Single nucleotide polymorphisms unravel hierarchical divergence and signatures of selection among Alaskan sockeye salmon (Oncorhynchus nerka) populations

<p>Abstract</p> <p>Background</p> <p>Disentangling the roles of geography and ecology driving population divergence and distinguishing adaptive from neutral evolution at the molecular level have been common goals among evolutionary and conservation biologists. Using single nucleotide polymorphism (SNP) multilocus genotypes for 31 sockeye salmon (<it>Oncorhynchus nerka</it>) populations from the Kvichak River, Alaska, we assessed the relative roles of geography (discrete boundaries or continuous distance) and ecology (spawning habitat and timing) driving genetic divergence in this species at varying spatial scales within the drainage. We also evaluated two outlier detection methods to characterize candidate SNPs responding to environmental selection, emphasizing which mechanism(s) may maintain the genetic variation of outlier loci.</p> <p>Results</p> <p>For the entire drainage, Mantel tests suggested a greater role of geographic distance on population divergence than differences in spawn timing when each variable was correlated with pairwise genetic distances. Clustering and hierarchical analyses of molecular variance indicated that the largest genetic differentiation occurred between populations from distinct lakes or subdrainages. Within one population-rich lake, however, Mantel tests suggested a greater role of spawn timing than geographic distance on population divergence when each variable was correlated with pairwise genetic distances. Variable spawn timing among populations was linked to specific spawning habitats as revealed by principal coordinate analyses. We additionally identified two outlier SNPs located in the major histocompatibility complex (MHC) class II that appeared robust to violations of demographic assumptions from an initial pool of eight candidates for selection.</p> <p>Conclusions</p> <p>First, our results suggest that geography and ecology have influenced genetic divergence between Alaskan sockeye salmon populations in a hierarchical manner depending on the spatial scale. Second, we found consistent evidence for diversifying selection in two loci located in the MHC class II by means of outlier detection methods; yet, alternative scenarios for the evolution of these loci were also evaluated. Both conclusions argue that historical contingency and contemporary adaptation have likely driven differentiation between Kvichak River sockeye salmon populations, as revealed by a suite of SNPs. Our findings highlight the need for conservation of complex population structure, because it provides resilience in the face of environmental change, both natural and anthropogenic.</p

The Role of Vaccination in the Prevention of Head and Neck Cancer

Human papillomavirus (HPV) is the main cause of cervical cancer and is also associated with head and neck cancer. The effect of prophylactic HPV vaccines on premalignant head and neck lesions is not measurable, but it is universally believed that HPV vaccines are able to prevent a considerable number of oropharyngeal cancers and a small proportion of oral cavity and larynx cancers. Recent studies on the effect of HPV vaccination on oral HPV infections provide further support of this hypothesis. The question then remains whether current vaccination programmes, in which only girls are vaccinated against HPV infections, should be extended to boys to increase the impact on future head and neck cancers. This question is particularly relevant because the burden of oropharyngeal cancer is on the rise in the United States and several other countries and it is disproportionally higher in men. The extension of a girls’ only HPV vaccination programme to a sex-neutral programme depends on a number of factors including herd effects received from the girls’ only programme and the price of the vaccine. HPV infection models predict a substantial impact of sex-neutral vaccination on future cancer in men and women when the coverage of the girls’ only vaccination programme is only 40–70%. At a higher uptake of 80%, a main argument in favour of sex-neutral vaccination is that it leads to near elimination of HPV16 and HPV18, thought to be responsible for the majority of the HPV-related head and neck cancers. Financial barriers to sex-neutral vaccination have been largely removed in countries that were successful in negotiating a low price for the vaccine

Fine-scale sampling reveals distinct isolation by distance patterns in chum salmon (Oncorhynchus keta) populations occupying a glacially dynamic environment

Populations with spatially restricted gene flow are characterized by genetic differentiation that may be positively correlated with the geographic distance separating populations, a pattern known as isolation by distance (IBD). Here we examined the fine-scale genetic structure of 66 chum salmon (Oncorhynchus keta) populations spawning in Alaska waterways and explored patterns of IBD using 90 nuclear and 3 mitochondrial single nucleotide polymorphisms. Estimating population structure of chum salmon in Alaska is of increasing concern because of fluctuating census sizes and the uncertain effects of harvest on specific populations. We hypothesized that IBD would be present because chum salmon spawn in coastal rivers that are distributed along a linear array and gene flow is spatially restricted due to homing. Evidence of very weak IBD was found throughout the region (R2 = 0.06, p < 0.0001) but the strength of the IBD relationship varied greatly over different spatial scales and geographic regions. Decomposed pairwise regression analyses identified nine outlier populations to regional IBD patterns, suggesting that geographic distance is not the only factor influencing genetic differentiation in the region. Instead, population structure appears to be heavily influenced by glacial history of the region and the presence of a glacial refugium on Kodiak Island