The phylogenetic position of an undescribed paedomorphic clupeiform taxon: Mitogenomic evidence

Ichthyological Research

Volumn 55, Issue 4, 2008, Pages 328-334

  Lavoué, Sébastien ^a   Miya, Masaki ^b   Kawaguchi, Akira ^c   Yoshino, Tetsuo ^c   Nishida, Mutsumi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b NATURAL HISTORY MUSEUM AND INSTITUTE   (Japan)

^c UNIVERSITY OF THE RYUKYUS   (Japan)

Author keywords

Clupeiformes; Evolution; Mitogenomics; Paedomorphism

Indexed keywords

CHIROCENTRUS; CLUPEIDAE; CLUPEIFORMES; CLUPEOIDEI; DUSSUMIERIINAE; ETRUMEUS; JENKINSIA; SPRATELLOIDES; SPRATELLOIDINI; SUNDASALANX; TELEOSTEI;

EID: 55549147929     PISSN: 13418998     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10228-008-0044-3     Document Type: Article

References (46)

1. DP Begle 1991 Relationships of the osmeroid fishes and the use of reductive characters in phylogenetic analysis Syst Zool 40 33 53
2. RE Broughton PC Reneau 2006 Spatial covariation of mutation and nonsynonymous substitution rates in vertebrate mitochondrial genomes Mol Biol Evol 23 1516 1524
3. S Cheng R Higuchi M Stoneking 1994 Complete mitochondrial genome amplification Nat Genet 7 350 351
4. WJEM Costa PY Le Bail 1999 Fluviphylax palikur: a new poeciliid from the Rio Oiapoque basin, northern Brazil (Cyprinodontiformes: Cyprinodontoidei), with comments on miniaturization in Fluviphylax and other neotropical freshwater fishes Copeia 1999 1027 1034
5. G Dingerkus LD Uhler 1977 Enzyme clearing of alcian blue stained whole small vertebrates for demonstration of cartilage Stain Technol 52 229 232
6. J Géry 1964 Une nouvelle famille de poissons dulçaquicoles africains; les Grasseichthyidae CR Acad Sci III 259 4805 4807
7. L Grande 1985 Recent and fossil clupeomorph fishes with materials for revision of the subgroups of clupeoids Bull Am Mus Nat Hist 181 231 372
8. J Hanken DB Wake 1993 Miniaturization of body-size-organismal consequences and evolutionary significance Ann Rev Ecol Syst 24 501 519
9. JP Huelsenbeck F Ronquist 2001 MrBAYES: Bayesian inference of phylogenetic trees Bioinformatics 17 754 755
10. JG Inoue M Miya K Tsukamoto M Nishida 2001 Complete mitochondrial DNA sequence of Conger myriaster (Teleostei: Anguilliformes): novel gene order for vertebrate mitochondrial genomes and the phylogenetic implications for anguilliform families J Mol Evol 52 311 320
11. JG Inoue M Miya K Tsukamoto M Nishida 2003 Evolution of the deep-sea gulper eel mitochondrial genomes: large-scale gene rearrangements originated within the eels Mol Biol Evol 20 1917 1924
12. JG Inoue M Miya K Tsukamoto M Nishida 2004 Mitogenomic evidence for the monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larva Mol Phylogenet Evol 32 274 286
13. NB Ishiguro M Miya M Nishida 2003 Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the " Protacanthopterygii" Mol Phylogenet Evol 27 476 488
14. NB Ishiguro M Miya JG Inoue M Nishida 2005 Sundasalanx (Sundasalangidae) is a progenetic clupeiform, not a closely-related group of salangids (Osmeriformes): mitogenomic evidence J Fish Biol 67 561 569
15. Johnson GD, Patterson C (1996) Relationships of lower euteleostean fishes. In: Stiassny MLJ, Parenti LR, Johnson GD (eds) Interrelationships of fishes. Academic Press, New York, pp 251-332
16. T Kon T Yoshino T Mukai M Nishida 2007 DNA sequences identify numerous cryptic species of the vertebrate: a lesson from the gobioid fish Schindleria Mol Phylogenet Evol 44 53 62
17. M Kottelat R Britz TH Hui KE Witte 2006 Paedocypris, a new genus of Southeast Asian cyprinid fish with a remarkable sexual dimorphism, comprises the world's smallest vertebrate Proc R Soc Lond B 273 895 899
18. S Lavoué M Miya JG Inoue K Saitoh N Ishiguro M Nishida 2005 Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: implications for higher-level relationships within the Otocephala Mol Phylogenet Evol 37 165 177
19. S Lavoué M Miya K Saitoh NB Ishiguro M Nishida 2007 Phylogenetic relationships among anchovies, sardines, herrings and their relatives (Clupeiformes), inferred from whole mitogenome sequences Mol Phylogenet Evol 43 1096 1105
