Jump to ContentJump to Main Navigation
Show Summary Details
More options …

DNA Barcodes

Ed. by Mitchell, Andrew

1 Issue per year


Emerging Science

Open Access
Online
ISSN
2299-1077
See all formats and pricing
More options …

Barcoding, phylogeography and species boundaries in clownfishes of the Indian Ocean

Kottila Veettil Dhaneesh
  • Corresponding author
  • Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai 608 502, Tamil Nadu, India
  • Department of Aquatic Biology and Fisheries, University of Kerala, Kariavattom, Thiruvananthapuram 695581, Kerala, India
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Thipramalai Thankappan Ajith Kumar
  • Corresponding author
  • Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai 608 502, Tamil Nadu, India
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Appukuttannair Biju Kumar
  • Corresponding author
  • Department of Aquatic Biology and Fisheries, University of Kerala, Kariavattom, Thiruvananthapuram 695581, Kerala, India
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2015-05-27 | DOI: https://doi.org/10.1515/dna-2015-0002

Abstract

In this study, barcoding of 13 clownfish species of the Indian Ocean was carried out to infer the phylogenetic relationships among them by analyzing cytochrome oxidase 1 (CO1) and cytochrome b mitochondrial gene sequences. The study also scrutinized species boundaries between four closely related species of the subgenus Phalerebus (Amphiprion akallopisos, A. perideraion, A. sandaracinos and A. nigripes ), three species of the subgenus Amphiprion (A. frenatus, A. melanopus and A. ephippium ) and two species of the subgenus Paramphiprion (A. sebae and A. polymnus ). In addition, phylogeographic structure of A. clarkii was calculated in terms of geographic isolation by phylogenetic analysis of mitochondrial control region and cytochrome b sequences. The genetic distances between the subgenus Phalerebus species were 0.165-0.233 in control region and 0.021-0.065 in cytochrome b ; and the genetic distance between the subgenus Amphiprion species was 0.122-0.171 in control region and 0.038-2.308 in cytochrome b . Species of the subgenus Paramphiprion had a genetic distance of 0.016 in control region and 2.185 in cytochrome b. A. clarkii collected from four regions have genetic distance of 0.019- 0.06 (control region) and 0-0.025 (cytochrome b ).

Keywords : Anemonefish; species identification; molecular phylogeny; Amphiprion; Premnas

References

  • [1] Hebert P.D.N., Gregory T.R., The promise of DNA bar-coding for taxonomy. Syst. Bio., 2005, 54, 852-859. CrossrefGoogle Scholar

  • [2] Nelson L.A., Wallman J.F., Dowton M., Using COI barcodes to identify forensically and medically important blowflies. Med. Vet. Ento., 2007, 21, 44-52. Web of ScienceGoogle Scholar

  • [3] Pfenninger M.C., Nowak C., Kley D., Steinke D., Streit B., Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus(Diptera) species. Mol. Ecol., 2007, 16, 1957-1968. CrossrefWeb of ScienceGoogle Scholar

  • [4] Corin S.E., Lester P.J., Abbott K.L., Ritchie P.A., Inferring historical introduction pathways with mitochondrial DNA: the case of introduced Argentine ants (Linepithema humile) into New Zealand. Divers. Distrib., 2007, doi: 10.1111/j.1472- 4642.2007.00355.x. Web of ScienceCrossrefGoogle Scholar

  • [5] Pons J., Barraclough T.G., Gomez-Zurita J., Cardoso A., Durand D.P., Hazell S., Kamoun S., Sumlin W.D., Vogler., Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst. Biol., 2006, 55, 595-606. CrossrefGoogle Scholar

  • [6] Allen G.R., Damselfishes of South Seas. T.F.H. Publications, Neptune City, NJ, 1975. Google Scholar

  • [7] Elliott J.K., Lougheed S.C., Bateman B., McPhee L.K., Boag P.T., Molecular phylogenetic evidence for the evolution of specialization in anemonefishes. Proc. R. Soc. Lond. B., 1999, 266, 677-685. Google Scholar

  • [8] Tang K.L., Phylogenetic relationships among Damselfishes (Teleostei: Pomacentridae) as determined by mitochondrial DNA data. Copeia., 2001, 3, 591-601. CrossrefGoogle Scholar

