Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

A simple, sufficient, and consistent method to score the status of threats and demography of imperiled species

Managers of large, complex wildlife conservation programs need information on the conservation status of each of many species to help strategically allocate limited resources. Oversimplifying status data, however, runs the risk of missing information essential to strategic allocation. Conservation status consists of two components, the status of threats a species faces and the species’ demographic status. Neither component alone is sufficient to characterize conservation status. Here we present a simple key for scoring threat and demographic changes for species using detailed information provided in free-form textual descriptions of conservation status. This key is easy to use (simple), captures the two components of conservation status without the cost of more detailed measures (sufficient), and can be applied by different personnel to any taxon (consistent). To evaluate the key’s utility, we performed two analyses. First, we scored the threat and demographic status of 37 species recently recommended for reclassification under the Endangered Species Act (ESA) and 15 control species, then compared our scores to two metrics used for decision-making and reports to Congress. Second, we scored the threat and demographic status of all non-plant ESA-listed species from Florida (54 spp.), and evaluated scoring repeatability for a subset of those. While the metrics reported by the U.S. Fish and Wildlife Service (FWS) are often consistent with our scores in the first analysis, the results highlight two problems with the oversimplified metrics. First, we show that both metrics can mask underlying demographic declines or threat increases; for example, ∼40% of species not recommended for reclassification had changes in threats or demography. Second, we show that neither metric is consistent with either threats or demography alone, but conflates the two. The second analysis illustrates how the scoring key can be applied to a substantial set of species to understand overall patterns of ESA implementation. The scoring repeatability analysis shows promise, but indicates thorough training will be needed to ensure consistency. We propose that large conservation programs adopt our simple scoring system for threats and demography. By doing so, program administrators will have better information to monitor program effectiveness and guide their decisions

Generic ecological impact assessments of alien species in Norway: a semi-quantitative set of criteria

The ecological impact assessment scheme that has been developed to classify alien species in Norway is presented. The underlying set of criteria enables a generic and semi-quantitative impact assessment of alien species. The criteria produce a classification of alien species that is testable, transparent and easily adjustable to novel evidence or environmental change. This gives a high scientific and political legitimacy to the end product and enables an effective prioritization of management efforts, while at the same time paying attention to the precautionary principle. The criteria chosen are applicable to all species regardless of taxonomic position. This makes the assessment scheme comparable to the Red List criteria used to classify threatened species. The impact of alien species is expressed along two independent axes, one measuring invasion potential, the other ecological effects. Using this two-dimensional approach, the categorization captures the ecological impact of alien species, which is the product rather than the sum of spread and effect. Invasion potential is assessed using three criteria, including expected population lifetime and expansion rate. Ecological effects are evaluated using six criteria, including interactions with native species, changes in landscape types, and the potential to transmit genes or parasites. Effects on threatened species or landscape types receive greater weightings

Dike intrusion and deformation during growth of the Half Dome pluton, Yosemite National Park, California

Meter-scale mapping of the Late Cretaceous Half Dome Granodiorite of the Tuolumne Intrusive Suite (TIS) near Tenaya Lake, Yosemite National Park, defines an intricate internal structure that reflects a combination of incremental pluton growth by diking and internal deformation as the pluton grew. At least four ages of dikes of layered granodiorite are defined by crosscutting relations. Because dikes thicker than 1 m invariably contain multiple cycles of layering that field relations indicate record multiple intrusive increments, dozens of discrete intrusive events are likely. The kinematic pattern of dilation across dikes, offset lithologic markers across dikes, shearing of mafic enclaves and magmatic layering, and folding of dikes defines a synintrusive bulk strain field characterized by E-W extension and N-S contraction, with net volume increase in the extension direction. The geometric and kinematic pattern of the deformation are consistent with current understanding of Late Cretaceous Cordilleran tectonics and suggest that regional tectonic dilation played a significant role in making upper-crustal space for the growing pluton. Narrow shear zones offset lithologic markers and produced extreme strains, yet no rock fabric is preserved in the zones. This indicates that late-magmatic to subsolidus recrystallization, previously inferred in the TIS based on textural and mineralogical observations, greatly modified rock textures and obscured both the intricate internal structure of the pluton and the importance of synemplacement deformation

Quantification of self pollution from two diesel school buses using three independent methods

We monitored two Seattle school buses to quantify the buses' self pollution using the dual tracers (DT), lead vehicle (LV), and chemical mass balance (CMB) methods. Each bus drove along a residential route simulating stops, with windows closed or open. Particulate matter (PM) and its constituents were monitored in the bus and from a LV. We collected source samples from the tailpipe and crankcase emissions using an on-board dilution tunnel. Concentrations of PM(1), ultrafine particle counts, elemental and organic carbon (EC/OC) were higher on the bus than the LV. The DT method estimated that the tailpipe and the crankcase emissions contributed 1.1 and 6.8 mug/m(3) of PM(2.5) inside the bus, respectively, with significantly higher crankcase self pollution (SP) when windows were closed. Approximately two-thirds of in-cabin PM(2.5) originated from background sources. Using the LV approach, SP estimates from the EC and the active personal DataRAM (pDR) measurements correlated well with the DT estimates for tailpipe and crankcase emissions, respectively, although both measurements need further calibration for accurate quantification. CMB results overestimated SP from the DT method but confirmed crankcase emissions as the major SP source. We confirmed buses' SP using three independent methods and quantified crankcase emissions as the dominant contributo