Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits

We present an approximate conditional and joint association analysis that can use summary-level statistics from a meta-analysis of genome-wide association studies (GWAS) and estimated linkage disequilibrium (LD) from a reference sample with individual-level genotype data. Using this method, we analyzed meta-analysis summary data from the GIANT Consortium for height and body mass index (BMI), with the LD structure estimated from genotype data in two independent cohorts. We identified 36 loci with multiple associated variants for height (38 leading and 49 additional SNPs, 87 in total) via a genome-wide SNP selection procedure. The 49 new SNPs explain approximately 1.3% of variance, nearly doubling the heritability explained at the 36 loci. We did not find any locus showing multiple associated SNPs for BMI. The method we present is computationally fast and is also applicable to case-control data, which we demonstrate in an example from meta-analysis of type 2 diabetes by the DIAGRAM Consortium.     

Biogeographic and taxonomic relationships among the mountain snails (Gastropoda: Oreohelicidae) of the central Great Basin

Described here are 4 species of mountain snails, Oreohelix , isolated on mountains in the central Great Basin of Nevada and Utah since the end of the Pleistocene. Forty-three mountains were searched during an 18-year period, resulting in 24 mountains found with no oreohelicids present. One population, Oreohelix loisae (19 mm to 23 mm in shell diameter), is described here as a new species related to, but geographically isolated from, the species Oreohelix nevadensis (17 mm to 22 mm diameter). Oreohelix loisae is present only in the Goshute Mountains while O. nevadensis is represented in 3 geographically adjacent ranges in the central Great Basin. These 2 species are possibly related to the Oreohelix haydeni group from the northern Wasatch Range. The subspecies Oreohelix strigosa depressa (15 mm to 21 mm diameter) is present on 11 ranges from western Utah west to east central Nevada. This subspecies is closely related to populations found today in the northern Wasatch Mountains of Utah. The smallest species in diameter (8 mm to 14 mm), Oreohelix hemphilli , is centered in the central Great Basin and found on 16 ranges often in sympatry with 1 or 2 of the larger conspecifics. Both qualitative and quantitative information on shell characters and soft anatomy is provided here for these 4 species. Shell characters, soft anatomy, geographical isolation, and statistical analysis suggest that 4 distinct species inhabit the central Great Basin today. Xeric and calciphilic species include O. hemphilli and O. loisae , while O. strigosa and O. nevadensis typically are associated with permanent water and both metamorphic and limestone mountains.     

Genome-wide association study identifies a new melanoma susceptibility locus at 1q21.3

We performed a genome-wide association study of melanoma in a discovery cohort of 2,168 Australian individuals with melanoma and 4,387 control individuals. In this discovery phase, we confirm several previously characterized melanoma-associated loci at MC1R, ASIP and MTAP-CDKN2A. We selected variants at nine loci for replication in three independent case-control studies (Europe: 2,804 subjects with melanoma, 7,618 control subjects; United States 1: 1,804 subjects with melanoma, 1,026 control subjects; United States 2: 585 subjects with melanoma, 6,500 control subjects). The combined meta-analysis of all case-control studies identified a new susceptibility locus at 1q21.3 (rs7412746, P = 9.0 × 10(-11), OR in combined replication cohorts of 0.89 (95% CI 0.85-0.95)). We also show evidence suggesting that melanoma associates with 1q42.12 (rs3219090, P = 9.3 × 10(-8)). The associated variants at the 1q21.3 locus span a region with ten genes, and plausible candidate genes for melanoma susceptibility include ARNT and SETDB1. Variants at the 1q21.3 locus do not seem to be associated with human pigmentation or measures of nevus density.     

Disruption of mouse Slx4, a regulator of structure-specific nucleases, phenocopies Fanconi anemia

The evolutionarily conserved SLX4 protein, a key regulator of nucleases, is critical for DNA damage response. SLX4 nuclease complexes mediate repair during replication and can also resolve Holliday junctions formed during homologous recombination. Here we describe the phenotype of the Btbd12 knockout mouse, the mouse ortholog of SLX4, which recapitulates many key features of the human genetic illness Fanconi anemia. Btbd12-deficient animals are born at sub-Mendelian ratios, have greatly reduced fertility, are developmentally compromised and are prone to blood cytopenias. Btbd12(-/-) cells prematurely senesce, spontaneously accumulate damaged chromosomes and are particularly sensitive to DNA crosslinking agents. Genetic complementation reveals a crucial requirement for Btbd12 (also known as Slx4) to interact with the structure-specific endonuclease Xpf-Ercc1 to promote crosslink repair. The Btbd12 knockout mouse therefore establishes a disease model for Fanconi anemia and genetically links a regulator of nuclease incision complexes to the Fanconi anemia DNA crosslink repair pathway.     

