Additional file
Tables
Table S1. Loci used in this study
Table S2. Summary statistics and neutrality tests of populations at species boundaries
Table S3. Other priors tested in IMa2
Table S4. Model evaluation for ecological niche modeling
Figures
Figure S1. Locations of occurrence data used for ecological niche modeling
Figure S2. Projection of current and past distribution of R. palmatus and R. grayanus using the
Maxent
Tables
Table S1. Loci used in this study
Loci used and summary statistics at species boundaries and contact zone (Table 1). The putative gene functions are annotated based on the database of
Arabidopsis thaliana reference proteins (min. threshold e-value was less than 10-20). bp: total length of sequence used for analysis; n(total) the total number
of phased sequences; S: the total number of segregating sites; fixed S: the number of segregating sites between species that are fixed within a species; FST :
population differentiation. COP1- and GSTF-homolog gene sequences included non-coding regions. Asterisk indicates chloroplast DNA region.
Contact Zones
putative gene
function
bp
n
S
number of
haplotype
θ(total)
π(total)
CO
305
154
6
9
0.0041
0.0067
COP1
276
158
5
6
0.0032
0.0046
CCNB1
hypothetical
protein
ETR
118
158
4
4
0.0060
0.0122
482
160
9
8
0.0035
0.0070
258
328
154
158
3
7
4
4
0.0021
0.0037
0.0026
0.0077
349
639
158
158
7
9
10
7
0.0036
0.0025
0.0054
0.0042
PHYA
416
362
160
158
10
7
5
6
0.0042
0.0034
0.0107
0.0077
PAL4
603
160
15
13
0.0044
0.0054
LDOX
393
154
4
4
0.0018
0.0035
PHR2
518
158
9
11
0.0038
0.0045
EXPA
237
160
4
5
0.0030
0.0047
XET
248
160
5
5
0.0036
0.0067
hypothetical
protein
276
154
2
3
0.0013
0.0034
IAA
351
160
3
4
0.0015
0.0026
TrnH_psbA*
238
80
3
2
0.0030
0.0053
F3H
F3GT
GI
GSTF
total
6302
112
Table S2. Summary statistics and neutrality tests of populations at species boundaries
Population summary statistics for the populations at the species boundaries (Table 1). The parameters shown are the number of haplotype studied: n; the
average number of segregating sites: S; nucleotide diversity (θ and π) for total, synonymous (s), non-synonymous (a), and non-cording. Tajima’s D and Fu &
Li D were also calculated and simulated. Mean values and lower and higher 95% intervals were simulated with 1000 coalescent simulations and compared
with the observed value to test its significance. +p<0.10, *p < 0.05, **p < 0.01.
Table S3. Other priors tested in IMa2
Other priors tested in this study and highest probability density (HPD) with 95% HPD in parentheses, in isolation with migration models of two species
populations (pop1 and pop2): divergence time in million years ago (t) of two focal populations, population size in thousands in population1 (θ1), population
2 (θ2), ancestral population (θA), and migration rate from population 2 to 1 (2NM1<2) and from population 1 to 2 (2NM1>2). Migration rates (2NM) were
tested by likelihood ratio tests (Nielsen and Wakeley, 2001); *p < 0.05, **p < 0.01, ***p < 0.001. We used two migration priors for independent runs; a
uniform distribution on [0,1] for migration rate, and an exponential distribution with mean m* = 0.05.
model
pop1, 2
run1
pYK, pEB
prior
θ
10
posterior
m t hn
1 4 20
1 5 40
run2
10
run3
10 0.05 5 40
4
2 2 20
10
1 5 40
5 0.05# 4 40
run4
#
gAM, gYK
run5
run6
run7
pYK, gAM
run8
run9
run10
pYK, gYK
t
θ1
θ2
θA
2NM1<2
2NM1>2
0.14 (0.03-3.63)
18.8 (9.3-32.0)
28.8 (16.1-45.7)
54.3 (0-255.2)
0.020 (0-0.216)
0.223 (0-0.362)
0.15 (0.03-4.54)
18.4 (9.3-32.0)
28.9 (13.6-45.7)
54.8 (0-288.4)
0.031 (0-0.215)
0.227 (0-0.363)
0.11 (0.05-0.21)
17.5 (8.4-31.1)
27.5 (14.8-46.1)
59.8 (34.8-96.1)
0.000 (0-0.035)
0.000 (0-0.073)
0.016 (0.003-0.13)
5.4 (1.3-14.1)
11.1 (2.9-27.6)
22.4 (7.9-42.6)
0.034 (0-0.235)
0.054 (0-0.477)
0.015 (0.006-0.07)
4.8 (1.5-14.0)
10.2 (2.7-26.5)
22.3 (8.9-40.2)
0.010 (0-0.104)
0.007 (0-0.212)
0.015 (0.006-0.065)
4.8 (1.5-13.5)
9.8 (2.7-26.5)
22.3 (9.4-40.2)
0.000 (0-0.013)
0.000 (0-0.025)
1 5 40
10 0.05# 5 40
10
1 5 40
1.15 (0.42-4.59)
42.2 (26.7-62.9)
12.9 (6.0-25.0)
20.9 (0-348.4)
0.000 (0-0.106)
0.000 (0-0.079)
0.99 (0.44-1.67)
45.1 (29.0-66.4)
15.8 (7.7-27.9)
34.2 (0-123.1)
0.000 (0-0.041)
0.000 (0-0.019)
1.00 (0.76-4.74)
12.7 (6.2-23.4)
13.9 (6.8-25.8)
12.1 (0-528.7) 0.072*** (0.028-0.131)
0.015** (0.001-0.070)
10 0.05# 5 40
1.07 (0.27-2.22)
17.5 (8.6-29.9)
16.9 (8.6-29.3)
0.9 (0 - 170.3) 0.022*** (0.005-0.057) 0.005** (0.0003-0.026)
10
Table S4. Model evaluation for ecological niche modeling
Averaged TSS, AUC and Kappa values for model evaluation. The values were averaged from 10 runs
of each modeling technique for each of 5 sets of pseudo-absence datasets.
model
GLM
GAM
MARS
CTA
RF
MAXENT
R. palmatus
TSS
AUC KAPPA
0.850
0.846
0.847
0.818
0.854
0.839
0.960
0.960
0.959
0.926
0.971
0.960
0.862
0.826
0.875
0.740
0.960
0.946
R. grayanus
TSS
AUC KAPPA
0.937
0.959
0.961
0.940
0.998
0.997
0.969
0.979
0.987
0.970
0.999
0.997
0.859
0.857
0.855
0.837
0.865
0.854
Figures
Figure S1. Locations of occurrence data used for ecological niche modeling. Red and green circles
represent occurrence data for R. palmatus and R. grayanus, respectively. Occurrence data were
obtained from GBIF (http://www.gbif.org) and also included the sampling sites for phylogeographic
analysis in this study.
0
25
50
75
100
Figure S2. Projection of current (a, b) and past (c, d) distribution of R. palmatus and R. grayanus
using the Maxent. Maxent is a modeling technique that use only presence data. A dozen of runs were
cross-validated with random seeds and averaged for each species projection.