Fwd: Australopithecus and orangutans

[Jason de Koning]

>> What kind of argument is: " if molecular characters can never be used  
>> for
>> evolutionary analysis, then why do they so frequently give phylogenies
>> that are congruent with "real cladistic analyses"? "
>>
>> For the same reason a stopped clock is correct twice a day is the  
>> answer to that argument.
>
> That is a poor analogy, given the vastness of treespace.  For 15 taxa,  
> there are ~2 x 10^14 possible rooted trees.  The probability of any  
> given morphological and molecular datasets from the same 15 taxa to  
> concur is thereby exceedingly and impossibly small, unless they  
> contain mutual information (that is, historical signal).  I assumed  
> that this would be a strawman argument for most people: an extreme  
> projection of what is being argued is that molecular data contains no  
> historical signal, which is preposterous.
>
> Since ultimately, the only way we have to really convince each other  
> is through experimental or analytic tests of theoretical predictions,  
> consider the several experimental phylogeny papers, where different  
> groups have subjected bacterial strains or viruses to serial  
> bottlenecks (or recently, generated mutants along a known phylogeny by  
> PCR), sequenced genes from some of those strains, and then correctly  
> reconstructed the historical process of simulated speciation.  See the  
> following paper for a recent study:
>
> Sanson et al., 2002.  Experimental phylogeny of neutrally evolving DNA  
> sequences generated by a bifurcate series of nested polymerase chain  
> reactions.
> http://www.ncbi.nlm.nih.gov:80/entrez/ 
> query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11801745&dopt=Abstract
>
> If one chooses to ignore molecular data out of principle, one must  
> confront their principles with evidence from in silico experiments  
> (simulation), in vitro experiments (PCR), in vivo experiments  
> (bacteriophage experiments), and from congruence between large  
> morphological and molecular datasets, which all suggest that the  
> cladistic analysis of molecular data (as defined conventionally) all  
> lead to known, correct, or congruent answers.
>
> - Jason
>