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© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Houstin, A., Zitterbart, D. P., Heerah, K., Eisen, O., Planas-Bielsa, V., Fabry, B., & Le Bohec, C. Juvenile emperor penguin range calls for extended conservation measures in the Southern Ocean. Royal Society Open Science, 9(8), (2022): 211708, https://doi.org/10.1098/rsos.211708., To protect the unique and rich biodiversity of the Southern Ocean, conservation measures such as marine protected areas (MPAs) have been implemented. Currently, the establishment of several additional protection zones is being considered based on the known habitat distributions of key species of the ecosystems including emperor penguins and other marine top predators. However, the distribution of such species at sea is often insufficiently sampled. Specifically, current distribution models focus on the habitat range of adult animals and neglect that immatures and juveniles can inhabit different areas. By tracking eight juvenile emperor penguins in the Weddell Sea over 1 year and performing a meta-analysis including previously known data from other colonies, we show that conservation efforts in the Southern Ocean are insufficient for protecting this highly mobile species, and particularly its juveniles. We find that juveniles spend approximately 90% of their time outside the boundaries of proposed and existing MPAs, and that their distribution extends beyond (greater than 1500 km) the species' extent of occurrence as defined by the International Union for Conservation of Nature. Our data exemplify that strategic conservation plans for the emperor penguin and other long-lived ecologically important species should consider the dynamic habitat range of all age classes., This study was funded by the Centre Scientifique de Monaco with additional support from the LIA-647 and RTPI-NUTRESS (CSM/CNRS/University of Strasbourg), by The Penzance Endowed Fund and The Grayce B. Kerr Fund in Support of Assistant Scientists and by the Deutsche Forschungsgemeinschaft (DFG) grant no. ZI1525/3-1 in the framework of the priority program ‘Antarctic research with comparative investigations in Arctic ice areas'.

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Houstin, A., Zitterbart, D., Winterl, A., Richter, S., Planas-Bielsa, V., Chevallier, D., Ancel, A., Fournier, J., Fabry, B., & Le Bohec, C. Biologging of emperor penguins-attachment techniques and associated deployment performance. PLoS One, 17(8), (2022): e0265849, https://doi.org/10.1371/journal.pone.0265849., An increasing number of marine animals are equipped with biologgers, to study their physiology, behaviour and ecology, often for conservation purposes. To minimise the impacts of biologgers on the animals’ welfare, the Refinement principle from the Three Rs framework (Replacement, Reduction, Refinement) urges to continuously test and evaluate new and updated biologging protocols. Here, we propose alternative and promising techniques for emperor penguin (Aptenodytes forsteri) capture and on-site logger deployment that aim to mitigate the potential negative impacts of logger deployment on these birds. We equipped adult emperor penguins for short-term (GPS, Time-Depth Recorder (TDR)) and long-term (i.e. planned for one year) deployments (ARGOS platforms, TDR), as well as juvenile emperor penguins for long-term deployments (ARGOS platforms) in the Weddell Sea area where they had not yet been studied. We describe and qualitatively evaluate our protocols for the attachment of biologgers on-site at the colony, the capture of the animals and the recovery of the devices after deployment. We report unprecedented recaptures of long-term equipped adult emperor penguins (50% of equipped individuals recaptured after 290 days). Our data demonstrate that the traditional technique of long-term attachment by gluing the biologgers directly to the back feathers causes excessive feather breakage and the loss of the devices after a few months. We therefore propose an alternative method of attachment for back-mounted devices. This technique led to successful year-round deployments on 37.5% of the equipped juveniles. Finally, we also disclose the first deployments of leg-bracelet mounted TDRs on emperor penguins. Our findings highlight the importance of monitoring potential impacts of biologger deployments on the animals and the need to continue to improve methods to minimize disturbance and enhance performance and results., This study was funded by the Centre Scientifique de Monaco with additional support from the LIA-647 and RTPI-NUTRESS (CSM/CNRS¬-University of Strasbourg), by The Penzance Endowed Fund and The Grayce B. Kerr Fund in Support of Assistant Scientists and by the Deutsche Forschungsgemeinschaft (DFG) grants ZI1525/3-1 in the framework of the priority program “Antarctic research with comparative investigations in Arctic ice areas”. Logistics and field efforts were supported by the Alfred Wegener Institute (AWI) within the framework of the program MARE.

