@article{condamine_origin_2015,
Author = {Condamine, Fabien L. and Nagalingum, Nathalie S. and
Marshall, Charles R. and Morlon, Hélène},
Title = {Origin and diversification of living cycads: a
cautionary tale on the impact of the branching process
prior in {Bayesian} molecular dating},
Journal = {BMC evolutionary biology},
Volume = {15},
Number = {1},
Pages = {65},
abstract = {BACKGROUND: Bayesian relaxed-clock dating has
significantly influenced our understanding of the
timeline of plant evolution. This approach requires the
use of priors on the branching process, yet little is
known about their impact on divergence time estimates.
We investigated the effect of branching priors using
the iconic cycads. We conducted phylogenetic
estimations for 237 cycad species using three genes and
two calibration strategies incorporating up to six
fossil constraints to (i) test the impact of two
different branching process priors on age estimates,
(ii) assess which branching prior better fits the data,
(iii) investigate branching prior impacts on
diversification analyses, and (iv) provide insights
into the diversification history of cycads. RESULTS:
Using Bayes factors, we compared divergence time
estimates and the inferred dynamics of diversification
when using Yule versus birth-death priors. Bayes
factors were calculated with marginal likelihood
estimated with stepping-stone sampling. We found
striking differences in age estimates and
diversification dynamics depending on prior choice.
Dating with the Yule prior suggested that extant cycad
genera diversified in the Paleogene and with two
diversification rate shifts. In contrast, dating with
the birth-death prior yielded Neogene diversifications,
and four rate shifts, one for each of the four richest
genera. Nonetheless, dating with the two priors
provided similar age estimates for the divergence of
cycads from Ginkgo (Carboniferous) and their crown age
(Permian). Of these, Bayes factors clearly supported
the birth-death prior. CONCLUSIONS: These results
suggest the choice of the branching process prior can
have a drastic influence on our understanding of
evolutionary radiations. Therefore, all dating analyses
must involve a model selection process using Bayes
factors to select between a Yule or birth-death prior,
in particular on ancient clades with a potential
pattern of high extinction. We also provide new
insights into the history of cycad diversification
because we found (i) periods of extinction along the
long branches of the genera consistent with fossil
data, and (ii) high diversification rates within the
Miocene genus radiations.},
doi = {10.1186/s12862-015-0347-8},
issn = {1471-2148},
language = {ENG},
month = apr,
pmid = {25884423},
shorttitle = {Origin and diversification of living cycads},
year = 2015
}
Author = {Condamine, Fabien L. and Nagalingum, Nathalie S. and
Marshall, Charles R. and Morlon, Hélène},
Title = {Origin and diversification of living cycads: a
cautionary tale on the impact of the branching process
prior in {Bayesian} molecular dating},
Journal = {BMC evolutionary biology},
Volume = {15},
Number = {1},
Pages = {65},
abstract = {BACKGROUND: Bayesian relaxed-clock dating has
significantly influenced our understanding of the
timeline of plant evolution. This approach requires the
use of priors on the branching process, yet little is
known about their impact on divergence time estimates.
We investigated the effect of branching priors using
the iconic cycads. We conducted phylogenetic
estimations for 237 cycad species using three genes and
two calibration strategies incorporating up to six
fossil constraints to (i) test the impact of two
different branching process priors on age estimates,
(ii) assess which branching prior better fits the data,
(iii) investigate branching prior impacts on
diversification analyses, and (iv) provide insights
into the diversification history of cycads. RESULTS:
Using Bayes factors, we compared divergence time
estimates and the inferred dynamics of diversification
when using Yule versus birth-death priors. Bayes
factors were calculated with marginal likelihood
estimated with stepping-stone sampling. We found
striking differences in age estimates and
diversification dynamics depending on prior choice.
Dating with the Yule prior suggested that extant cycad
genera diversified in the Paleogene and with two
diversification rate shifts. In contrast, dating with
the birth-death prior yielded Neogene diversifications,
and four rate shifts, one for each of the four richest
genera. Nonetheless, dating with the two priors
provided similar age estimates for the divergence of
cycads from Ginkgo (Carboniferous) and their crown age
(Permian). Of these, Bayes factors clearly supported
the birth-death prior. CONCLUSIONS: These results
suggest the choice of the branching process prior can
have a drastic influence on our understanding of
evolutionary radiations. Therefore, all dating analyses
must involve a model selection process using Bayes
factors to select between a Yule or birth-death prior,
in particular on ancient clades with a potential
pattern of high extinction. We also provide new
insights into the history of cycad diversification
because we found (i) periods of extinction along the
long branches of the genera consistent with fossil
data, and (ii) high diversification rates within the
Miocene genus radiations.},
doi = {10.1186/s12862-015-0347-8},
issn = {1471-2148},
language = {ENG},
month = apr,
pmid = {25884423},
shorttitle = {Origin and diversification of living cycads},
year = 2015
}