Cladogram comparison versus data combinality: A Comparative analysis of eight chloroplast genes, application to the phylogeny of the marine clade (Hydrocharitaceae)

We conducted separate parsimony analysis of eight chloroplast genes (atpA, atpB, atpE, psaB, psaI, cemA,rbcL, rps15) incorporating 16 genera in the aquatic plant family Hydrocharitaceae. Cladogram comparison in the assessment of phylogeny and branching patterns within the monophyletic group of seagrasses which comprises three genera (Enhalus, Thalassia, Halophila), depicted three various, distinct, well-resolved topologies in addition to a fully unresolved polytomy with regard to atpE gene. In order to elucidate causal events of gene tree discordance, we performed a range of additional analyses in a combined fashion, pooling the data in a step by step procedure approach. The result yielded in a fully-resolved and wellsupported total evidence tree. Conflicting signals and contributions of different characters were assessed through the distribution of synapomorphies among data sets for the node. While consensus trees by no means should be used to infer about diverging patterns and underlying evolutionary passways, merging different partitions not only does not hinder the phylogenetic inference but also helps the cryptic information to be uncovered in the total evidence tree, Nevertheless, separate analysis of individual data sets, though precluded resolving a robust phylogeny for the clade, simultaneous analysis of both approaches in a comparative study showed to provide important clues of diverse evolutionary processes in the chloroplast genome and thus gives us real insight in to sampling characters and assessing the consistency and effectiveness of different subsets of the data when conducting a phylogenetic analysis.

Keywords:

Seagrasses , Gene tree discordance , Phylogenetic inference , Total evidence , Evolutionary processes