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Table 2 Testing for diversification rate variation models by ∆AICRC test statistic

From: Nuclear and chloroplast DNA phylogeography suggests an Early Miocene southward expansion of Lithocarpus (Fagaceae) on the Asian continent and islands

ModelLog-likelihoodAICParameter
Both cpDNA and nrITS (Fig. 2a)
 PureBirth− 2.34196.684r1 = 0.101
 bd− 1.6821217.364r1 = 0.076, a = 0.405
 DDX− 1.9721697.944r1 = 0.065, x = − 0.136
 DDL− 2.3428.684r1 = 0.101, k = 1,168,951
 yule2rate− 1.0838.166r1 = 0.0687, r2 = 0.112, st1 = 14.894
 yule3rate1.8716.258r1 = 0.087, r2 = 9.936, r3 = 0.115, st1 = 5.939, st2 = 5.936
 ∆AICRC 0.426 
cpDNA (Fig. 3)
 PureBirth25.97718− 49.95435r1 = 0.120
 bd26.15159− 48.30319r1 = 0.105, a = 0.220
 DDX26.19223− 48.38446r1 = 0.091, x = − 0.082
 DDL25.97713− 47.95426r1 = 0.120, k = 1,428,290
 yule2rate27.806− 49.612r1 = 0.063, r2 = 0.130, st1 = 15.636
 yule3rate31.18926− 52.37852r1 = 0.063, r2 = 0.665, r3 = 0.124, st1 = 15.636, st2 = 15.017
 ∆AICRC 2.424 
nrITS (Fig. 4)
 PureBirth− 5.87024913.7405r1 = 0.086
 bd− 4.30351112.60702r1 = 0.058, a = 0.532
 DDX− 5.69561815.39124r1 = 0.061, x = − 0.105
 DDL− 5.87044315.74089r1 = 0.086, k = 1,284,297
 yule2rate− 2.42648610.85297r1 = 0.073, r2 = 0.148, st1 = 2.380
 yule3rate1.1895857.62083r1 = 0.075, r2 = 0.471, r3 = 0.112, st1 = 1.713, st2 = 1.457
 ∆AICRC 4.986 
cpDNA (Additional file 1: Figure S1A)
 PureBirth103.309− 204.617r1 = 0.121
 bd107.116− 210.231r1 = 0.076, a = 0.574
 DDX106.169− 208.338r1 = 0.046, x = − 0.251
 DDL103.308− 202.616r1 = 0.121, k = 2,195,621
 yule2rate108.500− 211.000r1 = 0.084, r2 = 0.153, st1 = 7.286
 yule3rate112.757− 215.514r1 = 0.095, r2 = 0.184, r3 = 0.024, st1 = 4.059, st2 = 0.328
 ∆AICRC 5.283 
nrITS (Additional file 1: Figure S1B)
 PureBirth27.403− 52.806r1 = 0.110
 bd31.284− 58.568r1 = 0.060, a = 0.667
 DDX29.731− 55.463r1 = 0.038, x = − 0.306
 DDL21.496− 38.991r1 = 0.140, k = 174
 yule2rate31.106− 56.213r1 = 0.103, r2 = 0.368, st1 = 0.227
 yule3rate34.049− 58.096r1 = 0.093, r2 = 9.384, r3 = 0.172, st1 = 2.055, st2 = 2.053
 ∆AICRC − 0.471 
  1. r1, r2, r3, net diversification rates at stages 1, 2, and 3; st1 and st2, the first and the second rate-shift times; a, the extinction fraction extinction rate/speciation rate; x, the x parameter in the density-dependent exponetial model; k, the K parameter in the logistic density dependent model
  2. PureBirth pure birth (Yule) model, bd rate-constant birth–death model, DDX and DDL exponential and logistic variants of the density-dependent speciation rate models, respectively, yule2rate and yule3rate multi-rate variants of the pureBirth model, ∆AICRC the difference in AIC score between the best rate-constant (AICRC) and rate-variable (AICRV) models. The overall best-fit models were indicated with italic AIC value