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*To*: dinosaur@usc.edu*Subject*: RE: Embarrassingly basic question about cladistic analysis*From*: Michael Mortimer <mickey_mortimer111@msn.com>*Date*: Tue, 03 Oct 2006 21:42:39 +0000*In-reply-to*: <20061003160547.31A75F3861@localhost.localdomain>*Reply-to*: mickey_mortimer111@msn.com*Sender*: owner-DINOSAUR@usc.edu

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.

Mickey Mortimer

**References**:**Embarrassingly basic question about cladistic analysis***From:*Mike Taylor <mike@indexdata.com>

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