Mitochondrial cytochrome b variation in sleeper sharks (Squaliformes: Somniosidae)

Sleeper sharks are a poorly studied group of deep-sea sharks. The subgenus, Somniosus, contains three morphologically similar species: S. microcephalus found in the Arctic and North Atlantic; S. pacificus in the North Pacific; and S. antarcticus in the Southern Ocean. These sharks have been reported mainly in temperate to polar waters and occasionally in subtropical locations. They have not been recorded in tropical waters. This study investigates the relationships among the accepted species of Somniosus through analysis of mitochondrial cytochrome b sequence variation. Seventy-five samples were examined from four sampling locations in the North Pacific, Southern Ocean and North Atlantic. Twenty-one haplotypes were found. A minimum spanning parsimony network separated these haplotypes into two divergent clades, an S. microcephalus and an S. pacificus/antarcticus clade, strongly supporting the distinction of S. microcephalus as a separate species from the Pacific sleeper shark species. Analysis of genetic structure within the S. pacificus/antarcticus clade (analysis of molecular variance, allele frequency comparisons, and a nested clade analysis) showed limited or no differences amongst three populations. Further examination of genetic variation at more variable mtDNA and nuclear markers is needed to examine the species status of S. pacificus and S. antarcticus.     

Allochthonous subsidy of periodical cicadas affects the dynamics and stability of pond communities

Periodical cicadas emerge from below ground every 13 or 17 years in North American forests, with individual broods representing the synchronous movement of trillions of individuals across geographic regions. Due to predator satiation, most individuals escape predation, die, and become deposited as detritus. Some of this emergent biomass falls into woodland aquatic habitats (small streams and woodland ponds) and serves as a high-quality allochthonous detritus pulse in early summer. We present results of a two-part study in which we (1) quantified deposition of Brood X periodical cicada detritus into woodland ponds and low-order streams in southwestern Ohio, and (2) conducted an outdoor mesocosm experiment in which we examined the effects of deposition of different amounts of cicada detritus on food webs characteristic of forest ponds. In the mesocosm experiment, we manipulated the amount of cicada detritus input to examine if food web dynamics and stability varied with the magnitude of this allochthonous resource subsidy, as predicted by numerous theoretical models. Deposition data indicate that, during years of periodical cicada emergence, cicada carcasses can represent a sizable pulse of allochthonous detritus to forest aquatic ecosystems. In the mesocosm experiment, cicada carcass deposition rapidly affected food webs, leading to substantial increases in nutrients and organism biomass, with the magnitude of increase dependent upon the amount of cicada detritus. Deposition of cicada detritus impacted the stability of organism functional groups and populations by affecting the temporal variability and biomass minima. However, contrary to theory, stability measures were not consistently related to the size of the allochthonous pulse (i.e., the amount of cicada detritus). Our study underscores the need for theory to further explore consequences of pulsed allochthonous subsidies for food web stability.     

All-in-one whole exome sequencing strategy with simultaneous copy number variant,single nucleotide variant and absence-of-heterozygosity analysis in fetuses with structural ultrasound anomalies: A 1-year experience

Objective

We performed a 1-year evaluation of a novel strategy of simultaneously analyzing single nucleotide variants (SNVs), copy number variants (CNVs) and copy-number-neutral Absence-of-Heterozygosity from Whole Exome Sequencing (WES) data for prenatal diagnosis of fetuses with ultrasound (US) anomalies and a non-causative QF-PCR result.

Methods

After invasive diagnostics, whole exome parent-offspring trio-sequencing with exome-wide CNV analysis was performed in pregnancies with fetal US anomalies and a non-causative QF-PCR result (WES-CNV). On request, additional SNV-analysis, restricted to (the) requested gene panel(s) only (with the option of whole exome SNV-analysis afterward) was performed simultaneously (WES-CNV/SNV) or as rapid SNV-re-analysis, following a normal CNV analysis.

