SMILE

Stochastic Models for the Inference of Life Evolution

Bibtex

@article{lambert_birthdeath_2013,
Author = {Lambert, Amaury and Stadler, Tanja},
Title = {Birth–death models and coalescent point processes:
{The} shape and probability of reconstructed
phylogenies},
Journal = {Theoretical Population Biology},
Volume = {90},
Pages = {113--128},
abstract = {Forward-in-time models of diversification (i.e.,
speciation and extinction) produce phylogenetic trees
that grow "vertically" as time goes by. Pruning the
extinct lineages out of such trees leads to natural
models for reconstructed trees (i.e., phylogenies of
extant species). Alternatively, reconstructed trees can
be modelled by coalescent point processes (CPPs), where
trees grow "horizontally" by the sequential addition of
vertical edges. Each new edge starts at some random
speciation time and ends at the present time;
speciation times are drawn from the same distribution
independently. CPPs lead to extremely fast computation
of tree likelihoods and simulation of reconstructed
trees. Their topology always follows the uniform
distribution on ranked tree shapes (URT). We
characterize which forward-in-time models lead to URT
reconstructed trees and among these, which lead to CPP
reconstructed trees. We show that for any "asymmetric"
diversification model in which speciation rates only
depend on time and extinction rates only depend on time
and on a non-heritable trait (e.g., age), the
reconstructed tree is CPP, even if extant species are
incompletely sampled. If rates additionally depend on
the number of species, the reconstructed tree is (only)
URT (but not CPP). We characterize the common
distribution of speciation times in the CPP
description, and discuss incomplete species sampling as
well as three special model cases in detail: (1) the
extinction rate does not depend on a trait; (2) rates
do not depend on time; (3) mass extinctions may happen
additionally at certain points in the past.},
doi = {10.1016/j.tpb.2013.10.002},
issn = {00405809},
language = {en},
month = dec,
shorttitle = {Birth–death models and coalescent point processes},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0040580913001056},
urldate = {2015-07-22},
year = 2013
}