Character independence and RFLPs vs DNA finger-prints

Neil Caithness neil at gecko.biol.wits.ac.za
Sat May 27 21:51:02 EST 1995

I’m having a debate with some colleagues about cladistics and character 
independence, and I would like to hear the opinion of readers of this group.

I think it's clear that one cannot treat RFLPs as caldistic character data 
due to the non-independence of fragment lengths (add one cut site between two 
others, and you loose one long fragment and gain two shorter ones).

But what about the "finger-prints" from transposable elements that _contain_ 
restriction sites? Does tagging just those fragments terminated by the 
insertion sequence (mostly at only one end) produce cladistic data? If the 
restriction sites within the transposable elements make up only a small 
proportion of the total number of restriction sites, then the fragment 
lengths produced at different insertion points are largely independent.

My first reaction was that a sub-set of data surely can’t tell you more than 
the complete set, but this is not an arbitrary sub-set, it is specifically 
the fragment lengths to the left and right of the insertion points of a 
transposable element. I argued against it, but I’m now not convinced.

There are several reasons that make finger-prints more desirable than direct 
sequencing; it’s easier, cheaper, and there are vastly more finger-prints 
already available than good sequences--but only if it produces good cladistic 

Neil Caithness
Epidemiology Research Unit, NCOH, Johannesburg, &
Dept. of Zoology, University of the Witwatersrand

E-mail:	neil at gecko.biol.wits.ac.za / neil at is.co.za

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