  • [9] Quenouille B., Bermingham E., Planes S., Molecular systematics of the damselfishes (Teleostei: Pomacentridae): Bayesian phylogenetic analyses of mitochondrial and nuclear DNA sequences. Mol. Phyl. Evol., 2004, 31, 66-88. Google Scholar

  • [10] Santini S., Polacco G., Finding Nemo: molecular phylogeny and evolution of the unusual life style of anemonefish. Gene., 2006, 385, 19-27. Google Scholar

  • [11] Mabuchi K., Nakabo T., Nishida M., Molecular phylogeny of the antitropical genus Pseudolabrus (Perciformes: Labridae): evidence for a Southern Hemisphere origin. Mol. Phyl. Evol., 2007, 32, 375-382. CrossrefGoogle Scholar

  • [12] Cummins J.M., Wakayama T., Yanagimachi R., Fate of microinjected spermatid mitochondria in the mouse oocyte and embryo. Zygote, 1997, 5, 301-308. CrossrefGoogle Scholar

  • [13] Eyre -Walker A., Awadalla P., Does human mtDNA recombine? J. Mol. Evol., 2001, 53, 430-435. CrossrefGoogle Scholar

  • [14] Ankel-Simons F., Cummins J.M., Misconception about mitochondria and mammalian fertilization: Implications for theories on human evolution. Proc. Natl. Acad. Sci., 1996, 93, 13859-13863. Google Scholar

  • [15] Hebert P.D.N., Gregory T.R., The promise of DNA barcoding for taxonomy. Syst. Biol., 2005, 54, 852–859. CrossrefGoogle Scholar

  • [16] Esposti D.M., De Vries S., Crimi M., Ghelli A., Patarnello T., Meyer A., Mitochondrial cytochrome b: evolution and structure of the protein. Biochim. Biophys. Acta., 1993, 1143, 243-271. Google Scholar

  • [17] Frankham R., Ballou J.D., Briscoe D.A., Introduction to Conservation Genetics, Cambridge Univ. Press, UK, 2002. Google Scholar

  • [18] Bernardi G., Holbrook S.J., Schmitt R.J., Crane N.L., DeMartini E., Species boundaries, populations and colour morphs in the coral reef three - spot damselfish (Dascyllus trimaculatus) species complex. Proc. R. Soc. Lond. B., 2002, 269, 599-605. Google Scholar

  • [19] Fautin D.G., Allen G.R., Anemonenfische und ihre Wirte, Tetra-Verlag, Melle, 1994. Google Scholar

  • [20] Chow S., Clarke M.E., Walsh P.J., PCR-RFLP analysis on thirteen western Atlantic snappers (Subfamily Lutjaninae): a simple method for species and stock identification. Fish. Bull., 1993, 91, 619-627. Google Scholar

  • [21] Miller S.A., Dykes D.D., Polesky H.F., A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res., 1988, 16, 12-15. Google Scholar

  • [22] Ward R., Zemlak T., Innes B., Last P., Hebert P., DNA barcoding Australia’s fish species. Philos. Trans. R. Soc. B. Biol. Sci., 2005, 360, 1847–1857. doi:10.1098/rstb.2005.1716. CrossrefGoogle Scholar

  • [23] Nelson J.S., Hoddell R.J., Chou L.M., Chan W.K., Phang V.P.E., Phylogeographic structure of false clownfish, Amphiprion ocellaris explained by sea level changes on the Sunda shelf. Mar. Biol., 2000, 137, 727-736. Google Scholar

  • [24] Kocher T.D., Thomas W.K., Meyer A., Edwards S.V., Paabo S.F., Villablanca F.X., Wilson A.C., Dynamics of mtDNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci., 1989, 86, 6196-6200. Google Scholar

  • [25] Lee W.J., Howell W.H., Kocher T.D., Structure and evolution of teleost mitochondrial control regions. J. Mol. Evol., 1995, 41, 54-66. Google Scholar

  • [26] Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S., MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol. Biol. Evol., 2011, (In Press). CrossrefWeb of ScienceGoogle Scholar

  • [27] Meyer C.P., Paulay G., DNA bar-coding: error rates based on comprehensive sampling. PLoS Biol., 2005, 3, e422. CrossrefGoogle Scholar

