Bibliography of Lower Actinopterygian Molecular Data

Initial Compilation by E. O. (Ed) Wiley 25 March 2005

 

Arnason U, Gullberg A, Janke A (2001) Molecular phylogenetics of gnathostomous (jawed) fishes: old bones, new cartilage. Zool Scripta 30: 249-255.

Arnason U, Gullberg A, Janke A, Joss J, Elmerot C (2004) Mitogenomic analyses of deep gnathostome divergences: a fish is a fish. Gene 333C: 61-70.

Arnason,U., Gullberg,A., Janke,A., Joss,J. and Elmerot,C. 2004.  Mitogenomic analyses of deep gnathostome divergences: a fish is a fish Gene 333, 61-70 (2004)

Bemis, W. E. & L. Grande. 2003. Phylogenetic relationships among the living species of gars (Acinopterygii: Lepisosteidae) inferred from mitochondrial DNA sequences. Abstract for the annual meeting of the Am Soc Ich Herp; Manaus, Brazil, June 2003.

Birstein, V. J., R. Hanner, and R. DeSalle. 1997. Phylogeny of the Acipenseriformes: cytogenetic and molecular approaches. Env. Biol. Fish. 48(1-4): 1270156.

Birstein, V.J., Betts, J. & DeSalle, R. 1998. Molecular identification of Acipenser sturio specimens: A warning note for recovery plans. Biological Conservation. 84(1): 97-101

Birstein, V.J. & DeSalle, R. 1998. Molecular phylogeny of Acipenserinae. Molecular Phylogenetics and Evolution. 9(1): 141-155.

Birstein, V.J., Doukakis, P., Sorkin, B. & DeSalle, R. 1998. Population aggregation analysis of three caviar-producing species of sturgeons and implications for the species identification of black caviar. Conserv. Biol. 12(4): 766-775.

Birstein, V. J., R. Hanner, and R. DeSalle. 1997. Phylogeny of the Acipenseriformes: cytogenetic and molecular approaches. Env. Biol. Fish. 48(1-4): 127-156.

Birstein, V.J., Betts, J. & DeSalle, R. 1998. Molecular identification of Acipenser sturio specimens: A warning note for recovery plans. Biological Conservation. 84(1): 97-101.

Booton, G. C., and P. Fuerst. 1994. The sequence of the nuclear 18S rRNA gene of the lake sturgeon (Acipenser fulvescens), and the molecular divergence of the Acipenseriformes. Poster abstracts from the Intl. Conf. Sturg. Biod. Cons., Am. Mus. Nat. Hist., NY.

Brinkmann,H., Denk,A., Zitzler,J., Joss,J.J. and Meyer,A. 2004. Complete mitochondrial genome sequences of the South American and the Australian lungfish: testing of the phylogenetic performance of mitochondrial data sets for phylogenetic problems in tetrapod relationships J. Mol. Evol. 59 (6), 834-848.

Brown, J. R., A. T. Beckenbach, and M. J. Smith. 1993. Intraspecific DNA sequence variation of the mitochondrial control region of white sturgeon (Acipenser transmontanus). Mol. Biol. Evol., 10(2): 326-341.

Brown, J. R., A. T. Beckenbach, and M. J. Smith. 1992. Mitochondrial DNA length variation and heteroplasmy in populations of white sturgeon (Acipenser transmontanus). Genetics, 132(1): 221-228.

Brown, J. R., D. J. Kowbel, A. T. Beckenbach, and M. J. Smith. 1988. Mitochondrial DNA polymorphism in white sturgeon (Acipenser transmontanus ) in the Fraser and Columbia Rivers. Aquaculture International Congress and Exposition, Vancouver, B.C. (Canada). Proc. Aquacult. Int. Congr. P. 57.

Brown, J. R., T. L. Gilbert, D. J. Kowbel, P. J. O'Hara, N. E. Buroker, A. T. Beckenbach & M. J. Smith. 1989. Nucleotide sequence of the apocytochrome B gene in white sturgeon mitochondrial DNA. Nucl. Acids Res. 17: 4389.

Brown, J. R., K. Beckenbach, A. T. Beckenbach, and M. J. Smith. 1996. Length variation, heteroplasmy and sequence divergence in the mitochondrial DNA of four species of sturgeon (Acipenser). Genetics, 142: 525-535.

