Biology subjects

Seeb, L. W.

Publications and source records attributed to Seeb, L. W..

3 recordsLinked to original sources

bioRxiv2019

Mixed-stock analyses among migratory, non-native Chinook salmon at-sea and assignment to natal sites in freshwater at their introduced range in South America

Invasive species with migratory behavior and complex life cycle represent a challenge for evaluating natal sites among individuals. Private and government-sponsored initiatives resulted in the successful introduction and naturalization of Chinook salmon (Oncorhynchus tshawytscha) throughout northern and southern Patagonia in South America. These migratory fish breed in freshwater, but spend most of their life at sea feeding, forming abundant populations in several watersheds draining into the southeast Pacific Ocean. We used single nucleotide polymorphisms (SNPs) combined with genetic structure and mixed-stock analyses to evaluate natal sites of Chinook salmon at-sea caught in one estuary and two coastal locations compared to reference populations from breeding sites in freshwater. Firstly, Bayesian individual-assignment analyses revealed no genetic structure among adults caught off the coast of the Tolten River and migrating (maturing) adults caught in Tolten River estuary, suggesting they likely belong to a single population. Secondly, mixed-stock genetic analyses revealed that most at-sea Chinook salmon caught in one estuary and two coastal locations likely originated from spawners from the nearest river (90-95%), with a small contribution from adjacent watersheds (5-10%). This appears consistent with Chinook salmon populations in their native range in which juveniles migrate short distances (100-200 km) from their river of origin to coastal feeding grounds, some of which became donor of propagules for non-native Chinook salmon populations under study. Mixed-stock genetic analyses provide considerable potential to identify the population of origin of Chinook salmon mixtures caught off the coast. They also seem an appropriate proof of concept to help identify potential immigrants from other watersheds as well as migration patterns and invasion pathways in a non-native species.

genetics↗

bioRxiv2019

Patterns of linkage disequilibrium reveal genome architecture in chum salmon

Many studies exclude loci exhibiting linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome inversions or sex-determining regions. Chromosome inversions and sex-determining regions are often involved in adaptation, allowing for the inheritance of co-adapted gene complexes and for the resolution of sexually antagonistic selection through sex-specific partitioning of genetic variants. Genomic features such as these can escape detection when loci with LD are removed; in addition, failing to account for these features can introduce bias to analyses. We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the signal of the sex-determining region was only obvious after restricting genetic analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. The results of this study highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of ignoring or excluding loci exhibiting LD.

genomics↗

bioRxiv2019

Y-chromosome haplotypes drive variation in size and age at maturity in male Chinook salmon

Variation in size and age at maturity is an important component of life history that is influenced both by environmental and genetic factors. In salmonids, large size confers a direct reproductive advantage through increased fecundity and egg quality in females, while larger males gain a reproductive advantage by monopolizing access to females. In addition, variation in size and age at maturity in males can be associated with different reproductive strategies; younger smaller males may gain reproductive success by sneaking in among mating pairs. In both sexes there is a trade-off between older age and increased reproductive success and increased risk of mortality by delaying reproduction. We identified four Y-chromosome haplogroups that showed regional and population-specific variation in frequency using RADseq data for 21 populations of Alaska Chinook salmon. We then characterized the range-wide distribution of these haplogroups using GT-seq assays. These haplogroups exhibited associations with size at maturity in multiple populations suggesting that the lack of recombination between X and Y-chromosomes has allowed Y-chromosome haplogroups to capture different alleles that influence size at maturity. Ultimately, conservation of life history diversity in Chinook salmon may require conservation of Y-chromosome haplotype diversity.

evolutionary biology↗