Patterns and relative rates of nucleotide and insertion/deletion evolution at six chloroplast intergenic regions in new world species of the Lecythidaceae

Molecular Biology and Evolution

Volumn 20, Issue 10, 2003, Pages 1710-1721

  Hamilton, Matthew B ^a,b   Braverman, John M ^c   Soria Hernanz, David F ^a  

^a GEORGETOWN UNIVERSITY   (United States)

^b INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA   (Brazil)

^c LOYOLA UNIVERSITY CHICAGO   (United States)

Author keywords

Chloroplast genome; Generation time effect; Homoplasy; Indel; Intergenic; Relative rate

Indexed keywords

NUCLEOTIDE; SPACER DNA; CHLOROPLAST DNA;

ARTICLE; CHLOROPLAST; DNA SEQUENCE; DNA STRUCTURE; GENE DELETION; GENE FLOW; GENE INSERTION; GENE MUTATION; GENETIC HETEROGENEITY; GENETIC MARKER; GENETIC VARIABILITY; HAPLOTYPE; LECYTHIDACEAE; MOLECULAR CLOCK; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; POPULATION STRUCTURE; REGRESSION ANALYSIS; SAPOTACEAE; GENETICS; PHYLOGENY; POINT MUTATION;

CORYTHOPHORA ALTA; LECYTHIDACEAE; SAPOTACEAE;

BASE SEQUENCE; CHLOROPLASTS; DNA, CHLOROPLAST; EVOLUTION, MOLECULAR; LECYTHIDACEAE; PHYLOGENY; POINT MUTATION; SEQUENCE DELETION; VARIATION (GENETICS);

EID: 3342931347     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg190     Document Type: Article

References (69)