Visual perception and memory systems: from cortex to medial temporal lobe

Visual perception and memory are the most important components of vision processing in the brain. It was thought that the perceptual aspect of a visual stimulus occurs in visual cortical areas and that this serves as the substrate for the formation of visual memory in a distinct part of the brain called the medial temporal lobe. However, current evidence indicates that there is no functional separation of areas. Entire visual cortical pathways and connecting medial temporal lobe are important for both perception and visual memory. Though some aspects of this view are debated, evidence from both sides will be explored here. In this review, we will discuss the anatomical and functional architecture of the entire system and the implications of these structures in visual perception and memory.     

Early life history of the sheepnose (Plethobasus cyphyus) (Mollusca: Bivalvia: Unionoida)

Managing a rare species can be improved with knowledge of its natural history. The sheepnose (Plethobasus cyphyus) is a freshwater mussel recently listed by the US as federally endangered. We used standard methods to study P. cyphyus brooding behaviour, host fishes in the laboratory and under natural conditions, and glochidial morphology. We monitored a population of P. cyphyus in the Chippewa River, WI during spring and summer 2007–2009 and 2011 and found brooding animals between mid-May and early August. Gravid individuals ranged between 5 and 27 yr (mean age ± 1 s.d. = 13 ± 4 yr). Plethobasus cyphyus brooded glochidia in outer gills, which varied in colour from red, orange, pink, cream, or white. We observed mature glochidia more commonly in individuals with cream or white gills and these glochidia were released in a clear, adhesive, mucus matrix. In laboratory trials we found several minnow and topminnow species (29 spp.) served as productive suitable native hosts. The mean number of juvenile mussels released per cyprinid per day was significantly higher for trials conducted at 22–25°C compared with those at 18–20°C, and 83% of trials conducted at 18–20°C using suitable host species produced no juveniles. Glochidia had a unique outline and shell morphometrics that distinguished P. cyphyus from seven other Chippewa River mussel species that produce similar sized glochidia. Using morphometrics we determined that mimic shiners (Notropis volucellus) were natural hosts for P. cyphyus, round pigtoe (Pleurobema sintoxia), and Wabash pigtoe (Fusconaia flava). Releasing mucus-bound glochidia has evolved in a variety of mussel species and may be more common than is currently realized. Our data show that P. cyphyus is a cyprinid host specialist, and propagation efforts for this species can be strengthened through improved access to mature glochidia by using females with cream-coloured gills and increased juvenile production through warmer fish holding temperatures.     

Riparian vegetation along the middle Snake River, Idaho: zonation, geographical trends, and historical changes

A baseline study was conducted on an 83-km free-flowing reach of the Snake River between Swan Falls Dam and the Idaho-Oregon border. The research had 2 components: (1) field characterization and inventory of existing riparian flora, vegetation, and environment (soils, topography, streamflow), and (2) determination and mapping, using a geographic information system, of historic changes in riparian vegetation based on a time series (1938-39, 1957, 1969, 1987) of aerial photographs. The flora was diverse, with 185 species of vascular plants identified, 63 of which were exotics. Vegetation was structured vertically along the riverbank gradient into lifeform-defined habitat types: emergent, riparian shrub-forb, tree, transitional grass-shrub, and upland. Riverbank seepage, probably of agricultural origin, blurred zonation patterns on some sites and added species to the overall flora. Upstream-downstream differences existed in the physical characteristics and vegetation of river subreaches. Coverage of riparian woodland, island riparian and total riparian vegetation, and area of islands increased since the 1930s, with the greatest changes in the 1969-1987 interval. Possible contributing facts were (1) significant declines in annual minimum flows since the 1950s, (2) decreases in peak flows following the completion of Swan Falls Dam and some upstream dams since the 1920s, (3) introduction and spread of exotic tree species ( Elaeagnus angustifolia and Tamarix spp.) and (4) possible effects of intensive agriculture on river sediment load and soil nutrients. The introduction and proliferation of purple loosestrife ( Lythrum salicaria ) could have considerable future effects on vegetation-channel dynamics in the middle Snake River.     

Habitat use of leatherside chub ( Gila copei ) in the presence of predatory brown trout ( Salmo trutta )

The objectives of this study were to (1) examine distribution and habitat use of leatherside chub ( Gila copei ) in a creek with high densities of predatory brown trout ( Salmo trutta ), and (2) compare study results with published accounts of leatherside chub habitat use in streams with few or no brown trout. A 14-km section of Diamond Fork Creek, Utah, was point-shocked to determine macrohabitat (main channel and lateral habitat) and microhabitat (current, depth, substrate, and cover) use of leatherside chug. At the macrohabitat level, leatherside chub were most common in lower reaches of Diamond Fork Creek where the channel was braided and lateral habitats (cutoff pools and backwaters) were abundant. Only a single leatherside chub was found in the main channel of Diamond Fork. Investigations in other systems lacking brown trout indicated that leatherside chub occupy main channel habitats. At the microhabitat level, we found significant positive associations between presence of leatherside chub and both habitat depth and silt. In addition, we found a significant negative association between presence of leatherside chub and number of brown trout. Our results suggest predation by brown trout may limit leatherside chub to lateral habitats that could provide refugia against predation. The introduction of brown trout to systems with little lateral habitat could have serious effects on persistence of resident leatherside chub populations.