The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.Oceans cover approximately 71% of the Earth's surface and harbour most of the phylum diversity of the animal kingdom. Understanding marine biodiversity and its evolution remains a major challenge. The Pacific oyster C. gigas (Thunberg, 1793) is a marine bivalve belonging to the phylum Mollusca, which contains the largest number of described marine animal species 1 . Molluscs have vital roles in the functioning of marine, freshwater and terrestrial ecosystems, and have had major effects on humans, primarily as food sources but also as sources of dyes, decorative pearls and shells, vectors of parasites, and biofouling or destructive agents. Many molluscs are important fishery and aquaculture species, as well as models for studying neurobiology, biomineralization, ocean acidification and adaptation to coastal environments under climate change 2,3 . As the most speciose member of the Lophotrochozoa, phylum Mollusca is central to our understanding of the biology and evolution of this superphylum of protostomes.As sessile marine animals living in estuarine and intertidal regions, oysters must cope with harsh and dynamically changing environments. Abiotic factors such as temperature and salinity fluctuate wildly, and toxic metals and desiccation also pose serious challenges. Filter-feeding oysters face tremendous exposure to microbial pathogens. Oysters do have a notable physical line of defence against predation and desiccation in the formation of thick calcified shells, a key evolutionary innovation making molluscs a successful group. However, acidification of the world's oceans by uptake of anthropogenic carbon dioxide poses a potentially serious threat to this ancient adaptation 4 . Understanding biomineralization and molluscan shell formation is, thus, a major area of interest 5 . Crassostrea gigas is also an interesting model for developmental biology owing to its mosaic development with typical molluscan stages, including trochophore and veliger larvae and metamorphosis.A complete genome sequence of C. gigas would enable a more th...

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To assess the role of human disturbances in species' extinction requires an understanding of the species population history before human impact. The passenger pigeon was once the most abundant bird in the world, with a population size estimated at 3-5 billion in the 1800s; its abrupt extinction in 1914 raises the question of how such an abundant bird could have been driven to extinction in mere decades. Although human exploitation is often blamed, the role of natural population dynamics in the passenger pigeon's extinction remains unexplored. Applying high-throughput sequencing technologies to obtain sequences from most of the genome, we calculated that the passenger pigeon's effective population size throughout the last million years was persistently about 1/10,000 of the 1800's estimated number of individuals, a ratio 1,000-times lower than typically found. This result suggests that the passenger pigeon was not always super abundant but experienced dramatic population fluctuations, resembling those of an "outbreak" species. Ecological niche models supported inference of drastic changes in the extent of its breeding range over the last glacial-interglacial cycle. An estimate of acorn-based carrying capacity during the past 21,000 y showed great year-to-year variations. Based on our results, we hypothesize that ecological conditions that dramatically reduced population size under natural conditions could have interacted with human exploitation in causing the passenger pigeon's rapid demise. Our study illustrates that even species as abundant as the passenger pigeon can be vulnerable to human threats if they are subject to dramatic population fluctuations, and provides a new perspective on the greatest human-caused extinction in recorded history

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Caspase-3 and caspase-7 are two key effector caspases that play important roles in apoptotic pathways that maintain normal tissue and organ development and homeostasis. However, little is known about the sequence, structure, activity, and function of effector caspases upon apoptosis in mollusks, especially marine bivalves. In this study, we investigated the possible roles of two executioner caspases in the regulation of apoptosis in the Pacific oyster Crassostrea gigas. A full-length capase-3–like gene named Cgcaspase-3 was cloned from C.gigas cDNA, encoding a predicted protein containing caspase family p20 and p10 domain profiles and a conserved caspase active site motif. Phylogenetic analysis demonstrated that both Cgcaspase-3 and Cgcaspase-1 may function as effector caspases clustered in the invertebrate branch. Although the sequence identities between the two caspases was low, both enzymes possessed executioner caspase activity and were capable of inducing cell death. These results suggested that Cgcaspase-3 and Cgcaspase-1 were two effector caspases in C. gigas. We also observed that nucleus-localized Cgcaspase-3, may function as a caspase-3–like protein and cytoplasm-localized Cgcaspase-1 may function as a caspase-7–like protein. Both Cgcaspase-3 and Cgcaspase-1 mRNA expression increased after larvae settled on the substratum, suggesting that both caspases acted in several tissues or organs that degenerated after oyster larvae settlement. The highest caspase expression levels were observed in the gills indicating that both effector caspases were likely involved in immune or metabolic processes in C. gigas.

