Penguin waste trajectories reveal insights into nest hygiene
Effective waste management is an often-overlooked but essential aspect of the penguin life cycle. Building on the groundbreaking 2003 study of penguin cloacal pressure, we investigated cloacal release behaviour in white-crested penguin, Archaeospheniscus lloydie, a little-known penguin species endemic to New Zealand’s sub-Antarctic islands. Using cloacal pressure sensors, high-speed video, and biodegradable tracing dyes, we quantified the range, angle, and cloacal release events in nesting adults during the breeding season. Our observations reveal that A. lloydie can project guano over distances exceeding 1.5 meters, with cloacal pressures reaching up to 32 kPa. Diet composition significantly influenced guano viscosity and range, with krill-based diets producing longer trajectories than fish-based diets. These findings suggest that projectile cloacal release is an adaptive behaviour that minimises nest contamination and parasite transmission. While focusing on a relatively understudied and once thought extinct species, this research highlights broader biomechanical and ecological principles relevant across penguin taxa. It underscores the importance of integrating physiology and behaviour to understand penguin life history and nest hygiene strategies.
Penguin waste trajectories exacerbate colony fouling: evidence against the projectile hygiene hypothesis
The hypothesis that projectile guano release serves as an adaptive mechanism to reduce nest contamination has gained recent attention (cf. Gushmore et al. 2025). Here, we present data from controlled field experiments and comparative nest surveys in Archaeospheniscus andreie demonstrating the opposite: cloacal propulsion is maladaptive, increasing rather than decreasing contamination risks. Using motion-triggered high-speed videography combined with nest hygiene assays, we documented that long-range guano events frequently overshoot intended targets and contaminate neighboring nests. Guano splatter events were strongly correlated with elevated parasite loads in adjacent brooding adults (χ² = 42.7, p < 0.001). Furthermore, diet-dependent differences in guano viscosity were shown to exacerbate fouling. Contrary to claims that krill-based diets promote cleaner trajectories, our viscosity assays revealed that krill guano adhered more strongly to plumage and nest material than fish-derived guano, doubling average parasite egg counts. We therefore reject the “projectile hygiene” hypothesis and propose instead the “fecal fallout” model: penguins trade local nest sanitation for colony-wide dispersal of waste, a strategy that may reduce individual nest fouling but propagates microbial exchange across colonies. These findings challenge the romantic notion of cloacal propulsion as a hygienic adaptation, suggesting instead that penguin waste management is governed more by physics than foresight.
Collateral damage in a cloacal arms race: non-breeding penguins under fire
While much recent debate has centered on whether cloacal propulsion reduces or exacerbates nest fouling, little attention has been paid to the plight of non-breeding penguins caught between feuding nest owners. In this study, we examined sub-colony “no penguin’s land,” where idle juveniles and failed breeders gather within range of high-velocity cloacal discharge. Using a combination of time-lapse drone imagery and trajectory modelling software adapted from military ballistics, we quantified the frequency, angle, and splatter radius of guano strikes impacting non-breeders. Our results reveal that up to 37% of idle penguins sustained direct hits during peak guano exchanges, with krill-fed adults demonstrating the greatest offensive range. Observed behaviours among non-breeders included ducking, sidestepping, and occasional retaliatory wing-flapping — none of which significantly reduced impact probability. These findings support the emerging hypothesis that cloacal propulsion has been co-opted as a form of social signalling and territorial defense, transforming guano into a projectile weapon with unintended collateral consequences. We propose a new framework, the “Excremental Arms Race Hypothesis,” in which penguins balance nest hygiene, social dominance, and neighbourly aggression through strategic deployment of cloacal firepower.
At the zoo, King penguins live longer, but age faster: methylation patterns reveal the cost of a sedentary life for an active bird.
