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Text Supplement: Trees & Comments Alexei S. Kassian ([email protected]), Mikhail Zhivlov, George Starostin, Artem A. Trofimov, Petr A. Kocharov, Anna Kuritsyna and Mikhail N. Saenko Rapid radiation of the Inner Indo-European languages: an advanced approach to Indo- European lexicostatistics Linguistics 59, 2021, https://doi.org/10.1515/ling-2020-0060 Text supplement: trees & comments 1. MrBayes commands .................... 2 2. Phylogenetic trees obtained by individual algorithms • StarlingNJ (Fig. S1a–f) ................ 3 • Bayesian MCMC (Fig. S2a–f) .............. 4 • Maximum parsimony (Fig. S3a–f) ............ 5 • DensiTree plots (Fig. S4-6) ............... 6 3. Bipartitions and their posterior probabilities for the Bayesian analysis 9 4. Basic information on the language groups ........... 10 5. Dating of the nodes and chronological constraints ........ 15 6. Linguistic comments on individual Swadesh forms ........ 19 7. Overview of lexical innovations in some Inner IE clades (Greek-Armenian, Balto-Slavic–Indo-Iranian, Italic-Germanic-Celtic) 110 8. Supplement references .................. 112 1 MrBayes commands The following commands for the MrBayes package were applied: FORMAT DATATYPE=RESTRICTION GAP=- MISSING=? lset coding=noabsencesites rates=gamma covarion=yes; calibrate Old_Hittite = uniform(3500, 3650); calibrate Tocharian_B = uniform(1100, 1600); calibrate Ancient_Attic_Greek = fixed(2375); calibrate Classical_Armenian = uniform(1500, 1600); calibrate Archaic_Latin = fixed(2200); calibrate Old_Irish = uniform(1100, 1300); calibrate Proto_Brittonic = uniform(1400, 1700); calibrate Proto_Germanic = uniform(2300, 2500); calibrate Proto_Slavic = uniform(1700, 2000); calibrate Proto_East_Baltic = uniform(2000, 2400); calibrate Old_Indic_Atharvaveda = uniform(3000, 3200); calibrate Proto_Iranian = uniform(3000, 3500); calibrate Albanian = fixed(50); prset clockratepr=exponential(3e5); prset speciationpr=exp(1); prset extinctionpr=beta(1,1) nodeagepr=calibrated; prset brlenspr=clock:fossilization clockvarpr=TK02; prset treeagepr = uniform(5500,10500); prset samplestrat=fossiltip; showmodel; mcmcp ngen=10000000 printfreq=10000 samplefreq=500 nruns=4 nchains=4 savebrlens=yes; mcmc; sumt relburnin=yes burninfrac=0.25; sump relburnin=yes burninfrac=0.25; 2 Phylogenetic trees obtained by individual algorithms (a) (b) Old Hittite Old Hittite Tokharian B −7080 Tokharian B Classical Armenian −7080 Albanian −6480 −5380 Anc ient At tic Greek 36 Classical Armenian 46 −5380 −5820 Proto-Slavic −6480 Anc i e nt At t ic Gr ee k −4140 Proto-East Baltic Archaic Latin Archaic Latin 37 Proto-Germanic −4920 −5030 −5770 Proto-Germanic 56 Old Irish −5700 −5140 −3260 Old Irish Proto-Brittonic −3260 −5700 Proto-Brittonic Proto-Slavic −4140 Albanian Proto-East Baltic −5650 Old Indic (Atharvaveda) Old Indic (Atharvaveda) −4150 −4150 Proto-Iranian Proto-Iranian -7000 -6000 -5000 -4000 -3000 -2000 -1000 yBP 0 -7000 -6000 -5000 -4000 -3000 -2000 -1000 yBP 0 (c) (d) Old Hittite Old Hittite Tokharian B Tokharian B −7080 −7080 Classical Armenian Albanian −6700 −5460 Ancient Att ic Greek 31 46 Classical Armenian −6700 −5460 Anc i e nt At t ic Gree k −6220 ArchaicLatin −4920 Proto-Germanic 53 Archaic Latin 42 −4920 −5500 −6100 Proto-Germanic Old Irish 20 −3500 −5500 Proto-Brittonic Old Irish −6180 −3500 Albanian Proto-Brittonic Proto-Slavic 94 Proto-Slavic −6000 −4390 −4390 Proto-East Baltic Proto-East Baltic 14 −5570 −5570 Old Indic (Atharvaveda) Old Indic (Atharvaveda) −4230 −4230 Proto-Iranian Proto-Iranian -7000 -6000 -5000 -4000 -3000 -2000 -1000 yBP 0 -7000 -6000 -5000 -4000 -3000 -2000 -1000 yBP 0 (e) (f) Old Hittite Old Hittite Tokharian B Tokharian B −7110 −7110 Classical Armenian Albanian −6710 −5460 47 Classical Armenian Ancient Attic Greek 34 −6710 −5460 Anc i e nt At t ic Gr ee k −6220 Archaic Latin −4920 Archaic Latin Proto-Germanic 66 41 −4920 −5540 −6150 Proto-Germanic Old Irish 23 −3570 −5540 Old Irish Proto-Brittonic −6180 −3570 Albanian Proto-Brittonic Proto-Slavic 93 Proto-Slavic −6060 −4450 −4450 Proto-East Baltic 21 Proto-East Baltic −5570 −5570 Old Indic (Atharvaveda) Old Indic (Atharvaveda) −4230 −4230 Proto-Iranian Proto-Iranian -7000 -6000 -5000 -4000 -3000 -2000 -1000 yBP 0 -7000 -6000 -5000 -4000 -3000 -2000 -1000 yBP 0 Fig. S1. Phylogenetic trees of the Indo-European language family produced by the StarlingNJ method from the multi- state matrix. Bootstrap values for the trees (b), (d), (f) are shown in italic near the branches (not shown for stable nodes with bootstrap value ≥ 95%). The trees are dated. Divergence times are given to the right of each node. Datasets with and without the Proto-Samoyed outgroup produce identical topologies and dates, thus only the trees for the proper Indo- European dataset are offered. Traditional subgroups are identified by color branches. • Stage-1 dataset with root cognacy (wind = veter, agni = ignis): (a) binary nodes; (b) neighboring nodes are joined if the distance between them is ≤ 300 years. • Stage-2 dataset without derivational drift (wind ≠ veter, agni = ignis): (c) binary nodes; (d) neighboring nodes are joined if the distance between them is ≤ 300 years. • Stage-3 homoplasy-optimized dataset (wind ≠ veter, agni ≠ ignis): (e) binary nodes; (f) neighboring nodes are joined if the distance between them is ≤ 300 years. For Stage-2 and Stage-3, no topological discrepancies between the trees, i.e., within the pairs (c) & (e), (d) & (f). 3 (a) (b) Proto_Samoyed Old_Hittite Old_Hittite Tocharian_B 11011.56 5757.62 Tocharian_B Ancient_Attic_Greek 0.86 3982.38 5793.55 Ancient_Attic_Greek 0.85 Classical_Armenian 4157.17 4903.69 Classical_Armenian Archaic_Latin 0.74 0.55 5217.874638.24 Archaic_Latin Proto_Germanic 4077.85 0.52 4202.87 Proto_Germanic 4806.84 Old_Irish Old_Irish 2208.09 0.88 2278.38 Proto_Brittonic 4872.16 Proto_Brittonic Albanian Albanian Proto_Slavic Proto_Slavic 0.61 3233.23 0.79 4457.47 4514.65 3294.66 Proto_East_Baltic Proto_East_Baltic Old_Indic_Atharvaveda Old_Indic_Atharvaveda 3792.39 3808.99 Proto_Iranian Proto_Iranian -7000 -6000 -5000 -4000 -3000 -2000 -1000 -14000 -13000 -12000 -11000 -10000 -9000 -8000 -7000 -6000 -5000 -4000 -3000 -2000 -1000 (c) (d) Proto_Samoyed Old_Hittite Old_Hittite Tocharian_B 10781.34 5747.77 Tocharian_B Albanian 5628.42 Albanian 0.7 Ancient_Attic_Greek 4974.48 0.89 3986.49 0.56 Ancient_Attic_Greek 5142.44 Classical_Armenian 4079.14 