Genome-wide linkage analysis of longitudinal phenotypes using σ<Superscript>2</Superscript><Subscript>A</Subscript> random effects (SSARs) fitted by Gibbs sampling

The study of change in intermediate phenotypes over time is important in genetics. In this paper we explore a new approach to phenotype definition in the genetic analysis of longitudinal phenotypes. We utilized data from the longitudinal Framingham Heart Study Family Cohort to investigate the familial aggregation and evidence for linkage to change in systolic blood pressure (SBP) over time. We used Gibbs sampling to derive sigma-squared-A-random-effects (SSARs) for the longitudinal phenotype, and then used these as a new phenotype in subsequent genome-wide linkage analyses. Additive genetic effects (sigma2A.time) were estimated to account for approximately 9.2% of the variance in the rate of change of SBP with age, while additive genetic effects (sigma2A) were estimated to account for approximately 43.9% of the variance in SBP at the mean age. The linkage results suggested that one or more major loci regulating change in SBP over time may localize to chromosomes 2, 3, 4, 6, 10, 11, 17, and 19. The results also suggested that one or more major loci regulating level of SBP may localize to chromosomes 3, 8, and 14. Our results support a genetic component to both SBP and change in SBP with age, and are consistent with a complex, multifactorial susceptibility to the development of hypertension. The use of SSARs derived from quantitative traits as input to a conventional linkage analysis appears to be valuable in the linkage analysis of genetically complex traits. We have now demonstrated in this paper the use of SSARs in the context of longitudinal family data.     

Quantifying Shark Distribution Patterns and Species-Habitat Associations: Implications of Marine Park Zoning

Quantifying shark distribution patterns and species-specific habitat associations in response to geographic and environmental drivers is critical to assessing risk of exposure to fishing, habitat degradation, and the effects of climate change. The present study examined shark distribution patterns, species-habitat associations, and marine reserve use with baited remote underwater video stations (BRUVS) along the entire Great Barrier Reef Marine Park (GBRMP) over a ten year period. Overall, 21 species of sharks from five families and two orders were recorded. Grey reef Carcharhinus amblyrhynchos, silvertip C. albimarginatus, tiger Galeocerdo cuvier, and sliteye Loxodon macrorhinus sharks were the most abundant species (>64% of shark abundances). Multivariate regression trees showed that hard coral cover produced the primary split separating shark assemblages. Four indicator species had consistently higher abundances and contributed to explaining most of the differences in shark assemblages: C. amblyrhynchos, C. albimarginatus, G. cuvier, and whitetip reef Triaenodon obesus sharks. Relative distance along the GBRMP had the greatest influence on shark occurrence and species richness, which increased at both ends of the sampling range (southern and northern sites) relative to intermediate latitudes. Hard coral cover and distance across the shelf were also important predictors of shark distribution. The relative abundance of sharks was significantly higher in non-fished sites, highlighting the conservation value and benefits of the GBRMP zoning. However, our results also showed that hard coral cover had a large effect on the abundance of reef-associated shark species, indicating that coral reef health may be important for the success of marine protected areas. Therefore, understanding shark distribution patterns, species-habitat associations, and the drivers responsible for those patterns is essential for developing sound management and conservation approaches.     

Extinction of anciently associated gut bacterial symbionts in a clade of stingless bees

Animal-microbe symbioses are often stable for millions of years. An example is the clade consisting of social corbiculate bees—honeybees, bumblebees, and stingless bees—in which a shared ancestor acquired specialized gut bacteria that subsequently diversified with hosts. This model may be incomplete, however, as few microbiomes have been characterized for stingless bees, which are diverse and ecologically dominant pollinators in the tropics. We surveyed gut microbiomes of Brazilian stingless bees, focusing on the genus Melipona, for which we sampled multiple species and biomes. Strikingly, Melipona lacks Snodgrassella and Gilliamella, bacterial symbionts ubiquitous in other social corbiculate bees. Instead, Melipona species harbor more environmental bacteria and bee-specific Starmerella yeasts. Loss of Snodgrassella and Gilliamella may stem from ecological shifts in Melipona or the acquisition of new symbionts as functional replacements. Our findings demonstrate the value of broadly sampling microbiome biodiversity and show that even ancient symbioses can be lost.Subject terms: Symbiosis, Microbiome, Microbial ecology, Metagenomics, Microbial ecology     

