Xanthium strumarium Divergence Time

Manzo, Eleonora & Tomasello, Salvatore, 2025, Recent Long-Distance-Dispersal Explains the Range Disjunction of the Old-Word Cockleburs (Xanthium strumarium), Journal of Biogeography (e 15104) 52 (5), pp. 1-16 : 7

2.5 | Xanthium strumarium Divergence Time

We used the concatenated dataset with the 732 regions obtained in the previous step and 26 samples from all recognised species of the genus ( Table 1). Input files for Beast2 ( Bouckaert et al. 2019) were prepared using BEAUti v.2.7.6 ( Bouckaert et al. 2019) and the “beast” template. We used the GTR + G as sequence substitution model, letting Beast2 optimise model parameters. The “Random Local Clock” was selected as clock model. In order to obtain absolute divergence times, we followed the approach used in Tomasello et al. (2020) and gave both an informative prior on the clock rate and a calibration point. Accordingly, we gave the “clockrates” a uniform distribution (min: 5.0 e− 5, max: 5.0 e− 7) with an initial value of 5.0 e− 6. Assuming a standard substitution rate of 5 e− 9 in plants (Wolfe et al. 1989), and since Xanthium plants are annuals, the clock rate will result in 5 e−6 mutations per site per thousand years (± an order of magnitude). As for the calibration point, we based it on the oldest Xanthium fossil, consisting of bur fragments found in Indiana ( USA) and dating back to the Upper Hemphillian/Blancan North American stages ( Farlow et al. 2001). Therefore, we applied to the root of the tree a lognormal prior distribution with mean 3.0 and standard deviation 2.9 (95% highest prior density ranging between 3000 and 8910 thousand years ago (ka)).

We ran two analyses for 100,000,000 generations, sampling every 10,000 iterations. Convergence between different analyses and effective sample size (ESS) were checked in Tracer v.1.7 (Rambaut et al. 2018). The tree files from the two independent runs were combined using LogCombiner v.2.7 ( Bouckaert et al. 2019). Finally, a maximum clade credibility tree was calculated in TreeAnnotator v.2.6 ( Bouckaert et al. 2019), applying 10% burn-in, a posterior probability limit of 0.5, and “Mean Heights” for node heights. Additional sets of analyses were performed using only the clock rates prior or the fossil calibration. This was done to assess the effect of using both calibration and clock-rate priors in the same analysis.