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Summary: Gene Conversion and the Evolution of Euryarchaeal Chaperonins: A Maximum
Likelihood-Based Method for Detecting ConŻicting Phylogenetic Signals
John M. Archibald,* Andrew. J. Roger
Canadian Institute1 for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology,
Dalhousie University, Halifax, Nova Scotia, Canada B3H 4H7
Received: 27 November 2001 / Accepted: 26 February 2002
Abstract. Recombination is well known as a com-
plicating factor in the interpretation of molecular
phylogenies. Here we describe a maximum likelihood
sliding window method based on a likelihood ratio
test for scanning DNA sequence alignments for re-
gions of incongruent phylogenetic signals, such as
those inŻuenced by recombination. Using this method,
we identify several instances of gene conversion be-
tween paralogous chaperonin genes in euryarchaeote
Archaea, many of which are not detected by two
other widely used methods. In the Thermococcus/
Pyrococcus lineage, where a gene duplication pro-
ducing a and b paralogues predates the divergence of
Thermococcus strains KS-1 and KS-8, gene conver-
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