• Energy Research

The Northern rockhopper penguin (also known as Moseley's rockhopper penguin or Moseley's penguin) is a small crested penguin closely related to the Eastern and Western rockhopper penguins. The Northern rockhopper penguin breeds on Amsterdam and Gough islands. They breed in colonies at sea level, on cliff sides and sometimes inland. Populations of the Northern rockhopper penguin have declined drastically, and the International Union for Conservation of Nature (IUCN) classifies them as endangered.We sequenced the genome of an adult Northern rockhopper penguin from Amsterdam Island, Southern Indian Ocean (provided by Yves Cherel) to a depth of approximately 139x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.23Gb, with the contig and scaffold N50 values of 20.86Kb and 2.14Mb respectively. We identified 16812 protein-coding genes.

The Australian fairy penguin (also known as little blue penguin, blue penguin and little penguin) is one of the smallest penguins. It is found widely along the southern coastlines of Australia and the Otago coast of New Zealand. They have a slate-blue plumage. Recent genetic, morphological and behavioral research has demonstrated that the Australian fairy penguin is a separate species to the New Zealand little blue penguin, however this still remains controversial. Populations have recently declined, and they are considered as Least Concern by the International Union for Conservation of Nature (IUCN), however this assessment still classifies the Australian and New Zealand species as conspecific.We sequenced the genome of an adult Fairy penguin from Phillip Island, Victoria, Australia (provided by Peter Dann) to a depth of approximately 137x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.28Gb, with the contig and scaffold N50 values of 119.59Kb and 27.92Mb respectively. We identified 17188 protein-coding genes.

AbstractAnticipating species’ responses to environmental change is a pressing mission in biodiversity conservation. Despite decades of research investigating how climate change may affect population sizes, historical context is lacking and the traits which mediate demographic sensitivity to changing climate remain elusive. We use whole-genome sequence data to reconstruct the demographic histories of 263 bird species over the past million years and identify networks of interacting morphological and life-history traits associated with changes in effective population size (Ne) in response to climate warming and cooling. Our results identify direct and indirect effects of key traits representing dispersal, reproduction, and survival on long-term demographic responses to climate change, thereby highlighting traits most likely to influence population responses to on-going climate warming.One-Sentence SummaryInteracting traits influence sensitivity of bird population sizes to climate warming and cooling over the past million years.

The Chinstrap penguin inhabits a variety of islands and shores in the Southern Pacific and the Antarctic Oceans. It has a narrow black band under its head. They breed in Antarctica, Argentina, Bouvet Island, Chile, the Falkland Islands, the French Southern Territories, and South Georgia and the South Sandwich Islands. Populations of Chinstrap penguin are considered to be decreasing overall, however in many sites the populations are increasing or stable. They are considered as Least Concern by the International Union for Conservation of Nature (IUCN).We sequenced the genome of an adult Chinstrap penguin from Thule Island, South Sandwich Islands (provided by Tom Hart) to a depth of approximately 125x 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 115.56Kb and 5.89Mb respectively. We identified 15488 protein-coding genes.

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.

Abstract Background Nearly one-quarter of all avian species is either threatened or nearly threatened. Of these, 73 species are currently being rescued from going extinct in wildlife sanctuaries. One of the previously most critically-endangered is the crested ibis, Nipponia nippon. Once widespread across North-East Asia, by 1981 only seven individuals from two breeding pairs remained in the wild. The recovering crested ibis populations thus provide an excellent example for conservation genomics since every individual bird has been recruited for genomic and demographic studies. Results Using high-quality genome sequences of multiple crested ibis individuals, its thriving co-habitant, the little egret, Egretta garzetta, and the recently sequenced genomes of 41 other avian species that are under various degrees of survival threats, including the bald eagle, we carry out comparative analyses for genomic signatures of near extinction events in association with environmental and behavioral attributes of species. We confirm that both loss of genetic diversity and enrichment of deleterious mutations of protein-coding genes contribute to the major genetic defects of the endangered species. We further identify that genetic inbreeding and loss-of-function genes in the crested ibis may all constitute genetic susceptibility to other factors including long-term climate change, over-hunting, and agrochemical overuse. We also establish a genome-wide DNA identification platform for molecular breeding and conservation practices, to facilitate sustainable recovery of endangered species. Conclusions These findings demonstrate common genomic signatures of population decline across avian species and pave a way for further effort in saving endangered species and enhancing conservation genomic efforts.

Global climate fluctuations have significantly influenced the distribution and abundance of biodiversity. During unfavorable glacial periods, many species experienced range contraction and fragmentation, expanding again during interglacials. An understanding of the evolutionary consequences of both historical and ongoing climate changes requires knowledge of the temporal dynamics of population numbers during such climate cycles. Variation in abundance should have left clear signatures in the patterns of intraspecific genetic variation in extant species, from which historical effective population sizes (N(e)) can be estimated. We analyzed whole-genome sequences of 38 avian species in a pairwise sequentially Markovian coalescent (PSMC, [5]) framework to quantitatively reveal changes in N(e) from approximately 10 million to 10 thousand years ago. Significant fluctuations in N(e) over time were evident for most species. The most pronounced pattern observed in many species was a severe reduction in N(e) coinciding with the beginning of the last glacial period (LGP). Among species, N(e) varied by at least three orders of magnitude, exceeding 1 million in the most abundant species. Several species on the IUCN Red List of Threatened Species showed long-term reduction in population size, predating recent declines. We conclude that cycles of population expansions and contractions have been a common feature of many bird species during the Quaternary period, likely coinciding with climate cycles. Population size reduction should have increased the risk of extinction but may also have promoted speciation. Species that have experienced long-term declines may be especially vulnerable to recent anthropogenic threats.