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Re: mtDNA - pros and cons


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Posted by troy h on December 12, 2002 at 13:49:07:

In Reply to: Re: mtDNA - pros and cons posted by WW on December 12, 2002 at 12:33:59:


:Considering the phylogenies of the different genes separately will certainly give us a better insight. Mroeover, there are approaches which allow you to reconstruct the species tree from multiple gene, different trees derived from multiple genes (gene tree parsimony). However, simply lining up the sequences end to end will obscure the differences bewteen the genes, and the final tree will simply show which particular set of gene histories was best represented.

:For example, if you used a 250 bp section of cytb and a 1000 bp section of a nuclear gene (just to give an example), and the genes had differnet histories, then the final tree would be most heavily influenced by the nuclear gene (assuming similar levels of divergence and %ages of inforamtive characters), and would represen the history of that gene, with cytb just adding noise. On the other hand, if you used 1000 bp of cytb and 250 bp of the nuclear gene, than the final "total evidence" tree would represent the mitochondrial gene phylogeny, with the nuclear gene just adding noise. A total evidence approach is inappropriate where different genes have different histories.

>>> so what you are saying is that you should instead develop a tree for each gene examined, and then combine them using parsimony? therefore treating each gene independently and weighting them equally?

:As far as independence is concerned, it acts as s single character, with a very high number of different character states. Of course, the information content of a sequence is huge, when compared with a simple presence/absence character!

>>>> so each gene is only 1 character? if this is so, then how could a gene tree (=1 character) be considered to provide as much information of as a tree based on a dozen or so morphological characters?


:I have not seen the Reeder/Wiens paper. If morphological or similar data come into it, then we are dealing with a whole new ball game, since morphological characters don't have a built in set of phylgoenetic infgormation each, unlike a sequence.

>>>> "built in" as in "sequence" opposed to "interpreted" as in "character states"?

:The point is, one should not uncritically combine conflicting gene sequences without testing whether they ahve different histories.

>>>> i think i'm getting where you're coming from with this. tell me if i've got it:

1. develop a gene tree for each gene
2. combine trees using total evidence approach
3. if you have trees developed from morphological or allozyme data, do the same

:That's not parsimony, that is total evidence. Yes, of course we should look for evidence from as wide a set of markers as possible. However, where different genes do have different histories, then fusing them together will give you a tree that represents the history of neither - not all that useful.

i would argue that the conflicting trees give conflicting information - and that neither tree would be particularly useful . . . so how does one evaluate which is useful and which isn't?

combining conflicting trees in a total evidence approach (sorry, i mis-used parsimony earlier) would certainly reveal polytomies and the trees would be unresolved . . . but at least that approach is honest - reflecting the reality that we have conflicting evidence and that we don't really know which better reflects the "true" phylogeny of the taxa involved.

troy

:Cheers,

:Wolfgang
:





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