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Botanica Marina

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Volume 58, Issue 4 (Aug 2015)

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DNA barcoding reveals high diversity in the Gelidiales of the Brazilian southeast coast

Cíntia Iha
  • Corresponding author
  • Instituto de Biociências, Departamento de Botânica, Universidade de São Paulo, São Paulo 05508-090, Brazil
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Daniela Milstein
  • Departamento de Ciências do Mar, Universidade Federal de São Paulo Campus Baixada Santista, Santos 11030-400, Brazil
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Silvia Maria P.B. Guimarães / D. Wilson Freshwater / Mariana Cabral Oliveira
  • Instituto de Biociências, Departamento de Botânica, Universidade de São Paulo, São Paulo 05508-090, Brazil
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2015-07-08 | DOI: https://doi.org/10.1515/bot-2014-0069

Abstract

Morphological identification of species in the order Gelidiales can be difficult and controversial because of phenotypic plasticity, the low numbers of reproductive specimens and poorly defined taxonomic boundaries. A DNA barcoding survey of Brazilian specimens of Gelidiales, employing neighbor-joining and Automatic Barcode Gap Discovery analyses, indicated the presence of 23 statistically robust primary species hypotheses (PSH). In addition to the cytochrome oxidase I gene (COI-5P), the chloroplast universal plastid amplicon (UPA) marker was also sequenced and submitted to the same analyses. Representatives of each COI-5P/UPA PSH were selected for rbcL sequence analysis to further corroborate the occurrence of 23 species and to infer their phylogenetic relationships. These analyses confirmed the identity of six species previously cited for Brazil: Gelidiella acerosa, G. ligulata, Gelidium crinale, G. floridanum, Pterocladiella bartlettii and P. capillacea. Three new reports for Brazil were also detected: Gelidium microdonticum, Pterocladiella beachiae and P. australafricanensis. Fourteen species remain unidentified and require detailed morphological evaluation.

This article offers supplementary material which is provided at the end of the article.

Keywords: COI-5P; DNA barcoding; Gelidiales; molecular markers; rbcL

References

  • Benson, D.A., M. Cavanaugh, K. Clark, I. Karsch-Mizrachi, D.J. Lipman, D.J. Ostell and E.W. Sayers. 2013. GenBank. Nucleic Acids Res. 41: D36–D42.Google Scholar

  • Boo, G.H., J.K. Park and S.M. Boo. 2013. Gelidiophycus (Rhodophyta: Gelidiales): a new genus of marine algae from East Asia. Taxon 62: 1105–1116.CrossrefGoogle Scholar

  • Boo, G.H., K.M. Kim, W.A. Nelson, R. Riosmena-Rodríguez, K.J. Yoon and S.M. Boo. 2014. Taxonomy and distribution of selected species of the agarophyte genus Gelidium (Gelidiales, Rhodophyta). J. Appl. Phycol. 26: 1243–1251.CrossrefGoogle Scholar

  • Bottalico, A., G.H. Boo, C. Russo, S.M. Boo and C. Perrone. 2014. Parviphycus albertanoae sp. nov. (Gelidiales, Rhodophyta) from the Mediterranean Sea. Phycologia 53: 243–251.CrossrefGoogle Scholar

  • Clarkston, B.E. and G.W. Saunders. 2010. A comparison of two DNA barcode markers for species discrimination in the red algal family Kallymeniaceae (Gigartinales, Florideophyceae), with a description of Euthora timburtonii sp. nov. Botany 88: 119–131.CrossrefGoogle Scholar

  • Clarkston, B.E. and G.W. Saunders. 2012. An examination of the red algal genus Pugetia (Kallymeniaceae, Gigartinales), with descriptions of Salishia firma gen. and comb. nov., Pugetia cryptica sp. nov. and Beringia wynnei sp. nov. Phycologia 51: 33–61.CrossrefGoogle Scholar

