Actinopterygii
July 6, 2017. Jun Inoue


Time tree derived from mitogenomic studies


Orthologous chromosomes

Review
Miya M, Nishida M. 2014.
The mitogenomic contributions to molecular phylogenetics and evolution of fishes: A 15-year retrospect. Ichthyological Research 61:1-43.

Sallan LC (2014)
Major issues in the origins of ray-finned fish (Actinopterygii) biodiversity. Biol. Rev.

Chen WJMayden RL 2010.
A Phylogenomic Perspective on the New Era of Ichthyology. Bioscience 60: 421-432. doi: Doi 10.1525/Bio.2010.60.6.6

Vega GC & Wiens JJ (2012)
Why are there so few fish in the sea? P Roy Soc B-Biol Sci 279(1737):2323-2329.

Parenti, L.R., 2008.
Life history patterns and biogeography: An interpretation of diadromy in fishes.
Annals of the Missouri Botanical Garden 95, 232-247.

Ilves KL & Randall DJ (2008)
WHY HAVE PRIMITIVE FISHES SURVIVED? Fish physiology 26:515–536.

Nelson, J. S. 2006.
Fishes of the World, fourth ed. [Amazon]
Wiley, New Jersey.

Stiassny, M.L.J, Wiley, E.O., Johnson, G.D., Carvalho, M.R., 2004.
Gnathostome fishes. In: Donaghue, M.J., Cracraft, J. (Eds.), Assembling the Tree of Life. Oxford University Press, New York, pp. 200-247.

Berra, T. M. 2001.
Freshwater Fish Distribution. [Amazon]
Academic Press, London.

FishBase

Catalog of Fishes

Fossil Fishes of Bear Gulch


Phylogenetic marker
Thomson RC, et al. 2010.
Genome-enabled development of DNA markers for ecology, evolution and conservation. Mol Ecol 19: 2184-2195. doi: Doi 10.1111/J.1365-294x.2010.04650.X

Li C, et al. 2010.
Exon-primed intron-crossing (EPIC) markers for non-model teleost fishes. BMC Evol Biol 10: 90. doi: 10.1186/1471-2148-10-90

Li, C., Orti, G., Zhang, G. & Lu, G. 2007
A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC Evol Biol 7, 44.

Chen WJ, et al. 2008.
Phylogenetic utility of two existing and four novel nuclear gene loci in reconstructing Tree of Life of ray-finned fishes: the order Cypriniformes (Ostariophysi) as a case study. Gene 423: 125-134. doi: 10.1016/j.gene.2008.07.016

Thomson RC, et al. 2008.
Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles. Mol Phylogenet Evol 49: 514-525. doi: 10.1016/j.ympev.2008.08.006


Fossil record from actinopterygian stem lineage
Benton, M. J., Donoghue, P. C. J., Asher, R. J., Friedman, M., Near, T. J., Vinther, J. (2015)
Constraints on the timescale of animal evolutionary history. Paleontologica Electronica 18.1.1FC

Long, JA, CHOO, B,YOUNG, GC. 2008.
A new basal actinopterygian fish from the Middle Devonian Aztec Siltstone of Antarctica.
Antarctic Science 20, 393–412.

Botella, H., H. Blom, M. Dorka, P. E. Ahlberg, and P. Janvier. 2007.
Jaws and teeth of the earliest bony fishes.
Nature 448: 583-586.

Lund, R. 2000.
The new Actinopterygian order Guildayichthyiformes from the Lower Carboniferous of Montana (USA).
Geodiversitas 22: 171-206.


Phylogenetic and divergence time estimation of actinopterygians
Malmstrom M, et al. (2016)
Evolution of the immune system influences speciation rates in teleost fishes. Nat. Genet. 48(10):1204-1210.

Dornburg A, Townsend JP, Friedman M, & Near TJ (2014)
Phylogenetic informativeness reconciles ray-finned fish molecular divergence times. BMC Evol. Biol. 14.

