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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 Evolutionary Biology, 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)

Mentioned by

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1 blog
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46 tweeters

Citations

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128 Dimensions

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186 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 Evolutionary Biology, 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.

Twitter Demographics

The data shown below were collected from the profiles of 46 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 186 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Mexico 3 2%
United States 2 1%
France 2 1%
Brazil 2 1%
Canada 2 1%
South Africa 1 <1%
Cameroon 1 <1%
China 1 <1%
Colombia 1 <1%
Other 1 <1%
Unknown 170 91%

Demographic breakdown

Readers by professional status Count As %
Researcher 37 20%
Student > Master 34 18%
Student > Bachelor 22 12%
Student > Ph. D. Student 22 12%
Professor > Associate Professor 13 7%
Other 38 20%
Unknown 20 11%
Readers by discipline Count As %
Agricultural and Biological Sciences 120 65%
Biochemistry, Genetics and Molecular Biology 15 8%
Environmental Science 11 6%
Earth and Planetary Sciences 7 4%
Computer Science 3 2%
Other 6 3%
Unknown 24 13%

Attention Score in Context

This research output has an Altmetric Attention Score of 34. 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 16 October 2021.
All research outputs
#823,158
of 19,404,461 outputs
Outputs from BMC Evolutionary Biology
#171
of 2,845 outputs
Outputs of similar age
#12,599
of 239,165 outputs
Outputs of similar age from BMC Evolutionary Biology
#1
of 1 outputs
Altmetric has tracked 19,404,461 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 2,845 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 10.9. This one has done particularly well, scoring higher than 94% 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 239,165 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 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them