Three genetic stocks of frigate tuna Auxis thazard thazard (Lacepede, 1800) along the Indian coast revealed from sequence analyses of mitochondrial DNA D-loop region

References

• Alvarado Bremer JR. 1994 . Assessment of morphological and genetic variation of the swordfish (Xiphias gladius Linnaeus): Evolutionary patterns of nucleotide substitution in the mitochondrial genome . PhD Thesis , University of Toronto , Ontario , Canada . 242 pages .
   Google Scholar
• Alvarado Bremer , JR , Mejuto , J and Baker , AJ. 1995 . Mitochondrial DNA control region sequences indicate extensive mixing of swordfish (Xiphias gladius L.) populations in the Atlantic Ocean . Canadian Journal of Fisheries and Aquatic Sciences , 52 : 1720 – 32 .
   Web of Science ®Google Scholar
• Alvarado Bremer , JR , Mejuto , J , Gómez-Márquez , J , Boán , F , Carpintero , P Rodráuez , JM . 2005 . Hierarchical analyses of genetic variation of samples from breeding grounds and feeding grounds confirm genetic partitioning northwest Atlantic and South Atlantic population of swordfish (Xiphias gladius L.) . Journal of Experimental Marine Biology and Ecology , 327 : 167 – 82 .
   Web of Science ®Google Scholar
• Alvarado Bremer , JR , Mejuto , J , Greig , TW and Ely , B. 1996 . Global population structure of the swordfish (Xiphias gladius L.) as revealed by analysis of the mitochondrial DNA control region . Journal of Experimental Marine Biology and Ecology , 197 : 295 – 310 .
   Web of Science ®Google Scholar
• Alvarado Bremer , JR , Stequert , B , Robertson , NW and Ely , B. 1998 . Genetic evidence for inter-oceanic subdivision of bigeye tuna (Thunnus obesus) populations . Marine Biology , 132 : 547 – 57 .
   Web of Science ®Google Scholar
• Asahida , T , Kobayashi , T , Saitoh , K and Nakayama , I. 1996 . Tissue preservation and total DNA extraction from fish stored at ambient temperature using buffers containing high concentration of urea . Fisheries Science , 62 : 727 – 30 .
   Web of Science ®Google Scholar
• Beerli , P and Palczewski , M. 2010 . Unified framework to evaluate panmixia and migration direction among multiple sampling locations . Genetics , 185 : 313 – 26 .
   PubMed Web of Science ®Google Scholar
• Brown , GG , Gadaleta , G , Pepe , G , Saccone , C and Sbisa , E. 1986 . Structural conservation and variation in D-loop-containing region of vertebrate mitochondrial DNA . Journal of Molecular Biology , 192 : 503 – 11 .
   PubMed Web of Science ®Google Scholar
• Catanese , G , Infante , C and Manchado , M. 2007 . Complete mitochondrial DNA sequences of the frigate tuna Auxis thazard and the bullet tuna Auxis rochei . DNA Sequence , 1 : 1 – 8 .
   Google Scholar
• Chiang , H-C , Hsu , C-C , Lin , H-D , Ma , GC , Chiang , T-Y and Yang , HY. 2006 . Population structure of bigeye tuna (Thunnus obesus) in South China Sea, Philippine Sea and Western Pacific Ocean inferred from mitochondrial DNA . Fisheries Research , 79 : 219 – 25 .
   Web of Science ®Google Scholar
• Chow , S , Okamoto , H , Miyabe , N , Hiramatsu , K and Barut , N. 2000 . Genetic divergence between Atlantic and Indo-Pacific stocks of bigeye tuna (Thunnus obesus) and admixture around South Africa . Molecular Ecology , 9 : 221 – 27 .
   PubMed Web of Science ®Google Scholar
• Collette , BB and Nauen , CE. 1983 . FAO species catalogue, vol. 2. Scombrids of the world. An annotated and illustrated catalogue of tunas, mackerels, bonitos, and related species known to date . FAO Fisheries Synopsis , 125 : 1 – 137 .
   Google Scholar
• Crosetti , D , Nelson , WS and Avise , JC. 1994 . Pronounced genetic structure of mitochondrial DNA among populations of the circumglobally distributed grey mullet (Mugil cephalus Linnaeus) . Journal of Fish Biology , 44 : 47 – 58 .
   Web of Science ®Google Scholar
• Dammannagoda , ST , Hurwood , DA and Mather , PB. 2008 . Evidence for fine geographical scale heterogeneity in gene frequency in yellowfin tuna (Thunnus albacares) from north Indian Ocean around Sri Lanka . Fisheries Research , 90 : 147 – 57 .
