Essentially the same tree topology was obtained in maximum likelihood and maximum parsimony trees Open image in new window Fig. 2 Genomic structures of four CaM genes (A to D) of the Pacific bluefin tuna.
MEGA 5.0 [47] was used to compute the Maximum Likelihood and Maximum Parsimony trees.
A heuristic search of the ACT1 gene sequences resulted in two maximum parsimony trees (Length 351, CI 0.855, RI 0.957); the URA5 gene produced 1152 maximum parsimony trees (Length 208, CI 0.897, RI 0.973); the PLB1 gene produced six maximum parsimony trees (Length 395, CI 0.922, RI 0.994); and the IDE gene produced 24 maximum parsimony trees (Length 113, CI 0.912, RI 0.993).
A heuristic search of the combined loci found 110 maximum parsimony trees (Length 1089, CI 0.864, RI 0.984) without introns and 1023 maximum parsimony trees (Length 1706, CI 0.866, RI 0.984) with introns.
A heuristic search of the ACT1 gene sequences found five maximum parsimony trees (Length 796, CI 0.884, RI 0.928).
At a higher substitution rate, maximum parsimony and union of maximum parsimony trees were the most accurate.
Phylogenetic trees were constructed both as unrooted neighbor joining (NJ) and maximum parsimony trees using a Dayhoff matrix substitution model.
The development of the UMP method to combine maximum parsimony trees into a single network appears to be quite appropriate.
The MP (Maximum parsimony) trees of median-joining networks of 13 hgs were constructed and shown in Figure S2 where MBWs were marked as solid circles.
The median-joining approach followed by the maximum parsimony (MP) option returns a network that corresponds most closely to the strict consensus of maximum parsimony trees found in phylogenetic analyses [72].
The Maximum Parsimony trees were calculated using the complete deletion option, all codon positions and a CNI level of 3 with an initial tree by random addition of sequences (10 replicates).
