You are where you live: Parasitic nematode mitochondrial genome size is associated with the thermal environment generated by hosts

Journal of Evolutionary Biology

Volumn 26, Issue 3, 2013, Pages 683-690

  Lagisz, M ^a   Poulin, R ^a   Nakagawa, S ^a  

^a UNIVERSITY OF OTAGO   (New Zealand)

Author keywords

Body size; Longevity; Metabolism; MtDNA; Temperature

Indexed keywords

HELMINTH DNA; MITOCHONDRIAL DNA;

BODY SIZE; ECTOTHERMY; ENDOTHERMY; EVOLUTIONARY BIOLOGY; GENOME; HOST-PARASITE INTERACTION; HYPOTHESIS TESTING; LONGEVITY; METABOLISM; MITOCHONDRIAL DNA; MUTATION; NATURAL SELECTION; NEMATODE; PROTEIN; TEMPERATURE EFFECT;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANIMAL; ARTICLE; BODY SIZE; CLASSIFICATION; DNA REPLICATION; ECOSYSTEM; FEMALE; GENE ORDER; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; GENOME SIZE; LONGEVITY; MALE; MITOCHONDRIAL GENOME; MITOCHONDRION; MOLECULAR EVOLUTION; NEMATODE; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPECIES DIFFERENCE; TEMPERATURE;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANIMALS; BASE SEQUENCE; BODY SIZE; DNA REPLICATION; DNA, HELMINTH; DNA, MITOCHONDRIAL; ECOSYSTEM; EVOLUTION, MOLECULAR; FEMALE; GENE ORDER; GENETIC VARIATION; GENOME SIZE; GENOME, MITOCHONDRIAL; LONGEVITY; MALE; MITOCHONDRIA; NEMATODA; PHYLOGENY; SELECTION, GENETIC; SPECIES SPECIFICITY; TEMPERATURE;

ANIMALIA; NEMATODA;

EID: 84873723676     PISSN: 1010061X     EISSN: 14209101     Source Type: Journal    
DOI: 10.1111/jeb.12068     Document Type: Article

References (53)

