Fig. 10.
Posterior means and 95% HPD CIs for the 16 parameters in the MSC model on species tree 1 (fig. 7) in analyses of the gibbon datasets under different clock models. Estimates of θs and τs are multiplied by 103. Each panel includes two replicate runs under six clock models as in figure 8, specified by (1) clock = 1 (strict clock, one rate for all loci); (2) locusrate = 1 0 0 5 iid, clock = 1 (strict clock, i.i.d. rates μi among loci); (3) locusrate = 1 0 0 5 iid, clock = 2 10 100 5 iid LN (clock 2, i.i.d. prior for μi and νi among loci, and log-normal kernel); (4) locusrate = 1 0 0 5 iid, clock = 2 10 100 5 iid G (clock 2, i.i.d. prior for μi and νi among loci, and gamma kernel); (5) locusrate = 1 0 0 5 dir, clock = 2 10 100 5 dir LN (clock 2, dir prior for μi and νi among loci, and log-normal kernel); (6) locusrate = 1 0 0 5 dir, clock = 2 10 100 5 dir G (clock 2, dir prior for μi and νi among loci, and gamma kernel). The panel for ν¯ shows two replicate runs for each of the four clock-2 analyses.

Posterior means and 95% HPD CIs for the 16 parameters in the MSC model on species tree 1 (fig. 7) in analyses of the gibbon datasets under different clock models. Estimates of θs and τs are multiplied by 103. Each panel includes two replicate runs under six clock models as in figure 8, specified by (1) clock = 1 (strict clock, one rate for all loci); (2) locusrate = 1 0 0 5 iid, clock = 1 (strict clock, i.i.d. rates μi among loci); (3) locusrate = 1 0 0 5 iid, clock = 2 10 100 5 iid LN (clock 2, i.i.d. prior for μi and νi among loci, and log-normal kernel); (4) locusrate = 1 0 0 5 iid, clock = 2 10 100 5 iid G (clock 2, i.i.d. prior for μi and νi among loci, and gamma kernel); (5) locusrate = 1 0 0 5 dir, clock = 2 10 100 5 dir LN (clock 2, dir prior for μi and νi among loci, and log-normal kernel); (6) locusrate = 1 0 0 5 dir, clock = 2 10 100 5 dir G (clock 2, dir prior for μi and νi among loci, and gamma kernel). The panel for ν¯ shows two replicate runs for each of the four clock-2 analyses.

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