1. Aldrich, J. A., B. W. Cherney, E. Merlin, and L. Christopherson. 1988. The role of insertions/deletions in the evolution of the intergenic region between psbA. and trnH in the chloroplast genome. Curr. Genet. 14:137-146.
2. Avise, J. C. 1991. Ten unorthodox perspectives on evolution prompted by comparative population genetic findings on mitochrondrial DNA. Annu. Rev. Genet. 25:45-69.
3. _. 1994. Molecular markers, natural history and evolution. Chapman and Hall, New York.
4. Ballard, J. W. O., and M. Kreitman. 1995. Is mitochondrial DNA a strictly neutral marker? Trends Ecol. Evol. 10:485-488.
5. Birky, C. W., P. Fuerst, and T. Maruyama. 1989. Organelle gene diversity under migration, mutation, and drift: equilibrium expectations, approach to equilibrium, effects of heteroplasmic cells, and comparison to nuclear genes. Genetics 121:613-627.
6. Birky, C. W., and J. B. Walsh. 1988. Effects of linkage on rates of molecular evolution. Proc. Natl. Acad. Sci. USA 85:6414-6418.
7. Bromham, L. D., D. Penny, A. Rambaut, and M. Hendy. 2000. The power of relative rates tests depends on the data. J. Mol. Evol. 50:296-301.
8. Caron, H., S. Dumas, G. Marque, C. Messier, E. Bandou, R. J. Petit, and A. Kremer. 2000. Spatial and temporal distribution of chloroplast DNA polymorphism in a tropical tree species. Mol. Ecol. 9:1089-1098.
9. Charlesworth, B. 1998. Measures of divergence between populations and the effect of forces that reduce variability. Mol. Biol. Evol. 15:538-543.
10. Clegg, M. T., B. S. Gaut, G. H. Learn, and B. R. Morton. 1994. Rates and patterns of chloroplast DNA evolution. Proc. Natl. Acad. Sci. USA 91:6795-6801.
11. Curtis, S. E., and M. T. Clegg. 1984. Molecular evolution of chloroplast DNA sequences. Mol. Biol. Evol. 1:291-301.
12. Demesure, B., N. Sodzi, and R. J. Petit. 1995. A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Mol. Ecol. 4:129-131.
13. Desplanque, B., F. Viard, J. Bernard, D. Forcioli, P. Saumitou-Laprade, J. Cuguen, and H. van Dijk. 2000. The linkage disequilibrium between chloroplast DNA and mitochondrial DNA haplotypes in Beta vulgaris ssp maritima (L.): the usefulness of both genomes for population genetic studies. Mol. Ecol. 9:141-154.
14. Doyle, J. J., M. Morgante, S. V. Tingey, and W. Powell. 1998. Size homoplasy in chloroplast microsatellites of wild perennial relatives of soybean (Glycine subgenus Glycine). Mol. Biol. Evol. 15:215-218.
15. Dumolin-Lapégue, S., M.-H. Pemonge, and R. J. Petit. 1997. An enlarged set of consensus primers for the study of organelle DNA in plants. Mol. Ecol. 6:393-397.
16. _. 1998. Association between chloroplast and mitochondrial lineages in Oaks. Mol. Biol. Evol. 15:1321-1331.
17. Dutech, C., L. Maggia, and H. I. Joly. 2000. Chloroplast diversity in Vouacapoua americana (Caesalpiniaceae), a neotropical forest tree. Mol. Ecol. 9:1427-1432.
18. Ennos, R. A., W. T. Sinclair, X.-S. Hu, and A. Langdon. 1999. Using organelle markers to elucidate the history, ecology and evolution of plant populations. Pp. 1-19 in P. M. Hollingsworth, R. M. Bateman, and R. J. Gornall, eds. Molecular systematics and plant evolution. Taylor and Francis Ltd., London.
19. Gascon, C., and R. O. Bierregaard. 2001. The Biological Dynamics of Forest Fragments Project: the study site, experimental design, and research activity. Pp. 31-42 in R. O. Bierregaard, C. Gascon, T. E. Lovejoy, and R. Mesquita, eds. Lessons from Amazonia: the ecology and conservation of a fragmented forest. Yale University Press, New Haven.
20. Gaut, B. S. 1998. Molecular clocks and nucleotide substitution rates in higher plants. Evol. Biol. 30:93-120.
21. Gaut, B. S., L. G. Clark, J. F. Wendel, and S. V. Muse. 1997. Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae). Mol. Biol. Evol. 14:769-777.
22. Goldstein, D. B., and D. D. Pollock. 1997. Launching microsatellites: a review of mutation processes and methods of phylogenetic interference. J. Hered. 88:335-342.
23. Golenberg, E. M., M. T. Clegg, M. L. Durbin, J. Doebley, et al. 1993. Evolution of a noncoding region of the chloroplast genome. Mol. Phylogenet. Evol. 2:52-64.
24. Graham, S., W. Reeves, P. A. Burns, and A. C. E. Olmstead. 2000. Microstructural changes in noncoding chloroplast DNA: interpretation, evolution, and utility of indels and inversions in basal angiosperm phylogenetic inference. Int. J. Plant Sci. 161:S83-S96.
25. Hamilton, M. B. 1999a. Tropical tree gene flow and seed dispersal. Nature 401:129-130.
26. _. 1999b. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Mol. Ecol. 8:521-523.
27. Hamilton, M. B., and J. M. Miller. 2002. Comparing relative rates of pollen and seed gene flow in the island model using nuclear and organelle measures of population structure. Genetics 162:1897-1909.
28. Hedrick, P. W. 1999. Perspective: highly variable loci and their interpretation in evolution and conservation. Evolution 53:313-318.
29. Huelsenbeck, J. B., and K. A. Crandall. 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst. 28:437-466.
30. Jarne, P., and P. J. L. Lagoda. 1996. Microsatellites, from molecules to populations and back. Trends Ecol. Evol. 11:424-429.
31. Kelchner, S. A. 2000. The evolution of non-coding chloroplast DNA and its application in plant systematics. Ann. Missouri Bot. Gard. 87:482-498.
32. Kimura, M. 1981. Estimation of evolutionary distances between homologous nucleotide sequences. Proc. Natl. Acad. Sci. USA 78:454-458
33. McCauley, D. E. 1994. Contrasting the distribution of chloroplast DNA and allozyme polymorphism among local populations of Silene alba: implications for studies of gene flow in plants. Proc. Natl. Acad. Sci. USA 91:8127-8131.
