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Myctophiformes
Phylogenetics of Myctophidae
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Ateleopodiformes
Lampridiformes
Polymixiiformes
Gadiformes
Phylogenetics of Macrouroidinae
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Round and pointed-head grenadier fishes (Actinopterygii : Gadiformes) represent a single sister group: Evidence from the complete mitochondrial genome sequences
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Complete mitochondrial genomes of 10 walleye pollocks
Yanagimoto, T., Kitamura, T., and Kobayashi, T.,
Complete nucleotide sequence and variation of mitochondrial DNA from 10 individuals of walleye pollock, Theragra chalcogramma.
FISHERIES SCIENCE 2004; 70 : 885-895.
Lophiiformes
Fossil records of lophiiforms
Carnevale G, Pietsch TW
Filling the gap: a fossil frogfish, genus Antennarius (Teleostei, Lophiiformes, Antennariidae), from the Miocene of Algeria
JOURNAL OF ZOOLOGY 270 (3): 448-457 NOV 2006
Zeiformes
Beryciformes
Stephanoberyciformes
Percomorpha
Gasterosteiformes
Phylogenetics of gasterosteiforms
Kawahara, Ryouka, Masaki Miya, Kohji Mabuchi, Sebastien Lavoue, Jun G. Inoue, Takashi P. Satoh, Akira Kawaguchi, and Mutsumi Nishida. 2007.
Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new pespective based on whole mitogenome sequences from 75 higher teleosts.
Molecular Phylogenetics and Evolution, (in press)
Phylogenetics of percomorphs
Phylogenetics of Elassoma
Near TJ, et al. 2012.
Nuclear gene-inferred phylogenies resolve the relationships of the enigmatic Pygmy Sunfishes, Elassoma (Teleostei: Percomorpha). Mol Phylogenet Evol 63: 388-395. doi: 10.1016/j.ympev.2012.01.011
Smith, W. L. and Wheeler, W. C. 2006. Venom Evolution Widespread in Fishes: A Phylogenetic Road Map for the Bioprospecting of Piscine Venoms. Journal of Heredity.
Miya, M., Takeshima, H., Endo, H., Ishiguro, N. B., Inoue, J. G., et al. 2003.
Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 26, 121-138.
Chen WJ, Bonillo C, Lecointre G.
Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa.
MOLECULAR PHYLOGENETICS AND EVOLUTION 26 (2): 262-288 FEB 2003
Wiley EO, Johnson GD, Dimmick WW
The interrelationships of Acanthomorph fishes: A total evidence approach using molecular and morphological data.
BIOCHEMICAL SYSTEMATICS AND ECOLOGY 28 (4): 319-350 APR 2000
Tang KL, Berendzen PB, Wiley EO, et al.
The phylogenetic relationships of the suborder Acanthuroidei (Teleostei : Perciformes) based on molecular and morphological evidence.
MOLECULAR PHYLOGENETICS AND EVOLUTION 11 (3): 415-425 APR 1999
Batrachoidiformes
Phylogenetic position of batrachoidiforms
Miya, Masaki, Takashi P. Satoh, and Mutsumi Nishida. 2005.
The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genomic sequences.
Biological Journal of Linnean Society, London, 85, 289-306.
Beloniformes
Phylogenetics of Oryzias
Takehana Y, Naruse K, Sakaizumi M
Molecular phylogeny of the medaka fishes genus Oryzias (Beloniformes : Adrianichthyidae) based on nuclear and mitochondrial DNA sequences
MOLECULAR PHYLOGENETICS AND EVOLUTION 36 (2): 417-428 AUG 2005
Percoidei
Phylogenetics of Sinipercids
Li CH, et al. 2010.
The phylogenetic placement of sinipercid fishes ("Perciformes") revealed by 11 nuclear loci. Mol Phylogen Evol 56: 1096-1104. doi: Doi 10.1016/J.Ympev.2010.05.017
Phylogenetics of Centropomidae
Li CH, et al. 2011.
Monophyly and interrelationships of Snook and Barramundi (Centropomidae sensu Greenwood) and five new markers for fish phylogenetics. Mol Phylogen Evol 60: 463-471. doi: Doi 10.1016/J.Ympev.2011.05.004
Divergence time estimation of black basses
Near TJ. et al. 2003.
