Detecting and characterizing gene conversions between multigene family members

Molecular Biology and Evolution

Volumn 16, Issue 10, 1999, Pages 1369-1390

  Drouin, Guy ^a   Prat, Frédéric ^b   Ell, Michael ^b   Clarke, G D Paul ^b  

^a UNIVERSITY OF OTTAWA   (Canada)

^b NONE

Author keywords

Co double; Gene conversion; Multigene families; Sawyer; SequEdit

Indexed keywords

ACTIN; DNA; GLOBIN; ZINC FINGER PROTEIN;

ARTICLE; COMPUTER PROGRAM; GENE CONVERSION; MAIZE; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIMATE; SPECIES DIFFERENCE; UNINDEXED SEQUENCE;

MAGNOLIOPHYTA; MAMMALIA; PRIMATES; ZEA MAYS;

EID: 0032826401     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026047     Document Type: Article

References (43)

1. AN, S. S., B. MÖPPS, K. WEBER, and D. BHATTACHARYA. 1999. The origin and evolution of green algae and plant actins. Mol. Biol. Evol. 16:275-285.
2. ANDERSSON, L., K. GUSTAFSSON, A.-K. JONSSON, and L. RASK. 1991a. Concerted evolution in a segment of the first domain exon of polymorphic MHC class II β loci. Immunogenetics 33:235-242.
3. _. 1991b. Concerted evolution of polymorphic MHC class II β loci: a comment to reviewer's reply. Immunogenetics 34:346-347.
4. BALDING, D. J., R. A. NICHOLS, and D. M. HUNT. 1992. Detecting gene conversion: primate visual pigment genes. Proc. R. Soc. Lond. B Biol. Sci. 249:275-280.
5. BETRÁN, E., J. ROZAS, A. NAVARRO, and A. BARBADILLA. 1997. The estimation of the number and the length distribution of gene conversion tracts from population DNA sequence data. Genetics 146:88-99.
6. DROUIN, G., and G. DOVER. 1990. Independent gene evolution in the potato actin gene family demonstrated by phylogenetic procedures for resolving gene conversions and the phylogeny of angiosperm actin genes. J. Mol. Evol. 31:132-150.
7. FELSENSTEIN, J. 1993. PHYLIP (phylogeny inference package). Version 3.5. Distributed by the author(ftp://evolution. genetics.washington.edu/), Department of Genetics, University of Washington, Seattle.
8. FITCH, D. H. A., and M. GOODMAN. 1991. Phylogenetic scanning: a computer assisted algorithm for mapping gene conversions and other recombinational events. CABIOS 7:207-215.
9. FITCH, D. H. A., C. MAINONE, M. GOODMAN, and J. L. SLIGHTOM. 1990. Molecular history of gene conversions in the primate fetal γ-globin genes. J. Biol. Chem. 265:781-793.
10. GAUT, S. B., and M. T. CLEGG. 1993. Molecular evolution of the Adh1 locus in the genus Zea. Proc. Natl. Acad. Sci. USA 90:5095-5099.
11. GRASSLY, N. C., and E. C. HOLMES. 1997. A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol. Biol. Evol. 14:239-247.
12. HAYASAKA, K., D. H. A. FITCH, J. L. SLIGHTOM, and M. GOODMAN. 1992. Fetal recruitment of anthropoid γ-globin genes. J. Mol. Biol. 224:875-881.
13. HEIN, J. 1993. A heuristic method to reconstruct the history of sequences subject to recombination. J. Mol. Evol. 36:396-405.
14. HOLM, S. 1979. A simple sequentially rejective multiple test procedure. Scand. J. Stat. 6:65-70.
15. HUGHES, A. L. 1991. Testing for interlocus genetic exchange in the MHC: a reply to Andersson and co-workers. Immunogenetics 33:243-246.
16. _. 1995. Origin and evolution of HLA class I pseudogenes. Mol. Biol. Evol. 12:247-258.
17. JAKOBSEN, I. B., and S. EASTEAL. 1996. A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. CABIOS 12:291-295.
18. JAKOBSEN, I. B., S. R. WILSON, and S. EASTEAL. 1997. The partition matrix: exploring variable phylogenetic signals along nucleotide sequence alignments. Mol. Biol. Evol. 14: 474-484.
19. KOOP, B. F., D. SIEMIENIAK, J. L. SLIGHTOM, M. GOODMAN, J. DUNBAR, P. C. WRIGHT, and E. L. SIMONS. 1989. Tarsius δ- and β-globin genes: conversions, evolution and systematic implications. J. Biol. Chem. 264:68-79.
