Genome‐wide selection components analysis in a fish with male pregnancy

A major goal of evolutionary biology is to identify the genome‐level targets of natural and sexual selection. With the advent of next‐generation sequencing, whole‐genome selection components analysis provides a promising avenue in the search for loci affected by selection in nature. Here, we implement a genome‐wide selection components analysis in the sex role reversed Gulf pipefish, Syngnathus scovelli. Our approach involves a double‐digest restriction‐site associated DNA sequencing (ddRAD‐seq) technique, applied to adult females, nonpregnant males, pregnant males, and their offspring. An F_ST comparison of allele frequencies among these groups reveals 47 genomic regions putatively experiencing sexual selection, as well as 468 regions showing a signature of differential viability selection between males and females. A complementary likelihood ratio test identifies similar patterns in the data as the F_ST analysis. Sexual selection and viability selection both tend to favor the rare alleles in the population. Ultimately, we conclude that genome‐wide selection components analysis can be a useful tool to complement other approaches in the effort to pinpoint genome‐level targets of selection in the wild.     

Sequencing improves our ability to study threatened migratory species: Genetic population assignment in California's Central Valley Chinook salmon

Effective conservation and management of migratory species requires accurate identification of unique populations, even as they mix along their migratory corridors. While telemetry has historically been used to study migratory animal movement and habitat use patterns, genomic tools are emerging as a superior alternative in many ways, allowing large‐scale application at reduced costs. Here, we demonstrate the usefulness of genomic resources for identifying single‐nucleotide polymorphisms (SNPs) that allow fast and accurate identification of the imperiled Chinook salmon in the Great Central Valley of California. We show that 80 well‐chosen loci, drawn from a pool of over 11,500 SNPs developed from restriction site‐associated DNA sequencing, can accurately identify Chinook salmon runs and select populations within run. No other SNP panel for Central Valley Chinook salmon has been able to achieve the high accuracy of assignment we show here. This panel will greatly improve our ability to study and manage this ecologically, economically, and socially important species and demonstrates the great utility of using genomics to study migratory species.     

The plasmid-encoded hydrogenase gene cluster in Alcaligenes eutrophus

Abstract Alcaligenes eutrophus strain H16 harbors a 450 kilobase pairs (kb) conjugative plasmid which codes for the ability of the organism to grow lithoautotrophically on hydrogen and carbon dioxide (reviewed in [1]). The genes for hydrogen oxidation, designated hox , are clustered on plasmid pHG1 in a DNA region of approximately 100-kb in size ([2], Fig. 1). The hox genes and their organization have been analyzed by isolation of Hox-deficient mutants, by complementation analysis, by cloning of hox genes, identification of hox -encoded polypeptides and, most recently, by DNA sequencing. The hox cluster is flunked by the two structural gene regions, hoxS and hoxP ; it contains a regulatory locus, hoxC , and additional genes like hoxN and hoxM whose products play a role in the formation of catalytically active hydrogenase proteins. Of four indigenous 1.3-kb insertion elements, two copies of IS491 map in the hox gene cluster. These elements may be involved in rearrangements and deletions which occur particularly frequently in this region of the megaplasmid (Schwartz, Kortlüke and Friedrich, unpublished).