Estimating the numbers of aquatic birds affected by oil spills: pre-planning, response, and post-incident considerations

Oil spills most visibly affect waterbirds and often the number of birds affected, a key measure of environmental damage from an incident, is required for public communication, population management, and legal reasons. We review and outline steps that can be taken to improve accuracy in the estimation of the number of birds affected in each of three phases: (1) pre-planning; (2) during a response; and (3) post-response. The more pre-planning undertaken, the more robust the estimates will be. Personnel involved in damage assessment efforts must have training in quantitative biology and need support during all three phases. The main approaches currently used to estimate the number of birds affected include probability exposure models and carcass sampling — both onshore and on the water. Probability exposure models can be used in the post-incident phase, particularly in offshore scenarios where beached bird surveys are not possible, and requires three datasets: (1) at-sea bird densities; (2) bird mortality; and (3) the spill trajectory. Carcass sampling using beached bird surveys is appropriate if trajectories indicate affected birds will reach shore. Carcass sampling can also occur via on-water transects and may overlap with risk assessment efforts. Damage assessment efforts should include a measure of sublethal effects following the post-acute phase of spills, yet this area has significant knowledge gaps. We urge jurisdictions worldwide to improve pre-incident planning. We provide guidance on how, in the absence of pre-incident data, quality data can be obtained during or after an incident. These recommendations are relevant for areas with aquatic-based industrial activities which can result in a spill of substances that could injure or kill waterbirds

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. 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; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation; analyses timings and patterns of tumour evolution; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity; and evaluates a range of more-specialized features of cancer genomes