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.

Population structure, genetic connectivity, and adaptation in the Olympia oyster (Ostrea lurida) along the west coast of North America

“…I specifically tested whether patterns of genetic variation suggest a smooth continuum of allele frequency shifts consistent with isolation-bydistance (IBD) (Malécot, 1968), regional blocks of genetic similarity that correspond to physical barriers (Hare & Avise, 1996), or the null model of no significant genetic differentiation (Grosberg & Cunningham, 2001). SNPs produced from high-throughput sequencing have led to the identification of previously undetected population structure in a number of marine and terrestrial species K E Y W O R D S connectivity, genotype-by-sequencing, management recommendations, Olympia oyster, outlier loci, population genomics (Everett et al, 2016;Reitzel, Herrera, Layden, Martindale, & Shank, 2013;Van Wyngaarden et al, 2016). Compared to the Atlantic coast of North America (Hoey & Pinsky, 2018), studies utilizing genomewide SNPs for marine taxa from the Pacific coast are far fewer in number and have been limited to regional spatial scales (De Wit & Palumbi, 2013;Drinan et al, 2018;Gleason & Burton, 2016;Larson et al, 2014;Martinez, Buonaccorsi, Hyde, & Aguilar, 2017) or in the number of sampling sites (Pespeni, Oliver, Manier, & Palumbi, 2010;Tepolt & Palumbi, 2015).…”

Population structure, genetic connectivity, and adaptation in the Olympia oyster (Ostrea lurida) along the west coast of North America

“…I specifically tested whether patterns of genetic variation suggest a smooth continuum of allele frequency shifts consistent with isolation-by-distance (IBD) (Malécot, 1968), regional blocks of genetic similarity that correspond to physical barriers (Hare and Avise, 1996), or the null model of no significant genetic differentiation (Grosberg and Cunningham, 2001). SNPs produced from high-throughput sequencing have led to the identification of previously undetected population structure in a number of marine and terrestrial species (Everett et al, 2016; Reitzel et al, 2013; Van Wyngaarden et al, 2016). Compared to the Atlantic coast of North America (Hoey and Pinsky, 2018), studies utilizing genome-wide SNPs for marine taxa from the Pacific coast are far fewer in number and have been limited to regional spatial scales (De Wit and Palumbi, 2013; Drinan et al, 2018; Gleason and Burton, 2016; Larson et al, 2014; Martinez et al, 2017) or in the number of sampling sites (Pespeni et al, 2010; Tepolt and Palumbi, 2015).…”

A review of gorgonian coral species (Cnidaria, Octocorallia, Alcyonacea) held in the Santa Barbara Museum of Natural History research collection: focus on species from Scleraxonia, Holaxonia, Calcaxonia – Part III: Suborder Holaxonia continued, and suborder Calcaxonia

“…This genus designation is incorrect; the specimen is the species Swiftiasimplex . While Nutting (1909) placed it in the genus Psammogorgia Verrill, 1868a, geographic location of specimen(s) he described, geographic locations of specimens examined here, appearance of sclerites, along with molecular work conducted by M Everett et al (2016), do not warrant that species designation either. While the WoRMS Database (Cordeiro et al 2019) did indicate an accepted status for this species designation under the genus Swiftia , it also showed accepted status for the species as Psammogorgiasimplex (Cordeiro et al 2018).…”

“…comm. and Everett et al 2016); this will certainly shed more light on the origins and dispersal of the genus. The discussion here, however, does not focus on how Swiftia member species came to be in the eastern North Pacific, or how they relate to other species in other parts of the world; the focus here is what has occurred morphologically within several member species since the migration and establishment of the genus in the eastern North Pacific.…”

“…These hypotheses are: 1) either these two species are in actuality the same species, with considerable transitional geographic variability seen from south to north within their distributional range (ecological morphs), 2) these two species are distinct species but show high degrees of intermediary form in areas where they overlap (perhaps similar enough to hybridize), 3) these two species are distinct species but display, in the center portion of their range, interesting examples of regional endemism or 4) that both are distinct species, highly subject to varying environmental/ecological parameters, sharing some responses to ecological factors in areas where they live together (factors such as colder water, and depth). In the case of Swiftiasimplex (a species that displays a whip-like colony form), it has been determined to be a single species (Everett et al 2016) but shows geographic and thus perhaps, ecological trends in its sclerite morphology over a vast distance.…”