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

• Published in: PloS one Vol. 11; no. 10; p. e0165279
• Main Authors: Everett, Meredith V, Park, Linda K, Berntson, Ewann A, Elz, Anna E, Whitmire, Curt E, Keller, Aimee A, Clarke, M Elizabeth
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 31.10.2016; Public Library of Science (PLoS)
• Subjects: Analysis; Animal behavior; Animals; Anthozoa - genetics; Base Sequence; Biodiversity; Bioinformatics; Biology and Life Sciences; Conservation biology; Continental shelves; Corals; Critical components; Data collection; Deep sea; Deoxyribonucleic acid; DNA; DNA sequencing; Earth Sciences; Ecology; Ecosystem biology; Ecosystems; Fisheries; Gene Flow; Gene sequencing; Genetics, Population; Genomes; Genomics; Genotyping; Genotyping Techniques; Geography; Heterozygote; Integrated software; Life history; Metadata; Oceans and Seas; People and places; Phylogeny; Polymorphism, Single Nucleotide - genetics; Population differentiation; Population genetics; Population structure; Population studies; Principal Component Analysis; Psammogorgia; Quality control; Reproducibility of Results; Research and analysis methods; Restriction Mapping; Sample Size; Science; Sequence Analysis, DNA; Single-nucleotide polymorphism; Species; Species Specificity; Structural analysis; Studies; Swiftia; Taxonomy; United States; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0165279

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.