  • [28] Saccone C., De Carla G., Gissi C., Pesole G., Reynes A., Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene, 1999, 238, 195-210. Google Scholar

  • [29] Yearsley G.K., Last P.R., Ward R.D., Australian seafood handbook: an identification guide to domestic species, Australia: CSIRO Marine Research. (Reprinted with minor corrections, 2001), 1999. Google Scholar

  • [30] Nei M., Kumar S., Molecular evolution and phylogenetics. Oxford, UK: Oxford University Press, 2000. Google Scholar

  • [31] Baer C.F., Miyamoto M.M., Denver D.R., Mutation rate variation in multicellular eukaryotes: causes and consequences. Nat. Rev. Gen., 2007, 8, 619-631. CrossrefWeb of ScienceGoogle Scholar

  • [32] Smith M.A., Wood D.M., Janzen D.H., Hallwachs W., Hebert P.D.N., DNA barcodes affirm that 16 species of apparently generalist tropical parasitoid flies (Diptera: Tachinidae) are not all generalists. Proc. Natl. Acad. Sci., 2007, 104, 4967-4972. Web of ScienceGoogle Scholar

  • [33] Farias I.P., Meyer A., Orti G., Total evidence: molecules, morphology, and the phylogenetics of cichlids fishes. J. Exp. Zool., 2000, 288, 76-92. Google Scholar

  • [34] Yoder A.D., Vilgalys R., Ruvolo M., Molecular evolutionary dynamics of cytochrome b in Strepsirrhine primates: the phylogenetic significance of third-position transversions. Mol. Biol. Evol., 1996, 13, 1339-1350. CrossrefGoogle Scholar

  • [35] Bernardi G., Holbrook S .J., Schmitt R.J., Gene flow at three spatial scales in acoral reef fish, the three-spot dascyllus, Dascyllus trimaculatus. Mar. Biol., 2001, 138, 457-465. Google Scholar

  • [36] Ehrlich P.R., The population biology of coral reef fishes. A. Rev. Ecol. Syst., 1975, 6, 211-248. CrossrefGoogle Scholar

  • [37] Shaklee J.B., Genetic variation and population structure in the damselfish Stegastes fasciolatus, throughout the Hawaiian Archipelago. Copeia, 1984, 629-640. CrossrefGoogle Scholar

  • [38] Bell L.J., Moyer J.T., Numachi K., Morphological and genetic variation in Japanese populations of the anemonefish, Amphiprion clarkii. Mar. Biol., 1982, 72, 99-108. Google Scholar

  • [39] Timm J., Figiel M., Kochzius M., Contrasting patterns in species boundaries and evolution of anemonefishes (Amphiprioninae, Pomacentridae) in the centre of marine biodiversity. Mol. Phyl. Evol., 2008, 49, 268-276. Web of ScienceGoogle Scholar

  • [40] Farias I.P., Orti G., Sampaio I., Schneider H., Meyer A., The cytochrome b gene as a phylogenetic marker: the limits of resolution for analyzing relationships among cichlid fishes. J. Mol. Evol., 2001, 53, 89-103. Google Scholar

  • [41] Bernardi G., Bucciarelli G., Molecular phylogeny and speciation of the surfperches (Embiotocidae, Perciformes). Mol. Phyl. Evol., 1999, 13, 77-81. CrossrefGoogle Scholar

  • [42] Kochzius M., Soller R., Khalaf M.A., Blohm D., Molecular phylogeny of the lionfish genera Dendrochirus and Pterois (Scorpaenidae: Pteroidae) based on mitochondrial DNA sequences. Mol. Phyl. Evol., 2003, 28, 396-403. CrossrefGoogle Scholar

About the article

Received: 2014-01-31

Accepted: 2015-01-20

Published Online: 2015-05-27


Citation Information: DNA Barcodes, ISSN (Online) 2299-1077, DOI: https://doi.org/10.1515/dna-2015-0002.

Export Citation

© 2015 Kottila Veettil Dhaneesh et al.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. BY-NC-ND 3.0

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

[1]
Pradipunt Thongtam na Ayudhaya, Narongrit Muangmai, Nuwadee Banjongsat, Worapong Singchat, Sommai Janekitkarn, Surin Peyachoknagul, and Kornsorn Srikulnath
Agriculture and Natural Resources, 2017

Comments (0)

Please log in or register to comment.
Log in