A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

uToL reconstructions from the numerical analysis of FSF domain age EvoPCO analysis was performed using Microsoft Excel XLSTAT plugin (125) . For this reconstruction, proteomes were treated as samples and FSFs as variables. Because proteomes are composed of FSFs of different ages (that is, nd values), we transformed the FSF occurrence matrix into an FSF occurrence* (1 − nd) matrix, making the matrix a multidimensional space of the evolutionary age of domains. The "reverse age" 1 − nd transformation ensured that we did not lose information about FSFs of very ancient origin (for example, c.37.1 that has an nd of 0 and could be confused with FSFs that were absent in a proteome). Similarly, the transformation ensured that FSF absences (domains that have not yet materialized) did not contribute age to the multidimensional temporal space. Next, we calculated Euclidean distances that described pairwise dissimilarity among proteomes. The pairwise phylogenetic distance matrix was used to calculate the first three principal coordinates that described maximum variability in data. Effectively, the evoPCO method provided the three most significant loadings that described how component parts (FSFs) contribute to the history of systems (proteomes). The evoPCO method should be considered "rooted" in time because the multidimensional space was centered on an nd parameter that correlates with geological time (56) . For reference, we added the previously reconstructed proteome of the last common ancestor of modern cells (57) as an additional sample.