Abstract
The phylogenetic relationships within the family Penaeidae are examined based on mitochondrial 16S rRNA gene sequence analysis of 30 species from 20 genera. The analysis generally supports the three-tribe scheme proposed by Burkenroad (1983) but it is not consistent with the five-group classification of Kubo (1949). Three clades are resolved: (Penaeus sensu stricto + Fenneropenaeus + Litopenaeus + Farfantepenaeus + Marsupenaeus + Melicertus + Funchalia + Heteropenaeus), (Metapenaeus + Parapenaeopsis + Xiphopenaeus + Rimapenaeus + Megokris + Trachysalambria) and (Metapenaeopsis + Penaeopsis + Parapenaeus), corresponding to the Penaeini, Trachypenaeini and Parapenaeini respectively, while the affinities of Atypopenaeus and Trachypenaeopsis are obscure. The molecular data support that Miyadiella represents the juvenile stage of Atypopenaeus. Within the Trachypenaeini, Trachypenaeus sensu lato is clearly paraphyletic, while the monophyly of Penaeus sensu lato in the Penaeini is questionable.References
Abele, L. (1991) Comparison of morphological and molecular phylogeny of the Decapoda. Memoirs of the Queensland Museum, 31, 101–108.
Burkenroad, M.D. (1983) Natural classification of Dendrobranchiata, with a key to recent genera. In: Schram, F.R. (Ed), Crustacean Issues I. Crustacean Phylogeny. A.A. Balkema, Rotterdam, pp. 279–290.
Camin, J.H. & Sokal, R.R. (1965) A method for deducing branching sequences in phylogeny. Evolution, 19, 311–326.
Chan, T.Y. (1998) Shrimps and prawns. In: Carpenter, K.E. & Niem, V.H. (Eds), FAO Species Identification Guide for Fishery Purposes. The Living Marine Resources of the Western Central Pacific. FAO, Rome, pp. 851–971.
Dall, W. (2007) Recent molecular research on Penaeus sensu lato. Journal of Crustacean Biology, 27, 380–382.
Dall, W., Hill, B.J., Rothlisberg, N.W. & Staples, D.J. (1990) The Biology of Penaeidae. Advances in Marine Biology, 27, 1–484.
Drummond, A.J. & Rambaut, A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
Felsenstein, J. (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 17, 368–376.
Flegel, T.W. (2007) The right to refuse revision in the genus Penaeus. Aquaculture, 264, 2–8.
Glaessner, M.F. (1969) Decapoda. In: Moore, R.C. (Ed), Treastise on Invertebrate Palaeontology Part R Arthropoda 4 Vol II. The Geological Society of America Inc and The University of Kansa Press, Bouder, Colorado, Lawrence, pp. 399–533.
Gleason, J.M., Caccone, A., Moriyama, E.N., White, K.P. & Powell, J.R. (1997) Mitochondrial DNA phylogenies for the Drosophila obscura group. Evolution, 51, 433–440.
Gascuel, O. (1997) BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Molecular Biology and Evolution, 14, 685–695.
Hayashi, K.I. (1992) Dendrobranchiata Crustaceans from Japanese Waters. Seibutsu Kenkyusha, Tokyo, pp.1–300.
Holthuis, L.B. (1980) FAO Species Catalogue. Volume 1. Shrimps and Prawns of the World. An Annotated Catalogue of Species of Interest to Fisheries. FAO Fisheries Synopsis No. 125, Vol. 1. FAO, Rome, pp.1–271.
Holthuis, L.B. (1993) The Recent Genera of the Caridean and Stenopodidean Shrimps (Crustacea, Decapoda): With an Appendix on the Order Amphionidacea. National Natuurhistorisch Museum, Leiden, pp. 1-328.
Jarman, S.N., Elliott, N.G., Nicol, S. & McMinn, A. (2000) Molecular phylogenetics of circumglobal Euphausia species (Euphausiacea: Crustacea). Canadian Journal of Fisheries and Aquatic Sciences, 57, 51–58.
Kishino, H. & Hasegawa, M. (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. Journal of Molecular Evolution, 29, 170–179.
Kubo, I. (1949) Studies on penaeids of Japan and its adjacent waters. Journal of the Tokyo University of Fisheries, 36, 178–192.
Lavery, S., Chan, T.Y., Tam, Y.K. & Chu, K.H. (2004) Phylogenetic relationships and evolutionary history of the shrimp genus Penaeus s.l. derived from mitochondrial DNA. Molecular Phylogenetics and Evolution, 31, 39–49.
Liu, J.Y. & Zhong, Z. (1986) Penaeoid Shrimps of the South China Sea. Agricultural Publishing House, Beijing, pp. 67–86 (in Chinese).
