New England and Corner Rise seamounts

Author Posting. © Oceanography Society, 2010. This article is posted here by permission of Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 23, 1 (2010): 104-105.One of the longest seamount tracks in the Atlantic Ocean was formed by the Great Meteor or New England hotspot. This more than 3000-km-long hotspot track formed both the New England and Corner Rise seamounts, with a pause in volcanism 83 million years ago as evidenced by the morphological gap between chains

Predicting RAD-seq marker numbers across the eukaryotic tree of life

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 7 (2015): 3207-3225, doi:10.1093/gbe/evv210.High-throughput sequencing of reduced representation libraries obtained through digestion with restriction enzymes—generically known as restriction site associated DNA sequencing (RAD-seq)—is a common strategy to generate genome-wide genotypic and sequence data from eukaryotes. A critical design element of any RAD-seq study is knowledge of the approximate number of genetic markers that can be obtained for a taxon using different restriction enzymes, as this number determines the scope of a project, and ultimately defines its success. This number can only be directly determined if a reference genome sequence is available, or it can be estimated if the genome size and restriction recognition sequence probabilities are known. However, both scenarios are uncommon for nonmodel species. Here, we performed systematic in silico surveys of recognition sequences, for diverse and commonly used type II restriction enzymes across the eukaryotic tree of life. Our observations reveal that recognition sequence frequencies for a given restriction enzyme are strikingly variable among broad eukaryotic taxonomic groups, being largely determined by phylogenetic relatedness. We demonstrate that genome sizes can be predicted from cleavage frequency data obtained with restriction enzymes targeting “neutral” elements. Models based on genomic compositions are also effective tools to accurately calculate probabilities of recognition sequences across taxa, and can be applied to species for which reduced representation data are available (including transcriptomes and neutral RAD-seq data sets). The analytical pipeline developed in this study, PredRAD (https://github.com/phrh/PredRAD), and the resulting databases constitute valuable resources that will help guide the design of any study using RAD-seq or related methods.This research was supported by the Office of Ocean Exploration and Research of the National Oceanic and Atmospheric Administration (NA09OAR4320129 to T.S.); the Division of Ocean Sciences of the National Science Foundation (OCE-1131620 to T.S.); the Astrobiology Science and Technology for Exploring Planets program of the National Aeronautics and Space Administration (NNX09AB76G to T.S.); and the Academic Programs Office (Ocean Ventures Fund to S.H.), the Ocean Exploration Institute (Fellowship support to T.M.S.), and the Ocean Life Institute of the Woods Hole Oceanographic Institution (internal grant to T.M.S. and S.H.)

Oceanographic drivers of deep-sea coral species distribution and community assembly on seamounts, islands, atolls, and reefs within the Phoenix Islands Protected Area

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Auscavitch, S. R., Deere, M. C., Keller, A. G., Rotjan, R. D., Shank, T. M., & Cordes, E. E. Oceanographic drivers of deep-sea coral species distribution and community assembly on seamounts, islands, atolls, and reefs within the Phoenix Islands Protected Area. Frontiers in Marine Science, 7, (2020): 42, doi:10.3389/fmars.2020.00042.The Phoenix Islands Protected Area, in the central Pacific waters of the Republic of Kiribati, is a model for large marine protected area (MPA) development and maintenance, but baseline records of the protected biodiversity in its largest environment, the deep sea (>200 m), have not yet been determined. In general, the equatorial central Pacific lacks biogeographic perspective on deep-sea benthic communities compared to more well-studied regions of the North and South Pacific Ocean. In 2017, explorations by the NOAA ship Okeanos Explorer and R/V Falkor were among the first to document the diversity and distribution of deep-water benthic megafauna on numerous seamounts, islands, shallow coral reef banks, and atolls in the region. Here, we present baseline deep-sea coral species distribution and community assembly patterns within the Scleractinia, Octocorallia, Antipatharia, and Zoantharia with respect to different seafloor features and abiotic environmental variables across bathyal depths (200–2500 m). Remotely operated vehicle (ROV) transects were performed on 17 features throughout the Phoenix Islands and Tokelau Ridge Seamounts resulting in the observation of 12,828 deep-water corals and 167 identifiable morphospecies. Anthozoan assemblages were largely octocoral-dominated consisting of 78% of all observations with seamounts having a greater number of observed morphospecies compared to other feature types. Overlying water masses were observed to have significant effects on community assembly across bathyal depths. Revised species inventories further suggest that the protected area it is an area of biogeographic overlap for Pacific deep-water corals, containing species observed across bathyal provinces in the North Pacific, Southwest Pacific, and Western Pacific. These results underscore significant geographic and environmental complexity associated with deep-sea coral communities that remain in under-characterized in the equatorial central Pacific, but also highlight the additional efforts that need to be brought forth to effectively establish baseline ecological metrics in data deficient bathyal provinces.Funding for this work was provided by NOAA Office of Ocean Exploration and Research (Grant No. NA17OAR0110083) to RR, EC, TS, and David Gruber

Population genomics of rapidly invading lionfish in the Caribbean reveals signals of range expansion in the absence of spatial population structure.

