Allium przewalskianum Regel. (Alliaceae) from the Qinghai-Tibet Plateau Organisms Diversity & Evolution

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Cryptic and repeated ‘allopolyploid’ speciation within Allium przewalskianum
Regel. (Alliaceae) from the Qinghai-Tibet Plateau
Organisms Diversity & Evolution
Qianlong Liang, Xiaoxiao Hu, Guili Wu, Jianquan Liu*
*
Corresponding author, e-mail: [email protected], postal address: MOE Key Laboratory
for Bio-resources and Eco-environment, College of Life Science, Sichuan University, 24´╝îSouth
Section 1, Yihuan Road, Chengdu 610065, China
Table S1 Details of the Allium przewalskianum diploid–tetraploid complex sampling
locations and sample sizes analyzed; P. denotes the population code.
Sample size(individual
P.
Location
Latitude(N)
Longitude(E)
number)
Altitude(m)
AFLP
ITS
CHS
1
Huzhu, QH
37°03′
102°24′
2378
7
1
1
2
Ledu, QH
36°25′
102°46′
2560
7
1
1
3
Xining,QH
36°34′
101°54′
2210
8
1
1
4
Haiyan,QH
36°51′
101°03′
2950
8
2
1
5
Lintao,GS
35°23′
103°50′
1880
5
1
2
6
Luqu,GS
34°36′
102°28′
3120
6
1
1
7
Tongren,QH
35°16′
101°53′
3170
6
1
1
8
Guoluo,QH
33°43′
100°49′
3500
6
1
2
9
Hongyuan,SC
33°01′
102°36′
3470
7
1
1
10
Shiqu,SC
33°00′
98°20′
3970
8
2
3
11
Jiangda,XZ
31°27′
98°09′
3640
8
2
1
12
Yushu,QH
31°51′
96°18′
3660
8
1
2
13
Lixian,SC
31°28′
103°07′
1954
6
1
1
14
Aerjinshan,GS
38°33′
90°10′
3358
4
1
1
15
Dangjinshan,GS
39°23′
94°20′
3930
2
1
1
16
Yumen,GS
39°48′
97°17′
3361
4
1
1
17
Delingha,QH
37°27′
97°20′
3310
4
1
1
18
Xinghai,QH
35°53′
99°41′
3760
5
1
1
19
Shandan,GS
38°06′
101°33′
2612
5
1
1
20
Zeku,QH
35°12′
100°55′
3500
7
1
1
21
Yushu,QH
33°51′
97°11′
4020
3
1
1
22
Yushu,QH
33°00′
97°19′
3610
5
1
1
23
Yushu,QH
32°21′
96°26′
3680
3
1
1
24
Dingqing,XZ
31°30′
95°23′
3770
6
1
1
25
Leiwuqi,XZ
31°12′
96°36′
3800
5
1
1
26
Ranwu,XZ
29°30′
96°46′
3950
5
1
1
27
Dangxiong,XZ
30°32′
91°08′
4310
4
1
1
28
Kangma,XZ
28°33′
89°43′
4430
5
1
1
Note: (1) Abbreviations: QH, Qinghai; GS, Gansu; SC, Sichuan; XZ, Xizang; YN,
Yunnan; (2) populations 1-12 are diploid; populations 13-28 are tetraploid and the
population codes are in bold.
Table S2 AFLP adapter and primer sequences used in this study
Code
Name
Sequence
E-F
EcoR 1-F(adapter)
5’-CTCGTAGACTGCGTACC-3’
E-R
EcoR 1-R(adapter)
5’-AATTGGTACGCAGTCTAC-3’
M-F
Mse 1-F(adapter)
5’-GACGATGAGTCCTGAG-3’
M-R
Mse 1-R(adapter)
5’-TACTCAGGACTCAT-3’
E-A
EcoR 1-A(Primer)
5’-GACTGCGTACCAATTCA-3’
M-C
Mse 1-C(Primer)
5’-GATGAGTCCTGAGTAAC-3’
E-ACC
EcoR 1-ACC(Primer)
5’-GACTGCGTACCAATTCACC-3’
M-CAC
Mse 1-CAC(Primer)
5’-GAT GAG TCC TGA GTA ACAC-3’
E-ACT
EcoR 1-ACT(Primer)
5’-GACTGCGTACCAATTCACT-3’
M-CTA
Mse 1-CTA(Primer)
5’-GAT GAG TCC TGA GTA ACTA-3’
Table S3 Population codes (P.), plant sources, and locality of the sequenced material;
ITS and CHS GenBank accession numbers for all sequences included in this study.
