Open Access Research article

Ecological transcriptomics of lake-type and riverine sockeye salmon (Oncorhynchus nerka)

Scott A Pavey12*, Ben JG Sutherland3, Jong Leong3, Adrienne Robb3, Kris von Schalburg3, Troy R Hamon1, Ben F Koop3 and Jennifer L Nielsen4

Author Affiliations

1 National Park Service, Katmai National Park; PO Box 7; King Salmon, AK 99613, USA

2 Department of Biological Sciences, Simon Fraser University; 8888 University Dr.; Burnaby, BC V5B 1S6 Canada

3 Centre for Biomedical Research, University of Victoria, 3800 Finnerty Rd.; Victoria, BC V8W 3N5, Canada

4 USGS Retired, 5817 Yeazell Rd KpS, Longbranch, WA 98351, USA

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BMC Ecology 2011, 11:31  doi:10.1186/1472-6785-11-31

Published: 2 December 2011



There are a growing number of genomes sequenced with tentative functions assigned to a large proportion of the individual genes. Model organisms in laboratory settings form the basis for the assignment of gene function, and the ecological context of gene function is lacking. This work addresses this shortcoming by investigating expressed genes of sockeye salmon (Oncorhynchus nerka) muscle tissue. We compared morphology and gene expression in natural juvenile sockeye populations related to river and lake habitats. Based on previously documented divergent morphology, feeding strategy, and predation in association with these distinct environments, we expect that burst swimming is favored in riverine population and continuous swimming is favored in lake-type population. In turn we predict that morphology and expressed genes promote burst swimming in riverine sockeye and continuous swimming in lake-type sockeye.


We found the riverine sockeye population had deep, robust bodies and lake-type had shallow, streamlined bodies. Gene expression patterns were measured using a 16K microarray, discovering 141 genes with significant differential expression. Overall, the identity and function of these genes was consistent with our hypothesis. In addition, Gene Ontology (GO) enrichment analyses with a larger set of differentially expressed genes found the "biosynthesis" category enriched for the riverine population and the "metabolism" category enriched for the lake-type population.


This study provides a framework for understanding sockeye life history from a transcriptomic perspective and a starting point for more extensive, targeted studies determining the ecological context of genes.