@article{lambert_phylogenetic_2014,
Author = {Lambert, Amaury and Alexander, Helen K. and Stadler,
Tanja},
Title = {Phylogenetic analysis accounting for age-dependent
death and sampling with applications to epidemics},
Journal = {Journal of Theoretical Biology},
Volume = {352},
Pages = {60--70},
abstract = {The reconstruction of phylogenetic trees based on
viral genetic sequence data sequentially sampled from
an epidemic provides estimates of the past transmission
dynamics, by fitting epidemiological models to these
trees. To our knowledge, none of the epidemiological
models currently used in phylogenetics can account for
recovery rates and sampling rates dependent on the time
elapsed since transmission, i.e. age of infection. Here
we introduce an epidemiological model where infectives
leave the epidemic, by either recovery or sampling,
after some random time which may follow an arbitrary
distribution. We derive an expression for the
likelihood of the phylogenetic tree of sampled
infectives under our general epidemiological model. The
analytic concept developed in this paper will
facilitate inference of past epidemiological dynamics
and provide an analytical framework for performing very
efficient simulations of phylogenetic trees under our
model. The main idea of our analytic study is that the
non-Markovian epidemiological model giving rise to
phylogenetic trees growing vertically as time goes by
can be represented by a Markovian "coalescent point
process" growing horizontally by the sequential
addition of pairs of coalescence and sampling times. As
examples, we discuss two special cases of our general
model, described in terms of influenza and HIV
epidemics. Though phrased in epidemiological terms, our
framework can also be used for instance to fit
macroevolutionary models to phylogenies of extant and
extinct species, accounting for general species
lifetime distributions.},
doi = {10.1016/j.jtbi.2014.02.031},
issn = {1095-8541},
language = {eng},
month = jul,
pmid = {24607743},
year = 2014
}