King penguins are famous for their outstanding metabolic abilities. In the wild, they can fast for up to 100 days a year, withstand hypoxia during deep foraging dives, actively swim for thousands of miles, and switch between acute obesity and extreme underweight several times year without visible adverse effect. Yet at the zoo, King penguins switch to a much more sedentary lifestyle: they don’t dive, feed as much as they like, barely exercise – but hey have medical care and don’t need to fret about predators. As a result, their lifespan can extend from 2 to nearly 4 decades. But this comes at the cost of a thorough life history reprogramming, including a much lowered reproductive success. Here, we take advantage of a known-age, known life-history population of electronically-monitored King penguins in the Crozet Archipelago, matched with known-age King penguins across European zoos, to understand the changes incurred through this radical lifestyle transition. Using whole-genome methyl-sequencing, we investigate the role of genome-wide methylation in adapting from wild to sedentary conditions. We find that paradoxically, lifespan extension at the zoo involves clear epigenetic age acceleration: sedentary birds live longer, but age faster. Our results underline the central role of epigenetic mechanisms in rapidly matching a common genomic background to widely divergent environmental challenges, and open the way for a finer understanding of the non-genetic determinants of adaptation in avian ecology.
Genetic analysis of HPAIV H5N1 clade 2.3.4.4b is Humboldt penguins, Chile 2023
In December 2022, HPAI H5N1 clade 2.3.4.4b emerged in Chile. The virus was first detected pelicans and gulls. After, cases on different avian species have been detected. Penguins has been found deceased or stranded in proximity of other positive animals and some of them have been confirmed positive to HPAIV H5N1. This study aims to investigate the genetic diversity of the highly pathogenic avian influenza virus (HPAIV) H5N1 detected in penguins in Chile. Between January and March 2023, 131 cases of suspected penguins were submitted for HPAIV diagnostic, involving the sampling of 270 animals. Positive samples were sequenced using MINION ONP technologies for whole genome sequencing and phylogenetic analysis. From the total cases, only four cases were positive for influenza detection, all of them HPAIV H5N1 positive. The positive samples were successfully sequenced, obtaining complete or near-to-complete genomes. Both were collected from different locations, one from Iquique and another from the Coquimbo Region. The sequences were identified as A/Humboldt penguin/Chile/238744-2/2023(H5N1) and A/Humboldt penguin/Chile/239590/2023(H5N1), which will be deposited in GenBank (In Process). The phylogeny was constructed with 90 reference sequences collected during the HPAIV H5N1 outbreak in Chile, from different hosts, to evidence the genetic relationship between them. The penguin sequences presented 99.5% identity on the HA segment between them. The phylogeny suggests that the penguin viruses belonged to different subclusters, highlighting the genetic diversity of the virus in the penguin population. These findings provide important insights into the genetic diversity of HPAIV H5N1 in penguins and can help improve our understanding of the transmission and evolution of the virus.
Genomes of banded penguins suggest islands of differentiation during ecological speciation.
Studies along the speciation continuum provide great opportunities to assess the contribution of neutral and adaptive evolution on the evolutionary history of species. When populations are geographically distant, the lower probability of random mating between populations would increase genetic divergence, by means of lower genetic connectivity and higher genetic drift. However, the increase of population divergence could also be related to adaptation to specific environmental conditions, and the contribution of each denotes the main drivers of speciation. Rockhopper penguins (genus Eudyptes) are crested penguins conformed by three main lineages, characterized by high vagility and low genetic divergence. Recently, it was found with a restricted set of genomic markers obtained from ddRAD sequencing, that these three major lineages represent three different species with low genomic variability. However, the main evolutionary processes that disentangle the drivers of speciation, such as introgression, incomplete lineage sorting and natural selection, have not been assessed with a robust and representative dataset. Here, we sequenced whole genomes of the Northern (n=12; E. moseleyi), Southern (n=21; E. chrysocome) and Eastern (n=26; E. filholi) rockhopper. Genetic structure analysis shows a clear lineage divergence between the three species, each with a characteristic demographic history trajectory, but with shared ancestry
At the zoo, King penguins live longer, but age faster: methylation patterns reveal the cost of a sedentary life for an active bird.