Chen W, -J. (2014) New insights on early evolution of spiny-rayed fishes (Teleostei: Acanthomorpha). Frontiers in Marine Science.

Betancur RR, Broughton RE, Wiley EO, Carpenter K, Lopez JA, Li C, Holcroft NI, Arcila D, Sanciangco M, Cureton Ii JC, Zhang F, Buser T, Campbell MA, Ballesteros JA, Roa-Varon A, Willis S, Borden WC, Rowley T, Reneau PC, Hough DJ, Lu G, Grande T, Arratia G, Orti G 2013.
The tree of life and a new classification of bony fishes. PLoS Curr 5.

Broughton RE, et al., 2013.
Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution. Plos Currents Tree of Life.

Near TJ, Eytan RI, Dornburg A, Kuhn KL, Moore JA, Davis MP, Wainwright PC, Friedman M, Smith WL 2012.
Resolution of ray-finned fish phylogeny and timing of diversification. Proc Natl Acad Sci U S A 109: 13698-13703.


Phylogenetic and divergence time estimation of model organisms
Santini, F, LJ Harmon, G Carnevale, ME Alfaro. 2009.
Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes. Bmc Evolutionary Biology 9:-.

Setiamarga, D. H. E., Miya, M., Inoue, J. G., Ishiguro, N. B., Mabuchi, K. & Nishida, M. 2009
Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates. Biology letters. in press.

Yamanoue, Y., Miya, M., Inoue, J. G., Matsuura, K., Nishida, M. 2006.
The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes.
Gene and Genetic Systems 81, 29-39. [doi:10.1266/ggs.81.29]

Steinke D, Salzburger W, Meyer A
Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs
JOURNAL OF MOLECULAR EVOLUTION 62 (6): 772-784 JUN 2006

Chen WJ, Orti G, Meyer A [Review]
Novel evolutionary relationship among four fish model systems.
TRENDS IN GENETICS 20 (9): 424-431 SEP 2004

Hedges SB, Kumar S [Review]
Vertebrate genomes compared
SCIENCE 297 (5585): 1283-1285 AUG 23 2002




Basal actinopterygians

Phylogenetics of ancient fish
Li, C., Lu, G. & Orti, G. 2008
Optimal Data Partitioning and a Test Case for Ray-finned Fishes (Actinopterygii) Based on Ten Nuclear Loci. Systematic Biology.

Li, C., Orti, G., Zhang, G. & Lu, G. 2007
A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC Evol Biol 7, 44.

Hurley IA, Mueller RL, Dunn, KA, Schmidt EJ, Friedman M, Ho RK, Prince VE, Yang Z, Thomas MG and Coates MI. (2007). *
A New Time-scale for Ray-Finned Fish Evolution.
Proceedings of the Royal Society B: Biological Sciences 274, 489-498.

Cavin L, Suteethorn V
A new semionotiform (Actinopterygii, Neopterygii) from Upper Jurassic Lower Cretaceous deposits of north-east Thailand, with comments on the relationships of semionotiforms
PALAEONTOLOGY 49: 339-353 Part 2 MAR 2006

Gardiner BG, Schaeffert B, Masserie JA
A review of the lower actinopterygian phylogeny

Kikugawa, K., S. Katoh, S. Kuraku, H. Sakurai, O. Ishida, N. Iwabe and T. Miyata. 2004.
Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes.
BMC Biology 2: Art. No. 3 MAR 11

Inoue, J. G., Miya, M., Tsukamoto, K., Nishida, M. 2003.
Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish."
Molecular Phylogenetics and Evolution
26, 110-120.

Venkatesh B, Erdmann MV, Brenner S., 2001
Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates.
Proc Natl Acad Sci USA, 98:11382-11387.

