Figure 3

Evolutionary relationship of the MSHORT1 elements in C2MC. A) The phylogenetic tree of all 193 MSHORT1 elements that are present in C2MC is shown. MSHORT1 copies are numbered from left to right for their location in C2MC. When a miRNA gene is present in the MSHORT, it is indicated as well. MSHORT1 copies in the central region of C2MC (see Figure 2C) are colored, while the MSHORT1 copies in two C2MC flanks are white. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The percentage of replicate trees in which the associated taxa clustered together is shown next to the branches. The scale bar represents 5% of sequence divergence. B) The sequential order of MSHORT1 copies is highlighted. The MSHORT1 units that belong to the same sub-cluster are listed in columns. Rows show the arrangement of MSHORT1 units in the corresponding MLONG1 copies. Please note that the first 31 MSHORT1 copies are located in the left flank of C2MC (Figure 2C), while copies 146-193 are in the right flank.