The evolution of mitochondrial genomes in subterranean caviomorph rodents: Adaptation against a background of purifying selection

Molecular Phylogenetics and Evolution

Volumn 61, Issue 1, 2011, Pages 64-70

  Tomasco, Ivanna H ^a   Lessa, Enrique P ^a  

^a UNIVERSIDAD DE LA REPÚBLICA   (Uruguay)

Author keywords

Caviomorpha; MtDNA; Positive selection; Purifying selection; Subterranean niche

Indexed keywords

MITOCHONDRIAL DNA; PROTEIN;

ADAPTATION; ANAEROBIC GROWTH; ANIMAL; ARTICLE; CLASSIFICATION; EVOLUTION; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; MITOCHONDRIAL GENOME; MITOCHONDRION; MOLECULAR EVOLUTION; PHYLOGENY; PHYSIOLOGY; RODENT;

ADAPTATION, PHYSIOLOGICAL; ANAEROBIOSIS; ANIMALS; BIOLOGICAL EVOLUTION; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME, MITOCHONDRIAL; MITOCHONDRIA; PHYLOGENY; PROTEINS; RODENTIA; SELECTION, GENETIC;

CAVIOMORPHA; CTENOMYIDAE; CTENOMYS; MAMMALIA; RODENTIA; SPALACOPUS; SPALACOPUS CYANUS;

EID: 79960616388     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2011.06.014     Document Type: Article

References (50)