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



Fossil record of polypteriforms
Gayet M, Meunier FJ, Werner C. 2002.
Diversification in Polypteriformes and special comparison with the Lepisosteiformes
PALAEONTOLOGY 45: 361-376 Part 2


Phylogenetics of acipenseriforms
Peng ZG, Ludwig A, Wang DQ, et al. 2007.
Age and biogeography of major clades in sturgeons and paddlefishes (Pisces : Acipenseriformes)
MOLECULAR PHYLOGENETICS AND EVOLUTION 42 (3): 854-862 MAR

Robles F, de la Herran R, Ludwig A, et al. 2004.
Evolution of ancient satellite DNAs in sturgeon genomes
GENE 338 (1): 133-142 AUG 18

Krieger J, Fuerst PA. 2002.
Evidence for a slowed rate of molecular evolution in the order Acipenseriformes
MOLECULAR BIOLOGY AND EVOLUTION 19 (6): 891-897

Ludwig A, Belfiore NM, Pitra C, et al.
Genome duplication events and functional reduction of ploidy levels in sturgeon (Acipenser, Huso and Scaphirhynchus).
GENETICS 158 (3): 1203-1215 JUL 2001

Krieger J, Fuerst PA, Cavender TM. 2000.
Phylogenetic relationships of the North American sturgeons (order Acipenseriformes) based on mitochondrial DNA sequences.
MOLECULAR PHYLOGENETICS AND EVOLUTION 16 (1): 64-72.

Birstein VJ, Hanner R, DeSalle R
Phylogeny of the Acipenseriformes: Cytogenetic and molecular approaches.
ENVIRONMENTAL BIOLOGY OF FISHES 48 (1-4): 127-156 MAR 1997.



Fossil record of acipenseriforms

Grande L, Jin F, Yabumoto Y, et al. 2002.
Protopsephurus liui, a well-preserved primitive paddlefish (Acipenseriformes : polyodontidae) from the lower cretaceous of Chinan.
JOURNAL OF VERTEBRATE PALEONTOLOGY 22 (2): 209-237.



Fossil record of lepisosteids

Wright JJ, et al. 2012.
Gene trees, species trees, and morphology converge on a similar phylogeny of living gars (Actinopterygii: Holostei: Lepisosteidae), an ancient clade of ray-finned fishes. Mol Phylogenet Evol 63: 848-856. doi: 10.1016/j.ympev.2012.02.033

Cavin L, Suteethorn V. 2006
A new semionotiform (Actinopterygii, Neopterygii) from Upper Jurassic Lower Cretaceous deposits of north-east Thailand, with comments on the relationships of semionotiforms
PALAEONTOLOGY 49: 339-353 Part 2

Kumar, K., Rana, R.S., Paliwal, B.S., 2005.
OSTEOGLOSSID AND LEPISOSTEID FISH REMAINS FROM THE PALEOCENE PALANA FORMATION, RAJASTHAN, INDIA.
Palaeontology, Vol. 48, Part 6, 2005, pp. 1187-1209.

Gayet M, Meunier FJ, Werner C. 2002
Diversification in Polypteriformes and special comparison with the Lepisosteiformes
PALAEONTOLOGY 45: 361-376 Part 2



Divergence time estimation of actinopterygians
Inoue, J. G.
, Kumazawa, Y., Miya, M. & Nishida, M. 2009.
The historical biogeography of the freshwater knifefishes using mitogenomic approaches: A Mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha). Mol Phylogenet Evol 51, 486-499.

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.

Hurley, I. A., R. L. Mueller, K. A. Dunn, E. J. Schmidt, M. Friedman, R. K. Ho, V. E. Prince, Z. Yang, M. G. Thomas, and M. I. Coates. 2007. *
A new time-scale for ray-finned fish evolution.
Proc. R. Soc. B 274: 489-498.

Inoue, J. G., Miya, M., Venkatesh, B., Nishida, M. 2005.
The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths.
Gene
349, 227-235.

Benton, M. J. 2005.
Vertebrate Palaeontology, third ed.
Backwell, Malden.