   Web of Science ®Google Scholar
• Dammannagoda , ST , Hurwood , DA and Mather , PB. 2011 . Genetic analysis reveals two stocks of skipjack tuna (Katsuwonus pelamis) in northwestern Indian Ocean . Canadian Journal of Fisheries and Aquatic Sciences , 68 : 210 – 23 .
   Web of Science ®Google Scholar
• Donaldson , KA and Wilson , RR. 1999 . Amphi-Panamaic geminates of snook (Percoidei: Centropomidae) provide a calibration of the divergence rates in the mitochondrial DNA control region of fishes . Molecular Phylogenetics and Evolution , 13 : 208 – 13 .
   PubMed Web of Science ®Google Scholar
• Dupanloup , I , Schneider , S and Excoffier , L. 2002 . A simulated annealing approach to define the genetic structure of populations . Molecular Ecology , 11 : 2571 – 81 .
   PubMed Web of Science ®Google Scholar
• Durand , JD , Collet , A , Chow , S , Guinand , B and Borsa , P. 2005 . Nuclear and mitochondrial DNA markers indicate unidirectional gene flow of Indo-Pacific to Atlantic bigeye tuna (Thunnus obesus) populations, and their admixture off southern Africa . Marine Biology , 147 : 313 – 22 .
   Web of Science ®Google Scholar
• Ely , B , Stoner , DS , Alvarado Bremer , JR , Dean , JM , Addis , P Cau , A . 2002 . Analyses of nuclear ldhA gene and mtDNA control region sequences of Atlantic northern bluefin tuna populations . Marine Biotechnology , 4 : 583 – 88 .
   PubMed Web of Science ®Google Scholar
• Excoffier , L , Laval , G and Schneider , S. 2005 . Arlequin version 3.11: An integrated software package for population genetics data analysis . Evolutionary Bioinformatics , 1 : 47 – 50 .
   PubMed Web of Science ®Google Scholar
• Excoffier , L , Smouse , PE and Quattro , JM. 1992 . Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data . Genetics , 131 : 479 – 91 .
   PubMed Web of Science ®Google Scholar
• Felsenstein , J. 1985 . Confidence limits on phylogenies: An approach using the bootstrap . Evolution , 39 : 783 – 91 .
   PubMed Web of Science ®Google Scholar
• Finnerty , JR and Block , BA. 1992 . Direct sequencing of mitochondrial DNA detects highly divergent haplotypes in blue marlin (Makaira nigricans) . Molecular Marine Biology and Biotechnology , 1 : 206 – 14 .
   PubMedGoogle Scholar
• Fu , YX. 1997 . Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection . Genetics , 147 : 915 – 25 .
   PubMed Web of Science ®Google Scholar
• Garber , AF , Tringali , MD and Franks , JS. 2005 . Population genetic and phylogeographic structure of wahoo, Acanthocybium solandri, from the western central Atlantic and central Pacific Oceans . Marine Biology , 147 : 205 – 14 .
   Web of Science ®Google Scholar
• Garber , AF , Tringali , MD and Stuck , KC. 2004 . Population structure and variation in red snapper (Lutjanus campechanus) from the Gulf of Mexico and Atlantic coast of Florida as determined from mitochondrial DNA control region sequence . Marine Biotechnology , 6 : 175 – 85 .
   PubMed Web of Science ®Google Scholar
• George , KC. 1989 . Results of ichthyoplankton surveys along the southwest coast of India with special reference to pelagic fish resources . Journal of Marine Biology Association of India , 31 : 119 – 72 .
   Google Scholar
• Grant , WS and Bowen , BW. 1998 . Shallow population histories in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation . Journal of Heredity , 89 : 415 – 26 .
   Web of Science ®Google Scholar
• Graves , JE and McDowell , JR. 1995 . Inter-ocean genetic-divergence of istiophorid billfishes . Marine Biology , 122 : 193 – 203 .
   Web of Science ®Google Scholar
• Guarniero , I , Franzellitti , S , Ungaro , N , Tommasini , S , Piccinetti , C and Tinti , F. 2002 . Control region haplotype variation in the central Mediterranean common sole indicates geographical isolation and population structuring in Italian stocks . Journal of Fish Biology , 60 : 1 – 16 .
   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 Symposium Series , 41 : 95 – 98 .
   Google Scholar
• Harpending , RC. 1994 . Signature of ancient population growth in a low resolution mitochondrial DNA mismatch distribution . Human Biology , 66 : 591 – 600 .
