Phylogenetic inference proposes an evolutionary hypothesis for a group of taxa which is usually represented as a phylogenetic tree. The use of several distinct biological evidence has shown to produce more resolved phylogenies than single evidence approaches. Currently, two conflicting paradigms are applied to combine biological evidence: taxonomic congruence (TC) and total evidence (TE). Although the literature recommends the application of these paradigms depending on the congruence of the input data, the resultant evolutionary hypotheses could vary according to the strategy used to combine the biological evidence biasing the resultant topologies of the trees. In this work, we evaluate the ability of different strategies associated with both paradigms to produce integrated evolutionary hypotheses by considering different features of the data: missing biological evidence, diversity among sequences, complexity, and congruence. Using datasets from the literature, we compare the resultant trees with reference hypotheses obtained by applying two inference criteria: maximum parsimony and likelihood. The results show that methods associated with TE paradigm are more robust compared to TC methods, obtaining trees with more similar topologies in relation to reference trees. These results are obtained regardless of (1) the features of the data, (2) the estimated evolutionary rates, and (3) the criteria used to infer the reference evolutionary hypotheses.
Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree.