  • Costa, E.S., E.M. Plastino, R. Petti, E.C. Oliveira and M.C. Oliveira. 2012. The Gracilariaceae Germplasm Bank of the University of São Paulo, Brazil – a DNA barcoding approach. J. Appl. Phycol. 24: 1643–1653.CrossrefGoogle Scholar

  • Fan, K.C. 1961. Morphological studies of the Gelidiales. Univ. Calif. Publ. Bot. 32: 315–368.Google Scholar

  • Fernandes, S. and S.M.P.B. Guimarães. 1998. Estudos taxonômicos de Gelidiales (Rhodophyta) do Estado do Espírito Santo, Brasil. Anais do IV Congresso Latino-Americano, II Reunião Ibero-Americana e VII Reunião Brasileira de Ficologia 2: 181–201.Google Scholar

  • Freshwater, D.W. and J. Rueness. 1994. Phylogenetic relationships of some European Gelidium (Gelidiales, Rhodophyta) species, based on rbcL nucleotide sequence analysis. Phycologia 33: 187–194.CrossrefGoogle Scholar

  • Freshwater, D.W., S. Fredericq and M.H. Hommersand. 1995. A molecular phylogeny of the Gelidiales (Rhodophyta) based on analysis of plastid rbcL nucleotide sequences. J. Phycol. 31: 616–632.CrossrefGoogle Scholar

  • Freshwater, D.W., K. Tudor, K. O’Shaughnessy and B. Wysor. 2010. DNA barcoding in the red algal order Gelidiales: comparison of COI with rbcL and verification of the “barcoding gap”. Cryptogam. Algol. 31: 435–449.Google Scholar

  • Garbary, D.J. and P.W. Gabrielson. 1990. Taxonomy and Evolution. In: (K. Cole and R.G. Sheath, eds) Biology of the red algae. Cambridge University Press, Cambridge. pp. 477–497.Google Scholar

  • Guiry, M.D. and G.M. Guiry. 2015. Algaebase. National University of Ireland, Galway. http://www.algaebase.org; Accesed on 24 April, 2014.

  • Guiry, M.D. and H.B.S. Womersley. 1993. Capreolia implexa gen. et sp. nov. (Gelidiales, Rhodophyta) in Australia and New Zealand; an intertidal mat-forming alga with unusual life history. Phycologia 32: 266–277.CrossrefGoogle Scholar

  • Hall, T.A. 1999. BioEdit: a user-friendly biological alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. 41: 95–98.Google Scholar

  • Hasegawa, M., H. Kishino and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22: 160–174.CrossrefGoogle Scholar

  • Hebert, P.D.N., A. Cywinska, S.L. Ball and J.R. DeWaard. 2003. Biological identifications through DNA barcodes. Proc. R. Soc. B. Biol. Sci. 270: 313–321.CrossrefGoogle Scholar

  • Hommersand, M.H. and S. Fredericq. 1988. An investigation of cystocarp development in Gelidium pteridifolium with a revised description of the Gelidiales (Rhodophyta). Phycologia 27: 254–272.CrossrefGoogle Scholar

  • Kim, K.M. and S.M. Boo. 2012. Phylogenetic relationships and distribution of Gelidium crinale and G. pusillum (Gelidiales, Rhodophyta) using cox1 and rbcL sequences. Algae 27: 83–94.CrossrefGoogle Scholar

  • Lanfear, R., B. Calcott, S.Y.W. Ho and S. Guindon. 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol. Biol. Evol. 29: 1695–1701.CrossrefGoogle Scholar

  • Le Gall, L. and G.W. Saunders. 2007. A nuclear phylogeny of the Florideophyceae (Rhodophyta) inferred from combined EF2, small subunit and large subunit ribosomal DNA: Establishing the new red algal subclass Corallinophycidae. Mol. Phylogenet. Evol. 43: 1118–1130.CrossrefGoogle Scholar

