Biology Reference
In-Depth Information
while the solution space is explored, with only the shortest MP trees being
retained. Since tree length in CMP methods is defined as the minimal
number of mutations in a given topology, the result will always be an inte-
ger. Likewise, in CC methods, the size of the largest clique will always be
an integer. Thus, in these methods, if intermediary trees are not immedi-
ately discarded, a strict consensus tree can be produced for a set consist-
ing of both the MP trees and the trees which are just one unit longer than
optimal (longer tree for CMP, smaller clique for CC).
s
Any branch of the
final tree that disappears in this consensus is considered a weak branch and
given a decay index of one. This method can be extended for trees which
are
z
units longer than optimal, yielding branches with a decay index of
z
,
until all of the branches have been given a decay index. A high decay index
indicates a high confidence level.
4.6. Recommended,Acceptable,and Unacceptable
Groupings of Taxons
The central objective of phylogenetics is the grouping of taxa, on the
basis of evolutionary criteria, in order to reconstruct an evolutionary tree.
As we have seen earlier (Sec. 2.4), an erroneous hypothesis of homology
could have been made. Clearly, such an error would entail mistaken
groupings of taxa. But groupings are not necessarily all wrong or all true.
There are nuances in plausibility, and some categories of grouping are
considered to be
a priori
of higher or lower theoretical quality according
to the classification rules of taxonomy, depending on the circumstances
and the classification objectives.
A grouping that contains the complete set of terminal nodes descen-
dant from a common ancestor is called holophyletic, and forms a holo-
phylon. This is a somewhat utopian concept, since we cannot really
be sure that all descendants of a given ancestor are known. A grouping
of terminal taxa in a dendrogram is called monophyletic if it contains all
s
There is no need to keep all intermediary trees in memory until the end of the
search. Since a strict consensus is used, only the preliminary consensus tree for each
score needs to be conserved.
