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Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating

Overview of attention for article published in BMC Ecology and Evolution, April 2015
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  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (94th percentile)
  • High Attention Score compared to outputs of the same age and source (91st percentile)

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1 blog
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40 X users
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6 Wikipedia pages

Citations

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194 Dimensions

Readers on

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208 Mendeley
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Title
Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating
Published in
BMC Ecology and Evolution, April 2015
DOI 10.1186/s12862-015-0347-8
Pubmed ID
Authors

Fabien L Condamine, Nathalie S Nagalingum, Charles R Marshall, Hélène Morlon

Abstract

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. 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. 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.

X Demographics

X Demographics

The data shown below were collected from the profiles of 40 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 208 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
France 2 <1%
Canada 2 <1%
Brazil 2 <1%
United States 2 <1%
Mexico 2 <1%
Cameroon 1 <1%
South Africa 1 <1%
Colombia 1 <1%
China 1 <1%
Other 1 <1%
Unknown 193 93%

Demographic breakdown

Readers by professional status Count As %
Researcher 41 20%
Student > Master 34 16%
Student > Ph. D. Student 25 12%
Student > Bachelor 23 11%
Student > Doctoral Student 14 7%
Other 39 19%
Unknown 32 15%
Readers by discipline Count As %
Agricultural and Biological Sciences 125 60%
Biochemistry, Genetics and Molecular Biology 16 8%
Environmental Science 13 6%
Earth and Planetary Sciences 8 4%
Computer Science 3 1%
Other 7 3%
Unknown 36 17%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 33. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 24 March 2024.
All research outputs
#1,217,254
of 25,551,063 outputs
Outputs from BMC Ecology and Evolution
#279
of 3,717 outputs
Outputs of similar age
#14,936
of 280,062 outputs
Outputs of similar age from BMC Ecology and Evolution
#7
of 74 outputs
Altmetric has tracked 25,551,063 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 95th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,717 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 12.5. This one has done particularly well, scoring higher than 92% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 280,062 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 94% of its contemporaries.
We're also able to compare this research output to 74 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 91% of its contemporaries.