Figure 4

A-F – Phylogenetic analysis of neighboring gene families. Examples of the phylogenetic relationship for six neighboring gene families A (ABLIM), B (ADAMTS), C (AP3), D (ZIMP), E (HNRNP) and F (LGI). The trees were constructed using the neighbor-joining method as implemented in MEGA 3.1 with pair-wise deletion of gaps and poisson-corrected distances [117] All datasets were bootstrapped 1000 times (percent bootstrap support are indicated below each node). Species abbreviations are: Dme (Drosophila melanogaster), Cel (Caenorhabditis elegans), Cin (Ciona intestinalis), Csa (Ciona savignyi), Tru (Takifugu rubripes), Tni (Tetraodon nigroviridis), Dre (Danio rerio), Mmu (Mus musculus), Hsa (Homo sapiens). Numbers refers to chromosome number or scaffold number (ScXX), letters after chromosomal/scaffold number was arbitrarily assigned to family members located on the same chromosome to tell them apart. The scale below every tree indicates numbers of substitutions/site.