20. KUMAR, S., K. TAMURA, and M. NEI. 1993. MEGA: molecular evolutionary genetics analysis. Version 1.01. The Pennsylvania State University, University Park.
21. LANFEAR, J., and P. W. H. HOLLAND. 1991. The molecular evolution of Zfy-related genes in birds and mammals. J. Mol. Evol. 32:310-315.
22. LI, W. H., and D. GRAUR. 1991. Fundamentals of molecular evolution. Sinauer, Sunderland, Mass.
23. MCDOWELL, J. M., S. HUANG, E. C. MCKINNEY, Y.-Q. AN, and R. B. MEAGHER. 1996. Structure and evolution of the actin gene family in Arabidopsis thaliana. Genetics 142: 587-602.
24. MCGUIRE, G., F. WRIGHT, and M. J. PRENTICE. 1997. A graphical method for detecting recombination in phylogenetic data sets. Mol. Biol. Evol. 14:1125-1131.
25. MAYNARD SMITH, J., and N. H. SMITH. 1998. Detecting gene conversion from gene trees. Mol. Biol. Evol. 15:590-599.
26. MEAGHER, R. B., S. BERRY-LOWE, and K. RICE. 1989. Molecular evolution of the small subunit of ribulose bisphosphate carboxylase: nucleotide substitution and gene conversion. Genetics 123:845-863.
27. MENOTTI-RAYMOND, M., M. W. T. STARMER, and D. T. SULLIVAN. 1991. Characterization of the structure and evolution of the Adh region of Drosophila hydei. Genetics 127:355-366.
28. MONIZ DE SÁ, M., and G. DROUIN. 1996. Phylogeny and substitution rates of angiosperm actin genes. Mol. Biol. Evol. 13:1198-1212.
29. OHTA, T. 1994. On hypervariability at the reactive center of proteolytic enzymes and their inhibitors. J. Mol. Evol. 39: 614-619.
30. OHTA, T., and C. J. BASTEN. 1992. Gene conversion generates hypervariability at the variable regions of kallikreins and their inhibitors. Mol. Phylogenet. Evol. 1:87-90.
31. PETES, T. D., R. E. MALONE, and L. S. SYMINGTON. 1991. Recombination in yeast. Pp. 407-521 in J. R. BROACH, J. R. PRINGLE, and E. W. JONES, eds. The molecular and cellular biology of the yeast Saccharomyces: genome dynamics, protein synthesis, and energetics. Vol. 1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
32. PRAT, F. 1997. Étude de la conversion génique chez les familles multigéniques. M.Sc. thesis, Université d'Ottawa, Ottawa, Ontario, Canada.
33. RICE, W. P. 1989. Analysing tables of statistical tests. Evolution 43:223-225.
34. SAWYER, S. 1989. Statistical tests for detecting gene conversion. Mol. Biol. Evol. 6:526-538.
35. SHIMMIN, L. C., B. H-J. CHANG, and W.-H. LI. 1994. Contrasting rates of nucleotide substitution in the X-linked and Y-linked zinc finger genes. J. Mol. Evol. 39:569-578.
36. Aγ- globin genes: complete nucleotide sequences suggest that DNA can be exchanged between these duplicated genes. Cell 21:627-638.
37. SLIGHTOM, J. L., T. W. THEISEN, B. F. KOOP, and M. GOODMAN. 1987. Orangutan fetal globin genes. J. Biol. Chem. 262: 7472-7483.
38. SNEATH, P. H. A., M. J. SACKIN, and R. P. AMBLER. 1975. Detecting evolutionary incompatibilities from protein sequences. Syst. Zool. 24:311-332.
39. STEPHENS, J. C. 1985. Statistical methods of DNA sequence analysis: detection of intragenic recombination of gene conversion. Mol. Biol. Evol. 2:539-556.
40. TAKAHATA, N. 1994. Comments on the detection of reciprocal recombination or gene conversion. Immunogenetics 39: 146-149.
41. THOMPSON, J. D., D. G. HIGGINS, and T. J. GIBSON. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gaps penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
42. VANDEKERCKHOVE, J., and K. WEBER. 1984. Chordate muscle actins differ distinctly from invertebrate muscle actins. J. Mol. Biol. 179:391-413.
43. WEILLER, G. F. 1998. Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Mol. Biol. Evol. 15:326-335.