Results

In total, 415 prenatal samples were included. Following a non-causative QF-PCR result, WES-CNV analysis was initially requested for 74.3% of the chorionic villus (CV) samples and 45% of the amniotic fluid (AF) samples. In case WES-CNV analysis did not reveal a causative aberration, SNV-re-analysis was requested in 41.7% of the CV samples and 17.5% of the AF samples. All initial analyses could be finished within 2 weeks after sampling. For SNV-re-analysis during pregnancy, turn-around-times (TATs) varied between one and 8 days.

Conclusion

We show a highly efficient all-in-one WES-based strategy, with short TATs, and the option of rapid SNV-re-analysis after a normal CNV result.     

Environmental Dependency of Inbreeding Depression: Implications for Conservation Biology

Inbreeding depression is environmentally dependent, such that a population may suffer from inbreeding depression in one environment but not another. We examined the phenotypic responses of 35 inbred ( F = 0.672) lineages of the red flour beetle Tribolium castaneum in two different climatic environments. We found a significant environmental effect on males but not females. More important, we found that the rank fitness order of lineages differs between environments; lineages of high fitness in one environment may have low fitness in another environment. This change in rank is evident in a significant genotype-by-environment interaction for inbreeding depression for both females and males. These results suggest that even if we know the average environmental effect of inbreeding depression in a population, for any particular lineage measurements of inbreeding depression in one environment may not predict the level of inbreeding depression in another environment. Conservation biologists need to be aware of the environmental dependency of inbreeding depression when planning wildlife refuges or captive propagation programs for small populations. Ideally, captive propagation programs should maintain separate lineages for release efforts. Refuge design programs should consider maintaining a range of habitat types.     

Adsorption of As(III) versus As(V) from aqueous solutions by cerium-loaded volcanic rocks

Environmental Science and Pollution Research - Contamination of drinking water with arsenic causes severe health problems in various world regions. Arsenic exists predominantly as As(III) and As(V)...     

Development of a distance-to-roadway proximity metric to compare near-road pollutant levels to a central site monitor

The primary objective of the Detroit Exposure and Aerosol Research Study (DEARS) was to compare air pollutant concentrations measured at various neighborhoods, or exposure monitoring areas (EMAs), throughout a major metropolitan area to levels measured at a central site or community monitor. One of the EMAs was located near a busy freeway (annual average daily traffic (AADT) of ～130,000) so that impacts of mobile sources could be examined. Air pollution concentrations from the roadway-proximate sites were compared to the central site monitor. The volatile organic compounds (VOCs) selected (benzene, toluene, ethylbenzene, m,p- and o-xylene, 1,3 butadiene, 1,3,5-trimethylbenzene and 4-ethyltoluene) are typically associated with mobile sources. Gradients were also evident that demonstrated the amplification of pollutant levels near the roadway compared to the community monitor. A novel distance-to-roadway proximity metric was developed to plot the measurements and model these gradients. Effective distance represents the actual distance an air parcel travels from the middle of a roadway to a site and varies as a function of wind direction, whereas perpendicular distance is a fixed distance oriented normal to the roadway. Perpendicular distance is often used as a proxy for exposures to traffic emissions in epidemiological studies.Elevated concentrations of all the compounds were found for both a summer and winter season. Effective distance was found to be a statistically significant (p < 0.05) univariate predictor for concentrations of toluene, ethylbenzene, m,p-xylene and o-xylene for summer 2005. For each of these pollutants, effective distance yielded lower p-values than the corresponding perpendicular distance models, and model fit improved. Results demonstrate that this near-road EMA had elevated levels of traffic-related VOCs compared to the community monitor, and that effective distance was a more accurate predictor of the degree to which they were elevated as a function of distance. Effective distance produced a range of distance-to-roadway values for a single site based on wind direction, thus increasing the number and range of values that could be used to plot and predict relative differences in pollutant concentrations between two sites.