Abstract. Systematic long-term studies on ecosystem dynamics are largely lacking from the East Antarctic Southern Ocean, although it is well recognized that they are indispensable to identify the ecological impacts and risks of environmental change. Here, we present a framework for establishing a long-term cross-disciplinary study on decadal timescales. We argue that the eastern Weddell Sea and the adjacent sea to the east, off Dronning Maud Land, is a particularly well suited area for such a study, since it is based on findings from previous expeditions to this region. Moreover, since climate and environmental change have so far been comparatively muted in this area, as in the eastern Antarctic in general, a systematic long-term study of its environmental and ecological state can provide a baseline of the current situation, which will be important for an assessment of future changes from their very onset, with consistent and comparable time series data underpinning and testing models and their projections. By establishing an Integrated East Antarctic Marine Research (IEAMaR) observatory, long-term changes in ocean dynamics, geochemistry, biodiversity, and ecosystem functions and services will be systematically explored and mapped through regular autonomous and ship-based synoptic surveys. An associated long-term ecological research (LTER) programme, including experimental and modelling work, will allow for studying climate-driven ecosystem changes and interactions with impacts arising from other anthropogenic activities. This integrative approach will provide a level of long-term data availability and ecosystem understanding that are imperative to determine, understand, and project the consequences of climate change and support a sound science-informed management of future conservation efforts in the Southern Ocean.

To protect the unique and rich biodiversity of the Southern Ocean, conservation measures such as marine protected areas (MPAs) have been implemented. Currently, the establishment of several additional protection zones is being considered based on the known habitat distributions of key species of the ecosystems including emperor penguins and other marine top predators. However, the distribution of such species at sea is often insufficiently sampled. Specifically, current distribution models focus on the habitat range of adult animals and neglect that immatures and juveniles can inhabit different areas. By tracking eight juvenile emperor penguins in the Weddell Sea over 1 year and performing a meta-analysis including previously known data from other colonies, we show that conservation efforts in the Southern Ocean are insufficient for protecting this highly mobile species, and particularly its juveniles. We find that juveniles spend approximately 90% of their time outside the boundaries of proposed and existing MPAs, and that their distribution extends beyond (greater than 1500 km) the species' extent of occurrence as defined by the International Union for Conservation of Nature. Our data exemplify that strategic conservation plans for the emperor penguin and other long-lived ecologically important species should consider the dynamic habitat range of all age classes.

Systematic long-term studies on ecosystem dynamics are largely lacking from the East Antarctic Southern Ocean, although it is well recognized that they are indispensable to identify the ecological impacts and risks of environmental change. Here, we present a framework for establishing a long-term cross-disciplinary study on decadal timescales. We argue that the eastern Weddell Sea and the adjacent sea to the east, off Dronning Maud Land, is a particularly well suited area for such a study, since it is based on findings from previous expeditions to this region. Moreover, since climate and environmental change have so far been comparatively muted in this area, as in the eastern Antarctic in general, a systematic long-term study of its environmental and ecological state can provide a baseline of the current situation, which will be important for an assessment of future changes from their very onset, with consistent and comparable time series data underpinning and testing models and their projections. By establishing an Integrated East Antarctic Marine Research (IEAMaR) observatory, long-term changes in ocean dynamics, geochemistry, biodiversity, and ecosystem functions and services will be systematically explored and mapped through regular autonomous and ship-based synoptic surveys. An associated long-term ecological research (LTER) programme, including experimental and modelling work, will allow for studying climate-driven ecosystem changes and interactions with impacts arising from other anthropogenic activities. This integrative approach will provide a level of long-term data availability and ecosystem understanding that are imperative to determine, understand, and project the consequences of climate change and support a sound science-informed management of future conservation efforts in the Southern Ocean

