Stochastic Models for Phylogenetic Trees
These pages form a complement to an old project
(with Lea Popovic and Maxim Krikun) we called
Coherent Stochastic Models for Macroevolution.
Part of the idea was that the behavior of higher-order
taxa (genera, families etc)
should emerge from a species-level model rather than being
Overview of project: model and results.
There was a
2004 draft document covering the whole project.
This was subsequently made into 3 papers.
A critical branching process model for biodiversity
deals with the species-level model.
One aspect of the model we emphasize is that qualitative behavior
of different realizations can appear quite different: see our
picture gallery of simulations.
Stochastic Models for Phylogenetic Trees on Higher-order Taxa
describes a way to combine the species-level model with schemes for classifying species into genera,
and starts analytic study of the resulting trees on genera.
Five statistical questions about the Tree of Life
is the final overview paper aimed at biologists;
the 5 questions we select are
For a clade on $n$ extant species, write $m \geq n$ for the maximum
number of coexisting species at any past time; how large do we expect
a priori that the ratio $m/n$ might be?
From a correct phylogeny of the extant species of a clade, what can
we deduce about past speciation and extinction rates?
What proportion of extant species are in fact descendants of still-extant ancestral species, and
how does this compare with predictions of models?
When one moves from trees on species to trees on
sets of species (whether traditional higher order taxa,
or clades within PhyloCode)
does one expect trees to become more unbalanced
as a purely logical consequence of
tree structure, without signifying any real biological phenomenon?
How do we expect that fluctuation
rates for counts of higher order taxa should compare to fluctuation rates for number of species?