Classical_Armenian Archaic_Latin 0.65 Archaic_Latin 4802.25 0.9 0.88 Proto_Germanic 4803.96 4128.44 0.9 4190.29 Proto_Germanic Old_Irish Old_Irish 2217.53 2263.93 Proto_Brittonic Proto_Brittonic Proto_Slavic Proto_Slavic 3331.58 3358.94 Proto_East_Baltic 0.69 0.77 Proto_East_Baltic 4366.44 4370.82 Old_Indic_Atharvaveda Old_Indic_Atharvaveda 3763.26 3761.56 Proto_Iranian Proto_Iranian -6000 -5000 -4000 -3000 -2000 -1000 -12000 -11000 -10000 -9000 -8000 -7000 -6000 -5000 -4000 -3000 -2000 -1000 (e) (f) Proto_Samoyed Old_Hittite Old_Hittite 10611.01 Tocharian_B Tocharian_B 5686.92 Ancient_Attic_Greek 5486.33 0.94 4015.39 Ancient_Attic_Greek 4019.09 0.7 Classical_Armenian 5011.9 0.61 Classical_Armenian 5032.25 Archaic_Latin Archaic_Latin Proto_Germanic 4080.98 0.8 4054.39 Proto_Germanic 4717.67 4657.36 Old_Irish Old_Irish 2243.16 2257.17 Proto_Brittonic Proto_Brittonic Albanian Albanian 0.54 Proto_Slavic 0.59 Proto_Slavic 4371.67 4320.16 3250.52 3245.92 Proto_East_Baltic Proto_East_Baltic 0.76 0.73 4241.16 4205.11 Old_Indic_Atharvaveda Old_Indic_Atharvaveda 3740.37 3724.95 Proto_Iranian Proto_Iranian -6000 -5000 -4000 -3000 -2000 -1000 0 -12000 -11000 -10000 -9000 -8000 -7000 -6000 -5000 -4000 -3000 -2000 -1000 Fig. S2. Phylogenetic trees of the Indo-European language family produced by the Bayesian MCMC method from the binary matrix in the MrBayes software (50% majority rule trees). No topological constraints. No chronological constraints for intermediate nodes; root is predefined within the range 10,500–5,500 yBP (for the proper IE dataset) and with the upper limit 10,000 yBP and mean 20,000 yBP (for the IE-Samoyed dataset). Bayesian posterior probabilities are shown in italic near the branches (not shown for stable branches with P ≥ 0.95). Blue bars represent the 95% highest probability density (HPD) for the divergence times; mean divergence times are given to the right of each node. Scale values repre- sent years before present (yBP). Traditional subgroups are identified by color branches. • Stage-1 dataset with root cognacy (wind = veter, agni = ignis): (a) proper IE, (b) IE-Samoyed. • Stage-2 dataset without derivational drift (wind ≠ veter, agni = ignis): (c) proper IE, (d) IE-Samoyed. • Stage-3 homoplasy-optimized dataset (wind ≠ veter, agni ≠ ignis): (e) proper IE, (f) IE-Samoyed. For Stage-2 and Stage-3, no topological discrepancies with and without Proto-Samoyed, i.e., within the pairs (c) & (d), (e) & (f). For Stage-1, topological discrepancies between (a) & (b) are insignificant. 4 (a) (b) Old_Hittite Proto_Samoyed Tocharian_B Old_Hittite Albanian Tocharian_B Ancient_Attic_Greek 93 Classical_Armenian 50 Ancient_Attic_Greek 62 Classical_Armenian 70 Archaic_Latin Archaic_Latin 28 24 Proto_Germanic Proto_Germanic 39 22 Old_Irish Old_Irish Proto_Brittonic Proto_Brittonic Albanian Proto_Slavic 10 Proto_Slavic Proto_East_Baltic 23 28 Proto_East_Baltic Old_Indic_Atharvaveda Old_Indic_Atharvaveda Proto_Iranian Proto_Iranian (c) (d) Old_Hittite Proto_Samoyed Tocharian_B Old_Hittite Tocharian_B Albanian Albanian Ancient_Attic_Greek 94 52 Ancient_Attic_Greek 34 60 Classical_Armenian 67 Classical_Armenian Archaic_Latin 41 Old_Irish Proto_Germanic
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