Kumazawa, Y., and M. Nishida. 2000. [Out of India Hypothesis]
Molecular phylogeny of osteoglossoids: a new model for gondwanian origin and plate tectonic transportation of the Asian arowana.
Mol. Biol. Evol. 17: 1869-1878.

Kumazawa, Y., M. Yamaguchi, and M. Nishida. 1999.
Mitochondrial molecular clocks and the origin of euteleostean biodiversity: familial radiation of perciforms may have predated the Cretaceous/Tertiary boundary.
in The Biology of Biodiversity (M. Kato, ed.) Springer-Verlag, Tokyo. Pages 35-52.



Basal teleosts
Fossil records
Gloria Arratia (2010)
Critical analysis of the impact of fossils on teleostean phylogenies, especially that of basal teleosts. In: Morphology, Phylogeny and Paleobiogeography of Fossil Fishes D. K. Elliott, J. G. Maisey, X. Yu & D. Miao (eds.): pp. 247-274, 15 figs., 6 tabs. Verlag Dr. Friedrich Pfeil, MuNnchen, Germany.
"In addition, the recognition of two families, the fossil †Anaethalionidae and the extant Elopidae was questioned. In the same paper, I studied also the phylogenetic relationships of 26 fossil and nine recent basal teleostean genera including †Anaethalion and Elops and the results showed that †Anaethalion and Elops are sister groups (Arratia 1997: figs. 99-102). "


Phylogenetics of basal teleosts
Steinke, D., W. Salzburger, and A. Meyer. 2006.
Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs. Journal of Molecular Evolution 62:772-784.

Inoue, J. G.,
Miya, M., Tsukamoto, K., Nishida, M. 2001.
A mitogenomic perspective on the basal teleostean phylogeny: resolving higher-level relationships with longer DNA sequences.
Molecular Phylogenetics and Evolution
20, 275-285.

Inoue, J. G., Miya, M. 2001.
Phylogeny of the basal teleosts, with special reference to the Elopomorpha.
Japanese Journal of Ichthyology 48, 75-91 (in Japanese with English abstract).



Osteoglossomorpha

Phylogenetics of osteoglossomorphs
Inoue, J. G., Kumazawa, Y., Miya, M. & Nishida, M. 2009.
The historical biogeography of the freshwater knifefishes using mitogenomic approaches: A Mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha). Mol Phylogenet Evol 51, 486-499.

Lavoue S, Sullivan JP. 2004.
Simultaneous analysis of five molecular markers provides a well-supported phylogenetic hypothesis for the living bony-tongue fishes (Osteoglossomorpha : Teleostei)
MOLECULAR PHYLOGENETICS AND EVOLUTION 33 (1): 171-185 OCT

Kumazawa, Y., and M. Nishida. 2000. [Out of India Hypothesis]
Molecular phylogeny of osteoglossoids: a new model for gondwanian origin and plate tectonic transportation of the Asian arowana.


Fossil record of osteoglossomorphs
Bonde, N. 2008.
Osteoglossomorphs of the marine Lower Eocene of Denmark with remarks on other Eocene taxa and their importance for palaeobiogeography. Geological Society, London 295:253-310.
http://sp.lyellcollection.org/cgi/reprint/295/1/253
[They found a lot of marine osteoglossomorph fossils]

Murray AM, Wilson MVH
Description of a new Eocene osteoglossid fish and additional information on Sigida jacksonoides Greenwood and Patterson, 1967 (Osteoglossomorpha), with an assessmant of their phylogenetic relationship
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 144 (2): 213-228 JUN 2005

Kumar, K., Rana, R.S., Paliwal, B.S., 2005.
OSTEOGLOSSID AND LEPISOSTEID FISH REMAINS FROM THE PALEOCENE PALANA FORMATION, RAJASTHAN, INDIA.
Palaeontology, Vol. 48, Part 6, 2005, pp. 1187-1209.

