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An alternative to ITS, a hypervariable, single-copy nuclear intron in corals, and its use in detecting cryptic species within the octocoral genus Carijoa

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Abstract

Here we report a highly variable nuclear marker that can be used for both soft and stony corals. Primers that amplify a ∼177 bp fragment from the nuclear gene encoding the 54 kDa subunit of the signal recognition particle (SRP54) were developed for the octocoral genus Carijoa. Cloning results from 141 individuals suggest that this hypervariable nuclear locus is a single-copy gene. Sequencing revealed a potential cryptic species previously thought to be Carijoa riisei. Results from an Analysis of Molecular Variance (AMOVA) based on mitochondrial DNA (mtDNA) explained <10% of the variation between Atlantic and Pacific samples of C. riisei (F st = 0.47), whereas the same comparison with SRP54 explained >33% of the variation (F st = 0.54). Using previously reported degenerate primers for SRP54, high levels of sequence variation were found at this locus across both scleractinian and octocorals. For example, pairwise sequence divergence within octocorals was ∼8–13 times greater with SRP54 than with mtDNA, and, up to 2.8% pairwise sequence divergence was found in SRP54 among individuals of Pocillopora whereas no variation at all was found in mtDNA markers. This case study with the octocoral C. riisei shows that variation in SRP54 appears sufficient to address questions of phylogeography as well as systematics of closely related species.

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Acknowledgments

We thank Phil Alderslade, Lori Bell, Yehuda Benayahu, Andrew Bowie, Bob Bruck, Steve Cairns, Barbara Calcinai, Steve Coles, John Earle, Zac Forsman, Shawn Fujimoto, Cathy McFadden, Gustav Paulay, John Perkner, Mike Rappé, Caroline Rogers, John Starmer, George Thompson, Peter Wirtz, the Coral Reef Research Foundation, members of the Toonen-Bowen laboratory, the Museum and Art Gallery of the Northern Territory, Australia, Sarah Daley and the NSF-EPSCoR Evolutionary Genetics facility at HIMB and Exotic Aquatics, Baltimore, MD. Figure 3a, b were provided courtesy of Gustav Paulay. Figure 3c was provided courtesy of Andrew Bowie. This paper is funded in part by a grant/cooperative agreement from the National Oceanic and Atmospheric Administration, Project #R/CR-11PD, which is sponsored by the University of Hawaii Sea Grant College Program, SOEST, under Institutional Grant No. NA36RG2254 from NOAA Office of Sea Grant, Department of Commerce (UNIHI-SEAGRANT-JC-04-31). Additional funding came from the Hawaii Coral Reef Initiative, NSF grant OCE#06-23678, the Hawaii Invasive Species Council #53780/53781, and NMSP MOA grant No. 2005-008/66882. The views expressed herein are those of the authors and do not necessarily reflect the views of NOAA or any of its sub-agencies. This is contribution 1294 from the Hawaii Institute of Marine Biology and SOEST 7185.

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  1. Hawaii Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, Kaneohe, HI, 96744, USA

    G. T. Concepcion, M. W. Crepeau, D. Wagner & R. J. Toonen

  2. Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, 96822, USA

    S. E. Kahng

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  1. G. T. Concepcion
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  2. M. W. Crepeau
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  3. D. Wagner
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  4. S. E. Kahng
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  5. R. J. Toonen
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Correspondence to G. T. Concepcion.

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Communicated by Biology Editor M. van Oppen.

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Concepcion, G.T., Crepeau, M.W., Wagner, D. et al. An alternative to ITS, a hypervariable, single-copy nuclear intron in corals, and its use in detecting cryptic species within the octocoral genus Carijoa . Coral Reefs 27, 323–336 (2008). https://doi.org/10.1007/s00338-007-0323-x

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