SPECIATION IN NORTH AMERICAN BLACK BASSES, MICROPTERUS (ACTINOPTERYGII: CENTRARCHIDAE).
Evolution. 57, 1610-1621.
Labroidei
Mabuchi, Kohji, Masaki Miya, Yoichiro Azuma, and Mutsumi Nishida.
Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes.
BMC Evolutionary Biology, 7:10. [doi:10.1186/1471-2148-7-10]
Phylogenetics of cichlids
Sparks JS, Smith WL
Phylogeny and biogeography of cichlid fishes (Teleostei : Perciformes : Cichlidae)
CLADISTICS 20 (6): 501-517 DEC 2004
Sparks JS
Molecular phylogeny and biogeography of the Malagasy and South Asian cichlids (Teleostei : Perciformes : Cichlidae)
MOLECULAR PHYLOGENETICS AND EVOLUTION 30 (3): 599-614 MAR 2004
Vences M, Freyhof J, Sonnenberg R, et al.
Reconciling fossils and molecules: Cenozoic divergence of cichlid fishes and the biogeography of Madagascar
JOURNAL OF BIOGEOGRAPHY 28 (9): 1091-1099 SEP 2001
Takahashi K, Terai Y, Nishida M, et al.
Phylogenetic relationships and ancient incomplete lineage sorting among cichlid fishes in Lake Tanganyika as revealed by analysis of the insertion of retroposons
MOLECULAR BIOLOGY AND EVOLUTION 18 (11): 2057-2066 NOV 2001
Farias IP, Orti G, Sampaio I, et al.
The cytochrome b gene as a phylogenetic marker: The limits of resolution for analyzing relationships among cichlid fishes
JOURNAL OF MOLECULAR EVOLUTION 53 (2): 89-103 AUG 2001
Farias IP, Orti G, Meyer A
Total evidence: Molecules, morphology, and the phylogenetics of cichlid fishes
JOURNAL OF EXPERIMENTAL ZOOLOGY 288 (1): 76-92 APR 15 2000
Ruber L, Verheyen E, Meyer A
Replicated evolution of trophic specializations in an endemic cichlid fish lineage from Lake Tanganyika
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 96 (18): 10230-10235 AUG 31 1999
Farias IP, Orti G, Sampaio I, et al.
Mitochondrial DNA phylogeny of the family Cichlidae: Monophyly and fast molecular evolution of the neotropical assemblage
JOURNAL OF MOLECULAR EVOLUTION 48 (6): 703-711 JUN 1999
Takahashi K, Terai Y, Nishida M, et al.
A novel family of short interspersed repetitive elements (SINEs) from cichlids: The patterns of insertion of SINEs at orthologous loci support the proposed monophyly of four major groups of cichlid fishes in Lake Tanganyika
MOLECULAR BIOLOGY AND EVOLUTION 15 (4): 391-407 APR 1998
Divergence time estimation of cichlids
Friedman M, Keck BP, Dornburg A, Eytan RI, Martin CH, Hulsey CD, Wainwright PC, Near TJ (2013)
Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting. Proc R Soc B 280:20131733
Hulsey CD, et al. 2011.
Species tree estimation and the historical biogeography of heroine cichlids. Mol Phylogenet Evol 58: 124-131. doi: 10.1016/j.ympev.2010.11.016
Martin J. Genner, Ole Seehausen, David H. Lunt, Domino A. Joyce, Paul W. Shaw, Gary R. Carvalho and George F. Turner. 2007.
Age of cichlids: New dates for ancient lake fish radiations.
Mol. Biol. Evol..
Azuma, Y., Kumazawa, Y., Miya, M., Mabuchi, K. & Nishida, M. 2008 Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences. BMC Evol. Biol. 8, 215.
Genner, M. J. et al.
Age of cichlids: New dates for ancient lake fish radiations. Mol.Biol. Evol. 24, 1269–1282 (2007).
Won YJ, Wang Y, Sivasundar A, et al.