JIANG-YONG, Z. 2004.
NEW FOSSIL OSTEOGLOSSOMORPH FROM NINGXIA, CHINA.
Journal of Vertebrate Paleontology 24(3):515-524.

Hilton EJ
Comparative osteology and phylogenetic systematics of fossil and living bony-tongue fishes (Actinopterygii, Teleostei, Osteoglossomorpha)
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 137 (1): 1-100 JAN 2003




Elopomorpha

Phylogenetic of elopomorphs
Inoue, J. G.,
Miya, M., Tsukamoto, K., Nishida, M. 2004.
Mitogenomic evidence for the monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larva.
Molecular Phylogenetics and Evolution
32, 274-286.

Obermiller LE, Pfeiler E
Phylogenetic relationships of elopomorph fishes inferred from mitochondrial ribosomal DNA sequences
MOLECULAR PHYLOGENETICS AND EVOLUTION 26 (2): 202-214 FEB 2003

Phylogenetic position of saccopharyngiforms
Inoue JG
, Miya M, Tsukamoto K, et al.
Evolution of the deep-sea gulper eel mitochondrial genomes: Large-scale gene rearrangements originated within the eels
MOLECULAR BIOLOGY AND EVOLUTION 20 (11): 1917-1924 NOV 2003



Phylogenetic relationships of anguilliforms
Lopez, J. A., Westneat, M. W. & Hanel, R. 2007
The phylogenctic affinities of the mysterious Anguilliform genera Coloconger and Thalassenchelys as supported by mtDNA sequences.
Copeia, 959-966.

Inoue, J. G., Miya, M., Tsukamoto, K. & Nishida, M. 2001
Complete mitochondrial DNA sequence of Conger myriaster (Teleostei: Anguilliformes): novel gene order for vertebrate mitochondrial genomes and the phylogenetic implications for anguilliform families.
Journal of Molecular Evolution 52, 311-320.

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.


Phylogenetics of Anguilla
Minegishi, Y. Aoyama, J., Inoue, J. G., Miya, M., Nishida, M., Tsukamoto, K. 2005.
Molecular phylogeny and evolution of the freshwater eels genus Anguilla based on the whole mitochondrial genome sequences.
Molecular Phylogenetics and Evolution
34, 134-146.

Aoyama, J., Nishida, M., Tsukamoto, K., 2001.
Molecular phylogeny and evolution of the freshwater eel, genus Anguilla.
Mol. Phylogenet. Evol. 20, 450-459.

Lin, Y.-S., Poh, Y.-P., Tzeng, C.-S., 2001.
A phylogeny of freshwater eels inferred from mitochondrial genomes.
Mol. Phylogenet. Evol. 20, 252-261.

Bastrop, R., Strehlow, B., Jurss, K., Sturmbauer, C., 2000.
A new molecular phylogenetic hypothesis for the evolution of freshwater eels.
Mol. Phylogenet. Evol. 14, 250-258.

Aoyama, J., Tsukamoto, K., 1997.
Evolution of the freshwater eels.
Naturwissenschaften 84, 17-21.





Clupeomorpha

Phylogenetic of clupeiforms
Lavoue S, Miya M, Saitoh K, et al.
Phylogenetic relationships among anchovies, sardines, herrings and their relatives (Clupeiformes), inferred from whole mitogenome sequences
MOLECULAR PHYLOGENETICS AND EVOLUTION 43 (3): 1096-1105 JUN 2007 [doi:10.1016/j.ympev.2006.09.018]

Phylogenetic position of Sundasalanx
Ishiguro, N. B., Miya, M., Inoue J. G., Nishida, M. 2005.
Sundasalanx
(Sundasalangidae) is a progenetic clupeiform, not a closely-related group of salangids (Osmeriformes): Mitogenomic evidence.
Journal of Fish Biology
67, 561-569.




Ostariophysi

Phylogenetics of gonorynchiforms
Lavoue, S., Miya, M., Inoue, J. G., Saitoh, K., Ishiguro, N. B., Nishida, M. 2005.
Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: Implications for higher-level relationships within the Otocephala.
Molecular Phylogenetics and Evolution 37, 165-177.


