Molinier Virginie1, van Tuinen Diederik1, Gollotte Armelle2, Wipf Daniel1, Redecker Dirk1

A multigene phylogeny demonstrates that Tuber aestivum and Tuber uncinatum are conspecific

1 UMR Agroécologie INRA 1347/Agrosup/Université de Bourgogne, Pôle «Interaction Plantes-Micro-organismes» ERL CNRS 6300, 17 rue Sully, BP 86510, 21065 Dijon Cedex, France.

2 Inoplant, 13 rue des Souhaits, 21110 Aiserey, France.

Corresponding authors:

Virginie Molinier

,

Phone number: +33(0)676528078

Supplementary Data 1: Detailed information on the implementation of all phylogenetic methods; Maximum likelihood (1.a) and Bayesian inference (1.b)

Maximum likelihood
Locus / Substition model / negative log likelihood - lnL / Akaike Information Criterion AIC / Number of
bootstrap
β-tubulin / HKY + G / 959.4455 / 2032.8911 / 1000
EF1α / HKY + G / 1707.8306 / 3533.6613 / 1000
ITS1 / HKY + G / 1021.188 / 2160.3767 / 1000
ITS2 / HKY + G / 1153.4642 / 3434.9284 / 1000
mt LSU / GTR + G / 1271.1085 / 2668.217 / 1000
mt SSU / F81 / 414.8745 / 943.7491 / 1000
nu LSU / GTR + G / 1160.3594 / 2446.7187 / 1000
nu SSU / K80 + G / 1000.905 / 2113.81 / 1000
RPB2 7_11 / GTR / 1321.1854 / 2766.3709 / 1000
Super Matrix / GTR + G / 10884.0899 / 21894.1799 / 1000
Bayesian inference
Locus / Substition model / mcmc generations / samplefreq / Average standard deviation of split frequencies / sump / sumt
β-tubulin / HKY + G / 10000000 / 1000 / 0.0066114 / 2500 / 2500
EF1α / HKY + G / 30000000 / 1000 / 0.008392 / 750 / 750
ITS1 / HKY + G / 1000000 / 1000 / 0.008643 / 250 / 250
ITS2 / HKY + G / 1000000 / 1000 / 0.008286 / 250 / 250
mt LSU / GTR + G / 1000000 / 1000 / 0.009510 / 250 / 250
mt SSU / F81 / 10000000 / 1000 / 0.003299 / 2500 / 2500
nu LSU / GTR + G / 1900000 / 1000 / 0.009731 / 475 / 475
nu SSU / K80 + G / 1100000 / 1000 / 0.009131 / 275 / 275
RPB2 7_11 / GTR / 2000000 / 1000 / 0.005810 / 500 / 500
Super Matrix / GTR + G / 2000000 / 1000 / 0.009159 / 500 / 500