphic character examined, with measurements...
Article
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Geographical range contraction is a fundamental ecological characteristic of species population decline, but relatively little investigation has been conducted into general trends in the dynamic properties of range collapse. The Yangtze River dolphin or baiji (Lipotes vexillifer), probably the first large mammal species to have become extinct in ov...
Article
A common paradigm in studies of human cooperation is that individuals mediate their investment in a public good according to the investments of others. However, most research on this topic has been conducted in artificial laboratory settings and has assumed that cooperation imposes relatively high monetary costs on players. As such, we do not yet k...
Article
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Recording the activity of animals as they migrate or forage has proven hugely advantageous to understanding how animals use their environment. Where animals cannot be directly observed, the problem remains of how to identify distinct behaviours that represent an animal’s decision-making process. An excellent example of this problem is that of forag...
Article
The nature of how behaviour at one time step influences the next is of great interest to behavioural ecologists, but rarely used for comparisons between animals. Time depth recorders (TDR) and other archival tags have been widely used to infer patterns of diving and foraging. However, while we can extract variables that describe individual dives, h...
Article
Local ecological knowledge can provide a unique source of data for conservation, especially in efforts to investigate the status of rare or possibly extinct species, but it is unlikely to remain constant over time. Loss of perspective about past ecological conditions caused by lack of communication between generations may create “shifting baseline...
Article
We report the characterization of 25 microsatellite loci isolated from the macaroni penguin (Eudyptes chrysolophus). Thirteen loci were arranged into four multiplex sets for future genetic studies of macaroni penguin populations. All 25 loci were tested separately in each of four other penguin species [Adélie penguin (Pygoscelis adeliae), chinstrap...
Article
Dimorphism in various morphological traits is widely used to sex birds. However, when a threshold is set and there is overlap in the distribution of traits between sexes, there will be an error rate. Macaroni Penguins show limited sexual dimorphism in size, with the distributions of most phenotypic traits overlapping between sexes, making using mor...

Citations

... Morphological data can be combined with a molecular matrix either based on a few loci (generated with Sanger techniques) [49] or based on hundreds of loci (generated with nextgeneration sequencing techniques) [80]. A morphological clock is then integrated, along with several molecular clocks, taking into account rate and clock heterogeneity across the dataset. ...
... Almost certainly, this reflects the scale of habitat use by baleen whales. At the smaller scale, i.e. at the scale of the GSGSSI 50 km buffer, Clucas et al. (2022) estimate that the dominant avian krill consumer on the SSI, the chinstrap penguin Pygoscelis antarctica, consumes approximately 258, 000 t of krill over the chick-rearing period, not accounting for the requirements of non-breeding adults or chicks. Therefore, minimum estimates suggest that close to the island, consumption may be equivalent to 31.8% of krill standing stock. ...
... However, a study in chicken has shown that activation of TLR15 involves proteolytic cleavage of the LRR ectodomain (de Zoete et al. 2011), suggesting that genetic variation in this domain could be functionally neutral. In addition, TLR15 has been revealed to cryptically pseudogenize in some birds (Fiddaman et al. 2021) which could partially explain the high sequence variation detected in this gene. We did, however, not detect any signs of pseudogenization of TLR15 in the mallard genome, and a test for relaxation of selection pressure (implemented in Datamonkey) on TLR15 in the mallard versus all other investigated taxa was not significant (K = 0.62, P = 0.67, LR = 0.18). ...
... Wildlife surveys using drones are promising techniques currently being developed for monitoring of animal abundance, trends and behaviour for many species (Colefax et al., 2018;Hodgson et al., 2018;Eikelboom et al., 2019;Lyons et al., 2019;Infantes et al., 2020;Gray et al., 2022). Drone observations also provide new possibilities for documenting animal behaviour as well as landscape features, in particular for species sensitive to human activity or aggressive to humans (Inman et al., 2019;Infantes et al., 2020), or at sites that are difficult to access (Dickens et al., 2021;Palomino-González et al., 2021). Although drone surveys collect detailed information rapidly, they still do not solve existing data analysis limitations. ...
... The Adélie (Pygoscelis adelieae), Chinstrap (Pygoscelis antarcticus) and Gentoo (Pygoscelis Papua) are the most usual penguin species on the Antarctic Peninsula (Barbosa et al. 2012). Adélie penguins are much more suited to ice environments and breed on average further South, while Chinstrap colonies are usually located in less icy areas situated in rocky valleys open to the sea, being restricted to the North of the peninsular region and the Scotia Arc islands (Clucas et al. 2014;Kokubun et al. 2015;Strycker et al. 2020). ...
... Andrews Bay, South Georgia have swiftly expanded their population and breeding ground into newly exposed ice-free areas following glacial retreat (Foley et al., 2018), as have gentoo penguins breeding on the Western Antarctic Peninsula (Herman et al., 2020), and Adélie penguins on Beaufort Island in the Ross Sea (Larue et al., 2013). The movement of penguins into new ice-free areas may then facilitate the establishment of other species in these areas via nutrient deposition, or perhaps, allow their old breeding sites to be colonized upon abandonment (Casanovas et al., 2013;Smykla et al., 2007;Tatur et al., 1997). ...
... Over the last several years, viral metagenomics has facilitated the discovery of hundreds of highly divergent single-stranded DNA (ssDNA) viruses that belong in the phylum Cressdnaviricota [7], also commonly referred to as circular replication-associated protein encoding single-stranded (CRESS) DNA viruses [3,[8][9][10][11][12]. In addition, a large number of ssDNA bacteriophages in the family Microviridae [13,14] have also been identified [15][16][17][18][19][20]. ...
... Punctuated environmental events may exhibit pronounced effects on some species, while affecting others very little. For example, large snowstorms can result in increased chick mortality when nests are inundated with snow -species that nest in areas prone to inundation, such as pygoscelid penguins or snow petrels (Chastel et al. 1993, Youngflesh 2018b, Youngflesh et al. 2021a) are likely more susceptible to these events than species that nest in well-draining areas, such as southern fulmars. This is one dimension of the niche separation which appears to be pronounced among the seabird species in the community. ...