Phylogenetics of ostariophysans
Saitoh, K., Miya, M., Inoue, J. G., Ishiguro, N. B., Nishida, M. 2003.
Mitochondrial genomics of ostariophysan fishes: perspectives on phylogeny and biogeography.
Journal of Molecular Evolution
56, 464-472.


Divergence time estimation of ostariophisans
Saitoh K, et al. 2011.
Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi). Zool J Linn Soc 161: 633-662. doi: Doi 10.1111/J.1096-3642.2010.00651.X


Divergence time estimation of characiforms
Arroyave JStiassny MLJ 2011.
Phylogenetic relationships and the temporal context for the diversification of African characins of the family Alestidae (Ostariophysi: Characiformes): Evidence from DNA sequence data. Mol Phylogen Evol 60: 385-397. doi: Doi 10.1016/J.Ympev.2011.04.016

Phylogenetics of characiforms
Oliveira C, et al. 2011.
Phylogenetic relationships within the speciose family Characidae (Teleostei: Ostariophysi: Characiformes) based on multilocus analysis and extensive ingroup sampling. BMC Evol Biol 11. doi: Artn 275
Doi 10.1186/1471-2148-11-275

Orti G, Meyer A
The radiation of characiform fishes and the limits of resolution of mitochondrial ribosomal DNA sequences
SYSTEMATIC BIOLOGY 46 (1): 75-100 MAR 1997


Phylogenetics of Cypriniformes
Saitoh, Kenji, Tetsuya Sado, Richard L. Mayden, Naoto Hanzawa, Kenji Nakamura, Mutsumi Nishida, and Masaki Miya.
Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The first evidence towards resolution of higher-level relationships of the world's largest freshwater-fish clade based on 59 whole mitogenome sequences.
Journal of Molecular Evolution, 63, 826-841. [doi:10.1007/s00239-005-0293-y]


Phylogenetics of Cyprinidae
Lukas Ruber, Maurice Kottelat, Heok Hui Tan, Peter KL Ng, Ralf Britz.
Evolution of miniaturization and the phylogenetic position of Paedocypris, comprising the worlds smallest vertebrate.
BMC Evolutionary Biology 2007, 7:38 doi:10.1186/1471-2148-7-38

Phylogenetics of Cyprinus
Mabuchi, K., H. Senou, and M. Nishida. 2008.
Mitochondrial DNA analysis reveals cryptic large-scale invasion of non-native genotypes of common carp (Cyprinus carpio) in Japan.
Molecular Ecology 17: 796-809.

Mabuchi K, Miya M, Senou H, et al.
Complete mitochondrial DNA sequence of the Lake Biwa wild strain of common carp (Cyprinus carpio L.): further evidence for an ancient origin
AQUACULTURE 257 (1-4): 68-77 JUN 30 2006 [doi:10.1016/j.aquaculture.2006.03.040]


Phylogenetic and divergence time estiomation of clariids (Siluriformes)
Jansen G, Devaere S, Weekers PHH, et al.
Phylogenetic relationships and divergence time estimate of African anguilliform catfish (Siluriformes : Clariidae) inferred from ribosomal gene and spacer sequences
MOLECULAR PHYLOGENETICS AND EVOLUTION 38 (1): 65-78 JAN 2006

Phylogenetic analysis of catfishes (Siluriformes)
Jondeung A, Sangthong P, Zardoya R
The complete mitochondrial DNA sequence of the Mekong giant catfish (Pangasianodon gigas), and the phylogenetic relationships among Siluriformes
GENE 387 (1-2): 49-57 JAN 31 2007

Hardman M
The phylogenetic relationships among non-diplomystid catfishes as inferred from mitochondrial cytochrome b sequences; the search for the ictalurid sister taxon (Otophysi : Siluriformes)
MOLECULAR PHYLOGENETICS AND EVOLUTION 37 (3): 700-720 DEC 2005