Bruno QuŽrat, Abdellah Sellouk and Christian Salmon. 2000.  Phylogenetic Analysis of the Vertebrate Glycoprotein Hormone Family Including New Sequences of Sturgeon (Acipenser baeri) § Subunits of the Two Gonadotropins and the Thyroid-Stimulating Hormone Biology of Reproduction 63, 222-228.

Buroker, N. E., J. R. Brown, T. A. Gilbert, P. J. O' Hara, A. T. Beckenbach, W. K. Thomas, and M. J. Smith. 1990. Length heteroplasmy of sturgeon mitochondrial DNA: An illegitimate elongation model. Genetics. 124(1):157-163.

Cao,Y., Waddell,P.J., Okada,N. and Hasegawa,M. 1998. The complete mitochondrial DNA sequence of the shark Mustelus manazo: evaluating rooting contradictions to living bony vertebrates Mol. Biol. Evol. 15 (12), 1637-1646.
Chang, Y.-S., F.-L. Huang, and T.-B. Lo. 1994. The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. J. Mol. Evol. 38:138-155.

Comincini, S., Lanfredi, M., Rossi, R. & Fontana, F. 1998. Use of RAPD markers to determine the genetic relationships among sturgeons (Acipenseridae, Pisces). Fish Sci. 64(1): 35-38.

Delarbre,C., Spruyt,N., Delmarre,C., Gallut,C., Barriel,V., Janvier,P., Laudet,V. and Gachelin,G. 1998. The complete nucleotide sequence of the mitochondrial DNA of the dogfish, Scyliorhinus canicula Genetics 150 (1), 331-344.
Delarbre,C., Rasmussen,A.S., Arnason,U. and Gachelin,G. 2001. The Complete Mitochondrial Genome of the Hagfish Myxine glutinosa:Unique Features of the Control Region. J. Mol. Evol. 53 (6), 634-641,

DeSalle, R. & V. J. Birstein. 1996. PCR identification of black caviar. Nature 381 :197-198.

Ferguson, M.M., L. Bernatchez, M. Gatt, B.R. Konkle, S. Lee, M.L. Malott & R.S. McKinley. 1993. Distribution of mitochondrial DNA variation in lake sturgeon (Acipenser fulvescens) from the Moose River basin, Ontario, Canada. J. Fish Biol. 43 (Suppl. A): 91-101.

Ferreiro, C., J. F. Medrano, and G. A. E. 1989. Gall. Genome analysis of rainbow trout and sturgeon with restriction enzymes and hybridization with a ZFY gene derived probe to identify sex. Aquaculture, 81(3-4): 245-251.

Folmar, L. C., N. D. Denslow, R. A. Wallace, G. Lafleur, T. S. Gross, S. Bonomelli, and C. V. Sullivan. 1995. A highly conserved N-terminal sequence for teleost vitellogenin with potential value to the biochemistry, molecular biology and pathology of vitellogenesis. J. Fish Biol., 46(2): 255-263.

Guenette, S., R. Fortin, E. Rassart. 1993. Mitochondrial DNA variation in Lake Sturgeon (Acipenser fulvescens) from the St. Lawrence river and James Bay drainage basins in Quebec, Canada. Can. J. Fish. Aquat. Sci., 50(3): 659-664.

Hillis, D. M., D. D. Pollock, J. A. McGuire, and D. J. Zwickl. 2003. Is sparse taxon sampling a problem for phylogenetic inference? Systematic Biology 52: 124-126.

Huelsenbeck, J., and F. Ronquist. 2001. MrBayes. Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755. (3.0 available at: http://morphbank.ebc.uu.se/mrbayes/info.php).

Holcroft, N. I. 2004. A molecular test of alternative hypotheses of tetraodontiform (Acanthomorpha: Tetraodontiformes) sister group relationships using data from the RAG1 gene. Mol. Phylo. Evol. 32:749-760.

Holcroft, N. I.  2005. A molecular analysis of the interrelationships of tetraodontiform fishes (Acanthomorpha: Tetraodontiformes). Mol. Phylogenet. Evol. 34:525-544.

Hurst, C. D., S. E. Bartlett, W. S. Davidson, and I. J. Bruce. 1999. The complete mitochondrial DNA sequence of the Atlantic salmon, Salmo salar. Gene 239:237-242.

Inoue JG, Miya M, Tsukamoto K, Nishida M. 2003. Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish." Mol. Phylogenet. Evol. 26:110-120.

