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It has been observed [ 5] that genomic signatures grouped organisms progressively better, with respect to 16S rRNA based phylogeny, when the oligonucleotide size increased.
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Alternative hypotheses for a mitochondrial sequence based phylogeny are not supported when the entire mitochondrial DNA sequence information is utilized.
The phylogeny of P. putida strains based on cpn60 confirmed the close relationship among P. putida strains, strengthening the 16S rRNA gene based phylogeny.
However, given the strong morphological convergence predicted with such repeated adaptive divergence patterns, it may be that there are many more cases awaiting discovery when examined in detail with molecular based phylogenies.
16S and 23S rRNA based phylogenies both showed a distinct cluster for strains associated with the "marine alpha" group.
Sequencing data used for chloroplast sequence based phylogenies.
The use of phylogenies based on molecules that may be subject of selection are considered to be potentially misleading to the hypothesis of species phylogeny, when compared to those based on neutrally evolving molecules.
Figure 6C presents an alternative phylogeny, based on the pigments and the morphological characters we identified.
Thus, we employ this Poisson-based inference when the empirical phylogeny we construct for a lineage (based on observed mutations) is consistent with a star phylogeny, and resort to the normal approximation only when the observed data contradicts a star phylogeny.
We tested the congruence between the rodent phylogeny and the Tlrs phylogeny based on the MrBayes approach using reconciliation analyses.
These phylogenies, when studied in the light of MLST based inferences, revealed distinct affinities between Peruvian Amerindian strains and Venezuelan Amerind strains, pointing thus to their common Asian origins.
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