1. Abascal, F., Zardoya, R. & Posada, D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104-2105.
2. Adachi, J., Cao, Y. & Hasegawa, M. 1993. Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: rapid evolution in warm-blooded vertebrates. J. Mol. Evol. 36: 270-281.
3. Blank, H.M., Li, C., Mueller, J.E., Bogomolnaya, L.M., Bryk, M. & Polymenis, M. 2008. An increase in mitochondrial DNA promotes nuclear DNA replication in yeast. PLoS Genet. 4: E1000047.
4. Blaxter, M. 2011. Nematodes: the worm and its relatives. PLoS Biol. 9: e1001050.
5. Boore, J.L. 1999. Animal mitochondrial genomes. Nucl. Acids Res. 27: 1767-1780.
6. Bourque, G. & Pevzner, P. 2002. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 12: 26-36.
7. Boyce, T.M., Zwick, M.E. & Aquadro, C.F. 1989. Mitochondrial DNA in the bark weevils: size, structure and heteroplasmy. Genetics 123: 825-836.
8. Bromham, L. & Penny, D. 2003. The modern molecular clock. Nat. Rev. Genet. 4: 216-224.
9. Burger, G., Gray, M.W. & Lang, B.F. 2003. Mitochondrial genomes: anything goes. Trends Genet. 19: 709-716.
10. Calow, P. 1983. Pattern and paradox in parasite reproduction. Parasitology 86: 197-207.
11. Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17: 540-552.
12. De Ley, P. & Blaxter, M.L. 2002. Systematic position and phylogeny. In: The Biology of Nematodes (D.L. Lee, ed.), pp. 1-30. Taylor and Francis, London.
13. Douzery, E.J.P., Snell, E.A., Bapteste, E., Delsuc, F. & Philippe, H. 2004. The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils? Proc. Natl. Acad. Sci. USA 101: 15386-15391.
14. Drummond, A.J., Suchard, M.A., Xie, D. & Rambaut, A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29: 1969-1973.
15. Estabrook, G.F., Smith, G.R. & Dowling, T.E. 2007. Body mass and temperature influence rates of mitochondrial DNA evolution in North American cyprinid fish. Evolution 61: 1176-1187.
16. Galtier, N., Jobson, R.W., Nabholz, B., Glémin, S. & Blier, P.U. 2009. Mitochondrial whims: metabolic rate, longevity and the rate of molecular evolution. Biol. Lett. 5: 413-416.
17. Gems, D. 2000. Longevity and ageing in parasitic and free-living nematodes. Biogerontology 1: 289-307.
18. Gilbert, D. 2003. Sequence file format conversion with command-line Readseq. Curr. Prot. Bioinf. Appendix 1E.
19. Gjetvaj, B., Cook, D.I. & Zouros, E. 1992. Repeated sequences and large-scale size variation of mitochondrial DNA: a common feature among scallops (Bivalvia: Pectinidae). Mol. Biol. Evol. 9: 106-124.
20. Griffith, O.L., Moodie, G.E. & Civetta, A. 2003. Genome size and longevity in fish. Exp. Gerontol. 38: 333-337.
21. Hadfield, J.D. 2010. MCMC methods for multi-response generalised linear mixed models: the MCMCglmm R Package. J. Stat. Softw. 33: 1-22.
22. Hadfield, J.D. & Nakagawa, S. 2010. General quantitative genetic methods for comparative biology: phylogenies, taxonomies, and multi-trait models for continuous and categorical characters. J. Evol. Biol. 23: 494-508.
23. Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser. 41: 95-98.
24. Khaidakov, M., Siegel, E.R. & Shmookler Reis, R.J. 2006. Direct repeats in mitochondrial DNA and mammalian lifespan. Mech. Ageing Dev. 127: 808-812.
25. Kirchner, T.B., Anderson, R.V. & Ingham, R.E. 1980. Natural selection and the distribution of nematode sizes. Ecology 61: 232-237.
26. Lynch, M. 1991. Methods for the analysis of comparative data in evolutionary biology. Evolution 45: 1065-1080.
27. Martin, A.P. & Palumbi, S.R. 1993. Body size, metabolic rate, generation time, and the molecular clock. Proc. Natl Acad. Sci. USA 90: 4087-4091.
28. McGaughran, A. & Holland, B.R. 2010. Testing the effect of metabolic rate on DNA variability at the intra-specific level. PLoS ONE 5: e9686.
29. Monaghan, P. & Metcalfe, N.B. 2000. Genome size and longevity. Trends Genet. 16: 331-332.
30. Nabholz, B., Glémin, S. & Galtier, N. 2008. Strong variations of mitochondrial mutation rate across mammals - the longevity hypothesis. Mol. Biol. Evol. 251: 120-130.
31. Nabholz, B., Glémin, S. & Galtier, N. 2009. The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals. BMC Evol. Biol. 9: 54.
32. Nakagawa, S. & Cuthill, I. 2007. Effect size, confidence interval and statistical significance: a practical guide for biologists. Biol. Rev. 82: 591-605.
33. Oliveira, P.L. & Oliveira, M.F. 2002. Vampires, Pasteur and reactive oxygen species. Is the switch from aerobic to anaerobic metabolism a preventive antioxidant defence in blood-feeding parasites? FEBS Lett. 525: 3-6.
34. Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature 401: 877-884.
35. Park, J.K., Sultana, T., Lee, S.H., Kang, S., Kim, H.K., Min, G.S. et al. 2007. Monophyly of clade III nematodes is not supported by phylogenetic analysis of complete mitochondrial genome sequences. BMC Genomics 12: 392.
36. Poulin, R. 2007. Evolutionary Ecology of Parasites, 2nd edn. Princeton University Press, Princeton, NJ.
37. R Development Core Team. 2011. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. (http://www.r-project.org).
38. Ragu, S., Faye, G., Iraqui, I., Masurel-Heneman, A., Kolodner, R.D. & Huang, M.E. 2007. Oxygen metabolism and reactive oxygen species cause chromosomal rearrangements and cell death. Proc. Natl Acad. Sci. USA 104: 9747-9752.
39. Rambaut, A. & Drummond, A.J. 2007. Tracer v1.4. (http://beast.bio.ed.ac.uk/Tracer).
40. Rand, D.M. 1993. Endotherms, ectotherms, and mitochondrial genome-size variation. J. Mol. Evol. 37: 281-295.
41. Rand, D.M. 1994. Thermal habit, metabolic rate and the evolution of mitochondrial DNA. Trends Ecol. Evol. 9: 125-131.
42. Rottenberg, H. 2007. Exceptional longevity in songbirds is associated with high rates of evolution of cytochrome b, suggesting selection for reduced generation of free radicals. J. Exp. Biol. 210: 2170-2180.
43. Samuels, D.C., Schon, E.A. & Chinnery, P.F. 2004. Two direct repeats cause most human mtDNA deletions. Trends Genet. 20: 393-398.
44. Selosse, M., Albert, B. & Godelle, B. 2001. Reducing the genome size of organelles favours gene transfer to the nucleus. Trends Ecol. Evol. 16: 135-141.
45. Signorovitch, A.Y., Buss, L.W. & Dellaporta, S.L. 2007. Comparative genomics of large mitochondria in Placozoans. PLoS Genet. 3: E13.
46. Smit, A.F.A., Hubley, R. & Green, P. 1996-2010. RepeatMasker Open-3.0. (http://www.repeatmasker.org).
47. Speakman, J.R. 2005. Body size, energy metabolism and life span. J. Exp. Biol. 208: 1717-1730.
48. Talavera, G. & Castresana, J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56: 564-577.
49. Tanabe, A.S. 2011. Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional, and separate models for combined molecular phylogenetic analyses of multilocus sequence data. Mol. Ecol. Res. 11: 914-921.
50. Thomas, W.K. & Beckenbach, A.T. 1989. Variation in salmonid mitochondrial DNA: evolutionary constraints and mechanisms of substitution. J. Mol. Evol. 29: 233-245.
51. Thompson, J.D., Higgins, D.G. & Gibson, T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
52. Tian, D., Wang, Q., Zhang, P., Araki, H., Yang, S., Kreitman, M. et al. 2008. Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. Nature 455: 105-108.
53. Welch, J.J., Bininda-Emonds, O.R. & Bromham, L. 2008. Correlates of substitution rate variation in mammalian protein-coding sequences. BMC Evol. Biol. 8: 53.