Evolution of mitochondrial-encoded cytochrome oxidase subunits in endothermic fish: The importance of taxon-sampling in codon-based models

Molecular Phylogenetics and Evolution

Volumn 63, Issue 3, 2012, Pages 679-684

  Little, Alexander G ^a   Lougheed, Stephen C ^a   Moyes, Christopher D ^a  

^a QUEEN S UNIVERSITY   (Canada)

Author keywords

Evolution; Lamnid sharks; Positive selection; Regional endothermy; Scombroids; Taxon sampling

Indexed keywords

CYTOCHROME C OXIDASE; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CODON; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; MOLECULAR TYPING; PERCIFORMES; PHYLOGENY; PHYSIOLOGY; PROTEIN SUBUNIT; SEQUENCE ALIGNMENT; SHARK;

ANIMALS; BAYES THEOREM; CODON; DNA, MITOCHONDRIAL; ELECTRON TRANSPORT COMPLEX IV; EVOLUTION, MOLECULAR; MODELS, GENETIC; MOLECULAR TYPING; PERCIFORMES; PHYLOGENY; PROTEIN SUBUNITS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SHARKS;

AVES; CHONDRICHTHYES; ISTIOPHORINAE; LAMNIDAE; MAMMALIA; PISCES; SCOMBRIDAE; VERTEBRATA; XIPHIIDAE;

EID: 84859812469     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.02.012     Document Type: Article

References (34)