P.
Voucher
Locality
ITS
1
1
1
2
2
2
3
3
3
4
4
4
5
5
5
5
6
6
7
7
7
7
7
7
7
8
8
8
8
8
8
9
9
10
10
10
J. Q. Liu-AO 01
China: Huzhu, QH
China: Huzhu, QH
China: Huzhu, QH
China: Ledu, QH
China: Ledu, QH
China: Ledu, QH
China: Xining, QH
China: Xining, QH
China: Xining, QH
China: Haiyan, QH
China: Haiyan, QH
China: Haiyan, QH
China: Lintao, GS
China: Lintao, GS
China: Lintao, GS
China: Lintao, GS
China: Luqu, GS
China: Luqu, GS
China: Tongren, QH
China: Tongren, QH
China: Tongren, QH
China: Tongren, QH
China: Tongren, QH
China: Tongren, QH
China: Tongren, QH
China: Guoluo, QH
China: Guoluo, QH
China: Guoluo, QH
China: Guoluo, QH
China: Guoluo, QH
China: Guoluo, QH
China: Hongyuan, SC
China: Hongyuan, SC
China: Shiqu, SC
China: Shiqu, SC
China: Shiqu, SC
KM189069
KM189070
KM189071
KM189072
KM189073
KM189074
KM189075
KM189076
KM189077
KM189078
KM189079
KM189080
KM189081
KM189082
KM189083
KM189084
KM189085
J. Q. Liu-AO 01
J. Q. Liu-AO 01
J. Q. Liu-AO 69
J. Q. Liu-AO 69
J. Q. Liu-AO 69
J. Q. Liu-AO 72
J. Q. Liu-AO 72
J. Q. Liu-AO 72
J. Q. Liu-AO 14
J. Q. Liu-AO 14
J. Q. Liu-AO 14
J. Q. Liu-AO 66
J. Q. Liu-AO 66
J. Q. Liu-AO 66
J. Q. Liu-AO 66
J. Q. Liu-2006033
J. Q. Liu-2006033
J. Q. Liu-AO 54
J. Q. Liu-AO 54
J. Q. Liu-AO 54
J. Q. Liu-AO 54
J. Q. Liu-AO 54
J. Q. Liu-AO 54
J. Q. Liu-AO 54
J. Q. Liu-AO 53
J. Q. Liu-AO 53
J. Q. Liu-AO 53
J. Q. Liu-AO 53
J. Q. Liu-AO 53
J. Q. Liu-AO 53
J. Q. Liu-2006026
J. Q. Liu-2006026
J. Q. Liu-AO 108
J. Q. Liu-AO 108
J. Q. Liu-AO 108
CHS
KM188957
KM188958
KM188959
KM188960
KM188961
KM188962
KM188963
KM188964
KM188965
KM188966
KM188967
KM188968
KM188969
KM188970
KM188971
KM188972
KM188973
KM188974
KM188975
KM188976
KM188977
KM188978
KM188979
KM188980
KM188981
KM188982
KM188983
KM188984
KM188985
KM188986
KM188987
KM188988
KM188989
KM188990
KM188991
10
10
10
10
11
11
11
11
12
12
13
13
13
13
13
14
14
14
14
14
15
15
15
15
16
16
16
16
16
17
17
17
17
17
17
18
18
18
18
18
19
19
19
19
J. Q. Liu-AO 108
J. Q. Liu-AO 108
J. Q. Liu-AO 108
J. Q. Liu-AO 108
J. Q. Liu-AO 117
J. Q. Liu-AO 117
J. Q. Liu-AO 117
J. Q. Liu-AO 117
J. Q. Liu-AO 106
J. Q. Liu-AO 106
J. Q. Liu-TB07024
J. Q. Liu-TB07024
J. Q. Liu-TB07024