Kikugawa, K., K. Katoh, K. Shigehiro, S. Hiroshi, I. Osamu, I. Naoyuki, and M. Takashi. 2004. Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes. BMC Biology 2004, 2:

Krieger, J., P.A. Fuerst, and T.M. Cavender. 2000. Phylogenetic Relationships of the North American Sturgeons (Order Acipenseriformes) Based on Mitochondrial DNA Sequences. Molecular Phylogenetics and Evolution, 16(1): 64-72.

J. Krieger and P. A. Fuerst. 2002. Evidence of multiple alleles of the nuclear 18S ribosomal RNA gene in sturgeon (Family: Acipenseridae). Journal of Applied Ichthyology. Volume 18 Issue 4-6 Page 290 

Le, H. L. V., G. Lecointre & R. Perasso. 1993. A 28S rRNA based phylogeny of the gnathostomes: first steps in the analysis of conflict and congruence with morphologically based cladograms. Mol. Phylog. Evol. 2: 31-51.

Lee,W.J. and Kocher,T.D. 1995. Complete sequence of a sea lamprey (Petromyzon marinus) mitochondrial genome: early establishment of the vertebrate genome organization Genetics 139 (2), 873-887 (1995)

Ludwig, A. & Krischbaum, F. 1998. Comparison of mitochondrial DNA sequences between the European and the Adriatic sturgeon. J. Fish Biol. 52(6): 1289-1291.

McMaster, D., M.A. Belenky, A.L. Polenov, K. Lederis. 1992. Isolation and amino acid sequence of urotensin II from the sturgeon Acipenser ruthenus. Gen. Comp. Endocrinol., 87(2): 275-285.

Meyer, A. 1993. Molecular phylogenetic studies of fishes. pp. 3-41. In: A. R. Beamumont (ed.) Evolution and Genetics of Aquatic Organisms, Chapman and Hall, London.

Meyer A. 1995. Molecular evidence on the origin of tetrapods and the relationships of the coelacanth. Trends Ecol. Evol. 10:111-16

Mikhailova, N. A., I. B. Lobov, O. I. Podgornaya, and V. J. Birstein. 1995. Restriction analysis of the nuclear DNA of three species of Acipenser. Sturg. Quart., 3(3): 8-9.

Miya, M., and M. Nishida. 2000. Use of mitogenomic information in teleostean molecular phylogenetics: A tree-based exploration under the maximum-parsimony optimality criterion. Mol. Phylogenet. Evol. 17:437-455.

Miya, M., A. Kawaguchi, and M. Nashida. 2001. Mitogenomic exploration of higher teleost phylogenies: A case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Mol. Biol. Evol. 18:1993-2009.

Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, et al. 2003. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial sequences. Mol. Phylogenet. Evol. 26:121-38.  

Noack K, Zardoya R, Meyer A. 1996. The complete mitochondrial DNA sequence of the bichir (Polypterus ornatipinnis), a basal ray-finned fish: ancient establishment of the consensus vertebrate gene order. Genetics 144:1165-80

Naylor, G. J. P., and D. C. Adams. 2001. Are the fossil data really at odds with the molecular data? Morphological evidence for Cetartiodactyla phylogeny reexamined. Systematic Biology 50:444-453.

Neill, D.F.O., Powell, J.F.F., Standen, E.M. et al. 1998. Gonadotropin-releasing hormone (GnRH) in ancient teleosts, the bonytongue fishes: Putative origin of salmon GnRH. General and Comparative Endocrinology. 112(3): 415 425.

Nesbo, C.L., Arab, M.O. & Jakobsen, K.S. 1998. Heteroplasmy, length and sequence variation in the mtDNA control regions of three percid fish species (Perca fluviatilis, Acerina cernua, Stizostedion lucioperca). Genetics 148(4): 1907-1919.

Nishii, M., B. Moverus, O. S. Bukovskaya, A. Takahashi, and H. Kawauchi. 1995. Isolation and Characterization of (Pro-2)Somatostatin-14 and Melanotropins from Russian Sturgeon, Acipenser gueldenstaedti Brandt. General and Comparative Endocrinology 99(1): 6-12.

Noack,K., Zardoya,R. and Meyer,A. 1996. The complete mitochondrial DNA sequence of the bichir (Polypterus ornatipinnis), a basal ray-finned fish: ancient establishment of the consensus vertebrate gene order. Genetics 144 (3), 1165-1180.