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bors, E. K., Herrera, S., Morris, J. A., Jr., & Shank, T. M. Population genomics of rapidly invading lionfish in the Caribbean reveals signals of range expansion in the absence of spatial population structure. Ecology and Evolution, 9(6), (2019):3306-3320, doi:10.1002/ece3.4952.Range expansions driven by global change and species invasions may have significant genomic, evolutionary, and ecological implications. During range expansions, strong genetic drift characterized by repeated founder events can result in decreased genetic diversity with increased distance from the center of the historic range, or the point of invasion. The invasion of the Indo‐Pacific lionfish, Pterois volitans, into waters off the US East Coast, Gulf of Mexico, and Caribbean Sea provides a natural system to study rapid range expansion in an invasive marine fish with high dispersal capabilities. We report results from 12,759 single nucleotide polymorphism loci sequenced by restriction enzyme‐associated DNA sequencing for nine P. volitans sampling areas in the invaded range, including Florida and other sites throughout the Caribbean, as well as mitochondrial control region D‐loop data. Analyses revealed low to no spatially explicit metapopulation genetic structure, which is partly consistent with previous finding of little structure within ocean basins, but partly divergent from initial reports of between‐basin structure. Genetic diversity, however, was not homogeneous across all sampled sites. Patterns of genetic diversity correlate with invasion pathway. Observed heterozygosity, averaged across all loci within a population, decreases with distance from Florida while expected heterozygosity is mostly constant in sampled populations, indicating population genetic disequilibrium correlated with distance from the point of invasion. Using an FST outlier analysis and a Bayesian environmental correlation analysis, we identified 256 and 616 loci, respectively, that could be experiencing selection or genetic drift. Of these, 24 loci were shared between the two methods.We thank the many participants of the Gulf and Caribbean Fisheries Institute for providing lionfish samples from around the Caribbean region, as well as Dr. Bernard Castillo at the University of the Virgin Islands and Kristian Rogers at the Biscayne Bay National Park. We would like to acknowledge Alex Bogdanoff at NOAA, Beaufort NC, for assistance with sample acquisition; Camrin Braun at WHOI, for assistance with the calculation of oceanic distances between sites; Dr. Tom Schultz at Duke Marine Lab and Dr. Margaret Hunter at USGS for discussions concerning ongoing population genetic projects; and Jack Cook at the WHOI Graphics department for his assistance in generating maps of the study area. We would like to extend a special thank you to Dr. John Wakeley of Harvard University for assistance in the interpretation of data. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. 1122374. Sequencing funding was provided in part by the PADI Foundation Grant No. 14904. Additional research support was provided by the Woods Hole Oceanographic Institution (WHOI) Ocean Ventures Fund, the Coastal Ocean Institute at WHOI, the National Science Foundation (OCE‐1131620 to TMS), and the James Education Fund for Ocean Exploration within the Ocean Exploration Institute at WHOI. Publication of this paper was supported, in part, by the Henry Mastin Graduate Student Fund administered by the Oregon State University Department of Fisheries and Wildlife. Finally, we sincerely thank the reviewers and editors who helped to strengthen this manuscript

Ancient DNA techniques : applications for deep-water corals

Author Posting. © University of Miami - Rosenstiel School of Marine and Atmospheric Science, 2007. This article is posted here by permission of University of Miami - Rosenstiel School of Marine and Atmospheric Science for personal use, not for redistribution. The definitive version was published in Bulletin of Marine Science 81 (2007): 351-359.The potential applications of ancient DNA (aDNA) techniques have been realized relatively recently, and have been revolutionized by the advent of pCR techniques in the mid 1980s. Although these techniques have been proven valuable in ancient specimens of up to 100,000 yrs old, their use in the marine realm has been largely limited to mammals and fish. Using modifications of techniques developed for skeletons of whales and mammals, we have produced a method for extracting and amplifying aDNA from sub-fossil (not embedded in rock) deep-water corals that has been successful in yielding 351 base pairs of the ITS2 region in sub-fossil Desmophyllum dianthus (Esper, 1794) and Lophelia pertusa (Linnaeus, 1758). The comparison of DNA sequences from fossil and live specimens resulted in clustering by species, demonstrating the validity of this new aDNA method. Sub-fossil scler-actinian corals are readily dated using U-series techniques, and so the abundance of directly-dateable skeletons in the world's oceans, provides an extremely useful archive for investigating the interactions of environmental pressures (in particular ocean circulation, climate change) on the past distribution, and the evolution of deep-water corals across the globe.Support for this project was provided by National Science Foundation grants OCE 0096373 (JFA), OCE 0095331 (Daniel Scheirer, USGS), OCE 0136871 [D. Yoerger (WH OI) and (TMS)], OCE 0624627 (TMS and RGW) and NOAA’s Office of Exploration grant NA05OAR4601054 (TMS, RGW, and JFA). We are also grateful for the enabling support of the Ocean Life Institute and the Ocean and Climate Change Institute of the Woods Hole Oceanographic Institutio

