The mitochondrial phylogeny of an ancient lineage of ray-finned fishes (Polypteridae) with implications for the evolution of body elongation, pelvic fin loss, and craniofacial morphology in Osteichthyes

BMC Evolutionary Biology

Volumn 10, Issue 1, 2010, Pages

  Suzuki, Dai ^a   Brandley, Matthew C ^b   Tokita, Masayoshi ^a,c  

^a KYOTO UNIVERSITY   (Japan)

^b YALE UNIVERSITY   (United States)

^c UNIVERSITY OF TSUKUBA   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN ANALYSIS; FINFISH; GENETIC ANALYSIS; GENETIC DIFFERENTIATION; MITOCHONDRION; MORPHOLOGY; MORPHOMETRY; PHYLOGENY;

ACTINOPTERYGII; ERPETOICHTHYS; OSTEICHTHYES; POLYPTERIDAE; POLYPTERUS; POLYPTERUS PALMAS; TETRAPODA;

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; BODY SIZE; DNA SEQUENCE; FISH; GENETICS; HISTOLOGY; MOLECULAR EVOLUTION; PHYLOGENY;

ANIMALS; BAYES THEOREM; BODY SIZE; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; FISHES; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 77149177675     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-10-21     Document Type: Article

References (97)

1. Vertebrate Paleontology. MJ Benton, Malden, MA: Blackwell Science 3 2004
2. Jaws and teeth of the earliest bony fishes. H Botella H Blom M Dorka PE Ahlberg P Janvier, Nature 2007 448 583 586 10.1038/nature05989 17671501
3. Developmental basis of evolutionary digit loss in the Australian lizard Hemiergis. MD Shapiro J Hanken N Rosenthal, J Exp Zool 2003 297 48 56 10.1002/jez.b.19
4. Integration and evolution of the cichlid mandible: the molecular basis of alternate feeding strategies. RC Albertson JT Streelman TD Kocher PC Yelick, Proc Natl Acad Sci USA 2005 102 16287 16292 10.1073/pnas.0506649102 16251275
5. The calmodulin pathway and evolution of elongated beak morphology in Darwin's finches. A Abzhanov WP Kuo C Hartmann BR Grant PR Grant CJ Tabin, Nature 2006 442 563 567 10.1038/nature04843 16885984
6. A single amino acid mutation contributes to adaptive beach mouse color pattern. HE Hoekstra RJ Hirschmann RA Bundey PA Insel JP Crossland, Science 2006 313 101 104 10.1126/science.1126121 16825572
7. Adaptive variation in beach mice produced by two interacting pigmentation genes. CC Steiner JN Weber HE Hoekstra, PLoS Biol 2007 5 219 10.1371/journal.pbio.0050219 17696646
8. Evolutionary origin and development of snake fangs. FJ Vonk JF Admiraal K Jackson R Reshef MA de Bakker K Vanderschoot I van den Berge M van Atten E Burgerhout A Beck PJ Mirtschin E Kochva F Witte BG Fry AE Woods MK Richardson, Nature 2008 454 630 633 10.1038/nature07178 18668106
9. A Novel Role for Mc1r in the parallel evolution of depigmentation in independent populations of the cavefish Astyanax mexicanus. JB Gross R Borowsky CJ Tabin, PLoS Genet 2009 5 1000326 10.1371/journal.pgen.1000326 19119422
10. Fishes of the World. JS Nelson, New York: Wiley 4 2006
11. On the homology of the posteriormost gill arch in polypterids (Cladistia, Actinopterygii). R Britz GD Johnson, Zool J Linn Soc 2003 138 495 503 10.1046/j.1096-3642.2003.t01-1-00067.x (Pubitemid 36990372)
12. New interpretations of the skull of a primitive bony fish Erpetoichthys calabaricus (Actinopterygii: Cladistia). KM Claeson WE Bemis JW Hagadorn, J Morphol 2007 268 1021 1039 10.1002/jmor.10567 17823913
13. The Genus Polypterus (Bichirs). A fish group diverged at the stem of ray-finned fishes (Actinopterygii). M Takeuchi M Okabe S Aizawa, Emerging Model Organisms: A Laboratory Manual New York: Cold Spring Harbor Laboratory Press 2009 1 447 467
14. Morphology and interrelationships of primitive actinopterygian fishes. C Patterson, Am Zool 1982 22 241 259
