Abstract
We infer a phylogeny of haemulid genera using mitochondrial COI and Cyt b genes and nuclear RAG1, SH3PX3, and Plagl2 genes from 56 haemulid species representing 18 genera of the expanded haemulids (including the former inermiids) and ten outgroup species. Results from maximum parsimony, maximum likelihood, and Bayesian analyses show strong support for a monophyletic Haemulidae with the inclusion of Emmelichthyops atlanticus. The former inermiids did not form a clade indicating that the highly protrusible upper jaw specialization to planktivory evolved more than once within Haemulidae. The subfamilies Haemulinae and Plectorhinchinae, currently diagnosed by eight morphological characters, most notably the number of chin pores and the origin of the retractor dorsalis, are also recovered from these analyses with the Haemulinae sister to the Plectorhinchinae. Plectorhinchus is monophyletic only with the inclusion of Diagramma. Within the Haemulinae, Pomadasys and Conodon are polyphyletic. In addition, Anisotremus is monophyletic only with the inclusion of Genyatremus and Conodon nobilis, and Haemulon is monophyletic only with the inclusion of Xenistius. These results suggest that further morphological and molecular studies are needed to revise the limits of several haemulid genera.References
Bernardi, G., Alva–Campbell, Y., Gasparini, J. & Floeter, S. (2008) Molecular ecology, speciation, and evolution of the reef fish genus Anisotremus. Molecular Phylogenetics and Evolution, 48, 929–935.
Bernardi, G. & Lape, J. (2005) Tempo and mode of speciation in the Baja California disjunct fish species Anisotremus davidsonii. Molecular Ecology, 14, 4085–4096.
Brandley, M.C., Schmitz, A. & Reeder, T.W. (2005) Partitioned Bayesian Analyses, Partition Choice, and the Phylogenetic Relationships of Scincid Lizards. Systematic Biology, 54, 373–390.
Courtenay, W.R.J. (1961) Western Atlantic fishes of the genus Haemulon (Pomadasyidae): Systematic status and juvenile pigmentation. Bulletin of Marine Science, 66–149.
Chen, D., Burleigh, J.G. & Fernández-Baca, D. (2007) Spectral Partitioning of Phylogenetic Data Sets Based on Compatibility. Systematic Biology, 56, 623–632.
Craig, M.T. & Hastings, P.A. (2007) A molecular phylogeny of the groupers of the subfamily Epinephelinae (Serranidae) with a revised classification of the Epinephelini. Ichthyological Research, 54, 1–17.
Dettai, A. & Lecointre, G. (2005) Further support for the clades obtained by multiple molecular phylogenies in the acanthomorph bush. C. R. Biologies, 328, 674–689.
Eschmeyer, W.N. (1990) Catalog of the Genera of Recent fishes: Special Publication, California Academy of Sciences, VI, 697 pp.
Gill, T.N. (1861) Catalogue of the fishes of the eastern coast of North America, from Greenland to Georgia. Proceedings of the Academy of Natural Sciences of Philadelphia, 13 (Suppl.), 1–63.
Girard, C.F. (1858) Notes upon various new genera and new species of fishes, in the museum of the Smithsonian Institution, and collected in connection with the United States and Mexican boundary survey: Major William Emory, Commissioner. . Proceedings of the Academy of Natural Sciences of Philadelphia, 10, 167–171.
Hall, B.G. (2004) Phylogenetic trees made easy: A how–to–manual (Vol. Second ed. ). Sinauer Associates, Inc. 221 pp.
Huelsenbeck, J.P. & Ronquist, F. (2001) MRBAYES: Bayesian inference of phylogeny. Bioinformatics, 17, 754–755.
Iwatsuki, Y., Kohno, H. & Ida, H. (1998) Redescription of a poorly–known haemulid fish, Pomadasys unimaculatus Tian, 1982, from Malaysia and comparison with P. maculatus (Bloch 1797) (Perciformes: Haemulidae). Ichthyological Research, 45, 195–200.
Iwatsuki, Y. & Nakabo, T. (2005) Redescription of Hapalogenys nigripinnis (Schlegel in Temminck & Schlegel 1843), a senior synonym of H. nitens Richardson, 1844, and a new species from Japan. Copeia, 4, 854–867.
Iwatsuki, Y. & Russell, B.C. (2006) Revision of the genus Hapalogenys (Teleostei: Perciformes) with two new species from the Indo–West Pacific. Memoirs of Museum Victoria, 63, 29–46.
Iwatsuki, Y., Satapoomin, U. & Amaoka, K. (2000) New Species: Hapalogenys merguiensis (Teleostei; Perciformes) from Andaman Sea. Copeia, 1, 129–139.
