A statistical method for excluding non-variable CpG sites in high-throughput DNA methylation profiling

Background  

High-throughput DNA methylation arrays are likely to accelerate the pace of methylation biomarker discovery for a wide variety of diseases. A potential problem with a standard set of probes measuring the methylation status of CpG sites across the whole genome is that many sites may not show inter-individual methylation variation among the biosamples for the disease outcome being studied. Inclusion of these so-called "non-variable sites" will increase the risk of false discoveries and reduce statistical power to detect biologically relevant methylation markers.     

Compensating for wetland losses in the United States

Impacts of climate change on US wetlands will add to those of historical impacts due to other causes. In the US, wetland losses and degradation result from drainage for agriculture, filling for urbanization and road construction. States that rely heavily on agriculture (California, Iowa, Illinois, Missouri, Ohio, Indiana) have lost over 80% of their historical area of wetlands, and large cities, such as Los Angeles and New York City, have retained only tiny remnants of wetlands, all of which are highly disturbed. The cumulative effects of historical and future degradation will be difficult to abate. A recent review of mitigation efforts in the US shows a net loss of wetland area and function, even though 'no net loss' is the national policy and compensatory measures are mandatory. US policy does not include mitigation of losses due to climate change. Extrapolating from the regulatory experience, one can expect additional losses in wetland areas and in highly valued functions. Coastal wetlands will be hardest hit due to sea-level rise. As wetlands are increasingly inundated, both quantity and quality will decline. Recognition of historical, current and future losses of wetland invokes the precautionary principal: avoid all deliberate loss of coastal wetland area in order to reduce overall net loss. Failing that, our ability to restore and sustain wetlands must be improved substantially.     

Delayed seed dispersal in Pinus torreyana (Torrey pine)

Summary Torrey pine exhibits a pattern of seed release intermediate between an open and closed-cone species. It was found that the cones open at maturity, but that seed fall from some cones continues for up to 13 years. Approximately 77% of the total seed crop was present in age classes one or more years past the time of seed maturity.Serotiny is thought to evolve in response to fire, and partial serotiny at the population level has been attributed to circumstances in which the strong selective pressure of fire is relaxed. We hypothesize that delayed seed dispersal in Torrey pine is a stable trait which is the result of a pattern of large relatively rare crown fires separated by intervals longer than one generation. The reduced serotiny observed in other conifers on headlands and islands in California seems consistent with our hypothesis.     

Declining Diversity in Natural and Restored Salt Marshes: A 30-Year Study of Tijuana Estuary

Between 1974 and 2004, Tijuana Estuary's natural salt marsh underwent pulse disturbance (an 8-month nontidal period in 1984), which caused the sudden loss of two short-lived halophytes ( Salicornia bigelovii [Sb] and Suaeda esteroa [Se]) and rapid dominance of a productive native succulent ( Sa. virginica [Sv]), plus ramp disturbance that led to gradual codominance by Jaumea carnosa (Jc) (another productive succulent) by 1994. Species richness was high in 1974 (4.2 species/0.25-m² plot), low in 1984 (1.4 species), and not fully recovered by 1994 (3.7 species) or 2004 (3.9 species). Restoration efforts (reseeding former habitat and excavating and planting new sites) did not recover the populations of Sb or Se. In a 1997 project, plantings of these and six other native halophytes survived initially, but by 2005, short-lived species were lost and Sv and Jc dominated, as in the natural marsh. In a 2000 restoration site, planting mortality was high for five species, but Sv recruited voluntarily and dominated by 2005. We attribute recent vegetation changes to frequent catastrophic storms, flooding, and sedimentation, which contrasted strongly with the benign conditions of decades prior to 1974. Sediment blocked tidal channels in 1984 and gradually elevated the marsh plain, degrading the diverse salt marsh and hindering efforts to restore it. Future restoration efforts will require even greater control over sediment inflows plus contouring sites to include natural topographic features that appear critical to sustaining high species richness and evenness.     

Cell surface composition,released polysaccharides,and ionic strength mediate fast sedimentation in the cyanobacterium Synechococcus elongatus PCC 7942

Cyanobacteria are photosynthetic prokaryotes of high ecological and biotechnological relevance that have been cultivated in laboratories around the world for more than 70 years. Prolonged laboratory culturing has led to multiple microevolutionary events and the appearance of a large number of ‘domesticated’ substrains among model cyanobacteria. Despite its widespread occurrence, strain domestication is still largely ignored. In this work we describe Synechococcus elongatus PCC 7942-KU, a novel domesticated substrain of the model cyanobacterium S. elongatus PCC 7942, which presents a fast-sedimenting phenotype. Under higher ionic strengths the sedimentation rate increased leading to complete sedimentation in just 12 h. Through whole genome sequencing and gene deletion, we demonstrated that the Group 3 alternative sigma factor F plays a key role in cell sedimentation. Further analysis showed that significant changes in cell surface structures and a three-fold increase in released polysaccharides lead to the appearance of a fast-sedimenting phenotype. This work sheds light on the determinants of the planktonic to benthic transitions and provides genetic targets to generate fast-sedimenting strains that could unlock cost-effective cyanobacterial harvesting at scale.     

