Evolutionary rate variation at multiple levels of biological organization in plant mitochondrial DNA

Molecular Biology and Evolution

Volumn 25, Issue 2, 2008, Pages 243-246

  Sloan, Daniel B ^a   Barr, Camille M ^b   Olson, Matthew S ^c   Keller, Stephen R ^a   Taylor, Douglas R ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

^b UNIVERSITY OF MONTANA   (United States)

^c UNIVERSITY OF ALASKA FAIRBANKS   (United States)

Author keywords

Molecular clock; mtDNA; Mutators; Silene latifolia; Silene noctiflora; Silene vulgaris

Indexed keywords

MITOCHONDRIAL DNA;

ANGIOSPERM; ARTICLE; CHLOROPLAST; DNA EXTRACTION; GENETIC ANALYSIS; GENOME; MITOCHONDRION; MUTATION RATE; NONHUMAN; PHYLOGENY; PLANT; SILENE;

CHLOROPLASTS; DNA, MITOCHONDRIAL; DNA, PLANT; EVOLUTION, MOLECULAR; PHYLOGENY; POLYMORPHISM, GENETIC; SILENE;

MAGNOLIOPHYTA; SILENE; SILENE LATIFOLIA; SILENE NOCTIFLORA; SILENE VULGARIS;

EID: 38949168470     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msm266     Document Type: Article

References (25)

1. Barr CM, Keller SR, Ingvarsson PK, Sloan DB, Taylor DR. 2007. Variation in mutation rate and polymorphism among mitochondrial genes in Silene vulgaris. Mol Biol Evol. 24:1783-1791.
2. Britten RJ. 1986. Rates of DNA sequence evolution differ between taxonomic groups. Science. 231:1393-1398.
3. Cho Y, Mower JP, Qiu YL, Palmer JD. 2004. Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants. Proc Natl Acad Sci USA. 101:17741-17746.
4. Eyre-Walker A, Gaut BS. 1997. Correlated rates of synonymous site evolution across plant genomes. Mol Biol Evol. 14:455-460.
5. Houliston GJ, Olson MS. 2006. Nonneutral evolution of organelle genes in Silene vulgaris. Genetics. 174:1983-1994.
6. Hudson RR. 1991. Gene genealogies and the coalescent process. In: Futuyma D, Antonovics J, editors. Oxford Surveys of Evolutionary Biology. Oxford: Oxford University Press. Vol. 7. p. 1-44.
7. Ingvarsson PK. 2004. Population subdivision and the hudson-kreitman- aguade test: testing for deviations from the neutral model in organelle genomes. Genet Res. 83:31-39.
8. Ingvarsson PK, Taylor DR. 2002. Genealogical evidence for epidemics of selfish genes. Proc Natl Acad Sci USA. 99:11265-11269.
9. Kimura M. 1983. The neutral theory of molecular evolution. Cambridge: Cambridge University Press.
10. Kumar S, Tamura K, Nei M. 2004. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5:150-163.
11. Martin AP, Palumbi SR. 1993. Body size, metabolic rate, generation time, and the molecular clock. Proc Natl Acad Sci USA. 90:4087-4091.
12. Mower JP, Touzet P, Gummow JS, Delph JS, Palmer JD. 2007. Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evol Biol. 7:135.
13. Palmer JD, Herbon LA. 1988. Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. J Mol Evol. 28:87-97.
14. Parkinson CL, Mower JP, Qiu YL, Shirk AJ, Song K, Young ND, DePamphilis CW, Palmer JD. 2005. Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae. BMC Evol Biol. 5:73.
15. Posada D. 2001. Unveiling the molecular clock in the presence of recombination. Mol Biol Evol. 18:1976-1978.
16. Posada D, Crandall KA. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics. 14:817-818.
17. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics. 19:2496-2497.
18. Städler T, Delph LF. 2002. Ancient mitochondrial haplotypes and evidence for intragenic recombination in a gynodioecious plant. Proc Natl Acad Sci USA. 99:11730-11735.
19. Tajima F. 1993. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics. 135:599-607.
20. Taylor DR, Keller SR. 2007. Historical range expansion determines the phylogenetic diversity introduced during contemporary species invasion. Evolution. 61:334-345.
21. Whittle CA, Johnston MO. 2002. Male-driven evolution of mitochondrial and chloroplastidial DNA sequences in plants. Mol Biol Evol. 19:938-949.
22. Wolfe KH, Li WH, Sharp PM. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA. 84:9054-9058.
23. Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Bioinformatics. 13:555.
24. Yoder AD, Yang Z. 2000. Estimation of primate speciation dates using local molecular clocks. Mol Biol Evol. 17:1081-1090.
25. Zuckerkandl E, Pauling L. 1965. Molecules as documents of evolutionary history. J Theor Biol. 8:357-366.