Johnson, G.D. (1981) The Limits and Relationships of Lutjanidae and Associated Families. In: Cox, C.S., Vincent, E.S., Fleminger, A. & Rosenblatt, R.H. (Eds), Bulletin of the Scripps Institution of Oceanography. University of California Press, Berkeley, pp. 1–112.
Johnson, G.D. (1984) Percoidei: development and relationships. In: Moser, H.G. et al. (Eds), American Society of Ichthyologists and Herpetologists Special Publication no. 1, pp. 464–498.
Jordan, D.S. & Bollman, C.H. (1890) Descriptions of new species collected at the Galapagos Islands and along the coast of the United States and Colombia. Proceedings of the United States National Museum, 12, 149–183.
Jordan, D.S. & Gilbert, C.H. (1882) Synopsis of the fishes of North America. Bulletin of the United States National Museum, 16, 1–1018.
Kass, R.E. & Raftery, A.E. (1995) Bayes Factors. Journal of the American Statistical Association, 90, 773–795.
Konchina, Y.V. (1976) The systematics and distribution of the grunts family (Pomadasyidae). Japanese Journal of Ichthyology, 16, 883–900.
Konchina, Y.V. (1977) Some data on the biology of grunts (Family Pomadasyidae). Japanese Journal of Ichthyology, 17, 548–558.
Li, C., Lu, G. & Ortí, G. (2008) Optimal Data Partitioning and a Test Case for Ray–Finned Fishes (Actinopterygii) Based on Ten Nuclear Loci. Systematic Biology, 57, 519–539.
Li, C. & Ortí, G. (2007) Molecular phylogeny of Clupeiformes (Actinopterygii) inferred from nuclear and mitochondrial DNA sequences. Molecular Phylogenetics and Evolution, 44, 386–398.
Li, C., Ortí, G., Zhang, G. & Lu, G. (2007) A practical approach to phylogenomics: the phylogeny of ray–finned fish (Actinopterygii) as a case study. BMC Evolutionary Biology, 7, 44.
Lindeman, K.C. (2006) CHAPTER 141 – INERMIIDAE: Bonnetmouths. In: Richards, W. J. (Ed), Early Stages of Atlantic Fishes: An Identification Guide for the Western Central North Atlantic, Two Volume Set. Taylor & Francis, CRC Press, USA, Boca Raton, FL., 1341pp.
Lindeman, K.C. & Toxey, C. (2003) Haemulidae – Grunts. In: Carpenter, K.E. (Ed), The living marine resources of the Western Central Atlantic. FAO species identification guide for fishery purposes and American Society of Ichthyologists and Herpetologists Special Publication No. 5, FAO, Rome, Italy, pp. 1375–2127.
López, J.A., Chen, W.–J. & Ortí, G. (2004) Esociform Phylogeny. Copeia, 3, 449–564.
Maddison, W.P. & Maddison, D.R. (2007) Mesquite: a modular system for evolutionary analysis. Version 2.71
Mahon, A.R. (2007) Molecular phylogenetics of perciform fishes using the nuclear recombination activating gene 1. PhD Dissertation, Norfolk, Virginia, USA, p. 303.
McEachran, J.D. & Fechhelm, J.D. (2005) Fishes of the Gulf of Mexico: Scorpaeniformes to Tetraodontiformes (Vol. 2). University of Texas Press, Austin, 228 pp.
McKay, R.J. (1984) Haemulidae. In: Fischer, W. & Bianchi, G. (Eds), FAO species identification sheets for fishery purposes. Western Indian Ocean (Fishing Area 51), p. pag. var.
McKay, R.J. (2001) Haemulidae (= Pomadasyidae). Grunts (also sweetlips, rubberlips, hotlips, and velvetchins). In: Carpenter, K.E. & Niem, V. (Eds), FAO species identification guide for fishery purposes. The living marine resources of the Western Central Pacific, FAO, Rome, Italy, p. 589.
McKay, R.J. & Schneider, M. (1995) Haemulidae. Burros, corocoros, chulas, gallinazos, roncos. In: Fischer, W., Krupp, F.,
Schneider, W., Sommer, C., Carpenter, K.E. & Niem, V. (Eds), Guia FAO para Identification de especies para lo fines de la pesca. Pacifico Centro–Oriental. Food and Agriculture Organization of the United Nations, Rome, Italy, pp. 1136–1173.
Miles, C. (1953) A New Pomadasid Fish from the Colombian Caribbean. Journal of the Linnean Society of London, 42, 273–275.
Nelson, J. (2006) Fishes of the world (Fourth ed.). John Wiley & Sons, Inc., Hoboken, New Jersey, 601 pp.
