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

Yang, Chih-Kai; Chiang, Yu-Chung; Huang, Bing-Hong; Ju, Li-Ping; Liao, Pei-Chun

doi:10.1186/s40529-018-0244-8

Botanical Studies

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

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

Model	Log-likelihood	AIC	Parameter
Both cpDNA and nrITS (Fig. 2a)
PureBirth	− 2.3419	6.684	r1 = 0.101
bd	− 1.682121	7.364	r1 = 0.076, a = 0.405
DDX	− 1.972169	7.944	r1 = 0.065, x = − 0.136
DDL	− 2.342	8.684	r1 = 0.101, k = 1,168,951
yule2rate	− 1.083	8.166	r1 = 0.0687, r2 = 0.112, st1 = 14.894
yule3rate	1.871	6.258	r1 = 0.087, r2 = 9.936, r3 = 0.115, st1 = 5.939, st2 = 5.936
∆AIC_RC		0.426
cpDNA (Fig. 3)
PureBirth	25.97718	− 49.95435	r1 = 0.120
bd	26.15159	− 48.30319	r1 = 0.105, a = 0.220
DDX	26.19223	− 48.38446	r1 = 0.091, x = − 0.082
DDL	25.97713	− 47.95426	r1 = 0.120, k = 1,428,290
yule2rate	27.806	− 49.612	r1 = 0.063, r2 = 0.130, st1 = 15.636
yule3rate	31.18926	− 52.37852	r1 = 0.063, r2 = 0.665, r3 = 0.124, st1 = 15.636, st2 = 15.017
∆AIC_RC		2.424
nrITS (Fig. 4)
PureBirth	− 5.870249	13.7405	r1 = 0.086
bd	− 4.303511	12.60702	r1 = 0.058, a = 0.532
DDX	− 5.695618	15.39124	r1 = 0.061, x = − 0.105
DDL	− 5.870443	15.74089	r1 = 0.086, k = 1,284,297
yule2rate	− 2.426486	10.85297	r1 = 0.073, r2 = 0.148, st1 = 2.380
yule3rate	1.189585	7.62083	r1 = 0.075, r2 = 0.471, r3 = 0.112, st1 = 1.713, st2 = 1.457
∆AIC_RC		4.986
cpDNA (Additional file 1: Figure S1A)
PureBirth	103.309	− 204.617	r1 = 0.121
bd	107.116	− 210.231	r1 = 0.076, a = 0.574
DDX	106.169	− 208.338	r1 = 0.046, x = − 0.251
DDL	103.308	− 202.616	r1 = 0.121, k = 2,195,621
yule2rate	108.500	− 211.000	r1 = 0.084, r2 = 0.153, st1 = 7.286
yule3rate	112.757	− 215.514	r1 = 0.095, r2 = 0.184, r3 = 0.024, st1 = 4.059, st2 = 0.328
∆AIC_RC		5.283
nrITS (Additional file 1: Figure S1B)
PureBirth	27.403	− 52.806	r1 = 0.110
bd	31.284	− 58.568	r1 = 0.060, a = 0.667
DDX	29.731	− 55.463	r1 = 0.038, x = − 0.306
DDL	21.496	− 38.991	r1 = 0.140, k = 174
yule2rate	31.106	− 56.213	r1 = 0.103, r2 = 0.368, st1 = 0.227
yule3rate	34.049	− 58.096	r1 = 0.093, r2 = 9.384, r3 = 0.172, st1 = 2.055, st2 = 2.053
∆AIC_RC		− 0.471

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
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, ∆AIC_RC the difference in AIC score between the best rate-constant (AIC_RC) and rate-variable (AIC_RV) models. The overall best-fit models were indicated with italic AIC value

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