  • Le Gall, L. and G.W. Saunders. 2010. DNA barcoding is a powerful tool to uncover algal diversity: a case study of the Phyllophoraceae (Gigartinales, Rhodophyta) in the Canadian flora. J. Phycol. 46: 374–389.CrossrefGoogle Scholar

  • Leliaert, F., H. Verbruggen, P. Vanormelingen, F. Steen, J.M. López-Bautista, G. C. Zuccarello and O. De Clerck. 2014. DNA-based species delimitation in algae. Eur. J. Phycol. 49: 179–196.CrossrefGoogle Scholar

  • Meier, R., G. Zhang and F. Ali. 2008. The use of mean instead of smallest interspecific distances exaggerates the size of the “barcoding gap” and leads to misidentification. Syst. Biol. 57: 809–813.CrossrefGoogle Scholar

  • Melo, R. 1998. Gelidium commercial exploitation: natural resources and cultivation. J. Appl. Phycol. 10: 303–314.CrossrefGoogle Scholar

  • Millar, A.J.K. and D.W. Freshwater. 2005. Morphology and molecular phylogeny of the marine algal order Gelidiales (Rhodophyta) from New South Wales, including Lord Howe and Norfolk Islands. Aust. Syst. Bot. 18: 215–263.CrossrefGoogle Scholar

  • Milstein, D. and G.W. Saunders. 2012. DNA barcoding of Canadian Ahnfeltiales (Rhodophyta) reveals a new species – Ahnfeltia borealis sp. nov. Phycologia 51: 247–259.CrossrefGoogle Scholar

  • Milstein, D., A.S. Medeiros, E.C. Oliveira and M.C. Oliveira. 2011. Will a DNA barcoding approach be useful to identify Porphyra species (Bangiales, Rhodophyta)? J. Appl. Phycol. 24: 837–845.CrossrefGoogle Scholar

  • Nelson, W.A., T.J. Farr and J.E.S. Broom. 2006. Phylogenetic diversity of New Zealand Gelidiales as revealed by rbcL sequence data. J. Appl. Phycol. 18: 653–661.CrossrefGoogle Scholar

  • Perrone, C., G.P. Felicini and A. Bottalico. 2006. The prostrate system of the Gelidiales: diagnostic and taxonomic importance. Bot. Mar. 49: 23–33.Google Scholar

  • Presting, G.G. 2006. Identification of conserved regions in the plastid genome: implications for DNA barcoding and biological function. Can. J. Bot. 84: 1434–1443.Google Scholar

  • Puckridge, M., N. Andreakis, S.A. Appleyard and R.D. Ward. 2013. Cryptic diversity in flathead fishes (Scorpaeniformes: Platycephalidae) across the Indo-West Pacific uncovered by DNA barcoding. Mol. Ecol. Resour. 13: 32–42.CrossrefGoogle Scholar

  • Puillandre, N., A. Lambert, S. Brouillet and G. Achaz. 2012a. ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Mol. Ecol. 21: 1864–1877.CrossrefGoogle Scholar

  • Puillandre, N., M.V. Modica, Y. Zhang, L. Sirovich, M.C. Boisselier, C. Cruaud, M. Holford and S. Samadi. 2012b. Large-scale species delimitation method for hyperdiverse groups. Mol. Ecol. 21: 2671–2691.CrossrefGoogle Scholar

  • Ratnasingham, S. and P.D.N. Hebert. 2007. BOLD: The Barcode of Life Data System (http://www.barcodinglife.org). Mol. Ecol. Notes 7: 355–364.Crossref

  • Robba, L., S.J. Russell, G.L. Barker and J. Brodie. 2006. Assessing the use of the mitochondrial cox1 marker for use in DNA barcoding of red algae (Rhodophyta). Am. J. Bot. 93: 1101–1108.Google Scholar

  • Ronquist, F. and J.P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574.CrossrefGoogle Scholar

  • Santelices, B. 1990. New and old problems in the taxonomy of the Gelidiales (Rhodophyta). Hydrobiologia 204/205: 125–135.Google Scholar