J. Q. Liu-TB07024
J. Q. Liu-TB07024
J. Q. Liu-TB07121
J. Q. Liu-TB07121
J. Q. Liu-TB07121
J. Q. Liu-TB07121
J. Q. Liu-TB07121
J. Q. Liu-TB07117
J. Q. Liu-TB07117
J. Q. Liu-TB07117
J. Q. Liu-TB07117
J. Q. Liu-TB07113
J. Q. Liu-TB07113
J. Q. Liu-TB07113
J. Q. Liu-TB07113
J. Q. Liu-TB07113
J. Q. Liu-AO 160
J. Q. Liu-AO 160
J. Q. Liu-AO 160
J. Q. Liu-AO 160
J. Q. Liu-AO 160
J. Q. Liu-AO 160
J. Q. Liu-AO 82
J. Q. Liu-AO 82
J. Q. Liu-AO 82
J. Q. Liu-AO 82
J. Q. Liu-AO 82
J. Q. Liu-TB07101
J. Q. Liu-TB07101
J. Q. Liu-TB07101
J. Q. Liu-TB07101
China: Shiqu, SC
China: Shiqu, SC
China: Shiqu, SC
China: Shiqu, SC
China: Jiangda, XZ
China: Jiangda, XZ
China: Jiangda, XZ
China: Jiangda, XZ
China: Yushu, QH
China: Yushu, QH
China: Lixian, SC
China: Lixian, SC
China: Lixian, SC
China: Lixian, SC
China: Lixian, SC
China: Aerjinshan, XJ
China: Aerjinshan, XJ
China: Aerjinshan, XJ
China: Aerjinshan, XJ
China: Aerjinshan, XJ
China: Dangjinshan, GS
China: Dangjinshan, GS
China: Dangjinshan, GS
China: Dangjinshan, GS
China: Yumen, GS
China: Yumen, GS
China: Yumen, GS
China: Yumen, GS
China: Yumen, GS
China: Delingha, QH
China: Delingha, QH
China: Delingha, QH
China: Delingha, QH
China: Delingha, QH
China: Delingha, QH
China: Xinghai, QH
China: Xinghai, QH
China: Xinghai, QH
China: Xinghai, QH
China: Xinghai, QH
China: Shandan, GS
China: Shandan, GS
China: Shandan, GS
China: Shandan, GS
KM189086
KM189087
KM189088
KM189089
KM189090
KM189091
KM189092
KM189093
KM189094
KM189095
KM189096
KM189097
KM189098
KM189099
KM189100
KM189101
KM189102
-
KM188992
KM188993
KM188994
KM188995
KM188996
KM188997
KM188998
KM188999
KM189000
KM189001
KM189002
KM189003
KM189004
KM189005
KM189006
KM189007
KM189008
KM189009
KM189010
KM189011
KM189012
KM189013
KM189014
KM189015
KM189016
KM189017
KM189018
KM189019
KM189020
KM189021
KM189022
KM189023
KM189024
KM189025
KM189026
KM189027
KM189028
KM189029
KM189030
KM189031
KM189032
KM189033
19
20
20
20
20
20
21
21
21
22
22
22
22
23
23
23
23
24
24
24
24
25
25
25
26
26
26
26
26
27
27
27
28
28
28
J. Q. Liu-TB07101
J. Q. Liu-AO 41
J. Q. Liu-AO 41
J. Q. Liu-AO 41
J. Q. Liu-AO 41
J. Q. Liu-AO 41
J. Q. Liu-AO 89
J. Q. Liu-AO 89
J. Q. