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The microbiome is a key factor in the health, well-being, and success of vertebrates, contributing to the adaptive capacity of the host. However, the impact of geographic and biotic factors that may affect the microbiome of wild birds in polar environments is not well defined. To address this, we determined the bacterial 16S rRNA gene sequence profiles in faecal samples from pygoscelid penguin populations in the Scotia Arc, focusing on gentoo penguins. This mesopredatory group breeds in defined colonies across a wide geographic range. Since diet could influence microbiome structure, we extracted dietary profiles from a eukaryotic 18S rRNA gene sequence profile. The bacterial microbiome profiles were considered in the context of a diverse set of environmental and ecological measures. Integrating wide geographic sampling with bacterial 16S and eukaryotic 18S rRNA gene sequencing of over 350 faecal samples identified associations between the microbiome profile and a suite of geographic and ecological factors. Microbiome profiles differed according to host species, colony identity, distance between colonies, and diet. Interestingly there was also a relationship between the proportion of host DNA (in relation to total 18S rRNA gene signal) and the microbiome, which may reflect gut passage time. Colony identity provided the strongest association with differences in microbiome profiles indicating that local factors play a key role in the microbiome structure of these polar seabirds. This may reflect the influence of local transfer of microbes either via faecal-oral routes, during chick feeding or other close contact events. Other factors including diet and host species also associate with variation in microbiome profile, and in at least some locations, the microbiome composition varies considerably between individuals. Given the variation in penguin microbiomes associated with diverse factors there is potential for disruption of microbiome associations at a local scale that could influence host health, productivity, and immunological competence. The microbiome represents a sensitive indicator of changing conditions, and the implications of any changes need to be considered in the wider context of environmental change and other stressors. [ABSTRACT FROM AUTHOR]

Aim: Delimiting recently diverged species is challenging. During speciation, genetic differentiation may be distributed unevenly across the genome, as different genomic regions can be subject to different selective pressures and evolutionary histories. Reliance on limited numbers of genetic markers that may be underpowered can make species delimitation even more challenging, potentially resulting in taxonomic inconsistencies. Rockhopper penguins of the genus Eudyptes comprise three broadly recognized taxa: northern (E. moseleyi), southern (E. chrysocome) and eastern rockhopper (E. filholi). Their taxonomic status has been controversial for decades, with researchers disagreeing about whether E. chrysocome and E. filholi are distinct species or conspecific. Our goal is to evaluate genome‐wide patterns of divergence to evaluate genetic differentiation and species delimitation in rockhopper penguins, and to assess which mechanisms may underlie previous discordance among nuclear versus mitochondrial analyses. Location: Sub‐Antarctic and temperate coastal regions of the Southern Hemisphere. Methods: We generated reduced‐representation genomic libraries using double digest restriction‐site associated DNA (ddRAD) sequencing to evaluate genetic differentiation, contemporary migration rates and admixture among colonies of rockhopper penguins. Results: The extent of genetic differentiation among the three taxa was consistently higher than population‐level genetic differentiation found within these and other penguin species. There was no evidence of admixture among the three taxa, suggesting the absence of ongoing gene flow among them. Species delimitation analyses based on molecular data, along with other lines of evidence, provide strong support for the taxonomic distinction of three species of rockhopper penguins. Main conclusions: Our results provide strong support for the existence of three distinct species of rockhopper penguins. The recognition of this taxonomic diversity is crucial for the management and conservation of this widely distributed species group. This study illustrates that widespread dispersive seabird lineages lacking obvious morphological differences may nevertheless have complex evolutionary histories and comprise cryptic species diversity. [ABSTRACT FROM AUTHOR]

