Variation in mutation rate and polymorphism among mitochondrial genes of Silene vulgaris

Molecular Biology and Evolution

Volumn 24, Issue 8, 2007, Pages 1783-1791

  Barr, Camille M ^a,b   Keller, Stephen R ^a   Ingvarsson, Pär K ^c   Sloan, Daniel B ^a   Taylor, Douglas R ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

^b UNIVERSITY OF MONTANA   (United States)

^c UMEÅ UNIVERSITY   (Sweden)

Author keywords

Mutation rate; Plant mitochondria; Polymorphism; Recombination; Silene vulgaris

Indexed keywords

ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE MUTATION; GENE SEGREGATION; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; GENETIC SELECTION; GENETIC VARIABILITY; GENOME; GEOGRAPHIC DISTRIBUTION; MITOCHONDRIAL GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; POPULATION SIZE; SILENE; SILENE VULGARIS;

BASE SEQUENCE; DNA, PLANT; EVOLUTION, MOLECULAR; GENES, MITOCHONDRIAL; GENES, PLANT; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MUTATION; PHYLOGENY; POLYMORPHISM, GENETIC; RECOMBINATION, GENETIC; SEQUENCE HOMOLOGY, NUCLEIC ACID; SILENE; VARIATION (GENETICS);

SILENE VULGARIS;

EID: 34547727793     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msm106     Document Type: Article

References (54)

