Estimating diversification rate changes and mass extinction
events in phylogenies
For a given phylogeny on present day data which is
calibrated to calendar-time, a method for estimating maximum
likelihood speciation and extinction processes is provided. The
method accounts for rate changes and mass extinction events:
Time is split into intervals. Throughout an interval, the
speciation and extinction rates stay constant. At the end of an
interval, the speciation and extinction rates may change, and a
fraction of the extant species may become extinct (mass
extinction). No species becoming extinct at the end of an
interval is a rate shift event without mass extinction. The
method estimates the maximum likelihood time intervals, the
speciation and extinction rates in each interval, and the
fraction of species going extinct (unless the fraction is known
and set to a predefined value). Note that the method takes into
account the whole phylogeny, in particular it accounts for the
"pull of the present" effect.

For a given phylogeny on present day data which is
calibrated to calendar-time, a method for estimating maximum
likelihood speciation and extinction processes is provided. The
method allows for non-constant rates. Rates may change (i) as a
function of time (rate shifts at specified times or mass
extinction events) or (ii) as a function of the number of
species (density-dependence). Note that the method takes into
account the whole phylogeny, in particular it accounts for the
"pull of the present" effect.

Estimating speciation and extinction rates based on phylogenies

For a given species phylogeny on present day data which is
calibrated to calendar-time, a method for estimating maximum
likelihood speciation and extinction processes is provided. The
method allows for non-constant rates. Rates may change (i) as a
function of time, i.e. rate shifts at specified times or mass
extinction events (implemented as bd.shifts.optim) or (ii) as a
function of the number of species, i.e. density-dependence
(implemented as bd.densdep.optim). Note that the method takes
into account the whole phylogeny, in particular it accounts for
the "pull of the present" effect. For a given phylogeny on
higher taxa, but where the number of species is known within
each higher taxa, speciation and extinction rates can be
estimated, under the assumption that these rates remained
constant (implemented as bd.groups.optim).