title: Large-Scale Genotyping-by-Sequencing Indicates High Levels of Gene Flow in the Deep-Sea Octocoral Swiftia simplex (Nutting 1909) on the West Coast of the United States.
abstract: Deep-sea corals are a critical component of habitat in the deep-sea, existing as regional hotspots for biodiversity, and are associated with increased assemblages of fish, including commercially important species. Because sampling these species is so difficult, little is known about the connectivity and life history of deep-sea octocoral populations. This study evaluates the genetic connectivity among 23 individuals of the deep-sea octocoral Swiftia simplex collected from Eastern Pacific waters along the west coast of the United States. We utilized high-throughput restriction-site associated DNA (RAD)-tag sequencing to develop the first molecular genetic resource for the deep-sea octocoral, Swiftia simplex. Using this technique we discovered thousands of putative genome-wide SNPs in this species, and after quality control, successfully genotyped 1,145 SNPs across individuals sampled from California to Washington. These SNPs were used to assess putative population structure across the region. A STRUCTURE analysis as well as a principal coordinates analysis both failed to detect any population differentiation across all geographic areas in these collections. Additionally, after assigning individuals to putative population groups geographically, no significant FST values could be detected (FST for the full data set 0.0056), and no significant isolation by distance could be detected (p = 0.999). Taken together, these results indicate a high degree of connectivity and potential panmixia in S. simplex along this portion of the continental shelf.
authors: National Research Council, under contract to Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America.
authors: Meredith V
authors: MV
authors: Everett
authors: Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America.
authors: Linda K
authors: LK
authors: Park
authors: Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America.
authors: Ewann A
authors: EA
authors: Berntson
authors: Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America.
authors: Anna E
authors: AE
authors: Elz
authors: Fishery Resource Analysis and Monitoring Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America.
authors: Curt E
authors: CE
authors: Whitmire
authors: Fishery Resource Analysis and Monitoring Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America.
authors: Aimee A
authors: AA
authors: Keller
authors: Office of the Science Director, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America.
authors: M Elizabeth
authors: ME
authors: Clarke
mesh_terms: D000818:Animals; D037421:Anthozoa / Q000235:genetics*; D001483:Base Sequence; D051456:Gene Flow; D005828:Genetics, Population; D060005:Genotyping Techniques; D005843:Geography; D006579:Heterozygote; D000071253:Metadata; D009792:Oceans and Seas; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D025341:Principal Component Analysis; D015203:Reproducibility of Results; D015183:Restriction Mapping; D018401:Sample Size; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D014481:United States