Diet of young Atlantic bluefin tuna (<Emphasis Type="Italic">Thunnus thynnus</Emphasis>) in eastern and western Atlantic foraging grounds

Atlantic bluefin tuna (Thunnus thynnus) are highly migratory predators whose abundance, distribution, and somatic condition have changed over the past decades. Prey community composition and abundance have also varied in several foraging grounds. To better understand underlying food webs and regional energy sources, we performed stomach content and stable isotope analyses on mainly juvenile (60–150 cm curved fork length) bluefin tuna captured in foraging grounds in the western (Mid-Atlantic Bight) and eastern (Bay of Biscay) Atlantic Ocean. In the Mid-Atlantic Bight, bluefin tuna diet was mainly sand lance (Ammodytes spp., 29% prey weight), consistent with historic findings. In the Bay of Biscay, krill (Meganyctiphanes norvegica) and anchovy (Engraulis encrasicolus) made up 39% prey weight, with relative consumption of each reflecting annual changes in prey abundance. Consumption of anchovies apparently declined after the local collapse of this prey resource. In both regions, stable isotope analysis results showed that juvenile bluefin tuna fed at a lower trophic position than indicated by stomach content analysis. In the Mid-Atlantic Bight, stable isotope analyses suggested that >30% of the diet was prey from lower trophic levels that composed <10% of the prey weights based upon traditional stomach content analyses. Trophic position was similar to juvenile fish sampled in the NW Atlantic but lower than juveniles sampled in the Mediterranean Sea in previous studies. Our findings indicate that juvenile bluefin tuna targeted a relatively small range of prey species and regional foraging patterns remained consistent over time in the Mid-Atlantic Bight but changed in relation to local prey availability in the Bay of Biscay.     

Evaluation of interference to conventional and real-time PCR for detection and quantification of fungi in dust

Advances in polymerase chain reaction (PCR) have permitted accurate, rapid and quantitative identification of microorganisms in pure cultures regardless of viability or culturability. In this study, a simple sample processing method was investigated for rapid identification and quantification of fungal spores from dust samples using both conventional and real-time PCR. The proposed method was evaluated for susceptibility to interference from environmental dust samples. Stachybotrys chartarum and Aspergillus fumigatus were used as test organisms. The sensitivity of detection in pure culture was 0.1 spore DNA equivalents per PCR reaction corresponding to 20 spores ml(-1) in the sample. However, 1 spore DNA equivalent per PCR reaction corresponding to 200 spores ml(-1) in the sample was the lowest amount of spores tested without interference in dust samples spiked with spores of either fungal species. The extent of inhibition was calculated using conventional and real-time PCR reactions containing fungal spores, specific primers, specific probes (for real-time PCR) and various amounts of dust. The results indicate that the extent of inhibition by dust on PCR varies with the type and amount of dust, and number of spores. No interference in the analysis of spiked samples was detected from 0.2 mg ml(-1) of four real-life dust samples at p-value >0.05 using 2 x 10(4) spores for conventional PCR and 2 x 10(5) spores for real-time PCR. However, samples containing >0.2 mg ml(-1) real-life dust compromised the PCR assay. These results suggest the potential usefulness of a simple sample processing method in conjunction with PCR for monitoring the fungal content of aerosols collected from indoor environments.     

Genomic erosion in a demographically recovered bird species during conservation rescue

The pink pigeon (Nesoenas mayeri) is an endemic species of Mauritius that has made a remarkable recovery after a severe population bottleneck in the 1970s to early 1990s. Prior to this bottleneck, an ex situ population was established from which captive-bred individuals were released into free-living subpopulations to increase population size and genetic variation. This conservation rescue led to rapid population recovery to 400–480 individuals, and the species was twice downlisted on the International Union for the Conservation of Nature (IUCN) Red List. We analyzed the impacts of the bottleneck and genetic rescue on neutral genetic variation during and after population recovery (1993–2008) with restriction site-associated sequencing, microsatellite analyses, and quantitative genetic analysis of studbook data of 1112 birds from zoos in Europe and the United States. We used computer simulations to study the predicted changes in genetic variation and population viability from the past into the future. Genetic variation declined rapidly, despite the population rebound, and the effective population size was approximately an order of magnitude smaller than census size. The species carried a high genetic load of circa 15 lethal equivalents for longevity. Our computer simulations predicted continued inbreeding will likely result in increased expression of deleterious mutations (i.e., a high realized load) and severe inbreeding depression. Without continued conservation actions, it is likely that the pink pigeon will go extinct in the wild within 100 years. Conservation rescue of the pink pigeon has been instrumental in the recovery of the free-living population. However, further genetic rescue with captive-bred birds from zoos is required to recover lost variation, reduce expression of harmful deleterious variation, and prevent extinction. The use of genomics and modeling data can inform IUCN assessments of the viability and extinction risk of species, and it helps in assessments of the conservation dependency of populations.     

