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Re: mtDNA - pros and cons

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Posted by troy h on December 12, 2002 at 11:41:45:

In Reply to: Re: mtDNA - pros and cons posted by WW on December 12, 2002 at 08:01:35:

:You certainly can, but only with some provisos. The problem is tat different markers, *especially* different DNA sequences, may well have different histories. There is a large literature on the problems of combining different sources of evidence in one analysis.

as a species may well have different histories, i would think that this would be an advantage in revealing the true history of a species evolutionary history and relationships. using a gene that has only one history, therefore, would seem to me more misleading, providing a researcher with the illusion of confidence that his tree represents a "true" history of that species or group of species.

:: seems to me that sequence data for several nuclear genes would only give you more characters that, because they may have been inherited differently, would give you a much more complete history for that population or species.

:Actually, they will give you a mish-mash, unless you go for gene tree parsimony approaches. For instance, if you wanted to trace the phylogeny of a set of species using a nuclear and a mitochondrialmarker, and one of the nuclear marker had been "injected" into the gene pool by a hybridisation event, then it would have a totally different history. Combining its sequence with that of another gene which represented organismal history and simply analysing everything in a total evidence approach would not make sense.

i can see where this might be a problem, but one that would be overcome by adding more evidence (more sequences). furthermore, this also points to problems mentioned above - if a gene enters due to a hybridization event, then don't we want to know that? doesn't that evidence give us a more exact representation of actual history of that species or group than a character like mtDNA which you state gives a better "organismal history"?

also, this points to another problem with sequence data in general - are these changes in gene sequences really independent characters? if a sequence is inherited intact, and each sequence has its own history - is a sequence really a bunch of independent characters or a single character?

:Most of the nuclear genome actually codes for nothing at all!

i am aware that much of the nuclear genome is introns . . . but the human genome does contain about 29,000 genes that do code for proteins - i haven't seen the proportion of noncoding regions to protein coding regions (genes) but that is still a lot of genetic information that is potentially useful.

:Most straightforward nuclear gene sequences used in phylogenetics are actually proteins used for various metabilic functions, just like the mitochondrial proteins. Factors such as the ones you mention are as often as not the result of different patterns of gene expression, not the individual gene sequences themselves.

ok, i'll buy that

:I would actually argue the opposite: using markers under strong selection pressure increases the chance of being misled by homoplasious characters. In other words, organimsms which independently evolved a similar life style (e.g., fossorial, arboreal or whatever) would tend to convergently evolve similarities in characters under selection pressure. At the molecular level, an example is that of many enzymes involved in metabolic functions. These tend to favour the monophyly of birds and mammals (which is very strongly and convincingly rejected by other markers, including both morphology and many protein/DNA sequences), simply because of convergent selection pressures due to endothermy.

true, to a degree. interpreting homoplasy is always something to be concerned about, in any phylogeny.

:In my view, selective neutrality is a strength if what you are trying to infer is the phylogeny. Obviously, if you are intrested in the process of speciation per se, as opposed to phylogeny, then you will be looking for different markers with direct selective relevance to that process.

ok . . .

:Thelatter is certainly true. However, the point is that mixing multiple markers with potentially different histories will not give you the correct organismal tree, it will give you nonsense.

i don't see how this is the case ... papers i read (again i'll cite reeder & weins) suggested that "whole data trees" gave the best phylogenies. others that i've seen (some of JACampbell's stuff) also concur.

one proviso i'd like to see in any single-gene paper is "based on the single gene i sequenced" the phylogeny is. of course, the next guy sequences a different gene and gets a different phylogeny because his gene has a different history. then we get to decide who is closer to true? that's why we have parsimony . . . combine data, get the closest answer based on all gene histories and all evidence - not just evidence of a single gene.


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