Figure 6

Results of a phylogenetic analysis of seven human EGF-SLC4A-FGF gene clusters. (a) EGF family; (b) FGF family; (c) SLC4A family; (d) inferred history of chromosomal duplications. Phylogenetic trees were constructed for each of the three gene families using four methods per family: neighbor-joining with uncorrected p, neighbor-joining with gamma correction, neighbor-joining with Poisson correction, and maximum parsimony. Non-bootstrap and 100-bootstrap inputs were used for each of the four methods. Therefore, 24 phylogenetic trees were constructed altogether. All phylogenetically informative orthologs known for each of the human genes were used. Human genes in the three families that did not map to any of the seven cluster loci are not shown. Alignments in MSF (text) format and the trees produced by PHYLIP from them can be found as additional data files available with the online version of this article. An intuitive interpretation of the unrooted trees is presented in a simplified cladogram format. Unlabeled nodes were supported by all four methods used. In (d), I, II, and III refer to three consecutive rounds of local duplication at the locus ancestral to 4q13. Nodes indicated by an asterisk (*) are supported solely by the three neighbor-joining trees. Nodes indicated by a hash mark (#) are supported by neighbor-joining with either gamma or Poisson correction only.