Gene trees, species trees, and morphology converge on a similar phylogeny of living gars (Actinopterygii: Holostei: Lepisosteidae), an ancient clade of ray-finned fishes

Molecular Phylogenetics and Evolution

Volumn 63, Issue 3, 2012, Pages 848-856

  Wright, Jeremy J ^a   David, Solomon R ^a   Near, Thomas J ^b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

Coalescence; Fishes; Gar; Lepisosteidae; Living fossil; Phylogeny

Indexed keywords

CYTOCHROME C OXIDASE; FISH PROTEIN;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; FISH; GENETICS; MITOCHONDRIAL GENE; MOLECULAR GENETICS; MULTILOCUS SEQUENCE TYPING; NUCLEOTIDE SEQUENCE; PHYLOGENY; STATISTICAL MODEL;

ANIMALS; BAYES THEOREM; ELECTRON TRANSPORT COMPLEX IV; FISH PROTEINS; FISHES; GENES, MITOCHONDRIAL; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MULTILOCUS SEQUENCE TYPING; PHYLOGENY;

ACTINOPTERYGII; HOLOSTEI; LEPISOSTEIDAE; LEPISOSTEUS OSSEUS; PISCES;

EID: 84859826164     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.02.033     Document Type: Article

References (65)

1. Alfaro M.E., Zoller S., Lutzoni F. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 2003, 20:255-266.
2. Altekar G., Dwarkadas S., Huelsenbeck J.P., Ronquist F. Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 2004, 20:407-415.
3. Avise J.C., Nelson W.S., Sugita H. A speciational history of "living fossils": molecular evolutionary patterns in horseshoe crabs. Evolution 1994, 46:1986-2001.
4. Barrientos-Villalobos J., Monteros A.E.D. Genetic variation and recent population history of the tropical gar Atractosteus tropicus Gill (Pisces: Lepisosteidae). J. Fish. Biol. 2008, 73:1919-1936.
5. Birstein V.J., DeSalle R. Molecular phylogeny of Acipenserinae. Mol. Phylogenet. Evol. 1998, 9:141-155.
6. Birstein V.J., Doukakis P., DeSalle R. Molecular phylogeny of Acipenseridae: nonmonophyly of Scaphirhynchinae. Copeia 2002, 287-301.
7. Bossu C.M., Near T.J. Gene trees reveal repeated instances of mitochondrial DNA introgression in Orangethroat Darters (Percidae: Etheostoma). Syst. Biol. 2009, 58:114-129.
8. Chow S., Hazama K. Universal PCR primers for S7 ribosomal protein gene introns in fish. Mol. Ecol. 1998, 7:1255-1256.
9. Dowling T.E., Demarais B.D. Evolutionary significance of introgressive hybridization in cyprinid fishes. Nature 1993, 362:444-446.
10. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
11. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. Relaxed phylogenetics and dating with confidence. PLOS Biol. 2006, 4:699-710.
12. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
13. Edwards S.V. Is a new and general theory of molecular systematics emerging?. Evolution 2009, 63:1-19.
14. Egger B., Koblmüller S., Sturmbauer C., Sefc K.M. Nuclear and mitochondrial data reveal different evolutionary processes in the Lake Tanganyika cichlid genus Tropheus. BMC Evol. Biol. 2007, 7:137.
15. Eldredge N., Thompson J.N., Brakefield P.M., Gavrilets S., Jablonski D., Jackson J.B.C., Lenski R.E., Lieberman B.S., McPeek M.A., Miller W. The dynamics of evolutionary stasis. Paleobiology 2005, 31:133-145.
16. Gould S.J. The Structure of Evolutionary Theory 2002, Harvard University Press, Cambridge.
17. Gould S.J., Eldredge N. Punctuated equilibria: the tempo and mode of evolution reconsidered. Paleobiology 1977, 3:115-151.
18. Graham S.W., Kohn J.R., Morton B.R., Eckenwalder J.E., Barrett S.C.H. Phylogenetic congruence and discordance among one morphological and three molecular data sets from Pontederiaceae. Syst. Biol. 1998, 47:545-567.
19. Grande L. An empirical and synthetic pattern study of gars (Lepisosteiformes) and closely related species, based mostly on skeletal anatomy. The resurrection of Holostei. Am. Soc. Ich. Herp. Spec. Pub. 2010, 6:1-871.
