Forest fire plumes over the North Atlantic: p-TOMCAT model simulations with aircraft and satellite measurements from the ITOP/ICARTT campaign

Intercontinental Transport of Ozone and Precursors (ITOP) (part of International Consortium for Atmospheric Research on Transport and Transformation (ICARTT)) was an intense research effort to measure long-range transport of pollution across the North Atlantic and its impact on O3 production. During the aircraft campaign plumes were encountered containing large concentrations of CO plus other tracers and aerosols from forest fires in Alaska and Canada. A chemical transport model, p-TOMCAT, and new biomass burning emissions inventories are used to study the emissions long-range transport and their impact on the troposphere O3 budget. The fire plume structure is modeled well over long distances until it encounters convection over Europe. The CO values within the simulated plumes closely match aircraft measurements near North America and over the Atlantic and have good agreement with MOPITT CO data. O3 and NOx values were initially too great in the model plumes. However, by including additional vertical mixing of O3 above the fires, and using a lower NO2/CO emission ratio (0.008) for boreal fires, O3 concentrations are reduced closer to aircraft measurements, with NO2 closer to SCIAMACHY data. Too little PAN is produced within the simulated plumes, and our VOC scheme's simplicity may be another reason for O3 and NOx model-data discrepancies. In the p-TOMCAT simulations the fire emissions lead to increased tropospheric O3 over North America, the north Atlantic and western Europe from photochemical production and transport. The increased O3 over the Northern Hemisphere in the simulations reaches a peak in July 2004 in the range 2.0 to 6.2 Tg over a baseline of about 150 Tg.

A new Snow-SVAT to simulate the accumulation and ablation of seasonal snow cover beneath a forest canopy

A new snow-soil-vegetation-atmosphere transfer (Snow-SVAT) scheme, which simulates the accumulation and ablation of the snow cover beneath a forest canopy, is presented. The model was formulated by coupling a canopy optical and thermal radiation model to a physically-based multi-layer snow model. This canopy radiation model is physically-based yet requires few parameters, so can be used when extensive in-situ field measurements are not available. Other forest effects such as the reduction of wind speed, interception of snow on the canopy and the deposition of litter were incorporated within this combined model, SNOWCAN, which was tested with data taken as part of the Boreal Ecosystem-Atmosphere Study (BOREAS) international collaborative experiment. Snow depths beneath four different canopy types and at an open site were simulated. Agreement between observed and simulated snow depths was generally good, with correlation coefficients ranging between r^2=0.94 and r^2=0.98 for all sites where automatic measurements were available. However, the simulated date of total snowpack ablation generally occurred later than the observed date. A comparison between simulated solar radiation and limited measurements of sub-canopy radiation at one site indicates that the model simulates the sub-canopy downwelling solar radiation early in the season to within measurement uncertainty.

Evaluation of forest snow processes models (SnowMIP2)

Thirty‐three snowpack models of varying complexity and purpose were evaluated across a wide range of hydrometeorological and forest canopy conditions at five Northern Hemisphere locations, for up to two winter snow seasons. Modeled estimates of snow water equivalent (SWE) or depth were compared to observations at forest and open sites at each location. Precipitation phase and duration of above‐freezing air temperatures are shown to be major influences on divergence and convergence of modeled estimates of the subcanopy snowpack. When models are considered collectively at all locations, comparisons with observations show that it is harder to model SWE at forested sites than open sites. There is no universal “best” model for all sites or locations, but comparison of the consistency of individual model performances relative to one another at different sites shows that there is less consistency at forest sites than open sites, and even less consistency between forest and open sites in the same year. A good performance by a model at a forest site is therefore unlikely to mean a good model performance by the same model at an open site (and vice versa). Calibration of models at forest sites provides lower errors than uncalibrated models at three out of four locations. However, benefits of calibration do not translate to subsequent years, and benefits gained by models calibrated for forest snow processes are not translated to open conditions.