Gentoo penguins (Pygoscelis papua) are found across the Southern Ocean with a circumpolar distribution and notable genetic and morphological variation across their geographic range. Whether this geographic variation represents species‐level diversity has yet to be investigated in an integrative taxonomic framework. Here, we show that four distinct populations of gentoo penguins (Iles Kerguelen, Falkland Islands, South Georgia, and South Shetlands/Western Antarctic Peninsula) are genetically and morphologically distinct from one another. We present here a revised taxonomic treatment including formal nomenclatural changes. We suggest the designation of four species of gentoo penguin: P. papua in the Falkland Islands, P. ellsworthi in the South Shetland Islands/Western Antarctic Peninsula, P. taeniata in Iles Kerguelen, and a new gentoo species P. poncetii, described herein, in South Georgia. These findings of cryptic diversity add to many other such findings across the avian tree of life in recent years. Our results further highlight the importance of reassessing species boundaries as methodological advances are made, particularly for taxa of conservation concern. We recommend reassessment by the IUCN of each species, particularly P. taeniata and P. poncetii, which both show evidence of decline. [ABSTRACT FROM AUTHOR]

Ornithogenic soils in Antarctica provide a biological archive of the occupation history and trophic ecology of penguins and other marine species over geological timescales. Hard prey remains and predator tissues, which are well preserved in ornithogenic soils, can act as paleoecological proxies of past environmental conditions. Here we examine ornithogenic soils from an active colony of Pygoscelis spp. penguins on Platter Island in the Danger Islands Archipelago along the northeastern side of the Antarctic Peninsula. We radiocarbon dated penguin tissues from excavated ornithogenic soils and parameterized an age-depth model of penguin occupation history. Hard prey remains were enumerated and recovered Pygoscelis spp. penguin and Antarctic fur seal (Arctocephalus gazella) tissues were analyzed for stable isotopes carbon (δ13C) and nitrogen (δ15N) analysis. The oldest recovered ornithogenic soils at Platter Island date to 502–653 years BP and coincide with the start of a period of increased warming and glacial discharge in the northeastern Antarctic Peninsula. Penguin tissues δ15N values increased between the oldest and youngest dated ornithogenic soils but seal tissues did not. This may indicate that the trophic level of penguins, but not seals, has increased over time, a hypothesis supported by the concurrent increase in the hard prey remains of fish and squid taxa common to penguin diets recovered from ornithogenic soils. Future studies of ornithogenic soils in the Danger Islands Archipelago are warranted to test this hypothesis and assess the potential confounding effects of varying ecosystem isotopic baselines and penguin species composition over time. [ABSTRACT FROM AUTHOR]

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 genomewide data obtained through RAD‐Seq to compare the patterns of connectivity among breeding colonies for five penguin species with shared ancestry, overlapping distributions and differing ecological niches, allowing an examination of the intrinsic and extrinsic barriers governing dispersal patterns. Our findings show that at‐sea range and oceanography underlie patterns of dispersal in these penguins. The pelagic niche of emperor (Aptenodytes forsteri), king (A. patagonicus), Adélie (Pygoscelis adeliae) and chinstrap (P. antarctica) penguins facilitates gene flow over thousands of kilometres. In contrast, the coastal niche of gentoo penguins (P. papua) limits dispersal, resulting in population divergences. Oceanographic fronts also act as dispersal barriers to some extent. We recommend that forecasts of extinction risk incorporate dispersal and that management units are defined by at‐sea range and oceanography in species lacking genetic data. [ABSTRACT FROM AUTHOR]

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 and dispersal. King penguins are long-lived seabirds that occupy a niche across the sub-Antarctic zone close to the Polar Front. Colonies have very different histories of exploitation, population recovery, and expansion. Results: We investigated the genetic population structure and patterns of colonisation of king penguins across their current range using a dataset of 5154 unlinked, high-coverage single nucleotide polymorphisms generated via restriction site associated DNA sequencing (RADSeq). Despite breeding at a small number of discrete, geographically separate sites, we find only very slight genetic differentiation among colonies separated by thousands of kilometers of open-ocean, suggesting migration among islands and archipelagos may be common. Our results show that the South Georgia population is slightly differentiated from all other colonies and suggest that the recently founded Falkland Island colony is likely to have been established by migrants from the distant Crozet Islands rather than nearby colonies on South Georgia, possibly as a result of density-dependent processes. Conclusions: The observed subtle differentiation among king penguin colonies must be considered in future conservation planning and monitoring of the species, and demographic models that attempt to forecast extinction risk in response to large-scale climate change must take into account migration. It is possible that migration could buffer king penguins against some of the impacts of climate change where colonies appear panmictic, although it is unlikely to protect them completely given the widespread physical changes projected for their Southern Ocean foraging grounds. Overall, large-scale population genetic studies of marine predators across the Southern Ocean are revealing more interconnection and migration than previously supposed. [ABSTRACT FROM AUTHOR]