20. Hardman M., Page L.M. Phylogenetic relationships among bullhead catfishes of the genus Ameiurus (Siluriformes: Ictaluridae). Copeia 2003, 2003:20-33.
21. Heled J., Drummond A.J. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 2010, 27:570-580.
22. Herrington S.J., Hettiger K.N., Heist E.J., Keeney D.B. Hybridization between longnose and alligator gars in captivity, with comments on possible gar hybridization in nature. Trans. Am. Fish. Soc. 2008, 137:158-164.
23. Holder M.T., Erdmann M.V., Wilcox T.P., Caldwell R.L., Hillis D.M. Two living species of coelacanths?. Proc. Natl. Acad. Sci. USA 1999, 96:12616-12620.
24. Hollingsworth P.R., Hulsey C.D. Reconciling gene trees of eastern North American minnows. Mol. Phylogenet. Evol. 2011, 61:149-156.
25. Huelsenbeck J.P., Rannala B. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst. Biol. 2004, 53:904-913.
26. Hulsey C.D., Keck B.P., Hollingsworth P.R. Species tree estimation and the historical biogeography of heroine cichlids. Mol. Phylogenet. Evol. 2011, 58:124-131.
27. Inoue J.G., Miya M., Tsukamoto K., Nishida M. Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish" Mol. Phylogenet. Evol. 2003, 26:110-120.
28. Jackson J.B.C., Cheetham A.H. Tempo and mode of speciation in the sea. Trends Ecol. Evol. 1999, 14:72-77.
29. Kammerer C.F., Grande L., Westneat M.W. Comparative and developmental functional morphology of the jaws of living and fossil gars (Actinopterygii: Lepisosteidae). J. Morphol. 2006, 267:1017-1031.
30. Keck B.P., Near T.J. A young clade repeating an old pattern: diversity in Nothonotus darters (Teleostei: Percidae) endemic to the Cumberland River. Mol. Ecol. 2010, 19:5030-5042.
31. Kikugawa K., Katoh K., Kuraku S., Sakurai H., Ishida O., Iwabe N., Miyata T. Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes. BMC Biol. 2004, 2:1-11.
32. Kubatko L.S., Gibbs H.L., Bloomquist E.W. Inferring species-level phylogenies and taxonomic distinctiveness using multilocus data in Sistrurus rattlesnakes. Syst. Biol. 2011, 60:393-409.
33. Kumazawa Y., Nishida M. Molecular phylogeny of osteoglossoids: a new model for Gondwanian origin and plate tectonic transportation of the Asian arowana. Mol. Biol. Evol. 2000, 17:1869-1878.
34. Kuo C.-H., Huang S., Lee S.-C. Phylogeny of hagfish based on the mitochondrial 16S rRNA gene. Mol. Phylogenet. Evol. 2003, 28:448-457.
35. Larget B., Simon D.L. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 1999, 16:750-759.
36. Larsen P.A., Marchan-Rivadeneira M.R., Baker R.J. Natural hybridization generates mammalian lineage with species characteristics. Proc. Natl. Acad. Sci. USA 2010, 107:11447-11452.
37. Lavoué S., Sullivan J.P. Simultaneous analysis of five molecular markers provides a well-supported phylogenetic hypothesis for the living bony-tongue fishes (Osteoglossomorpha: Teleostei). Mol. Phylogenet. Evol. 2004, 33:171-185.
38. Lê H.L.V., Lecointre G., Perasso R. A 28S rRNA-based phylogeny of gnathostomes: first steps in the analysis of conflict and congruence with morphologically based cladograms. Mol. Phylogenet. Evol. 1993, 2:31-51.
39. Li C.H., Ortí G., Zhang G., Lu G.Q. A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC Evol. Biol. 2007, 7:44.
40. Mavarez J., Linares M. Homoploid hybrid speciation in animals. Mol. Ecol. 2008, 17:4181-4185.
41. Meyer A., Salzburger W., Schartl M. Hybrid origin of a swordtail species (Teleostei: Xiphophorus clemenciae) driven by sexual selection. Mol. Ecol. 2006, 15:721-730.
42. Miya M., Pietsch T.W., Orr J.W., Arnold R.J., Satoh T.P., Shedlock A.M., Ho H.C., Shimazaki M., Yabe M., Nishida M. Evolutionary history of anglerfishes (Teleostei: Lophiiformes): a mitogenomic perspective. BMC Evol. Biol. 2010, 10.
43. Moyer G.R., Burr B.M., Krajewski C. Phylogenetic relationships of thorny catfishes (Siluriformes: Doradidae) inferred from molecular and morphological data. Zool. J. Linn. Soc. 2004, 140:551-575.
