Phylogenetic tree of BEL/Pao families. The phylogenetic tree is based on the concatenated amino acid sequence of the three protein domains protease, reverse transcriptase, and integrase. The tree is based on 893 transposable element families for which we could construct a consensus sequence for all three domains. In addition to data from these families, we used in this analysis all BEL/Pao elements from Repbase Update  where we could identify all three domains (total of 92 elements). Some of these Repbase Update elements are from species whose genomes we did not analyze here. Furthermore, we included 16 elements from the Gypsy element Database GyDB , in order to associate clades in the tree to previously described subclades of the BEL/Pao element class. A list of these elements is found in additional file 2. Different colors indicate major clades. A) Same phylogenetic tree as in A) but with major clades collapsed into triangles indicating superfamily divergence and statistical support values for the branches. We constructed the tree using PhyML with an approximate likelihood ratio test to estimate the statistical support of the tree topology . This statistical support is indicated by the numbers at the branches which range from 0 (least significant) to 1 (highly significant). All branches leading to the major clades have very high support. C) Same phylogenetic tree as in A) but without divergence triangles, and branches are reorganized to facilitate comparison with trees in D) and E). D) and E) Phylogenetic relationship of BEL/Pao clades as described by Copeland et al.  and Llorens et al , respectively. High resolution tree and graphic files are available from the authors upon request.
de la Chaux and Wagner BMC Evolutionary Biology 2011 11:154 doi:10.1186/1471-2148-11-154