Animal community dynamics at senescent and active vents at the 9° N East Pacific Rise after a volcanic eruption

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gollner, S., Govenar, B., Arbizu, P. M., Mullineaux, L. S., Mills, S., Le Bris, N., Weinbauer, M., Shank, T. M., & Bright, M. Animal community dynamics at senescent and active vents at the 9° N East Pacific Rise after a volcanic eruption. Frontiers in Marine Science, 6, (2020): 832, doi:10.3389/fmars.2019.00832.In 2005/2006, a major volcanic eruption buried faunal communities over a large area of the 9°N East Pacific Rise (EPR) vent field. In late 2006, we initiated colonization studies at several types of post eruption vent communities including those that either survived the eruption, re-established after the eruption, or arisen at new sites. Some of these vents were active whereas others appeared senescent. Although the spatial scale of non-paved (surviving) vent communities was small (several m2 compared to several km2 of total paved area), the remnant individuals at surviving active and senescent vent sites may be important for recolonization. A total of 46 meio- and macrofauna species were encountered at non-paved areas with 33 of those species detected were also present at new sites in 2006. The animals living at non-paved areas represent refuge populations that could act as source populations for new vent sites directly after disturbance. Remnants may be especially important for the meiofauna, where many taxa have limited or no larval dispersal. Meiofauna may reach new vent sites predominantly via migration from local refuge areas, where a reproductive and abundant meiofauna is thriving. These findings are important to consider in any potential future deep-sea mining scenario at deep-sea hydrothermal vents. Within our 4-year study period, we regularly observed vent habitats with tubeworm assemblages that became senescent and died, as vent fluid emissions locally stopped at patches within active vent sites. Senescent vents harbored a species rich mix of typical vent species as well as rare yet undescribed species. The senescent vents contributed significantly to diversity at the 9°N EPR with 55 macrofaunal species (11 singletons) and 74 meiofaunal species (19 singletons). Of these 129 species associated with senescent vents, 60 have not been reported from active vents. Tubeworms and other vent megafauna not only act as foundation species when alive but provide habitat also when dead, sustaining abundant and diverse small sized fauna.We received funding from the Austrian FWF (GrantP20190-B17; MB), the U.S. National Science Foundation (OCE-0424953; to LM, D. McGillicuddy, A. Thurnherr, J. Ledwell, and W. Lavelle; and OCE-1356738 to LM), and the European Union Seventh Framework Programme (FP7/2007-2013) under the MIDAS project, Grant Agreement No. 603418. Ifremer and CNRS (France) supported NL cruise participation and sensor developments. BG was supported by a postdoctoral fellowship from the Deep Ocean Exploration Institute at WHOI (United States). TS was supported by the U.S. National Science Foundation (OCE-0327261 to TS and OCE-0937395 to TS and BG)

Defining the word “seamount”

Author Posting. © Oceanography Society, 2010. This article is posted here by permission of Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 23, 1 (2010): 20-21.The term seamount has been defined many times (e.g., Menard, 1964; Wessel, 2001; Schmidt and Schmincke, 2000; Pitcher et al., 2007; International Hydrographic Organization, 2008; Wessel et al., 2010) but there is no “generally accepted” definition. Instead, most definitions serve the particular needs of a discipline or a specific paper

Seamount sciences : quo vadis?

Author Posting. © Oceanography Society, 2010. This article is posted here by permission of Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 23, 1 (2010): 212-213.Seamounts are fascinating natural ocean laboratories that inform us about fundamental planetary and ocean processes, ocean ecology and fisheries, and hazards and metal resources. The more than 100,000 large seamounts are a defining structure of global ocean topography and biogeography, and hundreds of thousands of smaller ones are distributed throughout every ocean on Earth

Autonomous and remotely operated vehicle technology for hydrothermal vent discovery, exploration, and sampling

Author Posting. © Oceanography Society, 2007. This article is posted here by permission of Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 20, 1 (2007): 152-161.Autonomous and remotely operated underwater vehicles play complementary roles in the discovery, exploration, and detailed study of hydrothermal vents. Beginning with clues provided by towed or lowered instruments, autonomous underwater vehicles (AUVs) can localize and make preliminary photographic surveys of vent fields. In addition to finding and photographing such sites, AUVs excel at providing regional context through fine-scale bathymetric and magnetic field mapping. Remotely operated vehicles (ROVs) enable close-up inspection, photomosaicking, and tasks involving manipulation of samples and instruments. Increasingly, ROVs are used to conduct in situ seafloor experiments. ROVs can also be used for fine-scale bathymetric mapping with excellent results, although AUVs are usually more efficient in such tasks