Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species

Background As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species’ potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis). Results Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus. Conclusion The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change

Genetic evidence for spatial structuring in a continuous African elephant (Loxodonta africana) population

Earlier studies on savannah elephants (Loxodonta africana) investigated the genetic structure of fragmented or isolated populations. Contrastingly, this study aimed to determine if there was genetic evidence for spatial structuring in a continuous elephant population in the Kavango-Zambezi Transfrontier Conservation Area (KAZA-TFCA). We sequenced one mtDNA gene region for 88 individuals and genotyped 100 individuals for ten nuclear microsatellite loci. Bayesian Clustering Algorithms in Geneland identified groups of genetically similar individuals. An analysis of molecular variance determined if these groups (sub-populations) were significantly differentiated. We identified geographic areas with high genetic divergence (genetic barriers) between samples using a GIS landscape genetic toolbox. There were three significantly differentiated mtDNA sub-populations (Fst = 0.787) and two nDNA sub-populations that were not significantly differentiated (Fst = -0.02; Rst = -0.045), implying obstructed mtDNA, but high nDNA gene flow across the study region. The KAZA-TFCA population has a genetic diversity (mtDNA pairwise number of differences (p) = 2.59; nDNA mean alleles/locus and He = 7.5, 0.71) higher than other southern African populations, and interpopulation movements may be responsible for maintaining this genetic diversity. We discount anthropogenic and geographic barriers as the primary drivers of genetic structuring in the KAZA-TFCA population and suggest that future studies should consider the influence of intrinsic factors (resource dependencies and social variables that limit movement) when investigating the genetic structure of elephant populations. We recommend continued support for conservation initiatives that aim at maintaining and restoring connectivity between populations, which in so doing may ensure inter-population gene flow and uphold the current genetic state of the KAZA-TFCA population.International Fund for Animal Welfare and the Conservation Foundation (Zambia).http://link.springer.com/journal/105922016-07-01hb201

Dopamine transporter DAT and receptor DRD2 variants affect risk of lethal cocaine abuse: a gene–gene–environment interaction

Epistatic gene–gene interactions could contribute to the heritability of complex multigenic disorders, but few examples have been reported. Here, we focus on the role of aberrant dopaminergic signaling, involving the dopamine transporter DAT, a cocaine target, and the dopamine D2 receptor, which physically interacts with DAT. Splicing polymorphism rs2283265 of DRD2, encoding D2 receptors, were shown to confer risk of cocaine overdose/death (odds ratio ∼3) in subjects and controls from the Miami Dade County Brain Bank.(1) Risk of cocaine-related death attributable to the minor allele of rs2283265 was significantly enhanced to OR=7.5 (P=0.0008) in homozygous carriers of the main 6-repeat allele of DAT rs3836790, a regulatory VNTR in intron8 lacking significant effect itself. In contrast, carriers of the minor 5-repeat DAT allele showed no significant risk (OR=1.1, P=0.84). DAT rs3836790 and DRD2 rs2283265 also interacted by modulating DAT protein activity in the ventral putamen of cocaine abusers. In high-linkage disequilibrium with the VNTR, DAT rs6347 in exon9 yielded similar results. Assessing the impact of DAT alone, a rare DAT haplotype formed by the minor alleles of rs3836790 and rs27072, a regulatory DAT variant in the 3′-UTR, occurred in nearly one-third of the cocaine abusers but was absent in African American controls, apparently conferring strong risk. These results demonstrate gene–gene–drug interaction affecting risk of fatal cocaine intoxication