  • Santelices, B. 2004. Parviphycus, a new genus in the Gelidiellaceae (Gelidiales, Rhodophyta). Cryptogam. Algol. 25: 313–326.Google Scholar

  • Santelices, B. and M.H. Hommersand. 1997. Pterocladiella, a new genus in the Gelidiaceae (Gelidiales, Rhodophyta). Phycologia 36: 114–119.CrossrefGoogle Scholar

  • Saunders, G.W. 2005. Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. Philos. Trans. R. Soc. B. 360: 1879–1888.Google Scholar

  • Saunders, G.W. 2008. A DNA barcode examination of the red algal family Dumontiaceae in Canadian waters reveals substantial cryptic species diversity. 1. The foliose Dilsea-Neodilsea complex and Weeksia. Botany 86: 773–789.CrossrefGoogle Scholar

  • Saunders, G.W. and T.E. Moore. 2013. Refinements for the amplification and sequencing of red algal DNA barcode and RedToL phylogenetic markers: a summary of current primers, profiles and strategies. Algae 28: 31–43.CrossrefGoogle Scholar

  • Sherwood, A.R. and G.G. Presting. 2007. Universal primers amplify a 23S rDNA plastid marker in Eukaryotic algae and cyanobacteria. J. Phycol. 43: 605–608.CrossrefGoogle Scholar

  • Sherwood, A.R., M.L. Vis, T.J. Entwisle, O. Necchi Jr and G.G. Presting. 2008. Contrasting intra versus interspecies DNA sequence variation for representatives of the Batrachospermales (Rhodophyta): Insights from a DNA barcoding approach. Phycol. Res. 56: 269–279.Google Scholar

  • Shimada, S., T. Horiguchi and M. Masuda. 1999. Phylogenetic affinities of genera Acanthopeltis and Yatabella (Gelidiales, Rhodophyta) inferred from molecular analyses. Phycologia 38: 528–540.CrossrefGoogle Scholar

  • Shimada, S., T. Horiguchi and M. Masuda. 2000. Two new species of Gelidium (Rhodophyta, Gelidiales), Gelidium tenuifolium and Gelidium koshikianum, from Japan. Phycol. Res. 48: 37–46.Google Scholar

  • Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei and S. Kumar. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28: 2731–2739.CrossrefGoogle Scholar

  • Taylor, W.R. 1969. Notes on the distribution of West Indian Marine Algae particularly in the Lesser Antilles: with a bibliography of recent works on Eastern American Tropical Algae. Contributions from the University of Michigan Herbarium. University of Michigan, Ann Arbor, MI.Google Scholar

  • Thiers, B. [continuously updated]. Index Herbariorum: A global directory of public herbaria and associated staff. New York Botanical Garden’s Virtual Herbarium. http://sweetgum.nybg.org/ih/; Accesed on 15 August 2014.

  • Thomas, D.T. and D.W. Freshwater. 2001. Studies of Costa Rican Gelidiales (Rhodophyta): four Caribbean taxa including Pterocladiella beachii sp. nov. Phycologia 40: 340–350.CrossrefGoogle Scholar

  • Thompson, J.D., D.G. Higgins and T.J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673–4680.CrossrefGoogle Scholar

  • Tronchin, E.M. and D.W. Freshwater. 2007. Four Gelidiales (Rhodophyta) new to southern Africa, Aphanta pachyrrhiza gen. et sp. nov., Gelidium profundum sp. nov., Pterocladiella caerulescens and P. psammophila sp. nov. Phycologia 46: 325–348.CrossrefGoogle Scholar

  • Tronchin, E.M., D.W. Freshwater, J.J. Bolton and R.J. Anderson. 2002. A reassessment and reclassification of species in the genera Onikusa Akatsuka and Suhria J. Agardh ex Endlicher (Gelidiales, Rhodophyta) based on molecular and morphological data. Bot. Mar. 45: 548–558.Google Scholar