Conspicuous colouration can evolve as a primary defence mechanism that advertises unprofitability and discourages predatory attacks. Geographic overlap is a primary determinant of whether individual predators encounter, and thus learn to avoid, such aposematic prey. We experimentally tested whether the conspicuous colouration displayed by Old World pachyrhynchid weevils (Pachyrhynchus tobafolius and Kashotonus multipunctatus) deters predation by visual predators (Swinhoe’s tree lizard; Agamidae, Japalura swinhonis). During staged encounters, sympatric lizards attacked weevils without conspicuous patterns at higher rates than weevils with intact conspicuous patterns, whereas allopatric lizards attacked weevils with intact patterns at higher rates than sympatric lizards. Sympatric lizards also attacked masked weevils at lower rates, suggesting that other attributes of the weevils (size/shape/smell) also facilitate recognition. Allopatric lizards rapidly learned to avoid weevils after only a single encounter, and maintained aversive behaviours for more than three weeks. The imperfect ability of visual predators to recognize potential prey as unpalatable, both in the presence and absence of the aposematic signal, may help explain how diverse forms of mimicry exploit the predator’s visual system to deter predation.

Aging is associated with an increased incidence and prevalence of renal glomerular diseases. Sirtuin (Sirt) 6, a nicotinamide adenine dinucleotide (NAD)-dependent histone deacetylase, has been shown to protect against multiple age-associated phenotypes; however it is unknown whether Sirt6 has a direct pathophysiologic role in the kidney. In the present study, we demonstrate that Sirt6 is expressed in the kidney and aging Sirt6-deficient mice exhibit renal hypertrophy with glomerular enlargement. Sirt6 deletion induces podocyte injury, including decreases in slit diaphragm proteins, foot process effacement, and cellular loss, resulting in proteinuria. Knockdown of Sirt6 in cultured primary murine podocytes induces shape changes with loss of process formation and cell apoptosis. Moreover, Sirt6 deficiency results in progressive renal inflammation and fibrosis. Collectively, these data provide compelling evidence that Sirt6 is important for podocyte homeostasis and maintenance of glomerular function, and warrant further investigation into the role of Sirt6 in age-associated kidney dysfunction.

Summary1. Through nest-site selection, mothers exert control over the incubation environment to which eggs are exposed, which in turn can affect offspring fitness. The strong relationship between offspring quality and incubation temperature in many ectotherms suggests that contemporary climate change could modify the fitness benefits gained from such behaviour. 2. We used life-history data from a tropical lizard (the long-tailed skink, Eutropis longicaudata) to show that a natural dichotomy in nesting habitat directly influences fitness, but that higher ambient temperatures in recent years are having a disproportionate impact on 'optimal' nest sites. 3. Gravid lizards either lay eggs beneath rocks in natural habitat or inside a concrete wall in human-modified habitat, where incubation temperatures are higher. Consequently, females using artificial habitat produced larger hatchlings that matured earlier and had higher rates of survival than conspecifics using natural habitat. 4. Ambient temperatures have impacted artificial habitats disproportionately over the last decade by increasing nest temperatures in artificial habitat three times that of natural habitat (1AE5 vs. 0AE5°C, respectively). This has reversed nest-site quality by lowering offspring viability of artificial nest sites, but has increased offspring viability of natural nest sites. 5. Climate change has overridden the fitness benefits derived from nesting in artificial habitats, but has caused a resultant increase in the fitness benefits derived from nesting in natural habitats. Laboratory incubation experiments confirm that these patterns are attributed to temperature. 6. Our study highlights the interactive effects of disparate human environmental impacts on fauna; by creating the concrete wall, human habitat modification initially conferred fitness benefits by increasing incubation temperatures, but human-induced climate change has raised nest temperatures above the point at which fitness is reduced. 7. Contemporary climate change is altering the location and availability of 'optimal' nesting habitat, thereby changing the ability of nesting females to adaptively manipulate the phenotypes of their offspring. Consequently, human-induced climate change can lead to some habitats becoming ecological traps.