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Application of DNA barcoding in biodiversity studies of shallow-water octocorals: molecular proxies agree with morphological estimates of species richness in Palau

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Abstract

The application of DNA barcoding to anthozoan cnidarians has been hindered by their slow rates of mitochondrial gene evolution and the failure to identify alternative molecular markers that distinguish species reliably. Among octocorals, however, multilocus barcodes can distinguish up to 70 % of morphospecies, thereby facilitating the identification of species that are ecologically important but still very poorly known taxonomically. We tested the ability of these imperfect DNA barcodes to estimate species richness in a biodiversity survey of the shallow-water octocoral fauna of Palau using multilocus (COI, mtMutS, 28S rDNA) sequences obtained from 305 specimens representing 38 genera of octocorals. Numbers and identities of species were estimated independently (1) by a taxonomic expert using morphological criteria and (2) by assigning sequences to molecular operational taxonomic units (MOTUs) using predefined genetic distance thresholds. Estimated numbers of MOTUs ranged from 73 to 128 depending on the barcode and distance threshold applied, bracketing the estimated number of 118 morphospecies. Concordance between morphospecies identifications and MOTUs ranged from 71 to 75 % and differed little among barcodes. For the speciose and ecologically dominant genus Sinularia, however, we were able to identify 95 % of specimens correctly simply by comparing mtMutS sequences and in situ photographs of colonies to an existing vouchered database. Because we lack a clear understanding of species boundaries in most of these taxa, numbers of morphospecies and MOTUs are both estimates of the true species diversity, and we cannot currently determine which is more accurate. Our results suggest, however, that the two methods provide comparable estimates of species richness for shallow-water Indo-Pacific octocorals. Use of molecular barcodes in biodiversity surveys will facilitate comparisons of species richness and composition among localities and over time, data that do not currently exist for any octocoral community.

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Acknowledgments

Many thanks to: Suheilah Abdalla and Anna Lee for laboratory support; Katherine Maloney, Michael Janes and the Coral Reef Research Foundation (Pat and Lori Colin) for collection assistance; and Yehuda Benayahu and Michael Janes for additional species identifications. Partial funding for this work was received from the Research Corporation for Science Advancement Multi-Investigator Cottrell College Science Award #10737 to K. Maloney and C. McFadden; Howard Hughes Medical Institute Undergraduate Science Program award 52006301; and a Merck/AAAS Undergraduate Science Research Program award to Harvey Mudd College.

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  1. Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA

    C. S. McFadden, A. S. Brown, C. Brayton & C. B. Hunt

  2. Naturalis Biodiversity Center, P. O. Box 9517, 2300 RA, Leiden, The Netherlands

    L. P. van Ofwegen

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  1. C. S. McFadden
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  2. A. S. Brown
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  3. C. Brayton
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Correspondence to C. S. McFadden.

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McFadden, C.S., Brown, A.S., Brayton, C. et al. Application of DNA barcoding in biodiversity studies of shallow-water octocorals: molecular proxies agree with morphological estimates of species richness in Palau. Coral Reefs 33, 275–286 (2014). https://doi.org/10.1007/s00338-013-1123-0

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