44. Moyer G.R., Sloss B.L., Kreiser B.R., Feldheim K.A. Isolation and characterization of microsatellite loci for alligator gar (Atractosteus spatula) and their variability in two other species (Lepisosteus oculatus and L-osseus) of Lepisosteidae. Mol. Ecol. Resour. 2009, 9:963-966.
45. Near T.J., Porterfield J.C., Page L.M. Evolution of cytochrome b and the molecular systematics of Ammocrypta (Percidae: Etheostomatinae). Copeia 2000, 2000:701-711.
46. Nelson J.S. Fishes of the World 2006, John Wiley, Hoboken.
47. Nolte A.W., Freyhof J., Stemshorn K.C., Tautz D. An invasive lineage of sculpins, Cottus sp. (Pisces, Teleostei) in the Rhine with new habitat adaptations has originated from hybridization between old phylogeographic groups. Proc. Roy. Soc. B 2005, 272:2379-2387.
48. Normark B.B., McCune A.R., Harrison R.G. Phylogenetic relationships of neopterygian fishes inferred from mitochondrial DNA sequences. Mol. Biol. Evol. 1991, 8:819-834.
49. Nylander, J.A.A., 2004. MrModeltest v2. Program Distributed by the Author. Evolutionary Biology Centre. Uppsala University.
50. Nylander J.A.A., Wilgenbusch J.C., Warren D.L., Swofford D.L. AWTY (are we there yet): a system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. Bioinformatics 2008, 24:581-583.
51. Poe S. Data set incongruence and the phylogeny of crocodilians. Syst. Biol. 1996, 45:393-414.
52. Rambaut, A., Drummond, A.J., 2009. Tracer 1.5. http://beast.bio.ed.ac.uk/Tracer.
53. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
54. Schelly R., Salzburger W., Koblmüller S., Duftner N., Sturmbauer C. Phylogenetic relationships of the lamprologine cichlid genus Lepidiolamprologus (Teleostei: Perciformes) based on mitochondrial and nuclear sequences, suggesting introgressive hybridization. Mol. Phylogenet. Evol. 2006, 38:426-438.
55. Shu D.-G., Luo H.-L., Morris S.C., Zhang X.-L., Hu S.-X., Chen L., Han J., Zhu M., Li Y., Chen L.-Z. Lower Cambrian vertebrates from South China. Nature 1999, 402:42-46.
56. Shu D.G., Morris S.C., Han J., Zhang Z.F., Yasui K., Janvier P., Chen L., Zhang X.L., Liu J.N., Li Y., Liu H.Q. Head and backbone of the Early Cambrian vertebrate Haikouichthys. Nature 2003, 421:526-529.
57. Stanley S.M. Macroevolution, Pattern and Process 1979, W.H. Freeman, San Francisco.
58. Stiassny M.L.J., Wiley E.O., Johnson G.D., Carvalho M.R.d. Gnathostome fishes. Assembling the Tree of Life 2004, 410-429. Oxford University Press, New York. J. Cracraft, M.J. Donoghue (Eds.).
59. Sudarto, Lalu X.C., Kosen J.D., Tjakrawidjaja A.H., Kusumah R.V., Sadhotomo B., Kadarusman, Pouyaud L., Slembrouck J., Paradis E. Mitochondrial genomic divergence in coelacanths (Latimeria): slow rate of evolution or recent speciation?. Mar. Biol. 2010, 157:2253-2262.
60. Suttkus R.D. Order Lepisostei. Fishes of the Western North Atlantic 1963, 61-88. Memoirs of the Sears Foundation of Marine Research, New Haven, CT. B. Bigelow, W.C. Schroeder (Eds.).
61. Suzuki D., Brandley M.C., Tokita M. 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 Evol. Biol. 2010, 10:21.
62. Venkatesh B., Erdmann M.V., Brenner S. Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates. Proc. Natl. Acad. Sci. USA 2001, 98:11382-11387.
63. Wiley E.O. The phylogeny and biogeography of fossil and recent gars (Actinopterygii: Lepisosteidae). Univ. Kansas Mus. Nat. Hist. Miscel. Publ. 1976, 64:1-111.
64. Williams S.T., Reid D.G., Littlewood D.T.J. A molecular phylogeny of the Littorininae (Gastropoda: Littorinidae): unequal evolutionary rates, morphological parallelism, and biogeography of the Southern Ocean. Mol. Phylogenet. Evol. 2003, 28:60-86.
65. Zardoya R., Meyer A. Evolutionary relationships of the coelacanth, lungfishes, and tetrapods based on the 28S ribosomal RNA gene. Proc. Natl. Acad. Sci. USA 1996, 93:5449-5454.