Normark, B. B., A. R. McCune & R. G. Harrison. 1991. Phylogenetic relationships of neopterygian fishes, inferred from mitochondrial DNA sequences. Mol. Biol. Evol. 8: 819-834.

O' Neill, D.F., Powell, J.F.F., Standen, E.M. et al. 1998. Gonadotropin-releasing hormone (GnRH) in ancient teleosts, the bonytongue fishes: Putative origin of salmon GnRH. Gener. Compar. Endocrinol. 112: 415-425.

O' Neill, D.F., Powell, J.F.F., Standen, E.M. et al. 1998. Gonadotropin-releasing hormone (GnRH) in ancient teleosts, the bonytongue fishes: Putative origin of salmon GnRH. Gener. Compar. Endocrinol. 112: 415-425.

Posada, D. and K. A. Crandall. 1998. Modeltest: testing the model of DNA substitutions. Bioinformatics 14(9): 817-818. (ModelTest 3.06, 2001 is available at: http://inbio.byu.edu/Faculty/kac/crandall_lab/modeltest.htm.)

Rasmussen A-S, Janke A, Arnason U (1998) The mitochondrial DNA molecule of the hagfish (Myxine glutinosa) and consideration of vertebrate phylogenetic relationships. J Mol Evol 46: 382-388.

Rasmussen A-S, Arnason U (1999a) Phylogenetic studies of complete mitochondrial DNA molecules place cartilaginous fishes within the tree of bony fishes. J Mol Evol 48: 118-123.

Rasmussen A-S, Arnason U (1999b) Molecular studies suggest that cartilaginous fishes have a terminal position in the piscine tree. Proc Natl Acad Sci USA 96: 2177-2182.

Robinson-Rechavi, M. O. Marchand, H. Escriva, P.-L. Bardet, D. Zelus, S. Hughes, and V. Laudet. 2001. Euteleost fish genomes are characterized by expansion of gene families. Genome Res. 11:781-788.

Rouille, Y., J. Chauvet, M. T. Chaeuvet, R. Acher. and A. L. Polenov. 1991. Neurohypophysial hormones as molecular evolutionary tracers: Investigations on the sturgeons Acipenser stellatus and Acipenser gueldenstaedti. Comp. Biochem. Physiol., B., 100B(4): 721-726.

Rouille, Y., J. Chauvet, M. T. Chaeuvet, R. Acher. and A. L. Polenov. 1991. Neurohypophysial hormones as molecular evolutionary tracers: Investigations on the sturgeons Acipenser stellatus and Acipenser gueldenstaedti. Comp. Biochem. Physiol., B., 100B(4): 721-726.

Rubin, D. A., J. H. Youson, L. E. Marra, and R. M. Dores. 1996. Cloning of a gar (Lepisosteus osseus) GH cDNA: Trends in actinopterygian GH structure. Journal of Molecular Endocrinology, 16(1): 73-80.

Rybin, V. K., L. P. Revina, and L. A. Baratova. 1992. Amino acid sequence comparison of sturgeon's triprotamines: Protamines from Acipenser stellatus. Mol. Biol. Moscow., 26(2): 300-306.

Sherwood, N. M., S. Doroshov, and V. Lance. 1991. Gonadotropin-releasing hormone (GnRH) in bony fish that are phylogenetically ancient: Reedfish (Calamoichthys calabaricus ), sturgeon (Acipenser transmontanus ), and alligator gar (Lepisosteus spatula). Gen. Comp. Endocrinol., 84(1): 44-57

Sherwood, N. M., S. I. Doroshov & V. Lance. 1991. Gonadotropin-releasing hormone (GnRH) in bony fish that are phylogenetically ancient: reedfish (Calamoichthys calabaricus), sturgeon (Acipenser transmontanus), and alligator gar (Lepisosteus spatula). Gen. Comp. Endocrinol. 84: 44-57.

Streelman, J.T.and S.A. Karl, 1997.  Reconstructing labroid evolution with single-copy nuclear DNA.  Proc. R. Soc. Lond. B (1997)264:1011–1020.

Swofford, D. L. 1998. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.

Tang, K. L., P. B. Berendzen, E. O. Wiley, J. F. Morrissey, R. Winterbottom, and G. D. Johnson. 1999. The phylogenetic relationships of the Suborder Acanthuroidei (Teleostei: Perciformes) based on morphological and molecular evidence. Mol. Phylogenet. Evol. 11(3): 415-425.

