Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Data from: Logging increases the functional and phylogenetic dispersion of understorey plant communities in tropical lowland rainforest

1. Logging is a major driver of tropical forest degradation, with severe impacts on plant richness and composition. Rarely have these effects been considered in terms of their impact on the functional and phylogenetic diversity of understorey plant communities, despite the direct relevance to community reassembly trajectories. Here, we test the effects of logging on functional traits and evolutionary relatedness, over and above effects that can be explained by changes in species richness alone. We hypothesised that strong environmental filtering will result in more clustered (under-dispersed) functional and phylogenetic structures within communities as logging intensity increases. 2. We surveyed understorey plant communities at 180 locations across a logging intensity gradient from primary to repeatedly-logged tropical lowland rainforest in Sabah, Malaysia. For the 691 recorded plant taxa, we generated a phylogeny to assess plot-level phylogenetic relatedness. We quantified 10 plant traits known to respond to disturbance (dispersal mode, fruit type, life-history mode, pollination syndrome, reproduction strategy and seed number) and affect ecosystem functioning (plant growth form, plant height, specific leaf area and wood density), and tested the influence of logging on functional and phylogenetic structure. 3. We found no significant effect of local- or landscape-scale forest canopy loss, or configuration of logging roads on species richness. By contrast, both the trait dispersion index (FDis) and net relatedness index (NRI) for phylogenetic dispersion showed strong gradients from clustered towards more randomly-assembled communities at higher logging intensity, independent of variation in species richness. All functional traits showed significant phylogenetic signals, indicating strong concordance between functional and phylogenetic dispersion. 4. Synthesis. We found a strong logging signal in the functional and phylogenetic structure of understorey plant communities, over and above species richness, but this effect was opposite to that predicted. Logging increased, rather than decreased, functional and phylogenetic dispersion in understorey plant communities. This effect was particularly pronounced for functional response traits, which directly link disturbance with plant community reassembly. Our study provides novel insight into the way logging affects understorey plant communities in tropical rainforest and highlights the importance of trait-based approaches to improve our understanding of the broad range of logging-associated impacts

Data from: Logging, exotic plant invasions, and native plant reassembly in a lowland tropical rain forest

Habitat modification and biological invasions are key drivers of global environmental change. However, the extent and impact of exotic plant invasions in modified tropical landscapes remains poorly understood. We examined whether logging drives exotic plant invasions, and whether their combined influences alter understory plant community composition in lowland rain forests in Borneo. We tested the relationship between understory communities and local- and landscape-scale logging intensity, using leaf area index (LAI) and above-ground biomass (AGB) data from 192 plots across a logging-intensity gradient from primary to repeatedly-logged forests. Overall, we found relatively low levels of exotic plant invasions, despite an intensive logging history. Exotic species were more speciose, had greater cover, and more biomass in sites with more local-scale canopy loss. Surprisingly, though, exotic species invasion was not related to either landscape-scale canopy loss nor road configuration. Moreover, logging and invasion did not seem to be acting synergistically on native plant composition, except that seedlings of the canopy-dominant Dipterocarpaceae family were less abundant in areas with higher exotic plant biomass. Current low levels of invasion, and limited association with native understory community change, suggest there is a window of opportunity to manage invasive impacts. We caution about potential lag effects and the possibly severe negative impacts of exotic plant invasions on the long-term quality of tropical forest, particularly where agricultural plantations function as permanent seed sources for recurrent dispersal along logging roads. We therefore urge prioritization of strategic management plans to counter the growing threat of exotic plant invasions in modified tropical landscapes

Matrix of biomass values for 691 species in 180 understorey vegetation plots in Borneo

This csv file contains a matrix of biomass values for 691 plant taxa sampled across 180 vegetation plots (2 x 2m) located at the Stability of Altered Forest Ecosystems (SAFE) project in Sabah, Malaysia

Species trait data for understorey plant species in Borneo

This csv file contains the complete list of species (691) sampled across 180 vegetation plots (2 x 2m) located at the Stability of Altered Forest Ecosystems (SAFE) project in Sabah, Malaysia, including their allocation to a range of plant functional traits as well as a distinction between native or exotic species origin

Plot characteristics for understorey vegetation plots in Borneo

This csv file contains the full database of characteristics for each of 180 vegetation plots including logging metrics, environmental variables as well as taxonomic, functional and phylogenetic diversity indices for understorey plants in Borneo

SpeciesDataBiotropica

This csv file contains the complete list of species (723) sampled across 192 vegetation plots (2 x 2m) located at the Stability of Altered Forest Ecosystems (SAFE) project in Sabah, Malaysia, including a distinction between native and exotic species origin

PlotDataBiotropica

This csv file contains the full database of characteristics for each of 159 vegetation plots including logging metrics, environmental variables as well as specific data on native and exotic plants

PlotSpeciesDataBiotropica

This csv file contains a matrix of biomass values for 723 plant taxa sampled across 192 vegetation plots (2 x 2m) located at the Stability of Altered Forest Ecosystems (SAFE) project in Sabah, Malaysia