In article ,
 Ron Okimoto  wrote:

> Brenton Thomas wrote:
> 
> > Being a physics maths IT type I don't have the background to even know
> > the right questions to ask, so was wondering if someone can help.
> >
> > If you make the assumption that each "branching" of the
phylogenetic
> > tree corresponds to a variation of some base type, then you could
> > classify how "evolved" how two organisms were by the number of
> > branchings from the root of the tree to the organism in question. Ie:
> > primitive organisms are pretty much the same now as they were millions
> > of years ago, more advanced organisms have undergone more changes
> > corresponding to more branches.
> >
> > Sounds easy and probably has been done before many times.
> >
> > With this concept in mind what is the most advanced "in terms of
> > number of branches" organism known and where do humans come in
> > comparison.
> >
> > Interestingly this problem corresponds to a problem in maths of
> > finding the longest path in a graph. Using computers is really hard.
> > But can be solved in analog fashion by "making" a tree
- say out of
> > string, where each branch is the same length and holding it in the air
> > by the root.  The longest path is the one closest to the ground.
> >
> > Also are their internet resources out there that you can use to see
> > the phylogentic tree as a whole entity and zoom in?
> >
> > Thanks in advance
> 
> You can't really think of a phylogenetic tree in this fashion.  Assume
> that there was some single common ancestor that existed and we inherited
> the universal genetic code from.  All extant taxa are equal distance from
> this common ancestor.  Species that went extinct half a billion years ago
> are half a billion years closer to the common ancestor.
> 
> What you can do is determine when one lineage branched (separated) from
> another.  The chimp lineage diverged from the human lineage on the order
> of 5 million years ago.  They both diverged from the lesser ape (gibbons)
> around 20 million years ago.  Since gibbons, chimps and humans all
> diverged from that common ancestor they are all equally distant from that
> common ancestor.  Chimps and humans just shared a lineage for around 15
> million years before going their separate ways.  You can make a list of
> the traits that have changed the most in these three lineages and make
> some statement that one lineage has diverged more from the common ancestor
> than another, but they all diverged at the same time and have all been
> evolving for the same amount of time.  All extant taxa are at the tips of
> the branches of the phylogenetic tree.  They have all been evolving the
> same length of time.
> 
> 
> 

There are two metrics one might use:

One is the number of nodes in the tree, or in other words, the number of 
branching points since the root. The problem with this is that we just 
don't know how many speciation events there are (each new species 
discovered in the fossil record adds a new event, as does each new 
species found in modern fauna), so at best we have a lower limit and 
nothing more. Moreover, what is being measured? Merely speciation rate. 
I do not think that is very informative.

The other is perhaps the overall distances on the tree, as calculated 
from Nei distance or similar. The problem here is that while these may 
be informative in short periods, they are neither objective (how many 
genes per unit of "evolution" is required? Answer, who knows? If they 
are regulatory genes, then massive changes can arise from small 
mutations. If they are junk DNA, then it is more informative perhaps, 
but only of phylogenetic relationships of the sampled taxa). Phenetic 
distances ("overall similarity") are totally arbitrary.

So, the primary question has to be - what is it we hope to measure here? 
If that can be answered, and the information can be recovered, then 
perhaps something might be done.
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