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Re: mtDNA - pros and cons

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Posted by WW on December 12, 2002 at 08:01:35:

In Reply to: Re: mtDNA - pros and cons posted by troy h on December 11, 2002 at 10:19:28:

::On the other hand, if you have one nuclear gene sequence, you cannot automatically add other nuclear sequences to create one phylogeny, since, due to lack of linkage, different nuclear genes may have different histories, one of which may or may not be an accurate representation of organismal history.

:why can you not combine multiple nuclear genes into a single phylogeny? you can combine mtDNA, along with morphological data, and allozyme data to get "whole data" trees (i.e. reeder & weins work with sceloporus).

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.

: 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.

:::3) mtDNA is not under the same sort of selection pressures as are nuclear DNA . . .

::What do you mean by that?

:i mean that presumably, since much of the nuclear genome codes for physical characteristics such as color or pattern or size/shape/performance characteristics,

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

: then those genes are subject to selection on those sorts of traits . . . whereas the mitichondrial genes such as cytochrome b are much less affected by selection . . .

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.

: and since its selection (presumably) that drives speciation (along with geographic isolation) then looking at genes under selection would show changes that are more important to delineating species than would be found on sequences or genes that are presumably not under such intense selection.

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.

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.

:::i do understand that using nuclear DNA is more difficult and time consuming (and expensive). . . but i think that this sort of DNA would reveal much better (i.e. closer to actual relationships) results in phylogenetic analyses.

::Actually, the contrary is true. For *allopatric* populations (i.e., where gene flow is not an issue), mitochondrial DNA is actually MORE likely to protray the true organismal phylogeny. The reason is that mtDNA has a smaller effective population size than any particular nuclear gene (due to being haploid and maternally inherited), and as a result, coalescence happens more rapidly than for any one nuclear gene. Consequently, a mtDNA gene tree is more likely to represent organismal history than a tree derived from any one nuclear gene.

:first off, what do you mean by coalescence?

This is difficultto put into words in an easily understandable manner - the link below will take you to a paper which shows it diagrammatically in Figure 1. Definitely a case where a pic is woth 1k words!

: i can see where using mtDNA would be more likely to give a "true" tree than a single nuclear gene . . . however, i don't see how it would be better than using multiple nuclear genes (or a mix of nuclear and mtDNA genes). Is it simply the case that right now mtDNA is cheaper, easier, and more convenient?

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.

:furthermore, i don't like to see morphology and/or allozymes ignored . . . the morphology and/or allozymes of the organism (barring nuclear sequencing) are the only "window" a researcher has into the "whole organism" while mtDNA is but a small sample of DNA . . . with the above-mentioned limitations.

AFLP and microsats are the other markers in the same categories. When it comes to inferring species boundaries, at least one of these is certainly (to my mind) required as additionalevidence to a mtDNA tree. See also the paper at the following link:

in which we warn against the uncritical use of mtDNA phylogenies to ifer species limits - the Burbrink phylogeography papers do exactly that in their attemprts to infer species limits.



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