15. Interrelationships of lower actinopterygian fishes. BG Gardiner B Schaeffer, Zool J Linn Soc 1989 97 135 187 10.1111/j.1096-3642.1989.tb00550.x
16. The complete mitochondrial DNA sequence of the bichir (Polypterus ornatipinnis), a basal ray-finned fish: Ancient establishment of the consensus vetebrate gene order. K Noack R Zardoya A Meyer, Genetics 1996 144 1165 1180 8913758
17. Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates. B Venkatesh MV Erdmann S Brenner, Proc Natl Acad Sci USA 2001 98 11382 11387 10.1073/pnas.201415598 11553795
18. Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish.". JG Inoue M Miya K Tsukamoto M Nishida, Mol Phylogenet Evol 2003 26 110 120 10.1016/S1055-7903(02)00331-7 12470943 (Pubitemid 36029258)
19. Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes. K Kikugawa K Katoh S Kuraku H Sakurai O Ishida N Iwabe T Miyata, BMC Evol Biol 2004 2 3
20. Insight into the phylogeny of African Clariidae (Teleostei, Siluriformes): Implications for their body shape evolution, biogeography, and taxonomy. JF Agnese GG Teugels, Mol Phylogenet Evol 2005 36 546 553 10.1016/j.ympev.2005.03.028 15886025
21. Phylogeny of the African representatives of the catfish family Clariidae (Teleostei, Siluriformes) based on a combined analysis: independent evolution towards anguilliformity. S Devaere G Jansen D Adriaens P Weekers, J Zool Syst Evol Res 2007 45 214 229 10.1111/j.1439-0469.2006.00399.x (Pubitemid 47087592)
22. Evolution of axial patterning in elongate fishes. AB Ward EL Brainerd, Biol J Linn Soc 2007 90 97 116 10.1111/j.1095-8312.2007.00714.x (Pubitemid 46089276)
23. Adaptive radiation of gobies in the interstitial habitats of gravel beaches accompanied by body elongation and excessive vertebral segmentation. T Yamada T Sugiyama N Tamaki A Kawakita M Kato, BMC Evol Biol 2009 9 145 10.1186/1471-2148-9-145 19558710
24. Digit reduction, body size, and paedomorphosis in salamanders. JJ Wiens JT Hoverman, Evol Dev 2008 10 449 463 10.1111/j.1525-142X.2008.00256.x 18638322
25. How lizards turn into snakes: a phylogenetic analysis of body-form evolution in anguid lizards. JJ Wiens JL Slingluff, Evolution 2001 55 2303 2318 11794789
26. Why does a trait evolve multiple times within a clade? Repeated evolution of snake-like body form in squamate reptiles. JJ Wiens MC Brandley TW Reeder, Evolution 2006 60 123 141 16568638
27. Rates and patterns in the evolution of snake-like body form in squamate reptiles: evidence for repeated re-evolution of lost digits and long-term persistence of intermediate body forms. MC Brandley JP Huelsenbeck JJ Wiens, Evolution 2008 62 2042 2064 10.1111/j.1558-5646.2008.00430.x 18507743
28. The origin and early radiation of terrestrial vertebrates. RL Carroll, J Paleontol 2001 75 1202 1213 10.1666/0022-3360(2001)075<1202:TOAERO>2.0. CO;2
29. Vestigial forelimbs and axial elongation in a 95 million-year old non-snake squamate. A Palci MW Caldwell, J Verteb Paleontol 2007 27 1 7 10.1671/0272-4634(2007)27[1:VFAAEI]2.0.CO;2 (Pubitemid 46542306)
30. Intraspecific variation in limblessness in vertebrates: a unique example of microevolution. D Adriaens S Devaere GG Teugels B Dekegel W Verraes, Biol J Linn Soc 2002 75 367 377 10.1111/j.1095-8312.2002.tb02078.x
31. Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. MD Shapiro ME Marks CL Peichel BK Blackman KS Nereng B Jánsson D Schluter DM Kingsley, Nature 2004 428 717 23 10.1038/nature02415 15085123
32. Developmental genetic basis for the evolution of pelvic fin loss in the pufferfish Takifugu rubripes. M Tanaka LA Hale A Amores YL Yan WA Cresko T Suzuki JH Postlethwait, Dev Biol 2005 15 227 39 10.1016/j.ydbio.2005.02.016 (Pubitemid 40719149)
33. Testing historical hypotheses of morphological change: biomechanical decoupling in Loricarioid catfishes. SA Schaefer GV Lauder, Evolution 1996 50 1661 1675 10.2307/2410902
34. Assessing morphological differences in an adaptive trait: a landmark-based morphometric approach. RC Albertson TD Kocher, J Exp Zool 2001 289 385 403 10.1002/jez.1020 11351326
35. Asymmetrical development of bones and soft tissues during eye migration of metamorphosing Japanese flounder, Paralichthys olivaceus. N Okada Y Takagi T Seikai M Tanaka M Tagawa, Cell Tissue Res 2001 304 59 66 10.1007/s004410100353 11383887
36. cimp1, a novel astacin family metalloproteinase gene from East African Cichlids, is differentially expressed between species during growth. T Kijimoto M Watanabe K Fujimura M Nakazawa Y Murakami S Kuratani Y Kohara T Gojobori N Okada, Mol Biol Evol 2005 22 1649 1660 10.1093/molbev/msi159 15858202
37. Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family Labridae. MW Westneat ME Alfaro PC Wainwright D Bellwood JR Grubich JL Fessler KD Clements LL Smith, Proc R Soc B 2005 272 993 1000 10.1098/rspb.2004.3013 16024356
38. Genetic and developmental basis of cichlid trophic diversity. RC Albertson TD Kocher, Heredity 2006 97 211 221 10.1038/sj.hdy.6800864 16835594
39. Morphological and biomechanical changes of the feeding apparatus in developing southern flounder, Paralichthys lethostigma. AW Francis Jr RG Turingan, J Morphol 2008 269 1169 1180 10.1002/jmor.10631 18473368
40. Continuous and arrested morphological diversification in sister clades of characiform fishes: a phylomorphospace approach. B Sidlauskas, Evolution 2008 62 3135 3156 10.1111/j.1558-5646.2008.00519.x 18786183
41. Form and function of damselfish skulls: rapid and repeated evolution into a limited number of trophic niches. WJ Cooper MW Westneat, BMC Evol Biol 2009 9 24 10.1186/1471-2148-9-24 19183467
42. Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution. C Chiu K Dewar GP Wagner K Takahashi F Ruddle C Ledje P Bartsch J-L Scemama E Stellwag C Fried SJ Prohaska PF Stadler CT Amemiya, Genome Res 2004 14 11 17 10.1101/gr.1712904 14707166
43. Catalogue of the freshwater fishes of Africa in the British Museum (Natural History). G Boulenger, London: Wheldon and Wesley 1909
44. Contribution l'étude systématique des Polyptèridae (première partie). M Poll, Revue de Zoologie et de Botanique Africaines 1941 35 141 179
45. Les tendances évolutives des Polyptères d'après l'étude systématique des espèces. M Poll, Annales de la Société Royale Zoologique de Belgique 1941 72 157 173
46. Contribution l'étude systématique des Polyptèridae (suite et fin). M Poll, Revue de Zoologie et de Botanique Africaines 1942 35 269 308
47. Essai de classification cladistique des Polyptéridés (Pisces, Branchiopterygii). J Daget M Desoutter, Bull Mus Natn Hist Nat Paris 1983 4 661 674
48. Evolutionary history of African lungfish: a hypothesis from molecular phylogeny. M Tokita T Okamoto T Hikida, Mol Phylogenet Evol 2005 35 281 286 10.1016/j.ympev.2004.11.025 15737597
49. Data partitions and complex models in Bayesian analysis: the phylogeny of gymnophthalmid lizards. TA Castoe TM Doan CL Parkinson, Syst Biol 2004 53 448 469 10.1080/10635150490445797 15503673
50. Bayesian phylogenetic analysis of combined data. JAA Nylander F Ronquist JP Huelsenbeck JL Nieves-Aldrey, Syst Biol 2004 5 47 67 10.1080/ 10635150490264699 (Pubitemid 38370420)
51. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. MC Brandley A Schmitz TW Reeder, Syst Biol 2005 54 373 390 10.1080/10635150590946808 16012105
52. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4.0b10. DL Swofford, Sunderland, MA: Sinauer Associates 2002 12504223