A comparison of three canopy interception models for a leafless mixed deciduous forest stand in the eastern United States

Canopy interception of incident precipitation is a critical component of the forest water balance during each of the four seasons. Models have been developed to predict precipitation interception from standard meteorological variables because of acknowledged difficulty in extrapolating direct measurements of interception loss from forest to forest. No known study has compared and validated canopy interception models for a leafless deciduous forest stand in the eastern United States. Interception measurements from an experimental plot in a leafless deciduous forest in northeastern Maryland (39°42'N, 75°5'W) for 11 rainstorms in winter and early spring 2004/05 were compared to predictions from three models. The Mulder model maintains a moist canopy between storms. The Gash model requires few input variables and is formulated for a sparse canopy. The WiMo model optimizes the canopy storage capacity for the maximum wind speed during each storm. All models showed marked underestimates and overestimates for individual storms when the measured ratio of interception to gross precipitation was far more or less, respectively, than the specified fraction of canopy cover. The models predicted the percentage of total gross precipitation (PG) intercepted to within the probable standard error (8.1%) of the measured value: the Mulder model overestimated the measured value by 0.1% of PG; the WiMo model underestimated by 0.6% of PG; and the Gash model underestimated by 1.1% of PG. The WiMo model’s advantage over the Gash model indicates that the canopy storage capacity increases logarithmically with the maximum wind speed. This study has demonstrated that dormant-season precipitation interception in a leafless deciduous forest may be satisfactorily predicted by existing canopy interception models.

Breeding distribution and population decline of globally threatened Grey-necked Picathartes Picathartes oreas in Mbam Minkom Mountain Forest, southern Cameroon

The Grey-necked Picathartes Picathartes oreas, considered 'Vulnerable', is an enigmatic ground-dwelling bird endemic to the central African equatorial rainforest and belongs to a family of only two species. Its distribution extends to the two Endemic Bird Areas within Cameroon (Guinea Congo forest biome and Cameroon mountain arc) and its population is thought to be in decline throughout its range due to increasing habitat fragmentation and disturbance. During March-April 2003 and June and October 2007 we surveyed Grey-necked Picathartes in the north-western region of the Mbam Minkom Mountain Forest. In January-March 2006 we surveyed the entire mountain range and found go breeding and 24 potential breeding sites, mostly located on the western slopes. From the complete survey, we estimated the population at 44 breeding individuals. Populations were highest in the north-west region but had apparently declined from 40 breeding individuals in 2003 to 20 in 2007. This region accounted for 41% of the entire population on the mountain range during the 2006 survey. The Mbam Minkom/Kala Important Bird Area was designated based on the presence of Grey-necked Picathartes but is under high pressure of imminent destruction from agricultural encroachment and illegal timber exploitation. These results have important implications for decision making in delimiting forest boundaries and core areas for protection in the development of management plans. We suggest possible remedial actions, appropriate repeatable methods for future monitoring and opportunities for community involvement in the management and conservation of the site.

The use of agricultural, open and forest habitats by juvenile Mauritius Kestrels Falco punctatus

Knowledge of tropical raptor habitat use is limited and yet a thorough understanding is vital when trying to conserve endangered species. We used a well studied, reintroduced population of the vulnerable Mauritius Kestrel Falco punctatus to investigate habitat preferences in a modified landscape. We constructed a high resolution digital habitat map and radiotracked 13 juvenile Kestrels to quantify habitat preferences. We distinguished seven habitat types in our study area and tracked Kestrels from 71 to 130 days old during which they dispersed from their natal territory and settled within a home-range after reaching independence. Mean home-range size was 0.95 km(2) characterized by a bimodal pattern of intensity around the natal site and post-independence home-range. Compositional analysis showed that home-ranges were located non-randomly with respect to habitat but there was no evidence to suggest differential use of habitats within home-ranges. Native and semi-invaded forest and grassland were consistently preferred, whereas agriculture was used significantly less than other habitats. No difference was found between the available length of edge dividing native forest and grassland within a home-range when compared to that available within a 2.35-km buffer around their nest-site, based on the maximum distance a juvenile was found to disperse. Repeating the analysis in three dimensions gave very similar results. Our results suggest that Mauritius Kestrels are not obligate forest dwellers as was once thought but can also exploit open habitats such as grassland. Kestrels may be using isolated mature trees within grassland as vantage points for hunting in the same way as they use the natural stratified forest structure. We suggest that the avoidance of agriculture is partly due to a lack of such vantage points. The conservation importance of forest degradation and agricultural encroachment is highlighted and comparisons with the habitat preferences of other tropical falcons are discussed.