Although mitochondrial DNA has been widely used in phylogeography, evidence has emerged that factors such as climate, food availability, and environmental pressures that produce high levels of stress can exert a strong influence on mitochondrial genomes, to the point of promoting the persistence of certain genotypes in order to compensate for the metabolic requirements of the local environment. As recently discovered, the gentoo penguins (Pygoscelis papua) comprise four highly divergent lineages across their distribution spanning the Antarctic and sub-Antarctic regions. Gentoo penguins therefore represent a suitable animal model to study adaptive processes across divergent environments. Based on 62 mitogenomes that we obtained from nine locations spanning all four gentoo penguin lineages, we demonstrated lineage-specific nucleotide substitutions for various genes, but only lineage-specific amino acid replacements for the ND1 and ND5 protein-coding genes. Purifying selection (dN/dS < 1) is the main driving force in the protein-coding genes that shape the diversity of mitogenomes in gentoo penguins. Positive selection (dN/dS > 1) was mostly present in codons of the Complex I (NADH genes), supported by two different codon-based methods at the ND1 and ND4 in the most divergent lineages, the eastern gentoo penguin from Crozet and Marion Islands and the southern gentoo penguin from Antarctica respectively. Additionally, ND5 and ATP6 were under selection in the branches of the phylogeny involving all gentoo penguins except the eastern lineage. Our study suggests that local adaptation of gentoo penguins has emerged as a response to environmental variability promoting the fixation of mitochondrial haplotypes in a non-random manner. Mitogenome adaptation is thus likely to have been associated with gentoo penguin diversification across the Southern Ocean and to have promoted their survival in extreme environments such as Antarctica. Such selective processes on the mitochondria

Natural catastrophic events such as tsunamis may induce drastic decreases in breeding success of animal populations. We evaluate the impacts of flooding on the reproductive success of king penguins (Aptenodytes patagonicus) in the Crozet Archipelago. On 26 December 2004, a magnitude-9 earthquake created a large tsunami that flooded a colony at 6,500 km from the epicentre of the earthquake. On 30 January 2005, severe waves again flooded the colony. About 17–20% of the surface of the colony was impacted during each flood and 44% of the breeding birds abandoned their egg or chick following the two floodings. Although about 11% of birds laid another egg after the tsunami, none reproduced again after the second flood that happened later in the breeding season. Our results show that the tsunami directly affected the reproductive success of seabirds nesting near the coast.

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Trathan, P. N., Wienecke, B., Barbraud, C., Jenouvrier, S., Kooyman, G., Le Bohec, C., Ainley, D. G., Ancel, A., Zitterbart, D. P., Chown, S. L., LaRue, M., Cristofari, R., Younger, J., Clucas, G., Bost, C., Brown, J. A., Gillett, H. J., & Fretwell, P. T. The emperor penguin - vulnerable to projected rates of warming and sea ice loss. Biological Conservation, 241, (2020): 108216, doi:10.1016/j.biocon.2019.108216., We argue the need to improve climate change forecasting for ecology, and importantly, how to relate long-term projections to conservation. As an example, we discuss the need for effective management of one species, the emperor penguin, Aptenodytes forsteri. This species is unique amongst birds in that its breeding habit is critically dependent upon seasonal fast ice. Here, we review its vulnerability to ongoing and projected climate change, given that sea ice is susceptible to changes in winds and temperatures. We consider published projections of future emperor penguin population status in response to changing environments. Furthermore, we evaluate the current IUCN Red List status for the species, and recommend that its status be changed to Vulnerable, based on different modelling projections of population decrease of ≥50% over the current century, and the specific traits of the species. We conclude that current conservation measures are inadequate to protect the species under future projected scenarios. Only a reduction in anthropogenic greenhouse gas emissions will reduce threats to the emperor penguin from altered wind regimes, rising temperatures and melting sea ice; until such time, other conservation actions are necessary, including increased spatial protection at breeding sites and foraging locations. The designation of large-scale marine spatial protection across its range would benefit the species, particularly in areas that have a high probability of becoming future climate change refugia. We also recommend that the emperor penguin is listed by the Antarctic Treaty as an Antarctic Specially Protected Species, with development of a species Action Plan., We thank Thomas J. Bracegirdle, Tony Phillips and Kevin Hughes for helpful comments on earlier drafts of this manuscript. PNT acknowledges the support of WWF-UK under GB095701 and SJ the support of NSF OPP1744794 and 1643901.

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 pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between different clades. In this study, we examine the diversity in a key family of innate immune genes - the Toll-like receptors (TLRs) - across the range of the Gentoo. The three TLRs that we investigated present varying levels of diversity, with TLR4 and TLR5 greatly exceeding the diversity of TLR7. We present evidence of positive selection in TLR4 and TLR5, which points to pathogen-driven adaptation to the local pathogen milieu. Finally, we demonstrate that two positively selected co-segregating sites in TLR5 are sufficient to alter the responsiveness of the receptor to its bacterial ligand, flagellin. Taken together, these results suggest that Gentoo penguins have experienced distinct pathogen-driven selection pressures in different environments, which may be important given the role of the Gentoo as a sentinel species in some of the world’s most rapidly changing environments.

