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For phylogenetic analyses, we rooted the trees with representatives of several cyprinids subfamilies.
Exceptions to this were artiodactyl-only, lipotyphlan-only and rodent-only trees (with representatives from at least three families), all of which were coded because the monophyly of each of these orders has been seriously challenged in recent years ([ 11, 18, 50] respectively).
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We then constructed phylogenetic trees with representative sequences of these OTUs according to phylum, which are shown in Figures 2A (for Firmicutes), 2B (for Actionobacteria), and 2C (Bacteroidetes).
This represents an unbalanced, right-ladderized tree with representatives of several vertebrate lineages, including the cartilaginous fishes, teleost fishes, amphibians, birds, and the mammalian lineage as represented by humans.
The phylogenetic analysis described here refers to the maximum likelihood tree with representative sequences (Fig. 2).
In order to confidently test whether the giant forms worldwide evolved independently from herbaceous ancestors, it seems vital to include a considerably larger representation of herbaceous taxa and to root the Lobelioideae tree with representative taxa from outside the subfamily.
The phylogenetic tree constructed with representatives of each family confirms this clustering (fig. 2).
The consensus gene tree (that is, consensus over all single-gene trees) made with representative proteins succeeded (included all accepted clades) on all problems except 4 and 9, and a consensus (over bootstraps) concatenated tree succeeded on all problems except 4. Randomly chosen proteins succeeded less often.
Trees were rooted with representatives from several related families based on the work of Yagishita and others [ 45, 50].
The tree was rooted with representatives of six other genera of trichomonads.
Several Bucks readers had questions about damage caused by trees, so we spoke with representatives of the Insurance Information Institute for some answers.
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