Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

The importance of the altricial – precocial spectrum for social complexity in mammals and birds:A review

Various types of long-term stable relationships that individuals uphold, including cooperation and competition between group members, define social complexity in vertebrates. Numerous life history, physiological and cognitive traits have been shown to affect, or to be affected by, such social relationships. As such, differences in developmental modes, i.e. the ‘altricial-precocial’ spectrum, may play an important role in understanding the interspecific variation in occurrence of social interactions, but to what extent this is the case is unclear because the role of the developmental mode has not been studied directly in across-species studies of sociality. In other words, although there are studies on the effects of developmental mode on brain size, on the effects of brain size on cognition, and on the effects of cognition on social complexity, there are no studies directly investigating the link between developmental mode and social complexity. This is surprising because developmental differences play a significant role in the evolution of, for example, brain size, which is in turn considered an essential building block with respect to social complexity. Here, we compiled an overview of studies on various aspects of the complexity of social systems in altricial and precocial mammals and birds. Although systematic studies are scarce and do not allow for a quantitative comparison, we show that several forms of social relationships and cognitive abilities occur in species along the entire developmental spectrum. Based on the existing evidence it seems that differences in developmental modes play a minor role in whether or not individuals or species are able to meet the cognitive capabilities and requirements for maintaining complex social relationships. Given the scarcity of comparative studies and potential subtle differences, however, we suggest that future studies should consider developmental differences to determine whether our finding is general or whether some of the vast variation in social complexity across species can be explained by developmental mode. This would allow a more detailed assessment of the relative importance of developmental mode in the evolution of vertebrate social systems

Field preference of Greylag geese Anser anser during the breeding season

Few studies address food preference of geese on agricultural land (utilization related to availability) and only a handful so for the breeding season. We studied Greylag geese Anser anser during the breeding season in an intensively farmed area in southern Sweden. Few of 22 available field types were truly preferred. Pastureland was the most consistently preferred, by goslings (with parents) as well as by nonbreeders. In some sampling periods, goslings also preferred grazed hay, ley, and carrot fields. Non-breeders exploited a greater variety of crops/fields, feeding also on barley, fallow, grazed hay, lettuce, oats, potatoes, and carrots. Most of these crops were preferred on at least one sampling occasion, except for fallow, grazed hay, and wheat, which were always used less than expected from availability. GLMs revealed that goslings rested more than they fed and preferred shorter vegetation before higher. Moreover, goslings occurred in higher densities in younger age classes than in older and preferred nearshore areas. In contrast, density of non-breeders was only related to field type and sampling occasion (higher densities as the season progressed). The maximum number of broods observed (106) implies a breeding success of 34% based on311 active nests earlier in the season. Brood size decreased from 3.5 to 2.1 during the study period. Our study shows that goose management during the breeding season should consider goslings and their parents separately from non-breeders, and it implies little potential conflict between Greylag geese and agriculture during the breeding period

Trans-Equatorial Migration Routes, Staging Sites and Wintering Areas of a High-Arctic Avian Predator:The Long-tailed Skua (Stercorarius longicaudus)

<p>The Long-tailed Skua, a small (</p>