King penguins are famous for their outstanding metabolic abilities. In the wild, they can fast for up to 100 days a year, withstand hypoxia during deep foraging dives, actively swim for thousands of miles, and switch between acute obesity and extreme underweight several times year without visible adverse effect. Yet at the zoo, King penguins switch to a much more sedentary lifestyle: they don’t dive, feed as much as they like, barely exercise – but hey have medical care and don’t need to fret about predators. As a result, their lifespan can extend from 2 to nearly 4 decades. But this comes at the cost of a thorough life history reprogramming, including a much lowered reproductive success. Here, we take advantage of a known-age, known life-history population of electronically-monitored King penguins in the Crozet Archipelago, matched with known-age King penguins across European zoos, to understand the changes incurred through this radical lifestyle transition. Using whole-genome methyl-sequencing, we investigate the role of genome-wide methylation in adapting from wild to sedentary conditions. We find that paradoxically, lifespan extension at the zoo involves clear epigenetic age acceleration: sedentary birds live longer, but age faster. Our results underline the central role of epigenetic mechanisms in rapidly matching a common genomic background to widely divergent environmental challenges, and open the way for a finer understanding of the non-genetic determinants of adaptation in avian ecology.
Genetic analysis of HPAIV H5N1 clade 2.3.4.4b is Humboldt penguins, Chile 2023
In December 2022, HPAI H5N1 clade 2.3.4.4b emerged in Chile. The virus was first detected pelicans and gulls. After, cases on different avian species have been detected. Penguins has been found deceased or stranded in proximity of other positive animals and some of them have been confirmed positive to HPAIV H5N1. This study aims to investigate the genetic diversity of the highly pathogenic avian influenza virus (HPAIV) H5N1 detected in penguins in Chile. Between January and March 2023, 131 cases of suspected penguins were submitted for HPAIV diagnostic, involving the sampling of 270 animals. Positive samples were sequenced using MINION ONP technologies for whole genome sequencing and phylogenetic analysis. From the total cases, only four cases were positive for influenza detection, all of them HPAIV H5N1 positive. The positive samples were successfully sequenced, obtaining complete or near-to-complete genomes. Both were collected from different locations, one from Iquique and another from the Coquimbo Region. The sequences were identified as A/Humboldt penguin/Chile/238744-2/2023(H5N1) and A/Humboldt penguin/Chile/239590/2023(H5N1), which will be deposited in GenBank (In Process). The phylogeny was constructed with 90 reference sequences collected during the HPAIV H5N1 outbreak in Chile, from different hosts, to evidence the genetic relationship between them. The penguin sequences presented 99.5% identity on the HA segment between them. The phylogeny suggests that the penguin viruses belonged to different subclusters, highlighting the genetic diversity of the virus in the penguin population. These findings provide important insights into the genetic diversity of HPAIV H5N1 in penguins and can help improve our understanding of the transmission and evolution of the virus.
Genomes of banded penguins suggest islands of differentiation during ecological speciation.
Studies along the speciation continuum provide great opportunities to assess the contribution of neutral and adaptive evolution on the evolutionary history of species. When populations are geographically distant, the lower probability of random mating between populations would increase genetic divergence, by means of lower genetic connectivity and higher genetic drift. However, the increase of population divergence could also be related to adaptation to specific environmental conditions, and the contribution of each denotes the main drivers of speciation. Rockhopper penguins (genus Eudyptes) are crested penguins conformed by three main lineages, characterized by high vagility and low genetic divergence. Recently, it was found with a restricted set of genomic markers obtained from ddRAD sequencing, that these three major lineages represent three different species with low genomic variability. However, the main evolutionary processes that disentangle the drivers of speciation, such as introgression, incomplete lineage sorting and natural selection, have not been assessed with a robust and representative dataset. Here, we sequenced whole genomes of the Northern (n=12; E. moseleyi), Southern (n=21; E. chrysocome) and Eastern (n=26; E. filholi) rockhopper. Genetic structure analysis shows a clear lineage divergence between the three species, each with a characteristic demographic history trajectory, but with shared ancestry
At the zoo, King penguins live longer, but age faster: methylation patterns reveal the cost of a sedentary life for an active bird.