Tang, K. L. 2001. Phylogenetic relationships among damselfishes (Teleostei: Pomacentridae) as determined by mitochondrial DNA data. Copeia 2001(3): 591-601.

Tang, K. L., K. M. McNyset, and N. I. Holcroft. 2004. The phylogenetic position of five genera (Acanthochromis, Azurina, Chrysiptera, Dischistodus, and Neopomacentrus) of the family Pomacentridae (Teleostei: Perciformes). Mol. Phylogenet. Evol.  30: 823–828.

 

Tohyama Y, Ichimiya T, Kasama-Yoshida H, Cao Y, Hasegawa M, et al. 2000. Phylogenetic relation of lungfish indicated by the amino acid sequence of myelin DM20. Brain Res. Mol. Brain Res. 80:256-59.

Tzeng, C.-S., C.-F. Hui, S.-C. Shen, and P. C. Huang. 1992. The complete nucleotide sequence of the Crossostoma lacustre mitochondrial genome: Conservation and variation among vertebrates. Nucleic Acids Res. 20:4853-4858.

Venkatesh B, Erdmann MV, Brenner S. 2001. Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates. Proc. Natl. Acad. Sci. USA 98:11382-87

Vladychenskaya, N. S., O. S. Kedrova, and N. B. Petrov. 1980. Organization of nucleotide sequences in the genome of the sterlet, Acipenser acipenser. Molek. Biol., 14: 986-1000 (Russian), Molec. Biol., 14: 774-786.

Waldman, J. R., K. Nolan, J. T. Hart and I. I. Wirgin. 1996b. Genetic differentiation of three key anadromous fish populations of the Hudson River. Estuaries 19 :759-768.

Wang, C. H., Kuo, C. H., Mok, H. K. & Lee, S. C. (2003). Molecular phylogeny of elopomorph fishes inferred from mitochondrial 12S ribosomal RNA sequences. — Zoologica Scripta, 32, 231–241.

Wiley, E. O., G. D. Johnson, and W. W. Dimmick. 1998. The phylogenetic relationships of lampridiform fishes (Teleostei: Acanthomorpha), based on a total-evidence analysis of morphological and molecular data. Mol. Phylo. Evol. 10:417-425.

Wirgin, I. I., Stabile, J. E. & Waldman, J. R. 1997. Molecular analysis in the conservation of sturgeons and paddlefish. Env. Biol. Fish., 48(1-4): 385-398.

Yasuda, A., K. Yamaguchi, T. Noso, H. Papkoff, A. L.Polenov, C. S. Nicoll, and H. Kawauchi. 1992. The complete amino acid sequence of growth hormone from sturgeon (Acipenser gueldenstaedti). Biochim. Biophys. Acta., 1120(3): 297-304.

Zardoya, R., A. Garrido-Pertierra, and J. M. Bautista. 1995. The complete nucleotide sequence of the mitochondrial genome of the rainbow trout, Oncorhynchus myskiss. J. Mol. Evol. 41:942-951.

Zardoya, R. and A. Meyer. 1996. Evolutionary relationships of the coelacant, lungfishes, and tetrapods based on the 28S ribosomal RNA gene. Proc. Natl. Acad. Sci. USA, 93: 5449-5454.

Zardoya,R. and Meyer,A. 1996. The complete nucleotide sequence of the mitochondrial genome of the lungfish (Protopterus dolloi) supports its phylogenetic position as a close relative of land vertebrates Genetics 142 (4), 1249-1263. 
Zardoya,R. and Meyer,A. 1997a. The complete DNA sequence of the mitochondrial genome of a 'living fossil,' the coelacanth (Latimeria chalumnae). Genetics 146 (3), 995-1010.

Zardoya R, Meyer A. 1997b. Molecular phylogenetic information on the identity of the closest living relative(s) of land vertebrates. Naturwissenschaften 84:389-97.

Zardoya R, Cao Y, Hasegawa M, Meyer A. 1998. Searching for the closest living relative(s) of tetrapods through evolutionary analyses of mitochondrial and nuclear data. Mol. Biol. Evol. 15:506-17

Zardoya, R. and A. Meyer, 2001. Vertebrate phylogeny: limits of inference of mitochondrial and nuclear rDNA sequende data due to an adverse phylogenetic signal/noise ratio. In: Ahlberg, P. E. (Ed). Major Events in Early Vertebrate Evolution. Taylor and Francis, London: 106-118.