Phylogenetics and biogeography of squeaker catfishes (Siluriformes)
Koblmuller S, Sturmbauer C, Verheyen E, et al.
Mitochondrial phylogeny and phylogeography of East African squeaker catfishes (Siluriformes : Synodontis)
BMC EVOLUTIONARY BIOLOGY 6: Art. No. 49 JUN 19 2006


Divergence time estimation of otocephalans
Peng ZG, He SP, Wang J, et al.
Mitochondrial molecular clocks and the origin of the major Otocephalan clades (Pisces : Teleostei): A new insight
GENE 370: 113-124 MAR 29 2006




Euteleostei

Li, C.,Orti, G., Zhang, G., Lu, G., 2007.
A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC Evolutionary Biology 7, 44.

Miya, M., Kawaguchi, A., Nishida, M., 2001.
Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly-determined complete mitochondrial DNA sequences.
Mol. Biol. Evol. 18, 1993-209.




Protacanthopterygii

Time estimation of protacanthopterygians
Campbell MA, López JA, Sado T, Miya M (2013)
Pike and salmon as sister taxa: detailed intraclade resolution and divergence time estimation of Esociformes + Salmoniformes based on whole mitochondrial genome sequences. Gene 530:57–65


Phylogenetics of protacanthopterygians
Brown KH, Drew RE, Weber LA, et al.
Intraspecific variation in the rainbow trout mitochondrial DNA genome
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 1 (2): 219-226 JUN 2006

Lopez JA, Chen WJ, Orti G
Esociform phylogeny
COPEIA (3): 449-464 AUG 20 2004

Ramsden SD, Brinkmann H, Hawryshyn CW, et al.
Mitogenomics and the sister of Salmonidae
TRENDS IN ECOLOGY & EVOLUTION 18 (12): 607-610 DEC 2003

Ishiguro, N. B., Miya M., Nishida, M., 2003.
Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the "Protacanthopterygii."
Mol. Phylogenet. Evol. 27, 476-488.

Phylogenetics of salmonids
Oakley TH, Phillips RB
Phylogeny of salmonine fishes based on growth hormone introns: Atlantic (Salmo) and Pacific (Oncorhynchus) salmon are not sister taxa
MOLECULAR PHYLOGENETICS AND EVOLUTION 11 (3): 381-393 APR 1999




Stomiiformes





Aulopiformes

Divergence time estimation for aulopiforms
Davis, MP, C Fielitz. 2010.
Estimating divergence times of lizardfishes and their allies (Euteleostei: Aulopiformes) and the timing of deep-sea adaptations. Molecular Phylogenetics and Evolution 57:1194-1208.

Phylogenetic position of Aulopiformes

Kawaguchi A, Miya M, Nishida M
Complete mitochondrial DNA sequence of Aulopus japonicus (Teleostei : Aulopiformes), a basal Eurypterygii: longer DNA sequences and higher-level relationships
ICHTHYOLOGICAL RESEARCH 48 (3): 213-223 AUG 25 2001




Myctophiformes

Phylogenetics of Myctophidae

Yamaguchi M, Miya M, Okiyama M, et al.
Molecular phylogeny and larval morphological diversity of the lanternfish genus Hygophum (Teleostei : Myctophidae)
MOLECULAR PHYLOGENETICS AND EVOLUTION 15 (1): 103-114 APR 2000




Ateleopodiformes




Lampridiformes




Polymixiiformes




Gadiformes


Phylogenetics of Macrouroidinae

Satoh TP, Miya M, Endo H, et al.
Round and pointed-head grenadier fishes (Actinopterygii : Gadiformes) represent a single sister group: Evidence from the complete mitochondrial genome sequences
MOLECULAR PHYLOGENETICS AND EVOLUTION 40 (1): 129-138 JUL 2006
[doi:10.1016/j.ympev.2006.02.014]


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