53. Estimating the dimension of a model. G Schwarz, Ann Statis 1978 6 461 464 10.1214/aos/1176344136
54. MRBAYES 3: Bayesian phylogenetic inference under mixed models. F Ronquist JP Huelsenbeck, Bioinformatics 2003 19 1572 1574 10.1093/bioinformatics/btg180 12912839
55. Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. G Altekar S Dwarkadas JP Huelsenbeck F Ronquist, Bioinformatics 2004 20 407 415 10.1093/bioinformatics/btg427 14960467
56. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. JAA Nylander JC Wilgenbusch DL Warren DL Swofford, Bioinformatics 2008 24 581 583 10.1093/bioinformatics/btm388 17766271
57. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. JP Huelsenbeck B Rannala, Syst Biol 2004 53 904 913 10.1080/10635150490522629 15764559
58. Advances in Morphometrics, NATO ASI Series A: Life Sciences, vol. 284. LF Marcus M Corti A Loy GJP Naylor DE Slice, New York: Plenum Press 1996
59. Geometric Morphometrics for Biologists: a Primer. ML Zeldich D Swiderski DH Sheets W Fink, Elsevier Academic Press, Amsterdam 2004 443
60. tpsDig2.10. FJ Rohlf, 2006 http://life.bio.sunysb.edu/morph/ 16929667
61. Coordgen6 h in Integrated Morphometrics Package (IMP). HD Sheets, Department of Physics, Canisius College 2006 http://www3.canisius.edu/ ∼sheets/moremorph.html
62. Pcagen6 h in Integrated Morphometrics Package (IMP). HD Sheets, Department of Physics, Canisius College 2007 http://www3.canisius.edu/ ∼sheets/moremorph.html
63. Mesquite: a modular system for evolutionary analysis. Version 2.6. WP Maddison DR Maddison, 2009 http://mesquiteproject.org 19199524
64. FishBase. version (09/2008). R Froese D Pauly, 2008 http://www.fishbase. org/search.php 18584209
65. Opening the black box: phylogenetics and morphological evolution of the Malagasy fossorial lizards of the subfamily "Scincinae". A Schmitz MC Brandley P Mausfeld M Vences F Glaw RA Nussbaum TW Reeder, Mol Phylogenet Evol 2005 34 118 133 10.1016/j.ympev.2004.08.016 15579386
66. Squared-change parsimony reconstructions of ancestral states for continuous-valued characters on a phylogenetic tree. WP Maddison, Syst Zool 1991 40 304 314 10.2307/2992324
67. Likelihood of ancestor states in adaptive radiation. D Schluter T Price AO Mooers D Ludwig, Evolution 1997 51 1699 1711 10.2307/2410994
68. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. M Pagel, Syst Biol 1999 48 612 622 10.1080/106351599260184
69. A likelihood approach to estimating phylogeny from discrete morphological character data. PO Lewis, Syst Biol 2001 50 913 925 10.1080/106351501753462876 12116640
70. Fresh-water fishes and West Indian zoogeography. GS Myers, Annual Report of the Board of Regents of the Smithsonian Institution 1938 92 339 364
71. Salt-tolerance of fresh-water fish groups in relation to zoogeographical problems. GS Myers, Bijdragen tot de Dierkunde 1949 28 315 322
72. Polypteridae. JP Gosse, Faune des poisons d'eaux douces et saumtres d'Afrique de l'Ouest I. ORSTOM 28, Lévèque C, Paugy D, Teugels GG, 1990 79 87
73. Subspecies in the Polypterus palmas complex (Brachiopterygii; Polypteridae) from West and Central Africa. MM Hanssens GG Teugels DFE Thys van den Audenaerde, Copeia 1995 1995 694 705 10.2307/1446767
74. Polypterus mokelembembe, a new species of bichir from the central Congo River basin (Actinopterygii: Cladistia: Polypteridae). UK Schliewen F Schäfer, Zootaxa 2006 1129 23 36
75. Gene trees reveal repeated instances of mitochondrial DNA introgression in orangethroat darters (Percidae:Etheostoma). CM Bossu TJ Near, Syst Biol 2009 58 114 129 10.1093/sysbio/syp014
76. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. DJ Funk KE Omland, Annu Rev Ecol Syst 2003 34 397 423 10.1146/annurev.ecolsys.34.011802.132421
