Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences.
BACKGROUND
Most phylogenetic methods assume that the sequences of nucleotides or amino acids have evolved under stationary, reversible and homogeneous conditions. When these assumptions are violated by the data, there is an increased probability of errors in the phylogenetic estimates. Methods to examine aligned sequences for these violations are available, but they are rarely used, possibly because they are not widely known or because they are poorly understood.


RESULTS
We describe and compare the available tests for symmetry of k-dimensional contingency tables from homologous sequences, and develop two new tests to evaluate different aspects of the evolutionary processes. For any pair of sequences, we consider a partition of the test for symmetry into a test for marginal symmetry and a test for internal symmetry. The proposed tests can be used to identify appropriate models for estimation of evolutionary relationships under a Markovian model. Simulations under more or less complex evolutionary conditions were done to display the performance of the tests. Finally, the tests were applied to an alignment of small-subunit ribosomal RNA sequences of five species of bacteria to outline the evolutionary processes under which they evolved.


BACKGROUND
Programs written in R to do the tests on nucleotides are available from http://www.maths.usyd.edu.au/u/johnr/testsym/
Ababneh
Faisal
F
School of Mathematics and Statistics, University of Sydney NSW 2006, Australia.
Jermiin
Lars S
LS
Ma
Chunsheng
C
Robinson
John
J
D020137:Base Pair Mismatch / Q000235:genetics*; D020029:Base Pairing / Q000235:genetics*; D001483:Base Sequence; D017124:Conserved Sequence; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid
D009711:Nucleotides