Botany online 1996-2004. No further update, only historical document of botanical science!

MADS Domain Protein Phylogeny Reconstructions

The phylogenetic trees linked from this page were constructed from alignments which were computed as outlined on the alignment page. All protein sequences from the genes listed in the MADS box gene list are included in this analysis. Phylogeny reconstruction was performed with the Phylogeny Inference Package (PHYLIP). Distance matrices were calculated from the alignments with the protdist program, and these were used to construct phylogenies by neighbor joining with the neighbor program. The trees are made available in the "New Hampshire" source format, which you may use to view the trees with programs like treetool or treeview. Additionally, PostScript graphics are provided, which you can view directly with your web browser if your browser can display PostScript or it is configured to use a viewer application, such as ghostview, for this purpose. As another option, we also provide GIF files which are generated from the PostScript graphics using ghostscript.

MADS domain tree: source, PostScript tree style or dendrogram style, GIF tree style or dendrogram style. This tree is constructed on the basis of an alignment MADS domain sequences (60 amino acids long). The MADS domain is the only sequence stretch that is clearly homologous among all MADS domain proteins from animals, fungi and plants. The tree allows a rough classification of genes into gene subfamilies.
MIK domain tree: source, PostScript tree style or dendrogram style, GIF tree style or dendrogram style. This tree is computed from an alignment of the MIK domain which, in addition to the MADS domain, also comprises the I region and the K domain, which are only found in plant MADS domain proteins. The MIK domain is approximately 170 amino acids long, length heterogeneity is particularly found in the rather variable I region. The phylogenetic tree provides some interesting hints about the radiation and evolution of MIK type genes in plants.

Jan T. Kim (kim@mpiz-koeln.mpg.de)