• Energy Research

The Macaroni penguin is a crested penguin with golden-yellow crests found widely on subantarctic islands to the Antarctic peninsula. The Macaroni penguin is often considered a separate species from the Royal penguin, given its unique black facial plumage and wide breeding range. Several recent genetic studies, however, have demonstrated that the Macaroni penguin and Royal penguin are probably incipient. They are the most numerous penguin species. However, widespread declines have been recorded in many populations and the International Union for Conservation of Nature (IUCN) classifies the Macaroni penguin as vulnerable.We sequenced the genome of an adult Macaroni penguin from Marion Island, Prince Edward Islands (provided by Peter Ryan) to a depth of approximately 109x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.25Gb, with the contig and scaffold N50 values of 160.01Kb and 13.16Mb respectively. We identified 16311 protein-coding genes.

The King penguin is the second largest species of penguin. They have a circumpolar range, breeding on the subantarctic islands at the northern reaches of Antarctica, South Georgia, and other temperate islands. They were heavily hunted for oil on Macquarie Island. King penguins appear to have suffered a major population declines, and 70% are expected to disappear in the next eighty years, however they are still considered as Least Concern by the International Union for Conservation of Nature (IUCN).We sequenced the genome of an adult King penguin from Fortuna Bay, South Georgia (provided by Tom Hart) to a depth of approximately 120x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.24Gb, with the contig and scaffold N50 values of 114.03Kb and 2.77Mb respectively. We identified 15195 protein-coding genes.

The Erect-crested penguin is endemic only to the New Zealand Antipodes Islands and Bounty Islands. It is a crested penguin closely related to the extinct Chatham Island crested penguin, and is named after its upright yellow crests. The Erect-crested penguin breeds in large colonies on rocky terrain. Little is known about its biology and breeding habits. Populations have recently declined and the International Union for Conservation of Nature (IUCN) classifies it as endangered. The Erect-crested penguin is a Taonga, or treasured possession in Mori culture.We sequenced the genome of an adult Erect-crested penguin from Antipodes Island, New Zealand sub-Antarctic (provided by Chris Rickard/Sarah Fraser) to a depth of approximately 131x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.25Gb, with the contig and scaffold N50 values of 67.93Kb and 1.83Mb respectively. We identified 15786 protein-coding genes.

The Humboldt penguin inhabits coastal Chile and Peru. They nest on islands and rocky coasts, holes in guano and in caves. Humboldt penguin populations are declining, and the International Union for Conservation of Nature (IUCN) classifies them as vulnerable.We sequenced the genome of an adult Humboldt penguin from Copenhagen Zoo, of Peru and Chile lineage (provided by Mads Bertelsen) to a depth of approximately 172x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.21Gb, with the contig and scaffold N50 values of 19.38Kb and 5.94Mb respectively. We identified 16587 protein-coding genes.

Distinguishing the relative influence of historic (i.e. natural) versus anthropogenic factors in metapopulation structure is an important but often overlooked step in management programs of threatened species. Biotas in freshwater wetlands and floodplains, such as those in the Murray–Darling Basin (MDB)—one of Australia’s most impacted ecosystems, are particularly susceptible to anthropogenic fragmentation. Here we present a comprehensive multilocus assessment of genetic variation in the threatened southern pygmy perch Nannoperca australis (578 individuals; 45 localities; microsatellite, allozyme and mitochondrial DNA datasets), an ecological specialist with low dispersal potential. We assess patterns of spatial structure and genetic diversity in populations spanning the highly fragmented MDB and test whether recent anthropogenic modification has disrupted range-wide connectivity. We detected strong and hierarchical population structure, very low genetic diversity and lack of contemporary gene flow across the MDB. In contrast, the apparent absence of pronounced or long-term phylogeographic structure suggests that observed population divergences generally do not reflect deeply historic natural fragmentation. Coalescent-based analyses supported this inference, revealing that divergence times between populations from the upper and lower MDB fall into the period of European settlement. It appears that the observed contemporary isolation of populations is partly explained by the severe modification of the MDB post-dating the onset of European settlement. Our integrated approach substantially improves the interpretation of how fragmentation impacts present-day biodiversity. It also provides novel contributions for risk-assessing management actions in the context of captive breeding and translocations of small freshwater fishes, a group of increasing global conservation concern.

Abstract 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 capabilities. With ~20 species among 6 genera, penguins range from the tropical Galápagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such diverse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive to climate change. Therefore, penguins provide an exciting target system for understanding the evolutionary processes of speciation, adaptation, and demography. Genomic data are an emerging resource for addressing questions about such processes. Results Here we present a novel dataset of 19 high-coverage genomes that, together with 2 previously published genomes, encompass all extant penguin species. We also present a well-supported phylogeny to clarify the relationships among penguins. In contrast to recent studies, our results demonstrate that the genus Aptenodytes is basal and sister to all other extant penguin genera, providing intriguing new insights into the adaptation of penguins to Antarctica. As such, our dataset provides a novel resource for understanding the evolutionary history of penguins as a clade, as well as the fine-scale relationships of individual penguin lineages. Against this background, we introduce a major consortium of international scientists dedicated to studying these genomes. Moreover, we highlight emerging issues regarding ensuring legal and respectful indigenous consultation, particularly for genomic data originating from New Zealand Taonga species. Conclusions We believe that our dataset and project will be important for understanding evolution, increasing cultural heritage and guiding the conservation of this iconic southern hemisphere species assemblage.

The Magellanic penguin breeds in coastal Argentina, Chile and the Falkland Islands. Nests are built under bushes or in burrows, and they lay eggs in warm places when the temperature remains over 20. Magellanic penguins travel in large flocks when hunting for food. The International Union for Conservation of Nature (IUCN) classifies the Magellanic penguin as near threatened.We sequenced the genome of an adult Magellanic penguin from Chiloe Island, Chile (provided by Juan Bouzat) to a depth of approximately 171x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.2Gb, with the contig and scaffold N50 values of 40.48Kb and 12.09Mb respectively. We identified 16795 protein-coding genes.