We argue the need to improve climate change forecasting for ecology, and importantly, how to relate long-term projections to conservation. As an example, we discuss the need for effective management of one species, the emperor penguin, Aptenodyptes forsteri. This species is unique amongst birds in that its breeding habit is critically dependent upon seasonal fast ice. Here, we review its vulnerability to ongoing and projected climate change, given that sea ice is susceptible to changes in winds and temperatures. We consider published projections of future emperor penguin population status in response to changing environments. Furthermore, we evaluate the current IUCN Red List status for the species, and recommend that its status be changed to Vulnerable, based on different modelling projections of population decrease of ≥50% over the current century, and the specific traits of the species. We conclude that current conservation measures are inadequate to protect the species under future projected scenarios. Only a reduction in anthropogenic greenhouse gas emissions will reduce threats to the emperor penguin from altered wind regimes, rising temperatures and melting sea ice; until such time, other conservation actions are necessary, including increased spatial protection at breeding sites and foraging locations. The designation of large-scale marine spatial protection across its range would benefit the species, particularly in areas that have a high probability of becoming future climate change refugia. We also recommend that the emperor penguin is listed by the Antarctic Treaty as an Antarctic Specially Protected Species, with development of a species Action Plan.

[Aim]: The conservation of biodiversity is hampered by data deficiencies, with many new species and subspecies awaiting description or reclassification. Population genomics and ecological niche modelling offer complementary new tools for uncovering functional units of phylogenetic diversity. We hypothesize that phylogenetically delineated lineages of gentoo penguins (Pygoscelis papua) distributed across Antarctica and sub-Antarctic Islands are subject to spatially explicit ecological conditions that have limited gene flow, facilitating genetic differentiation, and thereby speciation processes. [Location]: Antarctica and sub-Antarctic area. [Methods]: We identify divergent lineages for gentoo penguins using ddRAD-seq and mtDNA, and generated species distribution models (SDMs) based on terrestrial and marine parameters. Results: Analyses of our genomic data supports the existence of four major lineages of gentoo penguin: (i) spanning the sub-Antarctic archipelagos north of the Antarctic Polar Front (APF); (ii) Kerguelen Island; (iii) South America; and (iv) across maritime Antarctic and the Scotia Arc archipelagos. The APF, a major current system around Antarctica, acts as the most important barrier separating regional sister lineages. Our ecological analyses spanning both the terrestrial (breeding sites) and marine (feeding sites) realms recover limited niche overlap among the major lineages of gentoo penguin. We observe this pattern to correspond more closely with regional differentiation of marine conditions than to terrestrial macroenvironmental features. [Main conclusions]: Recognition of regional genetic lineages as discrete evolutionary entities that occupy distinct ecological niches and also differ morphologically should be considered a priority for conservation. Gentoo penguins provide a good example of how conservation policy can be directly impacted by new insights obtained through the integration of larger genomic datasets with novel approaches to ecologic

Penguins are the only extant family of flightless diving birds. They currently comprise at least 18 species, distributed from polar to tropical environments in the Southern Hemisphere. The history of their diversification and adaptation to these diverse environments remains controversial. We used 22 new genomes from 18 penguin species to reconstruct the order, timing, and location of their diversification, to track changes in their thermal niches through time, and to test for associated adaptation across the genome. Our results indicate that the penguin crown-group originated during the Miocene in New Zealand and Australia, not in Antarctica as previously thought, and that Aptenodytes is the sister group to all other extant penguin species. We show that lineage diversification in penguins was largely driven by changing climatic conditions and by the opening of the Drake Passage and associated intensification of the Antarctic Circumpolar Current (ACC). Penguin species have introgressed throughout much of their evolutionary history, following the direction of the ACC, which might have promoted dispersal and admixture. Changes in thermal niches were accompanied by adaptations in genes that govern thermoregulation and oxygen metabolism. Estimates of ancestral effective population sizes (Ne ) confirm that penguins are sensitive to climate shifts, as represented by three different demographic trajectories in deeper time, the most common (in 11 of 18 penguin species) being an increased Ne between 40 and 70 kya, followed by a precipitous decline during the Last Glacial Maximum. The latter effect is most likely a consequence of the overall decline in marine productivity following the last glaciation.