[Taxacom] Congruence of gene trees

[John Grehan]

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Jason Mate

> > 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. 

No, one usually chooses the best supported configuration (by whatever criterion) as most likely representing a differentiation sequence. The lineage sorting issue potentially applies as much to morphology as it does to molecules.

> Regarding Homo, Pan & Co. (sigh) IF there is incongruence between one
> dataset and another, this conflict is, of course, in need of more data.

Or different concepts or different perspectives on the data. More data does not necessarily provide a solution. If they dig up a hominid that is a clear precursor to the currently known bipedal morphologies, and this hominid looks even more like an orangutan than current hominids, I might say this additional data adds further support to the orangutan evidence, whereas molecular systematists might say that it is irrelevant in some way.

> 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.

Yes - if one is a pheneticist and rely on overall similarity through the law of large numbers. If the law of large numbers is applied to morphology one will get a human-African ape relationship every time, just as one might get a crocodile-lizard grouping every time. 


John Grehan