trnL-trnF cp DNA sequences from Pilea (Urticaceae)

Published: 9 August 2023| Version 1 | DOI: 10.17632/xhzgb287vd.1
Andrés Ernesto Ortiz-Rodriguez


The 76-accession dataset used for BEAST analyses in Lagos-Báez et al. (in process of publication)


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Divergence times were estimated under a Bayesian approach as implemented in BEAST v.1.8.1 (Drummond & Rambaut, 2007) using the trnL-F dataset. We include various representatives of Pilea and related genera of Urticaceae as available in the supplementary material of Fu et al. (2022). The 76-accession dataset (including 30 new sequences from Pilea pteridophylla) was prepared for BEAST using BEAUti with the optimum model setting determined by the results of jModeltest (Darriba et al., 2012). We used a lognormal calibration prior distribution, which assigned the highest probabilities to substantially older ages than the calibrated ages accounting for errors associated with the incompleteness and limited knowledge of the Urticaceae fossil record. In this way, the Urticaceae crown group was calibrated using the estimated mean age for the family (68.7 Ma; Wu et al., 2018) as offset and the shape of the lognormal distribution was defined with a median of 74.4 Ma and a 95 % probability interval between 69 and 136.4 Ma, using the unequivocal Angiosperm crown group pollen grain fossils (Hughes, 1994; Friis et al., 2010) as soft upper bound (offset: 68.7, mean: 17.6, log (Stdev): 1.5). An uncorrelated lognormal relaxed molecular clock (UCLD) and the Yule speciation tree prior were applied to all partitions. We ran 20 million generations for the cpDNA data set of the MCMC chain, with a sampling frequency of 1000 generations. Convergence of the posterior distributions of the parameters was evaluated by monitoring the effective sample sizes (ESS > 200) and trace plots in Tracer ( are/tracer/). A maximum credibility tree, which represents the maximum posterior topology, was calculated in TreeAnnotator (Drummond & Rambaut, 2007) after discarding the first 10 % of trees as burn-in.


Universidad Nacional Autonoma de Mexico


Genetics, Taxonomy, Angiosperm, Phylogeny