Large-Scale Genotyping-by-Sequencing Indicates High Levels of Gene Flow in the Deep-Sea Octocoral <i>Swiftia simplex</i> (Nutting 1909) on the West Coast of the United States

<div><p>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 <i>Swiftia simplex</i> 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, <i>Swiftia simplex</i>. 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 F_ST values could be detected (F_ST 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 <i>S</i>. <i>simplex</i> along this portion of the continental shelf.</p></div

Map of collection locations for all 29 individuals initially included in this study.

<p>Colored triangles indicate individuals included in the population analysis, with the individual colors representing putative geographic populations. Population one individuals are red, two are gold, three are blue and four are green. White circles are individuals that failed to pass quality control and were excluded from the population analysis.</p

Collection metadata for the twenty-nine individuals initially included in this study.

<p>Collection metadata for the twenty-nine individuals initially included in this study.</p

Maximum parsimony phylogeny obtained with the <i>MutS</i> sequence.

<p>The arrow indicates the branch containing all <i>S</i>. <i>simplex</i> individuals. Additional species are from our voucher collection (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165279#pone.0165279.s002" target="_blank">S1 Table</a>). Colored dots after each individual correspond to putative population groupings indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165279#pone.0165279.g001" target="_blank">Fig 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165279#pone.0165279.t001" target="_blank">Table 1</a>. Numbers at branch nodes are bootstrap values from 1,000 replicates. While there are four haplotypes of <i>S</i>. <i>simplex</i>, there is no correspondence with geographic grouping. Branch lengths are not scaled.</p

AMOVA between putative populations.

<p>AMOVA between putative populations.</p

Principal components analysis on RAD-tag genotypes.

<p>Colors correspond to putative geographic population groupings in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165279#pone.0165279.g001" target="_blank">Fig 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165279#pone.0165279.t001" target="_blank">Table 1</a>. A. Includes all 23 individuals. The three outliers are the three individuals with the most missing loci. PC1 and PC2 explain 10.5% and 5.5% of the total variance respectively. B. PCA after removing the three individuals with excess missing markers. The separations along PC1 in both cases are driven by missing genotypes. After removal PC1 and PC2 explain 6.7% and 6.6% of the variance.</p