Nylander, J.A.A., Ronquist, F., Huelsenbeck, J.P. & Nieves–Aldrey, J.L. (2004) Bayesian Phylogenetic Analysis of Combined Data. Systematic Biology, 53, 47–67.
Nylander, J.A.A., Wilgenbusch, J.C., Warren, D.L. & Swofford, D.L. (2008) AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics, 24, 581–583.
Ogden, J.C. & Ehrlich, P.R. (1977) The behavior of heterotypic resting schools of juvenile grunts (Pomadasyidae). Marine Biology, 42, 273–280.
Orrell, T.M., Carpenter, K.E., Musick, J.A. & Graves, J.E. (2002) Phylogenetic and Biogeographic Analysis of the Sparidae (Perciformes: Percoidei) from Cytochrome b Sequences. Copeia, 3, 618–631.
Rambaut, A. & Drummond, A. (2007) Tracer v1.4. Available from http://beast.bio.ed.ac.uk/Tracer (accessed 5 June 2010).
Ren, G. & Zhang, Q. (2007) Phylogeny of haemulid with discussion on systematic position of the genus Hapalogenys. Acta Zootaxonomica Sinica, 32, 835–841.
Richardson, J. (1844) Description of a genus of Chinese fish. Annals and Magazine of Natural History, 13, 461–462.
Rocha, L.A., Lindeman, K.C., Rocha, C.R. & Lessios, H.A. (2008) Historical biogeography and speciation in the reef fish genus Haemulon (Teleostei: Haemulidae). Molecular Phylogenetics and Evolution, 48, 918–928.
Ronquist, F. & Huelsenbeck, J. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572–1574.
Roux, C. (1981) Pomadasyidae. In: Fischer, W., Bianchi, G. & Scott, W.B (Eds), FAO species identification sheets for fishery purposes. Eastern Central Atlantic; fishing areas 34, 47 (in part). Department of Fisheries and Oceans Canada and FAO. Vol. 3. Bony fishes (Malacanthidae to Scombridae) FAO, Rome, Italy, p. pag. var.
Seutin, G., White, B.N. & Boag, P.T. (1990) Preservation of avian blood and tissue samples for DNA analysis. Canadian Journal of Zoology, 69, 82–90.
Smith, J.L.B. (1962) Fishes of the Family Gaterinidae of the Western Indian Ocean and the Red Sea with a Resume of all known Indo Pacific Species. Ichthyological Bulletin, 25, 469–502.
Smith, W.L. & Craig, M. (2007) Casting the Percomorph Net Widely: The Importance of Broad Taxonomic Sampling in the Search for the Placement of Serranid and Percid Fishes. Copeia, 1, 35–55.
Sorenson, M.D. & Franzosa, E.A. (2007) TreeRot, version 3. Boston University, Boston, MA.
Springer, V.G. & Raasch, M.S. (1995) Fishes, angling, and finfish fisheries on stamps of the world. American Topical Association. Handbook 129. Tucson, Arizona, 110 pp.
Swofford, D. (2002) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4.
Tavera, J.J., Pizarro, A.A., de la Cruz–Agüero, J. & Balart, E.F. (2011) Phylogeny and reclassification of the species of two neotropical grunt genera, Anisotremus and Genyatremus (Perciformes: Haemulidae), based on morphological evidence. Journal of Zoological Systematics and Evolutionary Research. DOI: 10.1111/j.1439-0469.2011.00622.x.
Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G. (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 24, 4876–4882.
Ward, R.D., Zemlak, T.S., Innes, B.H., Last, P.R. & Hebert, P.D.N. (2005) Barcoding Australia’s fish species. Philosophical Transactions of the Royal Society of London B, 360, 1847–1857.
Wiley, E.O. & Johnson, G.D. (2010) A teleost classification based on monophyletic groups. In: Nelson, J.S., Schultze, J.S. & Wilson, M.V.H. (Eds), Origin and Phylogenetic Interrelationships of Teleosts. Verlag Dr. Friedrich Pfeil, München, Germany, pp. 123–182.
Williams, A., Begg, G., Garrett, R., Larson, H. & Griffiths, S. (2004) Coastal Fishes. In: National Oceans Office. Description of key species groups in the Northern Planning Area. National Oceans Office, Hobart, Australia, p. 320.
Zhang, J. & Hanner, R. (2008) DNA Barcoding of fishes in the South China Sea. Unpublished.
Zhu, S.H., Zheng, W.J. & Zou, J.X. (2007) Molecular phylogenetic relationship of Carangidae based on sequence of complete mitochondrial cytochrome b gene. Zoology, 53, 641–650.
Zwickl, D.J. (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. The University of Texas at Austin, Austin, Texas.