  • Tronchin, E.M., D.W. Freshwater and J.J. Bolton. 2003. A re-evaluation of the genera Beckerella and Ptilophora (Gelidiales, Rhodophyta) based on molecular and morphological data. Phycologia 42: 80–89.CrossrefGoogle Scholar

  • Ugadim, Y. 1985. Estudos taxonômicos de Gelidium e Pterocladia (Gelidiaeae-Nemaliales-Rhodophyta) do Brasil. Universidade de São Paulo. pp. 218.Google Scholar

  • Ugadim, Y. 1987. Distribuição das espécies de Gelidium e Pterocladia (Gelidiaceae-Rhodophyta) no litoral brasileiro. Nerítica 2: 65–74.Google Scholar

  • Verbruggen, H., C.A. Maggs, G.W. Saunders, L. Le Gall, H.S. Yoon and O. De Clerck. 2010. Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life. BMC Evol. Biol. 10: 16.Google Scholar

  • Womersley, H.B.S. 1994. The marine benthic flora of southern Australia. Rhodophyta – Part III A – Bangiophyceae and Florideophyceae (Acrochaetiales, Nemaliales, Gelidiales, Hildenbrandiales and Gigartinales sensu lato). Flora of Australia. Supplementary Series Number 1. Australian Biological Resources Study, Canberra. p 508.Google Scholar

  • Zwickl, D.J. 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation, The University of Texas at Austin, Austin, TX.Google Scholar

About the article

Cíntia Iha

Cíntia Iha is a PhD student fellow at the Universidade de São Paulo. She was awarded a Master’s degree in Botany, with an emphasis in Phycology, by the Universidade de São Paulo for her work on phylogeny and taxonomy using molecular and morphological data of Gelidiales from the Brazilian southeast coast. Her more recent research has focused on phylogenomics of Gracilariales. She is interested in the evolution and diversity of Rhodophyta.

Daniela Milstein

Daniela Milstein is currently an Adjunct Professor at the Department of Marine Sciences (DCMar), Federal University of São Paulo (UNIFESP), Brazil. She was awarded a Master’s and a PhD degree in Botany from the University of São Paulo, Brazil, and a postdoctoral degree from the University of New Brunswick, Canada. Her research interests are molecular systematics, phylogeny and phylogeography of marine macroalgae.

Silvia Maria P.B. Guimarães

Silvia Maria P.B. Guimarães is an Associate Researcher at the Instituto de Botânica, São Paulo, Brazil. She received her Master’s degree and her PhD degree in Botany from the University of São Paulo for her work on the taxonomy of marine algae, mainly Rhodophyta. Presently, she works in the following areas: taxonomy of marine algae, algae of the infralittoral region and algae associated with rhodolith beds.

D. Wilson Freshwater

D. Wilson Freshwater is a researcher at the Center for Marine Science, University of North Carolina at Wilmington. His current research interests include molecular phylogeny and taxonomy of marine algae, application of DNA barcoding approaches in marine floristics, and ecology of marine hard bottom communities.

Mariana Cabral Oliveira

Mariana Cabral Oliveira is an Associate Professor at the University of São Paulo (USP), Brazil. She was awarded a PhD in Botany by USP for her work on the molecular phylogeny of Bangiales. Her main expertise is in molecular phylogeny and taxonomy of algae, and in the genomics of algae and bacteria, focusing mainly on red algae. She is interested in the origin, evolution and diversity of Rhodophyta. Presently, she integrates the coordination committee of the Biota-FAPESP program and is the head of the Botany Department at USP.


Corresponding author: Cíntia Iha, Instituto de Biociências, Departamento de Botânica, Universidade de São Paulo, São Paulo 05508-090, Brazil, e-mail:


Received: 2014-10-23

Accepted: 2015-06-02

Published Online: 2015-07-08

Published in Print: 2015-08-01


Citation Information: Botanica Marina, ISSN (Online) 1437-4323, ISSN (Print) 0006-8055, DOI: https://doi.org/10.1515/bot-2014-0069.

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