Documentaries have become so involving, entertaining and provocative that we almost forget the genre's root purpose: to document.
In my forthcoming book, Heart, Smarts, Guts and Luck, my co-authors and I discuss the notion of being connected to the "Heart" of a business — to its root purpose and its "why" as opposed to its "what" and "how". It is almost always easier for someone to state what they do for work than explain why they do what they do.
To identify a suitable outgroup of PBP-related sequences for rooting purpose, we selected more divergent, yet highly significant (E value<10−6), bacterial homolog sequences from a cyanobacterium, a firmicute, a beta and an alpha proteobacterium, none of them sharing the new subfamily signature.
(1) Transfer earmarked for grass roots purposes.
The matK matrix used to infer closest relatives consisted of 132 sequences of Phyllanthaceae plus a few Picrodendraceae, Euphorbiaceae, and Putranjivaceae for rooting purposes.
The translated protein sequences of the vlm data sets (Vlm1, Vlm1/2, Vlm2 and Vlm-combined) were also analyzed by MP in order to confirm the robustness of the nucleotide MP analysis and to identify a potential outgroup for rooting purposes.
This refinement is executed by running the entire pipeline using only those genomes represented by the node being refined (with additional sister taxa for rooting purposes).
The sequences for two deep-branching species, D. radiodurans and T. aquaticus [ 27], were included in this dataset for rooting purposes.
Additionally, since these network algorithms require rooted trees as input, selected trees were further required to contain at least one representative from domain Archaea to serve as an outgroup to the bacterial sequences for rooting purposes.
In the phylogenetic analysis, we included an extensive set of outgroups from both the Boletales (41 accessions) and its sister group the Atheliales, the latter used for rooting purposes (Dataset1).
Trees including this species as well as representatives from Dictyoglomi, Thermotogae, Aquificae and optionally other Clostridia were selected, with the additional requirement that Archaea be represented for rooting purposes (although interdomain transfers are certainly possible).
