Molecular Biology and Evolution, Vol 16, 1369-1390, Copyright © 1999 by Society for Molecular Biology and Evolution
G Drouin, F Prat, M Ell and GD Clarke
We used a variety of methods to detect known gene conversions in the actin
gene families of five angiosperm species, the beta-globin gene families of
two primate species, and the Zfx/Zfy gene families of seven mammalian
species. Our goal was to devise a working strategy which would allow the
analysis of the members of a multigene family in order to determine whether
there had been gene conversions between its members, identify the genes
involved in the gene conversions, establish the lengths of the converted
regions, and determine the polarities of the gene conversions. We show that
three phylogenetic methods and the homoplasy test of Maynard Smith and
Smith perform relatively poorly on our data sets because the sequences we
analyzed had large levels of multiple substitutions. The method of Sawyer,
the compatibility method of Jakobsen and Easteal, the partition matrix
method of Jakobsen, Wilson, and Easteal, and the co-double method of
Balding, Nichols, and Hunt can be used to identify the genes which have
been involved in gene conversions. The co-double method is more powerful
than other methods but requires orthologous sequences from related species.
Compatibility, phylogenetic, and nucleotide substitution distribution
statistics methods can be used to identify the location of the converted
region(s). Site-by-site compatibility analyses can also be used to identify
the direction of the conversion event(s). Combinations of these methods can
therefore be used to establish the presence, locations, and polarities of
gene conversions between multigene family members.
ORIGINAL ARTICLE
Detecting and characterizing gene conversions between multigene family members
Departement de biologie, Universite d'Ottawa, Ontario, Canada. guy@bio01.bio.uottawa.ca
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