1. Ballantyne J., Chamberlin M., Singer T. Oxidative metabolism in thermogenic tissues of the swordfish and mako shark. J. Exp. Zool. 1992, 261:110-114.
2. Bennet A.F., Ruben J.A. Endothermy and activity in vertebrates. Science 1979, 206:649-654.
3. Bernal D., Smith D., Lopez G., Weitz D., Grimminger T., Dickson K., Graham J.B. Comparative studies of high performance swimming in sharks II. Metabolic biochemistry of locomotor and myocardial muscle in endothermic and ectothermic sharks. J. Exp. Biol. 2003, 206:2845-2857.
4. Block B.A., Finnerty J. Endothermy in fishes, a phylogenetic analysis of constraints, credispositions, and selection pressures. Environ. Biol. Fishes 1994, 40:283-302.
5. Block B.A. Structure of the brain and eye heater tissue in marlins, sailfish, and spearfishes. J. Morph. 1986, 190:169-189.
6. Brown K. Fish mitochondrial genomics, sequence, inheritance and functional variation. J. Fish. Biol. 2008, 72:355-374.
7. Carlson J.K., Goldman K.J., Lowe C.G. Metabolism, energetic demand, and endothermy. The Biology of Sharks and Their Relatives 2004, 203-224. CRC Press, New York. J.C. Carrier, J.A. Musick, M.R. Heithaus (Eds.).
8. Castoe T.A., Jiang Z.J., Gu W., Wang Z.O., Pollock D.D. Adaptive evolution and functional redesign of core metabolic proteins in snakes. Plos One. 2008, 3:E2201.
9. Castoe T., De Koning A., Kim H. Evidence for an ancient adaptive episode of convergent molecular evolution. PNAS 2009, 106:8986-8991.
10. Christin P.A., Weinreich D.M., Besnard G. Causes and evolutionary significance of genetic convergence. TIG 2010, 26:400-405.
11. da Fonseca R.R., Johnson W.E., O'Brien S.J., Ramos M.J., Antunes A. The adaptive evolution of the mammalian mitochondrial genome. BMC Genom. 2008, 9:119.
12. Dalziel A.C., Moyes C.D., Fredriksson E., Lougheed S.C. Molecular evolution of cytochrome c oxidase in high-performance fish teleostei, scombroidei. J. Mol. Evol. 2006, 62:319-331.
13. Di Rocco F., Zambelli A.D., Vidal Rioja L.B. Identification of camelid specific residues in mitochondrial atp synthase subunits. J. Bioenerg. Biomembr. 2009, 41:223-228.
14. Dickson K., Graham J. Evolution and consequences of endothermy in fishes. Physiol. Biochem. Zool. 2004, 77:998-1018.
15. Donley J., Sepulveda C., Konstantinidis P. Convergent evolution in mechanical design of lamnid sharks and tunas. Nature 2004, 429:61-65.
16. Else P.L., Hulbert A.J. Comparison of the mammal machine and the reptile machine-energy-production. Am. J. Physiol. 1981, 240:R3-R9.
17. Gemballa S., Konstantinidis P., Donley J.M., Sepulveda C., Shadwick R.E. Evolution of high-performance swimming in sharks, transformations of the musculotendinous system from subcarangiform to thunniform swimmers. J. Morph. 2006, 267:477-493.
18. Gillooly J.F., Brown J.H., West G.B., Savage V.M., Charnov E.L. Effects of size and temperature on metabolic rate. Science 2001, 293(1):2248-2251.
19. Grossman L., Wildman D., Schmidt T., Goodman M. Accelerated evolution of the electron transport chain in anthropoid primates. TIG 2004, 20:578-585.
20. Havird J.C., Miyamoto M.M. The importance of taxon sampling in genomic studies, an example from the cyclooxygenases of teleost fishes. Mol. Phylogenet. Evol. 2010, 56:451-455.
21. Larkin M., et al. Clustal W and Clustal X version 20. Bioinformatics 2007, 23:2947-2948.
22. Little A.G., Lougheed S.C., Moyes C.D. Evolutionary affinity of billfishes xiphiidae and istiophoridae and flatfishes plueronectiformes, independent and trans-subordinal origins of endothermy in teleost fishes. Mol. Phylogenet. Evol. 2010, 56:897-904.
23. Little A.G., Kocha K.M., Lougheed S.C., Moyes C.D. Evolution of the nuclear-encoded cytochrome oxidase subunits in vertebrates. Physiol. Genom. 2010, 42:76-84.
24. Lu J., Zheng J., Xu Q., Chen K., Zhang C. Adaptive evolution of the vertebrate skeletal muscle sodium channel. Genet. Mol. Biol. 2011, 34:323-328.
25. Nespolo R.F., Bacigalupe L.D., Figueroa C.C., Koteja P., Opazo J.C. Using new tools to solve an old problem- the evolution of endothermy in vertebrates. Trends Ecol. Evol. Amst. 2011, 26:414-423.
26. Sanderson M.J., McMahon M.M., Steel M. Phylogenomics with incomplete taxon coverage, the limits to inference. BMC Evol. Biol. 2010, 10:155.
27. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 40. Mol. Biol. Evol. 2007, 24:1596-1599.
28. Uddin M., Opzao J., Wildman D., Sherwood C., Hof P. Molecular evolution of the cytochrome c oxidase subunit 5a gene in primates. BMC Evol. Biol. 2008, 8:8.
29. Walter I., Hegarty B., Seebacher F. Amp-activated protein kinase controls metabolism and heat production during embryonic development in birds. J. Exp. Biol. 2010, 213:3167-3176.
30. Walter I., Seebacher F. Endothermy in birds-underlying molecular mechanisms. J. Exp. Biol. 2009, 212:2328-2336.
31. Wolf N., Swift P., Carey F. Swimming muscle helps warm the brain of lamnid sharks. J. Comp. Physiol. B, Biochem. 1988, 157:709-715.
32. Wu W., Schmidt T.R., Goodman M., Grossman L.I. Molecular evolution of cytochrome c oxidase subunit i in primates, is there coevolution between mitochondrial and nuclear genomes?. Mol. Phylogenet. Evol. 2000, 17:294-304.
33. Ximena V.Z., Agnarsson I. Shark tales: A molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes). Mol. Phylogenet. Evol. 2011, 58:207-217.
34. Yang Z. PAML 4, Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 2007, 24:1586-1591.