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Seamounts are one of the largest biomes on earth, yet remain one of the least explored. They are known to be centers of increased biomass, species richness, endemism and speciation as well as areas of distinct community structure, as compared to surrounding areas. Much of this species richness may be due to the presence of structure-forming, deep-water corals on many seamounts. These corals act as ecosystem engineers, altering the local environment to the benefit of many other species. This is especially true in the waters of Alaska, where octocorals, the dominant deep water corals, form dense assemblages known as "coral gardens". Alaska is home to a 5.8 billion dollar commercial fishing industry, and 85% of commercially fished species have been shown to associate with structure-forming invertebrates. Octocorals, however, are very vulnerable to disturbance events from bottom contact fishing gear. It is therefore imperative that we understand the connectivity, community composition and distribution of octocoral species in Alaska. Both traditional morphological species identification and DNA barcoding techniques have been employed to study octocoral communities, but each method has serious issues when used with octocorals, and it is currently unclear how the two methods compare. Here I utilize a large dataset of Alaskan octocorals, covering a wide range of the Alaskan coast and the Gulf of Alaska, to show that genetic methods of study reveal community structure not identified by methods utilizing morphologic species designations. Analysis was performed on parallel datasets of specimens - one featuring species designations made using traditional morphological taxonomic methods and one featuring species designations made using a 3-gene barcode method - in order to increase the state of knowledge regarding Alaskan octocoral distributions and community structure, as well as to compare the results of these two widely used methods. Communities were shown to be distinct on a province level, with the Aleutian Island sites, the seamount sites and the slope sites each forming separate communities. The 3-gene barcode method also identified a distinct deep community that the morphologic methods failed to distinguish. Depth was found to be the strongest structuring gradient for all datasets. This work yields new insight into the connectivity of Alaskan octocorals and suggests that they may need to be managed in a 3-dimensional manner, taking depth into account when protecting this vital fisheries habitat.