Blair G. Flannery

The Application of Microsatellites for Stock Identification of Yukon River Chinook Salmon

Abstract In a cooperative project among three agencies, variation at 30 microsatellite loci was surveyed for 19 populations of Chinook salmon Oncorhynchus tshawytscha from the Yukon River. The observed number of alleles per locus ranged from 2 to 63. Loci with a greater number of alleles displayed lower genetic differentiation index (FST) values, but loci with lower FST values also tended to provide more-accurate estimates of stock composition. The observed number of alleles was related to the power of the locus for providing accurate estimates of stock composition of simulated single-population samples. Mean estimated stock compositions for these mixtures ranged from 38.9% for simulations of single loci with fewer than 10 alleles to 85.5% for simulated loci with more than 60 alleles. Reliable population-specific estimation of stock composition was obtained with a minimum of five loci. Comparison of microsatellite stock identification power with an existing nine-locus single-nucleotide polymorphism (SNP) ...

The influence of hydrographic structure and seasonal run timing on genetic diversity and isolation-by-distance in chum salmon (Oncorhynchus keta)

We used 20 microsatellite loci to compare genetic diversity and patterns of isolation-by-distance among three groups of chum salmon (Oncorhynchus keta) from two physically distinct watersheds in western Alaska, USA. The results were consistent with the hypothesis that gene flow decreases as the complexity of the hydrographic system increases. Specifically, higher gene flow was inferred among 11 populations from a nonhierarchical collection of short coastal rivers in Norton Sound compared with 29 populations from a complex hierarchical network of inland tributaries of the Yukon River. Within the Yukon River, inferred gene flow was highest among 15 summer-run populations that spawn in the lower drainage, compared with 14 fall-run populations that spawn in the upper drainage. The results suggest that the complexity of the hydrographic system may influence population connectivity and hence the level of genetic diversity of western Alaska chum salmon. Finally, evidence of isolation-by-time, when controlling fo...

The influence of hydrology and waterway distance on population structure of Chinook salmon Oncorhynchus tshawytscha in a large river

Adult Chinook salmon Oncorhynchus tshawytscha navigate in river systems using olfactory cues that may be influenced by hydrologic factors such as flow and the number, size and spatial distribution of tributaries. Thus, river hydrology may influence both homing success and the level of straying (gene flow), which in turn influences population structure. In this study, two methods of multivariate analysis were used to examine the extent to which four indicators of hydrology and waterway distance explained population structure of O. tshawytscha in the Yukon River. A partial Mantel test showed that the indicators of hydrology were positively associated with broad-scale (Yukon basin) population structure, when controlling for the influence of waterway distance. Multivariate multiple regression showed that waterway distance, supplemented with the number and flow of major drainage basins, explained more variation in broad-scale population structure than any single indicator. At an intermediate spatial scale, indicators of hydrology did not appear to influence population structure after accounting for waterway distance. These results suggest that habitat changes in the Yukon River, which alter hydrology, may influence the basin-wide pattern of population structure in O. tshawytscha. Further research is warranted on the role of hydrology in concert with waterway distance in influencing population structure in Pacific salmon.

Canadian-Origin Chinook Salmon Rearing in Nonnatal U.S. Tributary Streams of the Yukon River, Alaska

Abstract Yukon River Chinook salmon Oncorhynchus tshawytscha are described as having a “stream-type” life history strategy. After emergence from river gravel, juveniles typically feed and grow in tributary streams of the Yukon River throughout their first summer, overwinter in freshwater, and usually leave their rearing areas for marine waters during the second spring or summer. Nonnatal rearing has been described in the upper Canadian portion of the drainage, but information is lacking for downstream U.S. waters. In 2006–2007, a study was conducted to document nonnatal rearing and the genetic origin of Chinook salmon in U.S. tributary streams of the Yukon River. Eight nonspawning streams were selected for study, seven located in a 260-km segment between the U.S.–Canada border and Circle, Alaska, and one located 742 km downstream from the border. Age-0 juveniles were captured in all eight streams. Genetic stock composition analyses using 13 standardized microsatellite loci assigned the fish to Canadian so...

Mixed-Stock Analysis of Yukon River Chum Salmon: Application and Validation in a Complex Fishery

Abstract Yukon River chum salmon Oncorhynchus keta are managed under the Pacific Salmon Treaty (PST), which requires conservation and equitable sharing of this fishery resource by the USA and Canada. Fall chum salmon are of special concern because they spawn in both the United States and Canada, and the focus of the PST is on Canadian-origin salmon. Yukon River chum salmon were assayed for genetic variation at 22 microsatellite loci to establish a baseline for mixed-stock analysis (MSA) applications to assist in addressing conservation and allocation issues. The baseline has been applied yearly to estimate the stock composition of Yukon River fall chum salmon from samples collected in the Pilot Station test fishery. Accuracies in MSA simulations for 12 of 14 management regions exceeded 90%, with a range of 80–98%, for the 12 most informative loci. Stock composition estimates were within 10% of the actual proportions in a known-origin mixture analysis. Stock-specific abundance estimates, which were derived...

