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Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged improvements in mapping and genotyping methods to create a dense linkage map for Chinook salmon Oncorhynchus tshawytscha by assembling family data from different sources. We successfully mapped 14 620 SNP loci including 2336 paralogs in subtelomeric regions. This improved map was then used as a foundation to integrate genomic resources for gene annotation and population genomic analyses. We anchored a total of 286 scaffolds from the Atlantic salmon genome to the linkage map to provide a framework for the placement 11 728 Chinook salmon ESTs. Previously identified thermotolerance QTL were found to colocalize with several candidate genes including HSP70, a gene known to be involved in thermal response, as well as its inhibitor. Multiple regions of the genome with elevated divergence between populations were also identified, and annotation of ESTs in these regions identified candidate genes for fitness related traits such as stress response, growth and behaviour. Collectively, these results demonstrate the utility of combining genomic resources with linkage maps to enhance evolutionary inferences. [ABSTRACT FROM AUTHOR]

Gene sequence similarity due to shared ancestry after a duplication event, that is paralogy, complicates the assessment of genetic variation, as sequences originating from paralogs can be difficult to distinguish. These confounded sequences are often removed prior to further analyses, leaving the underlying loci uncharacterized. Salmonids have only partially rediploidized subsequent to a whole-genome duplication; residual tetrasomic inheritance has been observed in males. We present a maximum-likelihood-based method to resolve confounded paralogous loci by observing the segregation of alleles in gynogenetic haploid offspring and demonstrate its effectiveness by constructing two linkage maps for chum salmon (Oncorhynchus keta), with and without these newly resolved loci. We find that the resolved paralogous loci are not randomly distributed across the genome. A majority are clustered in expanded subtelomeric regions of 14 linkage groups, suggesting a significant fraction of the chum salmon genome may be missed by the exclusion of paralogous loci. Transposable elements have been proposed as drivers of genome evolution and, in salmonids, may have an important role in the rediploidization process by driving differentiation between homeologous chromosomes. Consistent with that hypothesis, we find a reduced fraction of transposable element annotations among paralogous loci, and these loci predominately occur in the genomic regions that lag in the rediploidization process. [ABSTRACT FROM AUTHOR]

The emerging field of next-generation sequencing (NGs) is rapidly expanding capabilities for cutting edge genomic research, with applications that can help meet marine conservation challenges of food security, biodiversity loss, and climate change. Navigating the use of these tools, however, is complex at best. Furthermore, applications of marine genomic questions are limited in developing nations where both marine biodiversity and threats to marine biodiversity are most concentrated. his is particularly true in southeast Asia. The first Pan-Pacific Advanced studies Institute (PacAsI) entitled "Genomic Applications to Marine science and resource Management in southeast Asia" was held in July 2012 in Dumaguete, Philippines, with the intent to draw together leading scientists from both sides of the Pacific Ocean to understand the potential of NGs in helping address the aforementioned challenges. Here we synthesize discussions held during the PacAsI to provide perspectives and guidance to help scientists new to NGs choose among the variety of available advanced genomic methodologies specifically for marine science questions. [ABSTRACT FROM AUTHOR]

Numerous empirical studies have reported lack of migration-drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ~13 000 years ago. The chum salmon's ( Oncorhynchus keta) range was fragmented by dramatic environmental changes during the Pleistocene. We investigated the population structure of chum salmon on the North Alaska Peninsula ( NAP) and, using both empirical data and simulations, evaluated the effects of colonization timing and founder population heterogeneity on patterns of genetic differentiation. We screened 161 single nucleotide polymorphisms and found evidence of nonequilibrium population structure when the slope of the isolation-by-distance relationship was examined at incremental spatial scales. In addition, simulations suggested that this pattern closely matched models of recent colonization of the NAP by secondary contact. Our results agree with geological and archaeological data indicating that the NAP was a dynamic landscape that may have been more recently colonized than during the last deglaciation because of dramatic changes in coastal hydrology over the last several thousand years. [ABSTRACT FROM AUTHOR]

