Molecular phylogeny of commercially important lobster species from Indian coast inferred from mitochondrial and nuclear DNA sequences

References

• Ahyong ST, O'Meally D. (2004). Phylogeny of the Decapoda Reptantia: Resolution using three molecular loci and morphology. Raff Bull Zool 52:673–93
   Web of Science ®Google Scholar
• Baisre JA. (1994). Phyllosoma larvae and the phylogeny of Palinuroidea (Crustacea: Decapoda): A review. Mar Freshwater Res 45:925–44
   Web of Science ®Google Scholar
• Ballard JW, Olsen GJ, Faith, DP, Odgers WA, Rowell DM, Atkinson PW. (1992). Evidence from 12S ribosomal RNA sequences that onychophorans are modified arthropods. Science 258:1345–8
   PubMed Web of Science ®Google Scholar
• Berry PF. (1974). A revision of the Panulirus homarus-group of spiny lobsters (Decapoda, Palinuridae). Crustaceana 27:31–42
   Google Scholar
• Botello A, Iliffe TM, Alvarez F, Juan C, Pons J, Jaume D. (2013). Historical biogeography and phylogeny of Typhlatya cave shrimps (Decapoda: Atyidae) based on mitochondrial and nuclear data. J Biogeogr 40:594–607
   Web of Science ®Google Scholar
• Burton TE, Davie PJF. (2007). A revision of the shovel-nosed lobsters of the genus Thenus (Crustacea: Decapoda: Scyllaridae), with descriptions of three new species. Zootaxa 1429:1–38
   Web of Science ®Google Scholar
• Carranza S, Giribet G, Ribera C, Baguña J, Riutort M. (1996). Evidence that two types of 18S rDNA coexist in the genome of Dugesia (Schmidtea) mediterranea (Platyhelminthes, Turbellaria, Tricladida). Mol Biol Evol 13:824–32
   PubMed Web of Science ®Google Scholar
• Chacko S. (1967). The central nervous system of Thenus orientalis (Leach). Mar Biol 1:113–17
   Web of Science ®Google Scholar
• Chan TY, Ho KC, Li CP, Chu KH. (2009). Origin and diversification of the clawed lobster genus Metanephrops (Crustacea: Decapoda: Nephropidae). Mol Phylogenet Evol 50:411–22
   PubMed Web of Science ®Google Scholar
• CMFRI. (2004--2014). Annual reports 2004--2014. Central Marine Fisheries Research Institute, Cochin, India
   Google Scholar
• CMFRI. (2014). Annual report 2013--2014. Central Marine Fisheries Research Institute, Cochin, India. p 16
   Google Scholar
• Cristescu MEA, Hebert PDN. (2002). Phylogeny and adaptive radiation in the Onychopoda (Crustacea, Cladocera): Evidence from multiple gene sequences. J Evol Biol 15:838–49
   Web of Science ®Google Scholar
• Da Silva JM, Creer S, Dos Santos A, Costa AC, Cunha MR, Costa FO, Carvalho GR. (2011). Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca). PLoS One 6:e19449
   PubMed Web of Science ®Google Scholar
• Daniels SR, Stewart BA, Gouws G, Cunningham M, Matthee CA. (2002). Phylogenetic relationships of the southern African freshwater crab fauna (Decapoda: Potamonautidae: Potamonautes) derived from multiple data sets reveal biogeographic patterning. Mol Phylogenet Evol 25:511–23
   PubMed Web of Science ®Google Scholar
• Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3:294–9
   PubMedGoogle Scholar
• Funk DJ, Omland KE. (2003). Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu Rev Ecol Evol Syst 34:397–423
   Web of Science ®Google Scholar
• George RW. (2006). Tethys origin and subsequent radiation of the spiny lobsters (Palinuridae). Crustaceana 79:397–422
   Web of Science ®Google Scholar
• George RW, Main AR. (1967). The evolution of spiny lobsters (Palinuridae): A study of evolution in the marine environment. Evolution 21:803–20
   PubMed Web of Science ®Google Scholar
• Hall TA. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–8
   Google Scholar
• Holthuis LB. (1991). Marine Lobsters of the world. An Annotated and illustrated catalogue of species of interest to fisheries known to date. FAO Species Catalog, FAO Fisheries and Synopsis, No. 125, vol. 13, FAO-UN, Rome
   Google Scholar
