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Re: ...and how ranks don't work was Re: Sauropodz r kewl




They're not measuring anything except taxonomists' mood swings. What you
need to measure biodiversity, unless you have a list of species under one
single species concept, is the sum of branch lengths that connect the
organisms you look at. You need a phylogenetic tree.
snip

My understanding of diversity from phylogeny is that it's the
difference between speciation rates and extinction rates, is that what
you're talking about, or do you mean something else (like the sum of
branch lengths is a good proxy for the differences between species)

I'm talking about the Phylogenetic Diversity Index. I should have made explicit that it uses the branch lengths of a timetree.

To quote from here http://dml.cmnh.org/2009Sep/msg00370.html :

Daniel P. Faith (1992): Conservation evaluation and phylogenetic
diversity. Biological Conservation 61, 1 -- 10.
(1994a): Genetic diversity and taxonomic priorities for conservation.
Biological Conservation 68, 69–74.
(1994b): Phylogenetic pattern and the quantification of organismal
biodiversity. Philosophical Transactions of the Royal Society of London,
Series B: Biological Sciences 345, 45–58.

And here an application:

K. Nehring&  C. Puppe (2004): Modelling phylogenetic diversity. Resource
and Energy Economics 26, 205–235.

The PDI uses topology and branch length to measure the uniqueness of an
OTU and the diversity represented by a tree. That's much better than
just counting species, even in the highly improbable event that they
were all named by a single person who used a single species concept
throughout!