King penguins are famous for their outstanding metabolic abilities. In the wild, they can fast for up to 100 days a year, withstand hypoxia during deep foraging dives, actively swim for thousands of miles, and switch between acute obesity and extreme underweight several times year without visible adverse effect. Yet at the zoo, King penguins switch to a much more sedentary lifestyle: they don’t dive, feed as much as they like, barely exercise – but hey have medical care and don’t need to fret about predators. As a result, their lifespan can extend from 2 to nearly 4 decades. But this comes at the cost of a thorough life history reprogramming, including a much lowered reproductive success. Here, we take advantage of a known-age, known life-history population of electronically-monitored King penguins in the Crozet Archipelago, matched with known-age King penguins across European zoos, to understand the changes incurred through this radical lifestyle transition. Using whole-genome methyl-sequencing, we investigate the role of genome-wide methylation in adapting from wild to sedentary conditions. We find that paradoxically, lifespan extension at the zoo involves clear epigenetic age acceleration: sedentary birds live longer, but age faster. Our results underline the central role of epigenetic mechanisms in rapidly matching a common genomic background to widely divergent environmental challenges, and open the way for a finer understanding of the non-genetic determinants of adaptation in avian ecology.
Genetic analysis of HPAIV H5N1 clade 2.3.4.4b is Humboldt penguins, Chile 2023
In December 2022, HPAI H5N1 clade 2.3.4.4b emerged in Chile. The virus was first detected pelicans and gulls. After, cases on different avian species have been detected. Penguins has been found deceased or stranded in proximity of other positive animals and some of them have been confirmed positive to HPAIV H5N1. This study aims to investigate the genetic diversity of the highly pathogenic avian influenza virus (HPAIV) H5N1 detected in penguins in Chile. Between January and March 2023, 131 cases of suspected penguins were submitted for HPAIV diagnostic, involving the sampling of 270 animals. Positive samples were sequenced using MINION ONP technologies for whole genome sequencing and phylogenetic analysis. From the total cases, only four cases were positive for influenza detection, all of them HPAIV H5N1 positive. The positive samples were successfully sequenced, obtaining complete or near-to-complete genomes. Both were collected from different locations, one from Iquique and another from the Coquimbo Region. The sequences were identified as A/Humboldt penguin/Chile/238744-2/2023(H5N1) and A/Humboldt penguin/Chile/239590/2023(H5N1), which will be deposited in GenBank (In Process). The phylogeny was constructed with 90 reference sequences collected during the HPAIV H5N1 outbreak in Chile, from different hosts, to evidence the genetic relationship between them. The penguin sequences presented 99.5% identity on the HA segment between them. The phylogeny suggests that the penguin viruses belonged to different subclusters, highlighting the genetic diversity of the virus in the penguin population. These findings provide important insights into the genetic diversity of HPAIV H5N1 in penguins and can help improve our understanding of the transmission and evolution of the virus.
Genomes of banded penguins suggest islands of differentiation during ecological speciation.
Studies along the speciation continuum provide great opportunities to assess the contribution of neutral and adaptive evolution on the evolutionary history of species. When populations are geographically distant, the lower probability of random mating between populations would increase genetic divergence, by means of lower genetic connectivity and higher genetic drift. However, the increase of population divergence could also be related to adaptation to specific environmental conditions, and the contribution of each denotes the main drivers of speciation. Rockhopper penguins (genus Eudyptes) are crested penguins conformed by three main lineages, characterized by high vagility and low genetic divergence. Recently, it was found with a restricted set of genomic markers obtained from ddRAD sequencing, that these three major lineages represent three different species with low genomic variability. However, the main evolutionary processes that disentangle the drivers of speciation, such as introgression, incomplete lineage sorting and natural selection, have not been assessed with a robust and representative dataset. Here, we sequenced whole genomes of the Northern (n=12; E. moseleyi), Southern (n=21; E. chrysocome) and Eastern (n=26; E. filholi) rockhopper. Genetic structure analysis shows a clear lineage divergence between the three species, each with a characteristic demographic history trajectory, but with shared ancestry
At the zoo, King penguins live longer, but age faster: methylation patterns reveal the cost of a sedentary life for an active bird.