Prostaglandin-E2 is produced by adult human epidermal melanocytes in response to UVB in a melanogenesis-independent manner

Excessive ultraviolet radiation (UVR) exposure induces erythema, mediated in part by prostaglandin-E₂ (PGE₂). While keratinocytes are a major PGE₂ source, epidermal melanocytes (EM) also express PGE₂-production machinery. It is unclear whether EM-produced PGE₂ contributes to UVR-induced skin inflammation, and whether this is correlated with melanogenesis. Epidermal melanocytes were cultured from skin phototype-1 and -4 donors, followed by assessment of PGE₂ production and melanogenesis. Epidermal melanocytes expressed cytoplasmic phospholipase-A₂, cyclooxygenase-1, cytoplasmic prostaglandin-E synthase and microsomal prostaglandin-E synthase-1, -2. Epidermal melanocytes produced PGE₂ under basal conditions, which increased further after arachidonic acid stimulation. Epidermal melanocytes expressed cyclooxygenase-2 (COX-2) mRNA and a selective COX-2 inhibitor (NS-398) reduced PGE₂ production. Ultraviolet B-induced PGE₂ production was positively correlated with skin phototype-1, despite variability between individual EM donors. By contrast, there was no correlation between PGE₂ production by EM and their melanogenic status. Thus, EM may contribute to UVR-induced erythema, with role of donor skin phototype more important than their melanogenic status.     

Growth of newly established alien populations: comparison of North American gypsy moth colonies with invasion theory

A common characteristic observed in many biological invasions is the existence of a lag between the time of arrival by the alien population and the time when established populations are noticed. Considerable advances have been made in modeling the expansion of invading species, and there is often remarkable congruence between the behavior of these models with spread of actual populations. While these models have been used to characterize expansion of very newly founded colonies, there have been few attempts to compare the behavior predicted from theory with spread in actual newly founded populations, largely due to the difficulty of sampling sparse populations. Models predict that time lags in the radial expansion of newly invaded populations may be due to time requirements for the population to grow from founding to detectable levels. Models also indicate that these time lags can be predicted based upon population parameters such as the intrinsic rate of population growth and diffusion coefficient. In this paper, we compared the behavior of these models with historical data on gypsy moth, Lymantria dispar, establishment and spread to show similarities between model predictions and observed population spread, both of which exhibited temporal lags of expansion. However, actual populations exhibited certain behaviors that were not predicted, and this could be due, in part, to the existence of Allee effects and stochasticity. Further work that incorporates these effects is needed to more fully understand the growth of incipient colonies of invading species. Ultimately, this information can be of critical importance in the selection of effective strategies for their detection and eradication.     

Effects of SPLAT® GM sprayable pheromone formulation on gypsy moth mating success

Several integrated pest management programs rely on the use of mating disruption tactics to control insect pests. Some programs specifically target non‐native species, such as the gypsy moth, Lymantria dispar (L.) (Lepidoptera: Lymantriidae). We evaluated SPLAT^® GM, a new sprayable formulation of the gypsy moth sex pheromone disparlure, for its ability to disrupt gypsy moth mating. The study was conducted in 2006, 2007, and 2008 in forested areas in Virginia, USA. Mating success of gypsy moth females was reduced by >99% and male moth catches in pheromone‐baited traps by >90%, in plots treated with SPLAT^® GM at dosages ranging from 15 to 75 g of active ingredient (a.i.) ha^?1. Dosage‐response tests conducted in 2008 indicated that SPLAT^® GM applied at a dosage of 7.5 g a.i. ha^?1 was as effective as a 15 g a.i. ha^?1 dosage.     

Human Hippocampal Neurogenesis Persists in Aged Adults and Alzheimer’s Disease Patients

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