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Journal of Biogeography
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Andean uplift drives diversification of the bothriurid scorpion genus Brachistosternus
Journal of Biogeography
Ceccarelli F.S., Ojanguren-Affilastro A.A, Ramírez M.J., Ochoa J.A., Mattoni C.I., Prendini L.
Appendix S2. Supplementary Materials and Methods: Time-calibrated tree-building,
priors and parameters.
A Markov chain Monte Carlo (MCMC) simulation of 100 million generations, sampling
every 5,000 generations, was conducted in two separate runs for the time-calibrated tree
reconstruction in BEAST. The dataset was partitioned by marker and the substitution models
unlinked, applying the appropriate model to each partition, as recommended by the Bayesian
Information Criterion (Schwarz, 1978), implemented in PartitionFinder v. 1.1.1 (Lanfear et al.,
2012). Clock models were also unlinked, applying an uncorrelated lognormal relaxed clock prior to
each partition. As there were no reliable clock rate data for Brachistosternus and the markers used in
this study, default settings for estimated mean clock rates with lognormal distributions were applied,
allowing for auto-optimisation as the runs progressed. Tree models were linked for the
mitochondrial markers and separately unlinked for the mitochondrial and each of the two nuclear
markers, considering the possibility of different genealogical histories for the two sources of DNA,
and a birth-death tree prior applied to all three partitions. Another set of MCMC runs was carried
out with the clock model prior linked for the mitochondrial gene markers, modelling evolutionary
rates across the entire mitochondrial partition.
Preliminary MCMC runs with an empty alignment were executed in BEAST to observe the
effect of the chosen priors on each other, as suggested by the program developers. TreeAnnotator
v.1.8.2 (Drummond et al., 2012) was used to choose the maximum clade credibility trees with the
“mean node heights” option applied to the 20,000 output trees from each of the two BEAST runs
combined in LogCombiner v1.8.2, with the first 5,000 trees from each run discarded as burn-in after
verifying the correct “mixing” of chains in Tracer v. 1.5, and establishing that the effective sample
sizes of the parameters were greater than 200. Tracer was also used to compare the likelihoods of
runs with mitochondrial clock rate priors linked and unlinked. Additionally, separate MCMC runs
were conducted for each marker in BEAST, to determine the genealogy and relative contribution to
the topological resolution of each marker, as well as an analysis with all markers linked for the tree
models, to obtain a single dated topology.
Based on the likelihood scores of the runs and ESS values, the rate obtained from the timecalibrated tree for the mitochondrial partition as a whole (i.e., with the three mitochondrial markers
linked) was used as a prior for the species tree analysis (see main text). BEAST was used for
calibrating molecular rates with node age constraints rather than *BEAST which did not initialise
with the calibration priors. Refer to the main text for information on the node age constraint for
calibrating molecular rates.
References
Drummond, A.J., Suchard, M.A., Xie, D. & Rambaut A. (2012) Bayesian phylogenetics with
BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 29, 1969–1973.
Lanfear, R., Calcott, B., Ho, S.Y.W. & Guindon, S. (2012) PartitionFinder: Combined selection of
partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology
and Evolution, 29, 1695–1701.
Schwarz, G. (1978) Estimating the dimension of a model. Annals of Statistics, 6, 461–464.