Until recently, single nucleotide polymorphism (SNP) discovery in nonmodel organisms faced many challenges, often depending upon a targeted-gene approach and Sanger sequencing of many individuals. The advent of next-generation sequencing technologies has dramatically improved discovery, but validating and testing SNPs for use in population studies remain labour intensive. Here, we detail a SNP discovery and validation pipeline that incorporates 454 pyrosequencing, high-resolution melt analysis (HRMA) and 5′ nuclease genotyping. We generated 4.59 × 10 bp of redundant sequence from transcriptomes of two individual chum salmon, a highly valued species across the Pacific Rim. Nearly 26 000 putative SNPs were identified-some as heterozygotes and some as homozygous for different nucleotides in the two individuals. For validation, we selected 202 templates containing single putative SNPs and conducted HRMA on 10 individuals from each of 19 populations from across the species range. Finally, 5′ nuclease genotyping validated 37 SNPs that conformed to Hardy-Weinberg equilibrium expectations. Putative SNPs expressed as heterozygotes in an ascertainment individual had more than twice the validation rate of those homozygous for different alleles in the two fish, suggesting that many of the latter may have been paralogous sequence variants. Overall, this validation rate of 37/202 suggests that we have found more than 4500 templates containing SNPs for use in this population set. We anticipate using this pipeline to significantly expand the number of SNPs available for the studies of population structure and mixture analyses as well as for the studies of adaptive genetic variation in nonmodel organisms. [ABSTRACT FROM AUTHOR]

A survey of mtDNA variation among populations of chum salmon Oncorhynchus keta around the Pacific Rim revealed four large population groups: Rim of the Sea of Japan, the Rim of the Okhotsk Sea and West Bering Sea, North-west Alaska and Gulf of Alaska. The observed population structure appears to reflect isolation by distance with limited gene flow between regions and larger amounts of gene flow between populations within these four regions. [ABSTRACT FROM AUTHOR]

Single nucleotide polymorphisms (SNPs) are appealing genetic markers due to several beneficial attributes, but uncertainty remains about how many of these bi-allelic markers are necessary to have sufficient power to differentiate populations, a task now generally accomplished with highly polymorphic microsatellite markers. In this study, we tested the utility of 37 SNPs and 13 microsatellites for differentiating 29 broadly distributed populations of Chinook salmon ( n = 2783). Information content of all loci was determined by In and , and the top 12 markers ranked by In were microsatellites, but the 6 highest, and 7 of the top 10 ranked markers, were SNPs. The mean ratio of random SNPs to random microsatellites ranged from 3.9 to 4.1, but this ratio was consistently reduced when only the most informative loci were included. Individual assignment test accuracy was higher for microsatellites (73.1%) than SNPs (66.6%), and pooling all 50 markers provided the highest accuracy (83.2%). When marker types were combined, as few as 15 of the top ranked loci provided higher assignment accuracy than either microsatellites or SNPs alone. Neighbour-joining dendrograms revealed similar clustering patterns and pairwise tests of population differentiation had nearly identical results with each suite of markers. Statistical tests and simulations indicated that closely related populations were better differentiated by microsatellites than SNPs. Our results indicate that both types of markers are likely to be useful in population genetics studies and that, in some cases, a combination of SNPs and microsatellites may be the most effective suite of loci. [ABSTRACT FROM AUTHOR]

This article focuses on the 20th Wakefield Symposium, "The Genetics of Subpolar Fish and Invertebrates," which is the successor of the 11th Wakefield Symposium. One of the predominant themes of both symposia was the descriptive study of population structure. Descriptive studies are an important step in developing management or conservation plans because they can provide markers for use in stock identification programs and because they can identify distinct productivity units in species that do not have convenient or obvious geographical boundaries, such as many marine species.

Genetic marking, the manipulation of allelic frequencies to tag fish stocks, was applied to chum salmon Oncorhynchus keta released in Kennedy Creek, a tributary to Totten Inlet in south Puget Sound, Washington. Our objectives were to conduct a Petersen mark-recapture population census of smolts residing in Totten Inlet and to identify the contribution of marked fish to subsequent spawning runs. Male spawners were selected for expression of the 115 allele of aspartate aminotransferase Aat 1,2 or the 90 allele of 6-phosphogluconate dehydrogenase Pgdh. The respective frequencies were thus increased from about 0.12 and 0.01 among the native fish to about 0.25 and 0.11 among the progeny of selected males. Eggs were incubated in streamside gravel box incubators and 11 x 106 hatched fish were released to Kennedy Creek during 1978-1980. Fish from the genetically marked broods made up 15-51% of the chum salmon smolts resident in Totten Inlet each spring, 1978-1980, and Petersen mark-recapture population estimates indicated that the total population size ranged from 2.2 x 106 to 4.3 x 106. In 1979-1981, 6-29% of adults returning to Kennedy Creek to spawn were fish from marked broods. This study validated the use of genetic marking as a tool for use in fisheries research and management. [ABSTRACT FROM AUTHOR]