77. Somite number and vertebrate evolution. MK Richardson SP Allen GM Wright A Raynaud J Hanken, Development 1998 125 151 160 9486789
78. The vertebrate segmentation clock: the tip of the iceburg. EM zbudak O Pourquié Curr Opin Genet Dev 2008 18 317 323 10.1016/j.gde.2008.06.007 18625313
79. Serpent clocks tick faster. FJ Vonk MK Richardson, Nature 2008 454 282 283 10.1038/454282a 18633402
80. Control of segment number in vertebrate embryos. C Gomez EM zbudak J Wunderlich D Baumann J Lewis O Pourquié Nature 2008 454 335 339 10.1038/nature07020 18563087
81. Larvae of polypterid fish Erpetoichthys Smith. HS Clausen, Nature 1956 178 932 933 10.1038/178932b0
82. On the reproduction and early development of Erpetoichthys calabaricus, Polypterus senegalus, and Polypterus ornatipinnis (Actinopterygii: Polypteridae). R Britz P Bartsch, Ichthyol Expl Freshwaters 1998 9 325 334
83. Developmental control of segment numbers in vertebrates. C Gomez O Pourquié J Exp Zool B Mol Dev Evol 2009 312 533 544 10.1002/jez.b.21305 19621429
84. Tetrapod limblessness: evolution and functional corollaries. C Gans, Am Zool 1975 15 455 467
85. Evolutionary mechanisms of limb loss in tetrapods. R Lande, Evolution 1978 32 73 92 10.2307/2407411
86. Developmental basis of limblessness and axial patterning in snakes. MJ Cohn C Tickle, Nature 1999 399 474 479 10.1038/20944 10365960
87. The developmental bases of limb reduction and body elongation in squamates. TJ Sanger JJ Gibson-Brown, Evolution 2004 58 2103 2106 15521466
88. Axial patterning in snakes and caecilians: evidence for an alternative interpretation of the Hox code. JM Woltering FJ Vonk H Müller N Bardine IL Tuduce MAG de Bakker WP Knöchel IO Sirbu AJ Durston MK Richardson, Dev Biol 2009 332 82 89 10.1016/j.ydbio.2009.04.031 19409887
89. Morphogenesis of the rudimentary hind-limb of the glass snake (Ophisaurus apodus Pallas). TM-Z Rahmani, J Embryol Exp Morphol 1974 32 431 443 4463212
90. Fibroblast growth factors (FGF-2) and delayed involution of the posterior limbs of the slow-worm embryo (Anguis fragilis, L.). A Raynaud P Kan G Bouche AM Duprat, Comptes rendus de l'Académie des sciences. Série III, Sciences de la vie 1995 318 573 578
91. Developmental basis for hind-limb loss in dolphins and origin of the cetacean bodyplan. JGM Thewissen MJ Cohn LS Stevens S Bajpai J Heyning WE Horton Jr, Proc Natl Acad Sci USA 2006 103 8414 8418 10.1073/pnas.0602920103 16717186
92. Parallel genetic origins of pelvic reduction in vertebrates. MD Shapiro MA Bell DM Kingsley, Proc Natl Acad Sci USA 2006 103 13753 13758 10.1073/pnas.0604706103 16945911
93. The BMP antagonists Chordin and Noggin have essential but redundant roles in mouse mandibular outgrowth. RW Stottmann RM Anderson J Klingensmith, Dev Biol 2001 240 457 473 10.1006/dbio.2001.0479 11784076
94. Genetic modifiers of otocephalic phenotypes in Otx2 heterozygous mutant mice. T Hide J Hatakeyama C Kimura-Yoshida E Tian N Takeda Y Ushio T Shiroishi S Aizawa I Matsuo, Development 2002 129 4347 4357 12183386
95. Fgf and Bmp signals repress the expression of Bapx1 in the mandibular mesenchyme and control the position of the developing jaw joint. J Wilson AS Tucker, Dev Biol 2004 266 138 150 10.1016/j.ydbio.2003.10.012 14729484
96. The genesis of cartilage size and shape during development and evolution. BF Eames RA Schneider, Development 2008 135 3947 3958 10.1242/dev.023309 18987028
97. barx1 is necessary for ectomesenchyme proliferation and osteochondroprogenitor condensation in the zebrafish pharyngeal arches. SM Sperber IB Dawid, Dev Biol 2008 321 101 110 10.1016/j.ydbio.2008.06.004 18590717