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RE: Embarrassingly basic question about cladistic analysis
Mike Taylor wrote-
I'm sure plenty of people here can answer this ...
When a paper presents a cladistic analysis and says something like
"This analysis produced 72 equally most parsimonious trees (MPTs) with
length = 783, consistency index (CI) = 0.526 and retention index (RI)
= 0.687", where are the CI and RI values taken from? Because as I
understand it, each of those 72 MPTs has its own CI and RI, correct?
Do people just pick one of the MPTs at random and report its
statistics? Do they take the highest CI and the lowest RI that occur
in any of the MPTs? Do they report the statistics of a consensus
tree? Or what.
The Consistancy Index is a ratio of the number of characters in the matrix
and tree length. Since equally parsimonious trees have the same length by
definition, and are based on the same character list, they have equal
consistancy indices. Similarly, the Retention Index is calculated using
these two numbers, plus the total number of 1's or 0's in the matrix (which
ever is smaller). So it will also be the same for any equally parsimonious
trees derived from a certain matrix.