Seed dormancy and germination of Ficus lundellii and tropical forest restoration

We investigated seed dormancy and germination in Ficus lundellii Standl. (Moraceae), a native species of Mexico's Los Tuxtlas tropical rain forest. In an 8-h photoperiod at an alternating diurnal (16/8 h) temperature of 20/30 degrees C, germination was essentially complete (96%) within 28 days, whereas in darkness, all seeds remained dormant. Neither potassium nitrate (0.05-0.2%) applied continuously nor gibberellic acid applied either continuously (10-200 ppm) or as a 24 hour pretreatment (2000 ppm) induced germination in the dark. Germination in the light was not reduced by a 24-h hydrochloric acid (0.1-1%) pretreatment, but it was reduced both by a 24-h pretreatment with either H2O2 (0. 1-5 M) or 5% HCl, or by more than 5 days of storage at 40 degrees C (4.5% seed water content). In a study with a 2-dimensional temperature gradient plate, seeds germinated fully and rapidly in the light at a constant temperature of 30 degrees C, and fully but less rapidly in the light at alternating temperatures with low amplitudes (< 12 degrees C) about the optimal constant temperature. The base, optimal and ceiling temperatures for rate of germination were estimated as 13.8, 30.1 and 41.1 degrees C, respectively. In all temperature regimes, light was essential for the germination of F lundellii seeds.

Gold mining in Ghana's forest reserves: a report on the current debate

This paper examines the debate surrounding a recent decision made by the Ghanaian government to permit gold exploration - and potentially, mining - in 'protected' forest reserves. In 2001, four mining companies were awarded mineral exploration concessions in forested regions of the country, and have since put forward applications to mine for gold. Notwithstanding the sharp divide in opinion on the issue, the continued uncertainty surrounding the implications of the proposed activities makes further research on the ground imperative in the short term. Work aiming to elicit indigenous perspectives on the projects, as well as research that facilitates dialogue between and/or among stakeholder parties, should be prioritized.

A novel parallel approach to the likelihood-based estimation of admixture in population genetics

Inferring population admixture from genetic data and quantifying it is a difficult but crucial task in evolutionary and conservation biology. Unfortunately state-of-the-art probabilistic approaches are computationally demanding. Effectively exploiting the computational power of modern multiprocessor systems can thus have a positive impact to Monte Carlo-based simulation of admixture modeling. A novel parallel approach is briefly described and promising results on its message passing interface (MPI)-based C implementation are reported.

100 years on: a century of genetics

In 2006 we celebrated the centenary of a remarkable year that saw the birth of genetics as a scientific discipline. This birth had its origins in horticulture and was supervised by a remarkable Cambridge academic, accompanied by a loyal group of female colleagues who worked together in underfunded conditions with little institutional support. Despite this deprivation, they established the foundations of an ongoing revolution, with huge academic and commercial consequences that we can recognize today in the shape of genomics and its application to biomedicine.

Development of a reverse genetics system enabling the rescue of recombinant avian influenza virus A/Turkey/England/50-92/91 (H5N1)

We previously described the use of an established reverse genetics system for the generation of recombinant human influenza A viruses from cloned cDNAs. Here, we have assembled a set of plasmids to allow recovery of the avian H5N1 influenza virus A/Turkey/England/50-92/91 entirely from cDNA. This system enables us to introduce mutations or truncations into the cDNAs to create mutant viruses altered specifically in a chosen gene. These mutant viruses can then be used in future pathogenesis studies in chickens and in studies to understand the host range restrictions of avian influenza viruses in humans.

Domestication of plants in the americas: Insights from mendelian and molecular genetics

Background Plant domestication occurred independently in four different regions of the Americas. In general, different species were domesticated in each area, though a few species were domesticated independently in more than one area. The changes resulting from human selection conform to the familiar domestication syndrome, though different traits making up this syndrome, for example loss of dispersal, are achieved by different routes in crops belonging to different families. Genetic and Molecular Analyses of Domestication Understanding of the genetic control of elements of the domestication syndrome is improving as a result of the development of saturated linkage maps for major crops, identification and mapping of quantitative trait loci, cloning and sequencing of genes or parts of genes, and discoveries of widespread orthologies in genes and linkage groups within and between families. As the modes of action of the genes involved in domestication and the metabolic pathways leading to particular phenotypes become better understood, it should be possible to determine whether similar phenotypes have similar underlying genetic controls, or whether human selection in genetically related but independently domesticated taxa has fixed different mutants with similar phenotypic effects. Conclusions Such studies will permit more critical analysis of possible examples of multiple domestications and of the origin(s) and spread of distinctive variants within crops. They also offer the possibility of improving existing crops, not only major food staples but also minor crops that are potential export crops for developing countries or alternative crops for marginal areas.