King penguins are famous for their outstanding metabolic abilities. In the wild, they can fast for up to 100 days a year, withstand hypoxia during deep foraging dives, actively swim for thousands of miles, and switch between acute obesity and extreme underweight several times year without visible adverse effect. Yet at the zoo, King penguins switch to a much more sedentary lifestyle: they don’t dive, feed as much as they like, barely exercise – but hey have medical care and don’t need to fret about predators. As a result, their lifespan can extend from 2 to nearly 4 decades. But this comes at the cost of a thorough life history reprogramming, including a much lowered reproductive success. Here, we take advantage of a known-age, known life-history population of electronically-monitored King penguins in the Crozet Archipelago, matched with known-age King penguins across European zoos, to understand the changes incurred through this radical lifestyle transition. Using whole-genome methyl-sequencing, we investigate the role of genome-wide methylation in adapting from wild to sedentary conditions. We find that paradoxically, lifespan extension at the zoo involves clear epigenetic age acceleration: sedentary birds live longer, but age faster. Our results underline the central role of epigenetic mechanisms in rapidly matching a common genomic background to widely divergent environmental challenges, and open the way for a finer understanding of the non-genetic determinants of adaptation in avian ecology.
Genetic analysis of HPAIV H5N1 clade 2.3.4.4b is Humboldt penguins, Chile 2023
In December 2022, HPAI H5N1 clade 2.3.4.4b emerged in Chile. The virus was first detected pelicans and gulls. After, cases on different avian species have been detected. Penguins has been found deceased or stranded in proximity of other positive animals and some of them have been confirmed positive to HPAIV H5N1. This study aims to investigate the genetic diversity of the highly pathogenic avian influenza virus (HPAIV) H5N1 detected in penguins in Chile. Between January and March 2023, 131 cases of suspected penguins were submitted for HPAIV diagnostic, involving the sampling of 270 animals. Positive samples were sequenced using MINION ONP technologies for whole genome sequencing and phylogenetic analysis. From the total cases, only four cases were positive for influenza detection, all of them HPAIV H5N1 positive. The positive samples were successfully sequenced, obtaining complete or near-to-complete genomes. Both were collected from different locations, one from Iquique and another from the Coquimbo Region. The sequences were identified as A/Humboldt penguin/Chile/238744-2/2023(H5N1) and A/Humboldt penguin/Chile/239590/2023(H5N1), which will be deposited in GenBank (In Process). The phylogeny was constructed with 90 reference sequences collected during the HPAIV H5N1 outbreak in Chile, from different hosts, to evidence the genetic relationship between them. The penguin sequences presented 99.5% identity on the HA segment between them. The phylogeny suggests that the penguin viruses belonged to different subclusters, highlighting the genetic diversity of the virus in the penguin population. These findings provide important insights into the genetic diversity of HPAIV H5N1 in penguins and can help improve our understanding of the transmission and evolution of the virus.
Genomes of banded penguins suggest islands of differentiation during ecological speciation.
Studies along the speciation continuum provide great opportunities to assess the contribution of neutral and adaptive evolution on the evolutionary history of species. When populations are geographically distant, the lower probability of random mating between populations would increase genetic divergence, by means of lower genetic connectivity and higher genetic drift. However, the increase of population divergence could also be related to adaptation to specific environmental conditions, and the contribution of each denotes the main drivers of speciation. Rockhopper penguins (genus Eudyptes) are crested penguins conformed by three main lineages, characterized by high vagility and low genetic divergence. Recently, it was found with a restricted set of genomic markers obtained from ddRAD sequencing, that these three major lineages represent three different species with low genomic variability. However, the main evolutionary processes that disentangle the drivers of speciation, such as introgression, incomplete lineage sorting and natural selection, have not been assessed with a robust and representative dataset. Here, we sequenced whole genomes of the Northern (n=12; E. moseleyi), Southern (n=21; E. chrysocome) and Eastern (n=26; E. filholi) rockhopper. Genetic structure analysis shows a clear lineage divergence between the three species, each with a characteristic demographic history trajectory, but with shared ancestry