1. Adams KL, Qui Y-L, Stoutemyer M, Palmer JD. 2002. Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc Natl Acad Sci. 99:9905-9912.
2. Barr CM, Neiman M, Taylor DR. 2005. Inheritance and recombination of mitochondrial genomes in plants, fungi and animals. New Phytol. 168:39-50.
3. Bazin E, Glemin S, Galtier N. 2006. Population size does not influence mitochondrial genetic diversity in animals. Science. 312:570-572.
4. Charlesworth B. 1994. The effect of background selection against deleterious mutations on weakly selected, linked variants. Genet Res. 63:213-227.
5. Charlesworth D. 2002. What maintains male-sterility factors in plant populations? Heredity. 89:408-409.
6. 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. 101:17741-17746.
7. Comeron JM. 2006. Weak selection and recent mutational changes influence polymorphic synonymous mutations in humans. Proc Natl Acad Sci. 103:6940-6945.
8. Conticello SG, Gilad Y, Avidan N, Ben-Asher E, Levy Z, Fainzilber M. 2001. Mechanisms for evolving hypervariability: the case of conopeptides. Mol Biol Evol. 18:120-131.
9. Davies TJ, Barraclough TG, Chase MW, Soltis PS, Soltis DE, Savolainen V. 2004. Darwin's abominable mystery: Insights from a supertree of the angiosperms. Proc Natl Acad Sci. 101:1904-1909.
10. Duminil J, Pemonge M-H, Petit RJ. 2002. A set of 35 consensus primer pairs amplifying genes and introns of plant mitochondrial DNA. Mol Ecol Notes. 2:428-430.
11. Endo T, Ikeo K, Gojobori T. 1996. Large-scale search for genes on which positive selection may operate. Mol Biol Evol. 13:685-690.
12. Eyre-Walker A, Smith NH, Maynard Smith J. 1999. How clonal are human mitochondria? Proc R Soc Lond., B. 266:477-483.
13. Galtier N, Enard D, Radondy Y, Bazin E, Belkhir K. 2006. Mutation hot spots in mammalian mitochondrial DNA. Genome Res. 16:215-222.
14. Gaut BS. 1998. Molecular clocks and nucleotide substitution rates in higher plants. In: Hecht MK, MacIntyre RJ, Clegg MT, editors. Evolutionary Biology. New York: Plenum Press. Vol. 30p. 93-120.
15. Gibbs MJ, Armstrong JS, Gibbs AJ. 2000. Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics. 16:573-582.
16. 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. 7p. 1-44.
17. Hudson RR, Kreitman M, Aguade M. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics. 116:153-159.
18. Hudson RR, Kaplan NL. 1985. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics. 111:147-164.
19. Ingvarsson PK. 2004. Population subdivision and the Hudson-Kreitman- Aguade test: testing for deviations from the neutral model in organelle genomes. Genet Res. Camb. 83:31-39.
20. Ingvarsson PK, Taylor DR. 2002. Genealogical evidence for epidemics of selfish genes. Proc Natl Acad Sci. 99:11265-11269.
21. Jolley KA, Feil EJ, Chan MS, Maiden MC. 2001. Sequence type analysis and recombinational tests (START). Bioinformatics. 17:1230-1231.
22. Jukes TH, Cantor CR. 1969. Evolution of protein molecules. In: Munro HN, editor. Mammalian Protein Metabolism. New York: Academic Press. p. 21-132.
23. Kubo T, Nishizawa S, Sugawara A, Itchoda N, Estiati A, Mikami T. 2000. The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNACys(GCA). Nucleic Acids Res. 28:2571-2576.
24. Kumar S, Tamura K, Nei M. 2004. MEGA3: Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence Alignment. Briefings in Bioinformatics. 5:150-163.
25. Laroche J, Li P, Maggia L, Bousquet J. 1997. Molecular evolution of angiosperm mitochondrial introns and exons. Proc Natl Acad Sci. 94:5722-5727.
26. Martin DP, Williamson C, Posada D. 2005. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics. 21:260-262.
27. Maynard Smith J. 1992. Analyzing the mosaic structure of genes. J Mol Evol. 34:126-129.
28. Maynard Smith J, Smith NH. 1998. Detecting recombination from gene trees. Mol Biol Evol. 15:590-599.
29. McCauley DE, Bailey MF, Sherman NA, Darnell MZ. 2005. Evidence for paternal transmission and heteroplasmy in the mitochondrial genome of Silene vulgaris, a gynodioecious plant. Heredity. 95:50-58.
30. McDonald J, Kreitman M. 1991. Adaptive protein evolution at adh locus in Drosophila. Nature. 351:652-654.
31. McVean G, Awadalla P, Fearnhead P. 2002. A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics. 160:1231-1241.
32. Muse SV. 2000. Examining rates and patterns of nucleotide substitution in plants. Plant Mol Biol. 42:25-43.
33. Nei M, Gojobori T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
34. Nielsen R. 2001. Statistical tests of selective neutrality in the age of genomics. Heredity. 86:641-647.
35. Nugent JM, Palmer JD. 1991. RNA-mediated transfer of the gene coxII from the mitochondrion to the nucleus during flowering plant evolution. Cell. 66:473-481.
36. Padidam M, Sawyer S, Fauquet CM. 1999. Possible emergence of new geminiviruses by frequent recombination. Virology. 265:218-225.
37. Palmer JD, Herbon LA. 1988. Plant mitochondrial DNA evolved rapidly in structure, but slowly in sequence. JMol Evol. 28:87-97.
38. Parkinson CL, Mower JP, Qiu Y-L, 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. 5:73-84.
39. Piganeau G, Eyre-Walker A. 2004. A reanalysis of the indirect evidence for recombination in human mitochondrial DNA. Heredity. 92:282-288.
40. Piganeau G, Gardner M, Eyre-Walker A. 2004. A broad survey of recombination in animal mitochondria. Mol Biol Evol. 21:2319-2325.
41. Posada D. 2002. Evaluation of methods for detecting recombination from DNA sequences: Empirical Data. Mol Biol Evol. 19:708-717.
42. Posada D, Crandall KA. 2001. Evaluation of methods for detecting recombination from DNA sequences: Computer simulations. Proc Natl Acad Sci. 98:13757-13762.
43. Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics. 19:2496-2497.
44. Salminen MO, Carr JK, Burke DS, McCutchan FE. 1995. Identification of breakpoints in intergenotypic recombinants of HIV type 1 by Bootscanning. AIDS Res Hum Retroviruses. 11:1423-1425.
45. Soltis DE, Soltis PS, Chase MW, Mort ME, Albach DC, Zanis M, Savolainen V, Hahn WH, Hoot SB, Fay MF, Axtell M, Swensen SM, Prince LM, Kress WJ, Nixon KC, Farris JS. 2000. Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Bot J Linn Soc. 133:381-461.
46. Stadler T, Delph LF. 2002. Ancient mitochondrial haplotypes and evidence for intragenic recombination in a gynodioecious plant. Proc Natl Acad Sci. 99:11730-11735.
47. Taberlet P, Gielly L, Pautou G, Bouvet J. 1991. Universal primers for amplification of three noncoding regions of chloroplast DNA. Plant Mol Biol. 17:1105-1109.
48. Taylor DR, Keller SR. 2007. Historical range expansion determines the phylogenetic diversity introduced during contemporary species invasion. Evolution. 61:334-345.
49. Watterson GA. 1975. On the number of segregating sites in genetical models without recombination. Theor Pop Biol. 7:256-276.
50. Wolfe KH, Li W-H, Sharp PM. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast. nuclear DNAs. Proc. Natl. Acad. Sci. 84:9054-9058.
51. Wolfe KH, Li W-H, Sharp PM. 1989. Mutation rates differ among regions of the mammalian genome. Nature. 0:283-285.
52. Wolstenholme DR, Fauron CM-R. 1995. Mitochondrial genome organization. In: Levings CS III, Vasil IK, editors. The Molecular Biology of Plant Mitochondria. The Netherlands: Kluwer Academic Publishers. p. 1-59.
53. Wright SI, Charlesworth B. 2004. The HKA test revisited: a maximum-likelihood-ratio test of the standard neutral model. Genetics. 168:1071-1076.
54. Yang Y-W, Lai K-N, Tai P-Y, Li W-H. 1999. Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages. J Mol Evol. 48:597-604.