Extended Data Figure 3. Substitution rate and tMRCA distributions.

a, Posterior density of the substitution rate. Shown with and without the use of sequences (outgroup) from outside the Americas. b–e, Posterior density of the date of the most recent common ancestor (MRCA) of sequences in four regions corresponding to those in Fig. 2c. Shown with and without the use of outgroup sequences. The use of outgroup sequences has little effect on estimates of these dates. f, Posterior density of the date of the MRCA of sequences in a clade consisting of samples from the Caribbean and continental United States. Shown with and without the sequence of DOM_2016_MA-WGS16-020-SER, a sample from the Dominican Republic that has only 3,037 unambiguous bases; this is the most ancestral sequence in the clade and its presence affects the tMRCA. In all panels, all densities are shown as observed with a relaxed clock model and with a strict clock model.