While reconciliation analysis serves to find the most parsimonious reconstruction of host and parasite evolutionary history by maximizing cospeciation events and minimizing the cost of the reconstruction, it can only identify possible scenarios describing the evolutionary history between associated taxa.
In our previous model-based data reconciliation analysis of the response to NADPH demand modulation, we showed that yeast cells responded to increases in NADPH demand by increasing flux through the PP and acetate pathways, which covered 80%and20%0% of the NADPH demand, respectively [ 5].
As 15 species do not have the predicted genes, a gene tree and a species tree of the remaining 19 species are subjected to reconciliation analysis.
We also address incongruence among the gene trees with gene tree reconciliation analysis, and assign estimated ages to the nodes of our tree.
A total of 34 genomes were subjected to the reconciliation analysis, comprising 25 fungi, one Oomycete, one bacterium, two archaea, two plants, and three animals.
The advent of parsimony-based reconciliation analysis has permitted many researchers to assess phylogenetic congruence in a wide array of host-parasite assemblages.
In order to elucidate evolutionary footprints, reconciliation analysis was performed with a species tree and an Argonaute gene tree.
The reconciliation analysis clearly identified duplication nodes giving rise to the first (N-terminal, node 1, red boxes) and final (third or fourth) (C-terminal, node 2, green boxes) A domains of both lineages (Fig. 3).
The reconciliation analysis identified a duplication at node 5 corresponding to this relationship (Fig. 3).
Therefore, contrary to the results of the reconciliation analysis, the divergence date estimates predict a much less parsimonious explanation of current primate louse distributions: a combination of the 'recent host switch' and 'pair of lice lost' hypotheses.