   PubMed Web of Science ®Google Scholar
• Infante , C , Catanese , G , Ponce , M and Manchado , M. 2004 . Novel method for the authentication of frigate tunas (Auxis thazard and Auxis rochei) in commercial canned products . Journal of Agricultural and Food Chemistry , 52 : 7435 – 43 .
   PubMed Web of Science ®Google Scholar
• James PSBR , Srinath M , Jayaprakash AA. 1987 . Stock assessment of tunas in the seas around India . Collective Volume of Working Document FAO/IPTP, II . 353 – 66 .
   Google Scholar
• Lin , W-F and Hwang , D. 2007 . Application of PCR-RFLP analysis on species identification of canned tuna . Food Control , 18 : 1050 – 57 .
   Web of Science ®Google Scholar
• Lindak , P and Paul , M. 1994 . Developments in molecular genetic techniques in fisheries . Reviews in Fish Biology and Fisheries , 4 : 272 – 99 .
   Web of Science ®Google Scholar
• Maguire JJ , Sissenwine M , Csirke J , Grainger R , Garcia S. 2006 . Highly Migratory Species . The State of World Highly Migratory, Straddling and Other High Seas Fishery Resources and Associated Species . Rome : Food and Agriculture Organization of the United Nations . 84 pages .
   Google Scholar
• Melissa , AP , McDowell , JR and Graves , JE. 2008 . Specific identification using COI sequence analysis of scombrid larvae collected off the Kona coast of Hawaii Island . Ichthyological Research , 55 : 7 – 16 .
   Web of Science ®Google Scholar
• Menezes , MR , Ikeda , M and Taniguchi , N. 2006 . Genetic variation in skipjack tuna Katsuwonus pelamis (L.) using PCR-RFLP analysis of mitochondrial DNA D-loop region . Journal of Fish Biology , 68 : 156 – 61 .
   Web of Science ®Google Scholar
• Menezes , MR , Kumar , G and Kunal , SP. 2012 . Population genetic structure of skipjack tuna Katsuwonus pelamis from the Indian coast using sequence analysis of the mitochondrial DNA D-loop region . Journal of Fish Biology , 80 : 2198 – 212 .
   PubMed Web of Science ®Google Scholar
• Morley , RJ and Flenley , JR. 1987 . “ Late Cainozoic vegetational and environmental changes in the Malay Archipelago ” . In Biogeographical Evolution of the Malay Archipelago , Edited by: Whitmore , TC . 50 – 59 . Oxford : Clarendon Press .
   Google Scholar
• Motomura , H and Senou , H. 2002 . Record of Polydactylus sexfilis (Perciformes: Polynemidae) from Hachijo-jima, Izu Islands, Japan with comments on morphological changes with growth and speciation of related species . Bulletin of the Kanagawa Prefectural Museum (Natural Sciences) , 31 : 27 – 31 .
   Google Scholar
• Pardini , AT , Jones , CS , Noble , LR , Kreiser , B , Malcolm , H Bruce , BD . 2001 . Sex-biased dispersal of great white sharks . Nature , 412 : 139 – 40 .
   PubMed Web of Science ®Google Scholar
• Pillai PP , Gopakumar G. 2003 . Tunas . In : Mohan Joseph M , Jayaprakash AA Status of Exploited Marine Fishery Resources of India . Central Marine Fisheries Research Institute , Kochi , 51 – 59 .
   Google Scholar
• Posada , D. 2008 . jModelTest: Phylogenetic model averaging . Molecular Biology and Evolution , 25 : 1253 – 56 .
   PubMed Web of Science ®Google Scholar
• Randall , JE and Satapoomin , U. 1999 . Archamia ataenia, a new species of cardinalfish (Perciformes: Apogonidae) from the Andaman Sea and Mentawai Islands . Research Bulletin of the Phuket Marine Biological Center , 62 : 1 – 8 .
   Google Scholar
• Ray , N , Currat , M and Excoffier , L. 2003 . Intra-deme molecular diversity in spatially expanding populations . Molecular Biology and Evolution , 20 : 76 – 86 .
   PubMed Web of Science ®Google Scholar
• Reeb , CA , Arcangeli , L and Block , BA. 2000 . Structure and migration corridors in Pacific populations of the Swordfish Xiphius gladius, as inferred through analyses of mitochondrial DNA . Marine Biology , 136 : 1123 – 31 .
   Web of Science ®Google Scholar
• Rice , WR. 1989 . Analyzing tables of statistical tests . Evolution , 43 : 223 – 25 .
   PubMed Web of Science ®Google Scholar
• Robertson , MD , Ovenden , JR and Barker , SC. 2007 . Identification of small juvenile scombrids from northwest tropical Australia using mitochondrial DNA cytochrome b sequences . Ichthyological Research , 54 : 246 – 52 .
