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Posted by troy h on December 11, 2002 at 10:19:28:
In Reply to: mtDNA - pros and cons posted by WW on December 11, 2002 at 03:03:08:
: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). 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.
::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, 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 . . . 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 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? 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?
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.