Maggioni, R., Rogers, A.D., Maclean, N. & D’Incao, F. (2001) Molecular phylogeny of western Atlantic Farfantepenaeus and Litopenaeus shrimp based on mitochondrial 16S partial sequences. Molecular Phylogenetics and Evolution, 18, 66–73.
Martin, J.W. & Davis, G.E. (2001) An Updated Classification of the Recent Crustacea. Science Series 39 Natural History Museum of Los Angeles County, Los Angeles, CA, USA, pp. 1–124.
Palumbi, S.R. & Benzie, J. (1991) Large mitochondrial DNA differences between morphologically similar penaeid shrimp. Molecular Marine Biology and Biotechnology, 1, 27–34.
Palumbi, S.R., Mable, B. & Moritz, C. (1996) The polymerase chain reaction. In: Hillis, D.M., Moritz, C. & Mable, B. (Eds), Molecular Systematics 2nd ed. Sinauer, Sunderland, Massachusetts, pp. 205–246.
Pérez Farfante, I. (1988) Illustrated key to the penaeoid shrimps of commerce in the Americas. NOAA Technical Reports NMFS, 64, 1–32.
Pérez Farfante, I. & Kensley, B. (1997) Penaeoid and Sergestoid Shrimps and Prawns of the World. Éditions du Muséum national d’Histoire naturelle, Paris, 152 pp.
Posada, D. & Crandall, K.A. (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics, 14, 817–818.
Quan, J., Zhuang, Z., Deng, J., Dai, J. & Zhang, Y. (2004) Phylogenetic relationships of 12 Penaeoidea shrimp species deduced from mitochondrial DNA sequences. Biochemical Genetics, 42, 331–345.
Rambaut, A. & Drummond, A.J. (2003) Tracer: MCMC Trace Analysis Tool, 1.2 ed. University of Oxford, Oxford.
Saiki, R., Gelfand, D.H., Stoffel, S., Scharf, S.J., Higuchi, R., Horn, G.T., Mullis, K.B. & Erlich, H.A. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science, 239, 487–491.
Saitou, N. & Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology Evolution, 4, 406–425.
Schram, F.R. (1977) Paleozoogeography of late Paleozoic and Triassic Malacostraca. Systematic Zoology, 26, 367–379.
Schram, F.R. (1982) The fossil record and evolution of Crustacea. In: Abele, L.G. (Ed), The Biology of Crustacea Vol 1. Academic Press, New York and London, pp. 241–304.
Shafer, A.B.A. & Stewart, D.T. (2007) Phylogenetic relationships among Nearctic shrews of the genus Sorex (Insectivora, Soricidae) inferred from combined cytochrome b and inter-SINE fingerprint data using Bayesian analysis. Molecular Phylogenetics and Evolution, 44, 192–203.
Shimodaira, H. & Hasegawa, M. (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16, 1114–1116.
Starobogatov, Y.I. (1972) Penaeidae (Crustacea Decapoda) of Tonking Gulf. Issledovanyia Fauny Morei, 10, 359–414 (in Russian).
Swofford, D.L. (1999) PAUP*: Phylogenetic Analysis using Parsimony (*and Other Methods), Version 4.0b 10. Sinauer Associates, Sunderland, Massachusetts.
Thompson, J.D., Higgins, D.G. & Gibson, T.J. (1994) Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673–4680.
Tong, J.G., Chan, T.Y. & Chu, K.H. (2000) A preliminary phylogenetic analysis of Metapenaeopsis (Decapoda: Penaeidae) based on mitochondrial DNA sequences of selected species from the Indo-West Pacific. Journal of Crustacean Biology, 20, 541–549.
Vázquez-Bader, A.R., Carrero, J.C., García Varela, M., Gracía, A. & Laclette, J.P. (2004) Molecular phylogeny of superfamily Penaeoidea Rafinesque-Schmaltz, 1815, based on mitochondrial 16S partial sequence analysis. Journal of Shellfish Research, 23, 911–917.
Voloch, C.M., Freire, P.R. & Russo, C.A.M. (2005) Molecular phylogeny of penaeid shrimps inferred from two mitochondrial markers. Genetics and Molecular Research, 4, 668–674.
Wilson, A.C., Carlso, S.S. & White, T.J. (1977) Biochemical evolution. Annual Review of Biochemistry, 46, 573–639.
Wilson, A.C., Sarich, V.M. & Maxson, L.R. (1974) The importance of gene rearrangement in evolution: Evidence from studies of rates of chromosomal, protein, and anatomical evolution. Proceedings of the National Academy of Sciences USA, 71, 3028–3030.
Yasuda, J. (1966) On the form of young stage of Atypopenaeus Compressipes (Henderson). Journal of Natural Scientific Society of Nagoya Keizai University and Ichimura Gakuen College, 1, 1–6.
Yu, H.P. & Chan, T.Y. (1986) The Illustrated Penaeoid Prawns of Taiwan. Southern Materials Center, Taipei, pp. 1–183.