   Web of Science ®Google Scholar
• Rogers , AR and Harpending , H. 1992 . Population growth makes waves in the distribution of pairwise genetic differences . Molecular Biology and Evolution , 9 : 552 – 69 .
   PubMed Web of Science ®Google Scholar
• Rosel , PE and Block , BA. 1996 . Mitochondrial control region variability and global population structure in the swordfish, Xiphias gladius . Marine Biology , 125 : 11 – 22 .
   Web of Science ®Google Scholar
• Rossi , AR , Capula , M and Crosetti , D. 1998 . Allozyme variation in global populations of striped mullet, Mugil cephalus (Pisces: Mugilidae) . Marine Biology , 131 : 203 – 12 .
   Web of Science ®Google Scholar
• Rozas , J , Sánchez-DelBarrio , JC and Messeguer-Rozas , R. 2003 . DnaSP, DNA polymorphism analyses by the coalescent and other methods . Bioinformatics , 19 : 2496 – 97 .
   PubMed Web of Science ®Google Scholar
• Saitou , N and Nei , M. 1987 . The neighbor-joining method: A new method for reconstructing phylogenetic trees . Molecular Biology and Evolution , 4 : 406 – 25 .
   PubMed Web of Science ®Google Scholar
• Schneider , S and Excoffier , L. 1999 . Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: Application to human mitochondrial DNA . Genetics , 152 : 1079 – 89 .
   PubMed Web of Science ®Google Scholar
• Sharp , GD. 1978 . “ Behavioral and physiological properties of tuna and their effects on vulnerability to fishing gear ” . In The Physiological Ecology of Tunas , Edited by: Sharp , GD and Dizon , AE . New York , NY : Academic Press . 485 pages
   Google Scholar
• Silas , EG , Pillai , PP , Srinath , M , Jayaprakash , AA , Muthiah , C Balan , V . 1986 . Population dynamics of tunas: Stock assessment . CMFRI Bulletin , 36 ( 3 ) : 20 – 27 .
   Google Scholar
• Sinclair , M and Iles , TD. 1989 . Population regulation and speciation in the oceans . Journal du Conseil International pour l’ Exploration de la Mer , 45 : 165 – 75 .
   Google Scholar
• Stepien , CA , Rosenblatt , RH and Bargmeyer , BA. 2001 . Phylogeography of the spotted sand bass, Paralabrax maculatofasciatus: Divergence of Gulf of California and Pacific coast populations . Evolution , 55 : 1852 – 62 .
   PubMed Web of Science ®Google Scholar
• Sudarsan D. 1993 . Tuna research in India – Present status and future approach . In : Sudarsan D , John ME Tuna Research in India . Fishery Survey of India , Bombay , 1 – 17 .
   Google Scholar
• Tajima , F. 1989 . Statistical method for testing the neutral mutation hypothesis by DNA polymorphism . Genetics , 10 : 512 – 26 .
   Google Scholar
• Tamura , K and Nei , M. 1993 . Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees . Molecular Biology and Evolution , 10 : 512 – 26 .
   PubMed Web of Science ®Google Scholar
• Tamura , K , Peterson , D , Peterson , N , Stecher , G , Nei , M and Kumar , S. 2011 . MEGA5: Molecular Evolutionary Genetics Analysis using likelihood, distance, and parsimony methods . Molecular Biology and Evolution , 28 : 2731 – 39 .
   PubMed Web of Science ®Google Scholar
• Thompson , JD , Higgins , DG and Gibson , TJ. 1994 . CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice . Nucleic Acids Research , 22 : 4673 – 80 .
   PubMed Web of Science ®Google Scholar
• Tringali MD , Ziemann , DA , Stuck KC. 2003 . Preliminary aspects of genetic management for Pacific threadfin (Polydactylis sexfilis) stock enhancement research in Hawaii . In : Nakamura Y , McVey JP , Leber K , Neidig C , Fox S , Churchhill K . Ecology of Aquaculture Species and Enhancement of Stocks . Proceedings of the 30th U.S.–Japan meeting on aquaculture . Washington , DC : National Oceanic and Atmospheric Administration , 55 – 76 .
   Google Scholar
• Ward , RD , Elliott , NG , Innes , BH , Smolenski , AJ and Grewe , PM. 1997 . Global population structure of yellowfin tuna Thunnus albacares, inferred from allozyme and mitochondrial DNA variation . Fishery Bulletin , 95 : 566 – 75 .
   Web of Science ®Google Scholar