Assessing ecological function in the context of species recovery

Species interactions matter to conservation. Setting an ambitious recovery target for a species requires considering the size, density, and demographic structure of its populations such that they fulfill the interactions, roles, and functions of the species in the ecosystems in which they are embedded. A recently proposed framework for an International Union for Conservation of Nature Green List of Species formalizes this requirement by defining a fully recovered species in terms of representation, viability, and functionality. Defining and quantifying ecological function from the viewpoint of species recovery is challenging in concept and application, but also an opportunity to insert ecological theory into conservation practice. We propose 2 complementary approaches to assessing a species’ ecological functions: confirmation (listing interactions of the species, identifying ecological processes and other species involved in these interactions, and quantifying the extent to which the species contributes to the identified ecological process) and elimination (inferring functionality by ruling out symptoms of reduced functionality, analogous to the red-list approach that focuses on symptoms of reduced viability). Despite the challenges, incorporation of functionality into species recovery planning is possible in most cases and it is essential to a conservation vision that goes beyond preventing extinctions and aims to restore a species to levels beyond what is required for its viability. This vision focuses on conservation and recovery at the species level and sees species as embedded in ecosystems, influencing and being influenced by the processes in those ecosystems. Thus, it connects and integrates conservation at the species and ecosystem levels.     

SAOZ measurements of NO2 at Aberystwyth

We present in this paper fifteen years' measurements, from March 1991 to September 2005, of stratospheric NO2 vertical columns measured by a SAOZ zenith-sky visible spectrometer. The instrument spent most of its time at Aberystwyth, Wales, with occasional excursions to other locations. The data have been analysed with the WinDOAS analysis program with low-temperature high-resolution NO2 cross-sections and fitting a slit function to each spectrum. Because of a change in detector in May 1998 there is some uncertainty about the relative changes before and after this date, which are partially constrained by the results of an intercomparison exercise. However, the effect of the Mt Pinatubo aerosol cloud is very evident in the data from 1991-94, with a decrease of 10% in NO2 in the summer of 1992 (the SAOZ was located in Lerwick, Scotland during the winter of 1991-92 and observed very low NO2 values but these cannot be directly compared to the Aberystwyth data). To focus more on interannual and long-term variations in NO2, a seasonal variation comprising an annual and semi-annual component was fitted to the morning and evening twilight separately from 1995 to the present. This fit yielded average NO2 columns of 4.08 x 10(15) cm(-2) and 2.68 x 10(15) cm(-2) for the evening and morning twilight, respectively, with a corresponding annual amplitude of +/-2.08 x 10(15) cm(-2) and +/-1.50 x 10(15) cm(-2). Departures from the fitted curve show a trend of 6% per decade, consistent with that reported elsewhere, for the period 1998-2003, but in the past two years a distinct interannual variation of amplitude of approximately 8% has emerged.     

Comparing the Extent and Permanence of Headwater Streams From Two Field Surveys to Values From Hydrographic Databases and Maps

Supreme Court cases have questioned if jurisdiction under the Clean Water Act extends to water bodies such as streams without year‐round flow. Headwater streams are central to this issue because many periodically dry, and because little is known about their influence on navigable waters. An accurate account of the extent and flow permanence of headwater streams is critical to estimating downstream contributions. We compared the extent and permanence of headwater streams from two field surveys with values from databases and maps. The first used data from 29 headwater streams in nine U.S. forests, whereas the second had data from 178 headwater streams in Oregon. Synthetic networks developed from the nine‐forest survey indicated that 33 to 93% of the channel lacked year‐round flow. Seven of the nine forests were predicted to have >200% more channel length than portrayed in the high‐resolution National Hydrography Dataset (NHD). The NHD and topographic map classifications of permanence agreed with ~50% of the field determinations across ~300 headwater sites. Classification agreement with the field determinations generally increased with increasing resolution. However, the flow classification on soil maps only agreed with ~30% of the field determination despite depicting greater channel extent than other maps. Maps that include streams regardless of permanence and size will aid regulatory decisions and are fundamental to improving water quality monitoring and models.     

An Evaluation of the Effects of Soil Characteristics on Mitigation and Restoration Involving Blue Elderberry, <Emphasis Type="Italic">Sambucus mexicana</Emphasis>

We conducted field surveys and laboratory analyses to test the effects of soil characteristics in habitat mitigation sites and natural sites on the growth and condition of blue elderberry (Sambucus mexicana), which is the sole host plant for the federally threatened Valley elderberry longhorn beetle (Desmocerus californicus dimorphus). Thirty mitigation and 16 natural sites were selected throughout the range of the beetle. We found that although plant relative growth rates were comparable between mitigation sites and a natural site, mitigation sites contained substantially less soil nutrients than mitigation sites. Within mitigation sites, elderberry health and growth were positively correlated with the amount of total nitrogen in soils and less strongly with other soil nutrients and soil moisture. Analyses demonstrated reductions in the relative growth rate of elderberry as mitigation sites aged, and that soil nutrients and soil moisture became depleted over time. For mitigation sites, it took approximately seven years to develop basal stem diameters that have been linked to successful beetle colonization. Mitigation sites have smaller shrubs than natural sites and growth slows as mitigation sites age, thus delaying convergence of conditions between natural and mitigation sites. Analyses of soil particle size and whether sites were within the 100-year floodplain (as an indicator of riparian conditions) were inconclusive. We recommend investigating fertilizing and optimum planting densities for elderberry at restoration and mitigation sites, as well as increasing the duration of irrigation and monitoring.