1. Adkins R.M., Honeycutt R.L. Evolution of the primate cytochrome c oxidase subunit II gene. J. Mol. Evol. 1994, 38:215-231.
2. Andrews T.D., Jermaine L.S., Easteal S. Accelerated evolution of cytB in simian primates: adaptive evolution in concert with other mitochondrial proteins?. J. Mol. Evol. 1998, 47:249-257.
3. Avise J.C. Phylogeography: The History and Formation of Species 2000, Harvard University Press, Cambridge, Massachusetts.
4. Ballard J.W., Whitlock M.C. The incomplete natural history of mitochondria. Mol. Ecol. 2004, 13:729-744.
5. Blier P.U., Dufresne F., Burton R.S. Natural selection and the evolution of mtDNA-encoded peptides: evidence for intergenomic co-adaptation. Trends Genet. 2001, 17:400-406.
6. Bromham L., Rambaut A., Harvey P.H. Determinants of rate variation in mammalian DNA sequence evolution. J. Mol. Evol. 1996, 43:610-621.
7. Buffenstein R. Ecophysiological responses of subterranean rodents to underground habitats. Life Underground, The Biology of Subterranean Rodents 2000, 63-110. University of Chicago Press, Chicago. E.A. Lacey, J.L. Patton, G.N. Cameron (Eds.).
8. Castillo A.H., Cortinas M.N., Lessa E.P. Rapid diversification of south american tuco-tucos (Ctenomys; Rodentia, Ctenomyidae): contrasting mitochondrial and nuclear intron sequences. J. Mammal. 2005, 86:170-179.
9. Chapple D.G., Ritchie P.A., Daugherty C.H. Origin, diversification, and systematics of the New Zealand skink fauna (Reptilia: Scincidae). Mol. Phylogenet. Evol. 2009, 52(2):470-487.
10. Cutrera A.P., Lacey E.A. Trans-species polymorphism and evidence of selection on class II MHC loci in tuco-tucos (Rodentia: Ctenomyidae). Immunogenetics 2007, 59:937-948.
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, 9:119-140.
12. Da Silva C.C., Tomasco I.H., Hoffmann F.G., Lessa E.P. Genes and ecology: accelerated rates of replacement substitutions in the cytochrome b gene of subterranean rodents. Open Evol. J. 2009, 3:17-30.
13. Dalziel A.C., Moyes C.D., Fredriksson E., Lougheed S.C. Molecular evolution of COX in high-performance fish (teleostei: Scombroidei). J. Mol. Evol. 2006, 62:319-331.
14. Di Rocco F., Parisi G., Zambelli A., Vida-Rioja L. Rapid evolution of cytochrome c oxidase subunit II in camelids (Tylopoda, Camelidae). J. Bioenerg. Biomembr. 2006, 38:293-297.
15. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
16. Gibson A., Gowri-Shankar V., Higgs P.G., Rattray M. A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods. Mol. Biol. Evol. 2005, 22:251-264.
17. Grossman L.I., Wildman D.E., Schmidt T.R., Goodman M. Accelerated evolution of the electron transport chain in anthropoid primates. Trends Genet. 2004, 20:578-585.
18. Hasegawa M., Kishino H., Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 1985, 22:160-174.
19. Honeycutt R.L., Rowe D.L., Gallardo M.H. Molecular systematics of the South American caviomorph rodents: relationships among species and genera in the family Octodontidae. Mol. Phylogenet. Evol. 2003, 26:476-489.
20. Huelsenbeck J.P., Ronquist F., Nielsen R., Bollback J.P. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 2001, 294:2310-2314.
21. Jobson R.W., Nielsen R., Laakkonen L., Wikstrom M., Albert V.A. Adaptive evolution of COX: infrastructure for a carnivorous plant radiation. Proc. Natl. Acad. Sci. USA 2004, 101:18064-18068.
22. Keane T.M., Creevey C.J., Pentony M.M., Naughton T.J., McInerney J.O. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol. 2006, 6:29.
23. Lessa E.P., Vassallo A.I., Verzi D.H., Mora M.S. Evolution of morphological adaptations for digging in living and extinct ctenomyid and octodontid rodents. Biol. J. Linn. Soc. Lond. 2008, 95:267-283.
24. Li W.-S., Ellsworth D.L., Krushkal J., Chang B.H.-J., Hewett-Emmett D. Rates of nucleotide substitutions in primates and rodents and the generation-time effect hypothesis. Mol. Phys. Evol. 1996, 5:182-187.
25. Luo Y., Gao W., Gao Y., Tang S., Huang Q., Tan X., Chen J., Huang T. Mitochondrial genome analysis of Ochotona curzoniae and implication of COX in hypoxic adaptation. Mitochondrion 2008, 8:352-357.
26. Martin A.P., Palumbi S.R. Body size, metabolic rate, generation time and the molecular clock. Proc. Natl. Acad. Sci. USA 1993, 90:4087-4091.
27. Martin A.P. Metabolic rate and directional nucleotide substitution in animal mitochondrial DNA. Mol. Biol. Evol. 1995, 12:1124-1131.
28. McClellan D.A., Palfreyman E.J., Smith M.J., Moss J.L., Christensen R.G., Sailsbery J.K. Physicochemical evolution and molecular adaptation of the cetacean and artiodactyl CytB proteins. Mol. Biol. Evol. 2005, 22:437-455.
29. Nevo E. Mosaic Evolution of Subterranean Mammals: Regression, Progression, and Global Convergence 1999, Oxford University Press, Oxford.
30. Opazo J.C. A molecular timescale for caviomorph rodents (Mammalia, Hystricognathi). Mol. Phylogenet. Evol. 2005, 37:932-937.
31. Osgood W.H. A new octodont rodent from the Paraguayan Chaco. Fieldiana Zool. 1946, 31:47-49.
32. Parada A., D'Elía G., Bidau C., Lessa E.P. Species groups and the evolutionary diversification of tuco-tucos, genus Ctenomys (Rodentia, Ctenomyidae). J. Mammal. 2011, 92:671-682.
33. Pearson O.P., Christie M.I. Los tuco-tucos (género Ctenomys) de los parques nacionales lanín y nahuel huapi, Argentina. Hist. Nat. 1985, 5:337-343.
34. Reig O.A., Busch C., Oteéis M.O., Contreras J.R. An overview of evolution, systematics, molecular biology and speciation in Ctenomys. Evolution of Subterranean Mammals at the Organismal and Molecular Levels 1990, 71-96. Wiley-Liss, New York. E. Nevo, O.A. Reig (Eds.).
35. Ronquist F., Huelsenbeck J.P. MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
36. Saccone C., Lanave C., Pesole G., Preparata G. Influence of base composition on quantitative estimates of gene evolution. Methods Enzymol. 1990, 183:570-583.
37. Shen Y.Y., Liang L., Zhu Z.H., Zhou W.P., Irwin D.M., Zhang Y.P. Adaptive evolution of energy metabolism genes and the origin of flight in bats. Proc. Natl. Acad. Sci. USA 2010, 107:8666-8671.
38. Slamovits C.H., Cook J.A., Lessa E.P., Rossi M.S. Recurrent amplifications and deletions of satellite DNA accompanied chromosomal diversification in South American tuco-tucos (genus Ctenomys, Rodentia: Octodontidae): a phylogenetic approach. Mol. Biol. Evol. 2001, 18:1708-1719.
39. Tamura K., Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 1993, 10:512-526.
40. Verzi D.H. The oldest South American tuco-tuco (late Pliocene, northwestern Argentina) and the boundaries of the genus Ctenomys (Rodentia, Ctenomyidae). Mammal. Biol. 2010, 75:243-252.
41. Vleck D. The energy cost of burrowing by the pocket gopher Thomomys bottae. Physiol. Zool. 1979, 52:122-136.
42. Woolley S., Johnson J., Smith M.J., Crandall K.A., McClellan D.A. TreeSAAP: selection on amino acid properties using phylogenetic trees. Bioinformatics 2003, 19:671-672.
43. Xu S.Q., Yang Y.Z., Zhou J., Jing G.E., Chen Y.T., Wang J., Yang H.M., Wang J., Yu J., Zheng X.G., Ge R.L. A mitochondrial genome sequence of the Tibetan antelope (Pantholops hodgsonii). Genom. Proteom. Bioinform. 2005, 3:5-17.
44. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 1997, 13:555-556.
45. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 2007, 24:1586-1591.
46. Yang Z., Nielsen R., Goldman N., Pedersen A.M.K. Codonsubstitution models for heterogeneous selection pressure at amino acid sites. Genetics 2000, 155:431-449.
47. Yang Z., Nielsen R. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J. Mol. Evol. 1998, 46:409-418.
48. Yang Z., Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 2002, 19:908-917.
49. Yang Z., Wong W.S.W., Nielsen R. Bayes empirical bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 2005, 22:1107-1118.
50. Zhang J., Nielsen R., Yang Z. Evaluation of an improved branchsite likelihood method for detecting positive selection at the molecular level. Mol. Biol. Evol. 2005, 22:2472-2479.