THE PARTITION MATRIX - EXPLORING VARIABLE PHYLOGENETIC SIGNALS ALONG NUCLEOTIDE-SEQUENCE ALIGNMENTS

The partition matrix is a graphical tool for comparative analysis of n ucleotide sequences following alignment. It is particularly useful for investigating the divergent phylogenies of sequence legions undergoin g reticulate evolution. A partition matrix is generated by determining the consistency of the parsimoniously informative sites in a set of a ligned sequences with the binary partitions inferred from the sequence s. Since the linear order of sites is maintained, the matrix can be us ed to assess whether the distribution of sites either supporting or co nflicting with particular partitions changes along the length of the a lignment. The usefulness of the matrix in allowing visual identificati on of differences in evolutionary history among regions depends on the order in which partitions are shown; several suitable ordering scheme s are proposed. We demonstrate the use of the partition matrix in inte rpreting the evolution of the pseudoautosomal boundary region on the s ex chromosome of catarrhine primates. Its routine use should help to a void attempts to derive single phylogenies from sequences whose evolut ion has been reticulate and to identify the gene conversion or recombi nation events underlying the reticulation. The method is relatively fa st. It is exploratory, and it can form the basis for more formal analy sis, which we discuss.