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, particularly focused on newly established colonies, provide a snapshot of colonization and can reveal the extent to which shifts in abundance and occupancy result from changes in demographic rates (e.g., reproduction and survival) or migration among suitable patches of habitat. Here, we describe the population structure of a colonial seabird breeding across a large latitudinal range in the Southern Ocean. Using multilocus microsatellite genotype data from 510 Gentoo penguin ( Pygoscelis papua) individuals from 14 colonies along the Scotia Arc and Antarctic Peninsula, together with mitochondrial DNA data, we find strong genetic differentiation between colonies north and south of the Polar Front, that coincides geographically with the taxonomic boundary separating the subspecies P. p. papua and P. p. ellsworthii. Using a discrete Bayesian phylogeographic approach, we show that southern Gentoos expanded from a possible glacial refuge in the center of their current range, colonizing regions to the north and south through rare, long-distance dispersal. Our findings show that this dispersal is important for new colony foundation and range expansion in a seabird species that ordinarily exhibits high levels of natal philopatry, though persistent oceanographic features serve as barriers to movement. [ABSTRACT FROM AUTHOR]

If not carefully managed, harvesting of Antarctic 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 archipelago. Some of the main krill predators breeding at the South Sandwich Islands are penguins, with five species breeding on the islands, the dominant species of which is the chinstrap penguin. In this paper we report on the results of ARGOS PTT deployments during the chinstrap penguin chick-rearing period, using the recorded foraging trips to develop habitat models. Foraging habitats used by chinstrap penguins during this period were best characterised by distance from the colony and sea surface temperature and, using these two covariates, we predicted the chick-rearing foraging habitat use around all islands. We show that the provisions of the South Georgia and South Sandwich Islands Marine Protected Area ensure that chinstrap penguins, and other krill-dependent predators with similar foraging ranges, likely have robust protection during the summer. During the winter, when krill predators are likely to forage further offshore, seasonal sea ice provides a physical barrier to exclude the fishery, again ensuring the islands' unique biodiversity receives strong protection. However, to the north of the marginal sea ice zone, competition between krill predators and the fishery could exist if the fishery were ever to explore new locations for resource extraction. We make a number of conclusions, including the need for winter tracking data to inform future management options. • Very little is known about penguin populations on the South Sandwich Islands (SSI). • We deployed 20 tracking devices on breeding chinstrap penguins to track their foraging trips. • Most foraging occurred up to 30 km offshore, with few trips exceeding 50 km offshore. • Distance from the colony and sea surface temperature determined habitat selection. • The SSI MPA likely provides robust protection to chinstrap penguins during breeding. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic caused the Port Lockroy post office, a popular Antarctic tourism destination, to close in 2020, creating a natural experiment to test human impacts on the local gentoo penguins. This study examines the abundance of nesting gentoo penguins before, during, and after the COVID-19 anthropause at different spatial scales centered around the post office. We found that the Port Lockroy population increased 83 % (∼450 nesting pairs) from 2018 to 2021, with areas of the island open to pedestrians seeing the greatest gains in the number of nests. Jougla Point, a site just 150 m away from Port Lockroy and located within the same harbor, increased 90 % (∼900 nesting pairs) during the closure, while two nearby sites outside the harbor decreased by 60 % and 59 % (∼1000 nesting pairs total). We conclude that gentoo penguins immigrated from neighboring sites into the Port Lockroy harbor. This apparent redistribution of nesting gentoo penguins immediately reversed itself when the post office re-opened in 2022. These findings, which are particularly striking given the assumed strong site fidelity of gentoo penguins, suggest that human activity can alter gentoo penguins' choice in nesting location, and that the spatial extent of disturbance is perhaps larger than previously appreciated. We suggest testing the impacts of ship and zodiac traffic on breeding behavior, the cumulative effects of tourism on sets of geographically proximate colonies, and the timing of tourism in relation to nest initiation to inform policies focusing on minimizing disturbances to gentoo penguins as Antarctic tourism resumes. [ABSTRACT FROM AUTHOR]