Variation in the Population Structure of Yukon River Chum and Coho Salmon: Evaluating the Potential Impact of Localized Habitat Degradation

Abstract We used microsatellite and mitochondri-al DNA–restriction fragment length polymorphism (mtDNA–RFLP) analyses to test the hypothesis that chum salmon Oncorhynchus keta and coho salmon O. kisutch in the Yukon River, Alaska, exhibit population structure at differing spatial scales. If the hypothesis is true, then the risk of losing genetic diversity because of habitat degradation from a gold mine near a Yukon River tributary could differ between the two species. For each species, collections were made from two tributaries in both the Innoko and Tanana rivers, which are tributaries to the lower and middle Yukon River. The results revealed a large difference in the degree and spatial distribution of population structure between the two species. For chum salmon, the microsatellite loci (F-statistic (F ST) = 0.021) and mtDNA (F ST = −0.008) revealed a low degree of interpopulation genetic diversity on a relatively large geographic scale. This large-scale population structure should minimize, although no...

Comparison of Radiotelemetry and Microsatellites for Determining the Origin of Yukon River Chinook Salmon

Abstract Chinook salmon Oncorhynchus tshawytscha support important subsistence and commercial fisheries throughout the Yukon River. Low returns and diverse user groups have made management of these fisheries contentious and have necessitated information on the origin of the spawning migration and harvest. Here we compare estimates of individual assignment and stock composition derived from genetic and radiotelemetry data collected from the same Chinook salmon. Radiotelemetry and genetic individual assignments were highly concordant. Agreement between methods for individual assignment was 79% to region and 93% to country when using the most probable genetic criterion, improving to 94% for region and 98% for country when using the ≥95% probability genetic criterion; however, under the more stringent criterion, fewer individuals could be assigned. Further analysis showed that estimates of stock composition based on radiotelemetry and genetic methods were within 6% of each other and were not significantly dif...

Variation of Amplified Fragment Length Polymorphisms in Yukon River Chum Salmon: Population Structure and Application to Mixed-Stock Analysis

Abstract The population structure of fall-run Yukon River chum salmon Oncorhynchus keta has been studied previously using allozyme, microsatellite, and mitochondrial markers. However, genetically similar populations from tributaries near the U.S.-Canadian border render mixed-stock analyses (MSAs) difficult in the fisheries from lower portions of the Yukon River; MSA simulation apportionment estimates are less than 90% accurate for the border region divided by country of origin. To increase the accuracy and precision of contribution estimates to harvests in the Yukon River and to improve our understanding of the population structure of fall-run chum salmon, we investigated the variation of amplified fragment length polymorphisms (AFLPs). Our results show that Yukon River chum salmon populations are structured by both seasonal race and geographic region. As expected, the MSA is most successful when mixtures are allocated to geographic regions. Both AFLP and microsatellites have better than 80% apportionment...

Using a Genetic Mixture Model to Study Phenotypic Traits: Differential Fecundity among Yukon River Chinook Salmon

Abstract Fecundity is a vital population characteristic that is directly linked to the productivity of fish populations. Historic data from Yukon River (Alaska) Chinook salmon Oncorhynchus tshawytscha suggest that length-adjusted fecundity differs among populations within the drainage and either is temporally variable or has declined. Yukon River Chinook salmon have been harvested in large-mesh gill-net fisheries for decades, and a decline in fecundity was considered a potential evolutionary response to size-selective exploitation. The implications for fishery conservation and management led us to further investigate the fecundity of Yukon River Chinook salmon populations. Matched observations of fecundity, length, and genotype were collected from a sample of adult females captured from the multipopulation spawning migration near the mouth of the Yukon River in 2008. These data were modeled by using a new mixture model, which was developed by extending the conditional maximum likelihood mixture model that...

Microsatellite Analysis of Population Structure in Alaska Eulachon with Application to Mixed-Stock Analysis

Abstract Estimation of genetic population structure, diversity, and effective population size (Ne ) is important for defining meaningful conservation units and assessing genetic health. Recent conservation concerns in Alaska have highlighted the need for research on Eulachon Thaleichthys pacificus, a species about which relatively little is known. Therefore, genetic variation was assayed at 14 microsatellite loci to investigate the genetic population structure of Alaska Eulachon. This analysis revealed a low degree of genetic divergence (G ST = 0.005) that is structured by broad-scale northern and southern geographic regions. Overall, there is a significant correlation between genetic and geographic distances, suggesting that gene flow is geographically restricted and follows an isolation-by-distance (IBD) model. However, closer analysis reveals an absence of IBD within regions and that gene flow is primarily restricted by the geographic distance between regions, a pattern that better approximates the hie...