Nuclear gene variation and molecular dating of the cichlid species flock of Lake Malawi
MOLECULAR BIOLOGY AND EVOLUTION 23 (4): 828-837 APR 2006
Phylogenetics of Labridae
Westneat MW, Alfaro ME
Phylogenetic relationships and evolutionary history of the reef fish family Labridae
MOLECULAR PHYLOGENETICS AND EVOLUTION 36 (2): 370-390 AUG 2005
Phylogenetics of Apogon
Mabuchi K, Okuda N, Nishida M
Molecular phylogeny and stripe pattern evolution in the cardinalfish genus Apogon
MOLECULAR PHYLOGENETICS AND EVOLUTION 38 (1): 90-99 JAN 2006
Phylogenetics of Atherinomorpha
Phylogeny and biogeography of the Malagasy and Australasian rainbowfishes (Teleostei : Melanotaenioidei): Gondwanan vicariance and evolution in freshwater
Sparks, JS; Smith, WL
MOLECULAR PHYLOGENETICS AND EVOLUTION. 33, 719-734 2004
Notothenioidei
Divergence time estimation of notothenioids.
Near TJ, et al. 2012.
Ancient climate change, antifreeze, and the evolutionary diversification of Antarctic fishes. Proceedings of the National Academy of Sciences of the United States of America 109: 3434-3439. doi: Doi 10.1073/Pnas.1115169109
Phylogenetics of notothenioids
Bargelloni L, Marcato S, Zane L, et al.
Mitochondrial phylogeny of notothenioids: A molecular approach to antarctic fish evolution and biogeography
SYSTEMATIC BIOLOGY 49 (1): 114-129 MAR 2000
BARGELLONI L, RITCHIE PA, PATARNELLO T, et al.
MOLECULAR EVOLUTION AT SUBZERO TEMPERATURES - MITOCHONDRIAL AND NUCLEAR PHYLOGENIES OF FISHES FROM ANTARCTICA (SUBORDER POTOTHENIOIDEI), AND THE EVOLUTION OF ANTIFREEZE GLYCOPEPTIDES
MOLECULAR BIOLOGY AND EVOLUTION 11 (6): 854-863 NOV 1994
Gobioidei
Phylogenetics of gobies
Gobius lagocephalus: The world's most widespread nomen dubium
Smith, WL; Sparks, JS
MOLECULAR PHYLOGENETICS AND EVOLUTION 43, 696-698, 2007
Kon, Takeshi, Tetsuo Yoshino, Takahiko Mukai, and Mutsumi Nishida.
DNA sequences identify numerous cryptic species of the vertebrate: A lesson from the gobioid fish Schindleria.
Molecular Phylogenetics and Evolution, (in press) [doi:10.1016/j.ympev.2006.12.007]
Ruber L, Van Tassell JL, Zardoya R
Rapid speciation and ecological divergence in the American seven-spined gobies (Gobiidae, Gobiosomatini) inferred from a molecular phylogeny
EVOLUTION 57 (7): 1584-1598 JUL 2003
Acanthuroidei
Phylogenetics of Poeciliidae
Meredith RW, et al. 2011.
Molecular phylogenetic relationships and the coevolution of placentotrophy and superfetation in Poecilia (Poeciliidae: Cyprinodontiformes). Mol Phylogen Evol 59: 148-157. doi: Doi 10.1016/J.Ympev.2011.01.014
Phylogenetics of siganids
Kuriiwa, Kaoru, Naoto Hanzawa, Tesuo Yoshino, Seishi Kimura, and Mutsumi Nishida. 2007.
Phylogenetic relationships and natural hybridization in rabbitfishes (Teleostei: Siganidae) inferred from mitochondrial and nuclear DNA analyses.
Molecular Phylogenetics and Evolution, (in press)
Tetraodontiformes
Phylogenetics of tetraodontiforms
Yamanoue, Yusuke, Masaki Miya, Keiichi Matsuura, Naoki Yagishita, Kohji Mabuchi, Harumi Sakai, Masaya Katoh, and Mutsumi Nishida. 2007
Phylogenetic position of tetraodontiform fishes within the higher teleosts: Bayesian inferences based on 44 whole mitochondrial genome sequences.
Molecular Phylogenetics and Evolution, (in press)
Holcroft NI
A molecular analysis of the interrelationships of tetraodontiform fishes (Acanthomorpha : Tetraodontiformes).
MOLECULAR PHYLOGENETICS AND EVOLUTION 34 (3): 525-544 MAR 2005
Phylogenetics of Molidae
Yamanoue Y, Miya M, Matsuura K, et al.
Mitochondrial genomes and phylogeny of the ocean sunfishes (Tetraodontiformes : Molidae)
ICHTHYOLOGICAL RESEARCH 51 (3): 269-273 AUG 2004
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