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Alaskan harbour seal populations are currently listed as a species of special concern. Although there is evidence of recent stabilization or even partial recovery of harbour seal numbers in areas of historic decline, most populations have not made substantial recoveries. To date, few data exist regarding spatial and seasonal changes in blubber fatty acids (FAs) for Alaskan harbour seal populations. The purpose of this study was to qualitatively investigate harbour seal blubber FA profiles for regional, seasonal and age class differences. Blubber FA concentrations were analysed using MANOVA and linear discriminant analysis (LDA) from 760 individual harbour seals across Bristol Bay, Kodiak, Prince William Sound and Southeast Alaska from 1997 to 2010. Our results suggest spatial and seasonal differences are largely driven by monounsaturated FAs, most notably 14:1n-5, 16:1n-7 and 18:1n-7. In addition, our data revealed a progression in blubber FAs from pups to adults, with a shift from saturated FAs and short-chained monounsaturated FAs in the pup blubber to more long-chain monounsaturated FAs and polyunsaturated FAs in adults. Lastly, harbour seals pups had elevated saturated FA 16:0 concentrations when compared to other age classes, regardless of location or period. With this vast spatial and seasonal FA information, we believe future sampling of blubber FAs from Alaskan harbour seal populations could be a useful tool in assessing the response of this species and its ecosystem to changes associated with natural and anthropogenic pressures. [ABSTRACT FROM AUTHOR]