• Hwang UW, Kim W. (1999). General properties and phylogenetic utilities of nuclear ribosomal DNA and mitochondrial DNA commonly used in molecular systematics. Korean J Parasitol 37:215–28
   PubMedGoogle Scholar
• Jeena NS, Gopalakrishnan A, Radhakrishnan EV, Lijo J, Joe KK, Basheer VS, Shoba JK, et al. (2011). Molecular phylogeny of commercially important lobster species from Indian waters deduced from mitochondrial and nuclear DNA sequences. Abstract No. GB-O 04. Book of Abstracts, 9th Indian Fisheries Forum, December 19–23, Chennai, India
   Google Scholar
• Kartavtsev YP. (2013). Sequence diversity at Cyt-b and Co-1 mtDNA genes in animal taxa proved neo-Darwinism. J Phylogenet Evol Biol 1:120. doi:10.4172/2329-9002.1000120
   Google Scholar
• Lavalli KL, Spanier E, editors. (2007). The biology and fisheries of the slipper lobster, vol. 17. USA: CRC Press
   Google Scholar
• Librado P, Rozas J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–2
   PubMed Web of Science ®Google Scholar
• Lin FJ, Liu Y, Sha Z, Tsang LM, Chu KH, Chan TY, Cui Z. (2012). Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes. BMC Genomics 13:631
   PubMed Web of Science ®Google Scholar
• Machida RJ, Miya MU, Nishida M, Nishida S. (2002). Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda). Mar Biotechnol 4:406–17
   PubMed Web of Science ®Google Scholar
• McWilliam PS. (1995). Evolution in the phyllosoma and puerulus phases of the spiny lobster genus Panulirus White. J Crust Biol 15:542–57
   Web of Science ®Google Scholar
• Mon TR, Joseph MV, Huxley VAJ. (2011). 18S rRNA gene polymorphisms of Panulirus homarus populations from different geographic regions of Peninsular India. J Theor Exp Biol 8:85–93
   Google Scholar
• MPEDA. (2009). Statistics of marine products 2009. Kochi, Kerala, India: The Marine Exports Development Authority (Government of India, Ministry of Commerce and Industry). p 25, 59
   Google Scholar
• Munasinghe DHN, Murphy NP, Austin CM. (2003). Utility of mitochondrial DNA sequences from four gene regions for systematic studies of Australian freshwater crayfish of the genus Cherax (Decapoda: Parastacidae). J Crust Biol 23:402–17
   Web of Science ®Google Scholar
• Nigro L, Solignac M, Sharp P. (1991). Mitochondrial DNA sequence divergence in the Melanogaster and Oriental species subgroups of Drosophila. J Mol Evol 33:156–62
   PubMed Web of Science ®Google Scholar
• Ovenden JR, Booth JD, Smolenski AJ. (1997). Mitochondrial DNA phylogeny of red and green rock lobsters (genus Jasus). Mar Freshwater Res 48:1131–6
   Web of Science ®Google Scholar
• Palacios-Theil E, Cuesta JA, Campos E, Felder DL. (2009). Molecular genetic re-examination of subfamilies and polyphyly in the family Pinnotheridae (Crustacea: Decapoda). Crustacean Issues 18:423–42
   Google Scholar
• Palero F, Crandall KA, Abelló P, Macpherson E, Pascual M. (2009). Phylogenetic relationships between spiny, slipper and coral lobsters (Crustacea, Decapoda, Achelata). Mol Phylogenet Evol 50:152–62
   PubMed Web of Science ®Google Scholar
• Palero F, Guerao G, Clark PF, Abelló P. (2011). Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. J Mar Biol Assoc UK 91:485–92
   Web of Science ®Google Scholar
• Palumbi SR, Martin A, Romano S, McMillan WO, Stice L, Grabowski G. (1991). The simple fool's guide to PCR, Version 2.0. Hawaii, Honolulu: Privately Published, University
   Google Scholar
• Parker TJ. (1884). On the structure of the head in Palinurus with special reference to the classification of the genus. Nature 29:189–90
   Google Scholar
• Patek SN, Oakley TH. (2003). Comparative tests of evolutionary trade-offs in a palinurid lobster acoustic system. Evolution 57:2082–100
   PubMed Web of Science ®Google Scholar
• Pedraza-Lara C, Doadrio I, Breinholt JW, Crandall KA. (2012). Phylogeny and evolutionary patterns in the dwarf crayfish subfamily (Decapoda: Cambarellinae). PLoS One 7:e48233
