Analyses reported in Fig. 5 of the main text were performed using BEAST, while those in Fig. 6 were done using MrBayes. Here, I provide a part of the log of a MrBayes analysis with mostly the same settings as the BEAST analysis reported in Fig. 5(a). (The two differ in using differ- ent wide priors on the speciation rate). Comparison of the clade posteriors between the log below and Fig. 5(a) in the main text shows that both software packages correctly sample from essentially one and the same posterior, as expected. Furthermore, the tree height is almost exactly the same (BEAST: [0.1191, 0.1332] 95% HPDI, MrBayes: [0.1196, 0.1333] 95% HPDI), though the inferred speciation rates differ (BEAST: [6.8348, 18.204] 95% HPDI, MrBayes: [3.9682, 10.5462] 95% HPDI.) The difference in the speciation rate goes in the direction we expect it to be given the influence of the prior (the exponential(1) prior in the MrBayes analysis depresses the rate compared to the uniform prior in the BEAST analysis.) Model settings: Data not partitioned -- Datatype = Standard Coding = Noabsencesites # States = Variable, up to 10 State frequencies are fixed to be equal Rates = Equal Active parameters: Parameters ------------------ Statefreq 1 Ratemultiplier 2 Topology 3 Brlens 4 Speciationrate 5 Extinctionrate 6 Clockrate 7 ------------------ 1 -- Parameter = Alpha_symdir Type = Symmetric diricihlet/beta distribution alpha_i parameter Prior = Symmetric dirichlet with fixed(-1.00) variance parameter 2 -- Parameter = Ratemultiplier Type = Partition-specific rate multiplier Prior = Fixed(1.0) 3 -- Parameter = Tau Type = Topology Prior = All topologies equally probable a priori Subparam. = V 4 -- Parameter = V Type = Branch lengths Prior = Clock:Birthdeath Tree age has a Uniform(0,infinity) distribution Node ages are not constrained 5 -- Parameter = Net_speciation Type = Speciation rate Prior = Exponential(1.00) 6 -- Parameter = Relative_extinction Type = Extinction rate Prior = Fixed(0.00) 7 -- Parameter = Clockrate Type = Base rate of clock Prior = Fixed(1.000000) The clock rate is constant (strict clock) <...> List of taxa in bipartitions: 1 -- Finnish 2 -- Karelian 3 -- Veps 4 -- Estonian 5 -- Livonian 6 -- Northern_Sami 7 -- Ume_Sami 8 -- Skolt_Sami 9 -- Erzya_Mordvin 10 -- Meadow_Mari 11 -- Komi-Zyrian 12 -- Udmurt 13 -- Hungarian 14 -- Northern_Mansi 15 -- Eastern_Khanty 16 -- Tundra_Nenets 17 -- Selkup Key to taxon bipartitions (saved to file "Uralic/Full_woProtoU.Yule.codingNoAbs.parts"): ID -- Partition ----------------------- 0 -- ***************** 1 -- *................ 2 -- .*............... 3 -- ..*.............. 4 -- ...*............. 5 -- ....*............ 6 -- .....*........... 7 -- ......*.......... 8 -- .......*......... 9 -- ........*........ 10 -- .........*....... 11 -- ..........*...... 12 -- ...........*..... 13 -- ............*.... 14 -- .............*... 15 -- ..............*.. 16 -- ...............*. 17 -- ................* 18 -- .....***......... 19 -- .............**.. 20 -- ..........**..... 21 -- ...**............ 22 -- ***.............. 23 -- *****............ 24 -- ...............** 25 -- ********......... 26 -- **............... 27 -- .....**.......... 28 -- **********....... 29 -- *********........ 30 -- ............***.. 31 -- ************..... 32 -- .............**** 33 -- ..........*****.. 34 -- ........**....... 35 -- ************...** 36 -- ..........******* 37 -- **********.....** 38 -- ************.**** 39 -- ............***** 40 -- ***************.. 41 -- ..........***.... 42 -- ********.*....... ----------------------- Summary statistics for informative taxon bipartitions (clades) (saved to file "Uralic/Full_woProtoU.Yule.codingNoAbs.tstat"): ID #obs Probab. Sd(s)+ Min(s) Max(s) Nruns ---------------------------------------------------------------- 18 1802 1.000000 0.000000 1.000000 1.000000 2 19 1802 1.000000 0.000000 1.000000 1.000000 2 20 1802 1.000000 0.000000 1.000000 1.000000 2 21 1802 1.000000 0.000000 1.000000 1.000000 2 22 1802 1.000000 0.000000 1.000000 1.000000 2 23 1802 1.000000 0.000000 1.000000 1.000000 2 24 1802 1.000000 0.000000 1.000000 1.000000 2 25 1802 1.000000 0.000000 1.000000 1.000000 2 26 1802 1.000000 0.000000 1.000000 1.000000 2 27 1802 1.000000 0.000000 1.000000 1.000000 2 28 1280 0.710322 0.014126 0.700333 0.720311 2 29 1097 0.608768 0.019620 0.594895 0.622642 2 30 877 0.486681 0.008633 0.480577 0.492786 2 31 545 0.302442 0.018050 0.289678 0.315205 2 32 504 0.279689 0.012557 0.270810 0.288568 2 33 400 0.221976 0.023544 0.205327 0.238624 2 34 374 0.207547 0.009418 0.200888 0.214206 2 35 371 0.205882 0.011772 0.197558 0.214206 2 36 340 0.188679 0.021974 0.173141 0.204218 2 37 322 0.178690 0.003139 0.176471 0.180910 2 38 319 0.177026 0.008633 0.170921 0.183130 2 39 304 0.168701 0.000000 0.168701 0.168701 2 40 295 0.163707 0.013342 0.154273 0.173141 2 41 223 0.123751 0.002354 0.122087 0.125416 2 42 179 0.099334 0.007063 0.094340 0.104329 2 ---------------------------------------------------------------- + Convergence diagnostic (standard deviation of split frequencies) should approach 0.0 as runs converge.