Abstract
BackgroundBayesian relaxed-clock dating has significantly influenced our understanding of the timeline of biotic 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.ResultsUsing 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.ConclusionsThese 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0347-8) contains supplementary material, which is available to authorized users.
Highlights
Bayesian relaxed-clock dating has significantly influenced our understanding of the timeline of biotic evolution
“Cycads are to the vegetable kingdom what Dinosaurs are to the animal, each representing the culmination in Mesozoic times of the ruling Dynasties in the life of their age.”
Nodes within genus radiations were recovered with lower posterior probabilities (PP), which was expected because the genetic divergence among cycad species within genera is low (Cycas: [95,96]; Ceratozamia: [52]; Dioon: [56]; Encephalartos: [97]; Macrozamia: [98]; Zamia: [99])
Summary
Bayesian relaxed-clock dating has significantly influenced our understanding of the timeline of biotic evolution This approach requires the use of priors on the branching process, yet little is known about their impact on divergence time estimates. The advent of molecular dating approaches has fostered an explosion of studies constructing time-calibrated trees for diverse plant clades like bryophytes [2], ferns [3,4], gymnosperms [5,6,7,8] and angiosperms [9,10,11] These dated trees have permitted the study of character evolution via the reconstruction of ancestral traits [11], inference of biogeographical history [7], as well as estimates of diversification rates. The use of explicit prior distributions is central to the Bayesian perspective; the critical role of prior selection in Bayesian analysis is not always fully appreciated [17]
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