Q on fast evolving sequences

Nicolas_Galtier galtier at acnuc.univ-lyon1.fr
Wed Jun 4 01:15:50 EST 1997

Thorsten Burmester writes:

> Hi there,
> I have a question on the construction of phylogenetic trees with sequence
> data using parsimony: 
> Is there theoretical basis why sequences that evolve faster than the
> others tend to branch off "earlier" in a tree instead of joining their
> actual "relatives"?

Yes. The theoritical reason was given by Joe Felsenstein in the 70's
and 80's and called "Long branch attraction" (LBA). A discussion took
place after Felsenstein's 1978 paper. Felsenstein argued that
parsimony was inconsistant in case of unequal evolutionary rates among
lineages unless rates are small enough, and that a maximum likelihood 
approach is better. Several cladists including Farris and Sober 
advocated for the use of parsimony anyway, considering Felsenstein's
result as non-conclusive. This somewhat vehement debate undoubtedly 
raised our knowledge about how tree-building methods work. A few 
references are given below (maybe Joe has some more...).

Let me try to explain the LBA effect again. Suppose the actual tree is :

		_________ sp1
	       |_ sp2
	  |    |_ sp3
	__|    |
	  |    |_ sp4
	  |_________ O

This example includes a multifurcation, but you can imagine any resolution
provided that the lengths of newly resolved branches are very short.

sp2, sp3 and sp4 evolve slowly: they are quite similar to their ancestor,
and similar to each other. Therefore most characters will suit the following

	  O:  ?
	sp1:  ?
	sp2:  A
	sp3:  A
	sp4:  A

where A denotes any character state.

Now, look at what kind of parsimony-informative characters can occur, assuming
this scheme. A single one is allowed :

	  O:  B
	sp1:  B
	sp2:  A
	sp3:  A
	sp4:  A

supporting a tree where sp1 branches off near O, namely as an outgroup to sp2,
sp3 and sp4. This (homoplasic) character type can outnumber synapomorphies 
and make parsimony inconsistant if rates are rally different.
The Maximum Likelihood method is less (not) sensitive to this problem.

The long branch attraction effect may apply whatever the location of the root.
Usually, the outgroup branch is a long one, so that long branch attraction becomes
attraction toward the root.

Hope this helps,

Nicolas Galtier
Laboratoire de Biometrie, Genetique et Biologie des Populations
Universite C.Bernard

Felsenstein 1978 Syst. Zool. 27:401-410
Felsenstein 1979 Syst. Zool. 28:49-62
Farris 1986 Cladistics 2:14-27
Felsenstein and Sober 1986 Syst. Zool. 35:617-626.

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