Set‐backs in Replacing Phalaris arundinacea Monotypes with Sedge Meadow Vegetation

Reed canary grass (Phalaris arundinacea) invades wetlands, forms monotypes, and resists control efforts, suggesting that strong feedbacks sustain its dominance, as in the alternative states model. In nine field experiments, we tested the hypothesis that applying a graminicide (sethoxydim) for three years would progressively reduce Phalaris abundance, and that seeding sedge meadow species (except grasses) would reestablish native plant dominance. The graminicide prevented Phalaris from flowering, reduced its height by 50% and reduced its cover, often to less than 40%. However, only two of the nine sites showed progressive declines over the three‐year experiment. The first setback was that Phalaris recovered annually in nearly all treatment plots. A second setback was that seeding did not reestablish sedge meadow. In five sites, unseeded plots had similar numbers of native species as those seeded with either forbs, forbs and graminoids, or graminoids. In four formerly agricultural sites, however, non‐native weeds increased in species richness and cover (a third setback). In only one site did the graminicide's effect on Phalaris allow native species to increase in number and cover. But short‐term gains were not long‐lasting. In year four, three sites that developed high native‐species cover were again strongly dominated by Phalaris (a fourth setback). The feedbacks that sustain this invader include resistance to the graminicide aboveground and rapid and robust regrowth from rhizomes and seeds belowground. The weak effect of this graminicide was a surprise; hence, we recommend stronger management actions to control Phalaris.     

Organisation of the soil seed bank in mixed chaparral

Seed densities, estimated from germinations under glasshouse conditions, were determined for fire-treated and control soils sampled from north and south facing stands of mixedAdenostoma fasciculatum-Ceanothus greggii chaparral that last burned 10, 17, 36, 62 and 86 years before 1987. A total of 53 species was recorded. Total germinable seed density was not influenced by aspect nor by an experimental fire treatment, however, densities varied significantly, but not predictably, over the time since fire sequence. Species diversity was significantly lower in the 86 year old stand, but neither diversity or richness was influenced by the fire treatment. Soils from north facing slopes supported a higher species diversity overall, and seed densities of six species were significantly higher on north than on south slopes.We identify two functional groups in the seed bank on the basis of the direct effects of fire on seed densities: a fire-dependent group, comprising 6 species and about 21% of the total seed bank, in which germinable densities increased after the fire treatment, and a fire-independent group, made up of 11 species and almost two-thirds of the seed bank. The fire-independent group is further separated into two: a shrub-centred sub-group (Crassula erecta, Filago californica, Pterostegia drymarioides, Streptanthus heterophyllus andCryptantha intermedia) maintained larger seed banks in older stands and was associated with shrub cover; and an opportunistic sub-group (Camissonia hirtella, Gnaphalium chilense, Mimulus pilosus andSenecio vulgaris) tended to have larger seed banks in younger stands and was associated with canopy gaps.Overall, the soil seed assemblage from this mixed chaparral does not appear to be tightly coupled to fire-generated opportunities for recruitment. The reason for this is that the fire-dependent group represents only 6 species. In addition, among the fire-independent species, the shrub-centred group of 5 annuals made up almost 40% of total soil seed density. This group shows ecological and taxonomic affinities with desert annuals.     

Monitoring Wetland Habitat Restoration in Southern California Using Airborne Multi spectral Video Data

Remote sensing provides a complementary approach to field sampling to assess whether restored wetland areas provide suitable habitat for the Light-footed Clapper Rail (Rallus longirostris levipes). Habitat requirements for the clapper rail are specified by the composition of vegetation species and their spatial extent in its nesting home range. A major salt marsh construction project has been completed at the Sweetwater Marsh National Wildlife Refuge (“the refuge”), San Diego County. In this paper we describe the application of image classification techniques to high-spatial-resolution digital video imagery (0.8-m pixels) to delimit patches of different marsh vegetation at the refuge. Using maps of vegetation types derived from multi spectral imagery, we estimated the area occupied by each vegetation type in potential clapper rail home ranges. Preliminary field-checking results indicate that this approach is an accurate, noninvasive and cost-efficient means of providing ecological information for restoration monitoring in southern California's remnant wetlands.