34. _. 1995. The use of cloroplast DNA polymorphism in studies of gene flow in plants. Trends Ecol. Evol. 10:198-202.
35. _. 1998. The genetic structure of a gynodioecious plant: nuclear and cytoplasmic genes. Evolution 52:255-260.
36. McGuire, G., M. C. Denham, and D. J. Balding. 2001. Models of sequence evolution for DNA sequences containing gaps. Mol. Biol. Evol. 18:481-490.
37. Mon, S. A., P. Becker, and D. Kincaid. 2001. Lecythidaceae of a central Amazonian lowland forest. Pp. 54-67 in R. O. Bierregaard, C. Gascon, T. E. Lovejoy, R. Mesquita, eds. Lessons from Amazonia: the ecology and conservation of a fragmented forest. Yale University Press, New Haven, Conn.
38. Morton, B. R. 1995. Neighboring base composition and transversion/ transition bias in a comparison of rice and maize chloroplast noncoding regions. Proc. Natl. Acad. Sci. USA 92:9717-9721.
39. _. 2000. Codon bias and the context dependency of nucleotide substitutions in the evolution of plastid DNA. Evol. Biol. 31:55-103.
40. Morton, B. R., and M. T. Clegg. 1995. Neighboring base composition in strongly correlated with base substitution in a region of the chloroplast genome. J. Mol. Evol. 41:597-603.
41. Morton, C. M., S. A. Mori, G. T. Prance, K. G. Karol, and M. W. Chase. 1997. Phylogenetic relationships of Lecythidaceae: a cladistic analysis using rbcL sequence and morphological data. Am. J. Bot. 84:530-540.
42. Muloko-Ntoutoume, N., R. J. Petit, L. White, and K. Abernethy. 2000. Chloroplast DNA variation in a rainforest tree (Aucoumea klaineana, Burseraceae) in Gabon. Mol. Ecol. 9:359-363.
43. Muse, S. V. 2000. Examining rates and patterns of nucleotide substitution in plants. Plant Mol. Biol. 42:25-43.
44. Muse, S. V., and B. S. Gaut. 1997. Comparing patterns of nucleotide substitution rates among chloroplast loci using the relative ratio test. Genetics 146:393-399.
45. Muse, S. V., and B. S. Weir. 1992. Testing for equality of evolutionary rates. Genetics 132:269-276.
46. Nei, M., and S. Kumar. 2000. Molecular evolution and phylogenetics. Oxford University Press, Oxford, U.K.
47. Oddou-Muratorio, S., R. J. Petit, B. Le Guerroue, D. Guesnet, and B. Demesure. 2001. Pollen- versus seed-mediated gene flow in a scattered forest tree species. Evolution 55:1123-1135
48. Palmer, J. D. 1990. Contrasting modes and tempos of genome evolution in land plant organelles. Trends Genet. 6:115-20.
49. Parker, P. G., A. A. Snow, M. D. Schug, G. C. Booton, and P. A. Fuerst. 1998. What molecules can tell us about populations: choosing and using a molecular marker. Ecology 79:361-382.
50. Petit, R. J., A. Kremer, and D. B. Wagner. 1993. Finite island model for organelle and nuclear genes in plants. Heredity 71:630-641.
51. Posada, D., and K. A. Crandall. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.
52. _. 2001. Selecting models of nucleotide substitution: an application to human immunodeficiency virus (HIV-1). Mol. Biol. Evol. 18:897-906.
53. Powell, W., M. Morgante, R. McDevitt, G. G. Vendramin, and J. A. Rafalski. 1995. Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proc. Natl. Acad. Sci. USA 92:7759-7763.
54. Provan J., W. Powell, and P. M. Hollingsworth. 2001. Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol. Evol. 16:142-147.
55. Rand, D. M. 1993. Endotherms, ectotherms, and mitochondrial genome-size variation. J. Mol. Evol. 37:281-295.
56. Rice, W. R. 1989. Analyzing tables of statistical tests. Evolution 43:223-225.
57. Saitou, N., and S. Ueda. 1994. Evolutionary rates of insertion and deletion in noncoding nucleotide sequences of primates. Mol. Biol. Evol. 11:504-512.
58. Sarich, V. M., and A. C. Wilson. 1973. Generation time and genomic evolution in primates. Science 179:1144-1147.
59. Savolainen, V., M. W. Chase, S. B. Hoot, C. M. Morton, D. E. Soltis, C. Bayer, M. F. Fay, A. Y. de Bruijn, S. Sullivan, and Y.-L. Qiu. 2000. Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences. Systemat. Biol. 49:306-362.
60. Savolainen, V., J. F. Manen, E. Douzery, and R. Spichiger. 1994. Molecular phylogeny of families related to Celastrales based on rbcL 5′ flanking sequences. Mol. Phylogenet. Evol. 3: 27-37.
61. Simmons, M. P., and H. Ochoterena. 2000. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49:369-381.
62. Stephan, W., L. Xing, D. A. Kirby, and J. M. Braverman. 1998. A test of the background selection hypothesis based on nucleotide data from Drosophila ananassae. Proc. Natl. Acad. Sci. USA 95:5649-5654.
63. Swofford, D. L. 2002. PAUP*. phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Mass.
64. Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pp. 407-514 in D. M. Hillis, C. Moritz, and B. K. Mable, eds. Molecular systematics. 2nd Edition. Sinauer Associates, Sunderland, Mass.
65. Taberlet, P., L. Gielly, G. Pautou, and J. Bouvet. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol. Biol. 17:1105-1109.
66. Tajima, F. 1993. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135:599-607.
67. Tajima, F., and M. Nei. 1984. Estimation of evolutionary distance between nucleotide sequences. Mol. Biol. Evol. 1:269-285.
68. Thome, J. L., H. Kishinmo, and J. Felsenstein. 1992. An evolutionary model for maximum likelihood alignment of DNA sequences. J. Mol. Evol. 34:3-16.
69. Whittle, C.-A., and M. O. Johnston. 2003. Broad-scale analysis contradicts the theory that generation time affects molecular evolutionary rates in plants. J. Mol. Evol. 56:223-233.