   PubMed Web of Science ®Google Scholar
• Phillips BF. (2006). Lobsters: Biology, management, aquaculture and fisheries. Oxford: Blackwell Publishing
   Google Scholar
• Ptacek MB, Sarver SK, Childress MJ, Herrnkind WF. (2001). Molecular phylogeny of the spiny lobster genus Panulirus (Decapoda: Palinuridae). Mar Freshwater Res 52:1037–47
   Web of Science ®Google Scholar
• Radhakrishnan EV, Manisseri MK. (2003). Lobsters. In: Status of exploited marine fishery resources of India. Cochin: CMFRI. p 195–202
   Google Scholar
• Radhakrishnan EV, Deshmukh VD, Manisseri MK, Rajamani M, Kizhakudan JK, Thangaraja R. (2005). Status of the major lobster fisheries in India. New Z J Mar Fresh 39:723–32
   Web of Science ®Google Scholar
• Ratnasingham S, Hebert PD. (2007). BOLD: The Barcode of Life Data System ( http://www.barcodinglife.org). Mol Ecol Notes 7:355–64
   PubMed Web of Science ®Google Scholar
• Ravago RG, Juinio-Meñez MA. (2003). Phylogenetic position of the striped-legged forms of Panulirus longipes (A. Milne-Edwards, 1868) (Decapoda, Palinuridae) inferred from mitochondrial DNA sequences. Crustaceana 75:1047–59
   Web of Science ®Google Scholar
• Sambrook J, Russell DW. (2001). Molecular cloning: A laboratory manual, 3rd ed. New York: Cold Spring Harbor Laboratory Press
   Google Scholar
• Schubart CD, Cannicci S, Vannini M, Fratini S. (2006). Molecular phylogeny of grapsoid crabs (Decapoda, Brachyura) and allies based on two mitochondrial genes and a proposal for refraining from current superfamily classification. J Zool Sys Evol Res 44:193–9
   Web of Science ®Google Scholar
• Simon C, Frati F, Beckenbach A, Crespi B, Liu H, Floors P. (1994). Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann Entomol Soc Am 87:651–701
   Web of Science ®Google Scholar
• Steel MA, Lockhart PJ, Penny D. (1993). Confidence in evolutionary trees from biological sequence data. Nature (Lond) 364:440–2
   PubMed Web of Science ®Google Scholar
• Tamura K, Nei M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–26
   PubMed Web of Science ®Google Scholar
• Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–9
   PubMed Web of Science ®Google Scholar
• Toon A, Finley M, Staples J, Crandall KA. (2009). Decapod phylogenetics and molecular evolution. In: Martin JW, Crandall KA, Felder DL, editors. Decapod crustacean phylogenetics. Crustacean Issues. Koenemann, S. (series editor), vol. 18. Boca Raton, London, New York: CRC Press, Taylor & Francis Group. p 15–28
   Google Scholar
• Torres AP, Palero F, Dos Santos A, Abelló P, Blanco E, Boné A, Guerao G. (2014). Larval stages of the deep-sea lobster Polycheles typhlops (Decapoda, Polychelida) identified by DNA analysis: Morphology, systematic, distribution and ecology. Helgol Mar Res 68:379–97
   Web of Science ®Google Scholar
• Tsoi KH, Chan TY, Chu KH. (2011). Phylogenetic and biogeographic analysis of the spear lobsters Linuparus (Decapoda: Palinuridae), with the description of a new species. Zool Anz 250:302–15
   Web of Science ®Google Scholar
• Vijayakumaran M, Radhakrishnan EV. (2011). Slipper lobsters. In: Recent advances and new species in aquaculture. Chichester, England: Wiley-Blackwell. p 85–114
   Google Scholar
• Webber WR, Booth JD. (2007). Taxonomy and evolution. In: The biology and fisheries of the slipper lobster. USA: CRC Press. p 26–52
   Google Scholar
• Whiting MF. (2002). Mecoptera is paraphyletic: Multiple genes and phylogeny of Mecoptera and Siphonaptera. Zool Scripta 31:93–104
   Web of Science ®Google Scholar
• Yang CH, Bracken-Grissom H, Kim D, Crandall KA, Chan TY. (2012). Phylogenetic relationships, character evolution, and taxonomic implications within the slipper lobsters (Crustacea: Decapoda: Scyllaridae). Mol Phylogenet Evol 62:237–50
   PubMed Web of Science ®Google Scholar