20. JS Lee M Miya YS Lee CG Kim EH Park Y Aoki M Nishida 2001 The complete DNA sequence of the mitochondrial genome of the self-fertilizing fish Rivulus marmoratus (Cyprinodontiformes, Rivulidae) and the first description of duplication of a control region in fish Gene 280 1 7
21. C Li G Ortí 2007 Molecular phylogeny of Clupeiformes (Actinopterygii) inferred from nuclear and mitochondrial DNA sequences Mol Phylogenet Evol 44 386 398
22. A Löytynoja MC Milinkovitch 2003 A hidden Markov model for progressive multiple alignment Bioinformatics 19 1505 1513
23. K Mabuchi M Miya TP Satoh MW Westneat M Nishida 2004 Gene rearrangements and evolution of tRNA pseudogenes in the mitochondrial DNA of the parrotfish (Teleostei: Perciformes: Scaridae) J Mol Evol 59 287 297
24. JR Macey A Larson NB Ananjeva ZL Fang TJ Papenfuss 1997 Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome Mol Biol Evol 14 91 104
25. M Miya M Nishida 1997 Speciation in the open ocean Nature 389 803 804
26. M Miya M Nishida 1999 Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei: Stomiiformes): first example of transfer RNA gene rearrangements in bony fishes Mar Biotechnol 1 416 426
27. M Miya 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
28. M Miya A Kawaguchi M Nishida 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 2009
29. M Miya H Takeshima H Endo NB Ishiguro JG Inoue T Mukai TP Satoh M Yamaguchi A Kawaguchi K Mabuchi SM Shirai M Nishida 2003 Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences Mol Phylogenet Evol 26 121 138
30. M Miya TP Satoh M 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 genome sequences Biol J Linn Soc 85 289 306
31. C Moritz TE Dowling WM Brown 1987 Evolution of animal mitochondrial DNA-relevance for population biology and systematics Ann Rev Ecol Syst 18 269 292
32. MJ Phillips F Delsuc D Penny 2004 Genome-scale phylogeny and the detection of systematic biases Mol Biol Evol 21 1455 1458
33. D Posada KA Crandall 1998 MODELTEST: testing the model of DNA substitution Bioinformatics 14 817 818
34. TR Roberts 1981 Sundasalangidae, a new family of minute freshwater salmoniform fishes from Southeast Asia Proc Calif Acad Sci 42 295 302
35. TR Roberts 1984 Amazonsprattus scintilla, new genus and species from the Rio Negro, Brazil, the smallest known clupeomorph fish Proc Calif Acad Sci 43 317 321
36. F Ronquist JP Huelsenbeck 2003 MrBayes 3: Bayesian phylogenetic inference under mixed models Bioinformatics 19 1572 1574
37. K Saitoh T Sado RL Mayden N Hanzawa K Nakamura M Nishida M Miya 2006 Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): the first evidence toward resolution of higher-level relationships of the world's largest freshwater fish clade based on 59 whole mitogenome sequences J Mol Evol 63 826 841
38. TP Satoh M Miya H Endo M Nishida 2006 Round and pointed-head grenadier fishes (Actinopterygii: Gadiformes) represent a single sister group: evidence from the complete mitochondrial genome sequences Mol Phylogenet Evol 40 129 138
39. DJ Siebert 1997 Notes on the anatomy and relationships of Sundasalanx Roberts (Teleostei, Clupeidae), with descriptions of four new species from Borneo Bull Br Mus (Nat Hist) Zool 63 13 26
40. A Stamatakis 2006 RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models Bioinformatics 22 2688 2690
41. JP Sullivan S Lavoué CD Hopkins 2002 Discovery and phylogenetic analysis of a riverine species flock of African electric fishes (Mormyridae: Teleostei) Evolution 56 597 616
42. WR Taylor 1967 An enzyme method of clearing and staining small vertebrates Proc US Nat Mus 122 1 17
43. CS Tzeng CF Hui SC Shen PC Huang 1992 The complete nucleotide-sequence of the Crossostoma Lacustre mitochondrial genome-conservation and variations among vertebrates Nucleic Acids Res 20 4853 4858
44. PJP Whitehead 1963 A contribution to the classification of clupeoid fishes Ann Mag Nat Hist 5 737 750
45. Y Yamanoue M Miya K Matsuura M Katoh H Sakai M Nishida 2004 Mitochondrial genomes and phylogeny of the ocean sunfishes (Tetraodontiformes: Molidae) Ichthyol Res 51 269 273
46. Z Yang 1994 Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods J Mol Evol 39 306 314