[Taxacom] Congruence of gene trees

[Jason Mate]

> Interesting. So you are saying that an ancestor that is morphologically
> polymorphic gives rise to multiple descendants that reflect those
> polymorphisms variously. AND are you also saying that an ancestor that
> is molecularly polymorphic also gives rise to multiple descendants with
> various distributions of those molecular polymorphisms? 

I haven´t read Michael´s paper (I would like to read a PDF though :)) But the crux is that new species tend to arise from the bossom of a metapopulation and in this way the relationship of each character (and the genes that encode them) has followed a different path. I intensely dislike (hate is not very PC nowadays) the absurdity of statements such as "the first Aus bus". It gives the impression that one species suddenly became another one or was born like that and can be traced back in this way. If you look at a single mutation, if complex (and therefore improbable) enough then I am sure that it had such an origin but 

> THUS are you also saying that any group of, say, three exemplars that
> are supported in three different ways by different gene lineages are all
> derived from that same ancestor. SO if there is evidence that there is
> differential lineage sorting, then molecular analysis cannot be used to
> distinguish a correct species tree for the taxa involved because there
> is no one correct species tree and all the taxa are derived from a joint
> ancestor with polymorphic genes? 
> So if John Grehan can find differential lineage sorting with
> well-supported but different gene trees for configurations of orang,
> man, chimp and gorilla, then the molecular evidence cannot be used to
> disprove or decide against a morphological analysis of relationships? 
> Are you implying this? Are you saying that if there are many gene trees
> supporting one tree and only are few supporting other configurations,
> then we should not choose the configuration (topology) of the one
> supported by the most or the overwhelming number of gene trees from
> different genes?

This is probably (I am not sure at this point) John´s position. However the average of many genes (how many is anybody´s guess) should give you an acceptable average of how the population that became Aus bus diverged from Cus bus. Of course the question in itself is meaningless for species don´t split-off cleanly. Gene barriers (mountains, seas, etc) don´t come into existence instantly.
Regarding Homo, Pan & Co. (sigh) IF there is incongruence between one dataset and another, this conflict is, of course, in need of more data. That said I go back to my second line. If the average of hundreds of genes (or whole genomes as Kenneth pointed out) gives one result that conflicts with morphology then you have to argue that the weight (sheer volume) of data should be the trump card.
 
> This is NOT following dogma, Michael! Doubtless one of the excellent
> phylogeneticists among us will explain why my take (above) on your
> message is totally wrong.

Michael´s statement is, in my humble opinion, true but equally applicable to all sources of data. The key is that this problem is only, well problematic, when you are working with species pairs or trios. The effects of gene sorting and metapopulation dynamics only apply to the splitting of sister species... and it ties nnicely with mono vs paraphyletic species and species concepts. So we will just tuck it back nicely into Pandora´s box before something else escapes. ;)

Jason

_________________________________________________________________
With Windows Live, you can organize, edit, and share your photos.
http://www.microsoft.com/middleeast/windows/windowslive/products/photo-gallery-edit.aspx