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Posted by WW on December 11, 2002 at 03:03:08:
In Reply to: mtDNA - problems . . . posted by troy h on December 10, 2002 at 12:09:49:
:perhaps it would be nice if Rick Staub or someone else working with mtDNA data sets would get on here and contribute to this discussion . . . but for now, i'd like to point out a few limitations of mtDNA analyses . . .
Not Rick Staub, but working with mtDNA sequences, so allow me to butt in ;-)
:1) since mtDNA is matrilineal (i.e. its all inherited from your mother), use mtDNA underestimates gene flow. as you know, females of most species are more sedentary than males (of herps in particular) - most females grow up and live their lives in a relatively small home range. its males that get up and move around - much of animal dispersal and therefore gene flow is due to movement of young males away from their birthplace.
Correct. That's not necessarily a negative aspect though. The important point is to be aware of this property of mtDNA and not to ask it questions that it cannot answer by itself.
What mtDNA does extremely well is portray historical partitions of a species' range, as well as later dispersal events. Where there are deep phylogenetic splits in the mtDNA of a wide-ranging species (or species complex), and there is a geographical pattern to the distrbution of haplotype clades, then one can confidently infer past range partitioning. Thus, the *historical/biogeographical* interpretations of Burbrink are entirely appropriate - his data strongly support past vicariance in E. obsoleta and E. guttata. This applies where gene flow right across the species range (as seen in wide-ranging turtles or whales, for instance) is not an issue.
What is inappropriate is to regard the populations representing different haplotype clades as genetically closed, independently evolving units. As you mention, male-mediated gene flow can merrily cross mtDNA clade boundaries, and the existence of parapatric or sympatric mtDNA haplotype clades does not necessarily indicate reproductive isolation and lack of genetic exchange.
:2) every gene on mtDNA is inherited as a unit because the mtDNA is a single loop of DNA
Correct. Again, that can be an advantage as well as a disadvantage.
The important point is to differentiate between a gene tree and an organismal tree.
The fact that all mtDNA genes are inherited as a single linake unit means that you can build a more robust mtDNA phylogeny by sequencing more mitochondrial genes. For instance, if sequencing only cytochrome b leaves a lot of nodes unresolved, or at least not statistically significantly supported, then sequencing further mitochondrial genes ought to resolve that problem. Since all mitochondrial genes share the same history, one can confidently analyse all data in a single analysis, and thus arrive at a very robustly supported gene tree - with the caveat that this may not be representative of the organismal tree.
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.
:3) mtDNA is not under the same sort of selection pressures as are nuclear DNA . . .
What do you mean by that?
: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.
If one is intereted in elucidating patterns of genetic exchange between different populations (e.g., mtDNA clades in Elaphe), then different nuclear markers have to be used, such as microsatellites of AFLPs. Howeverm these are not gene sequences, and not normally interpreted phylogenetically, but in terms of gene flow. These would be markers of choice for testing whetehr the new Elaphe taxa should be considered as species or not. Of course, good old allozymes could also do this...
Hope this helps.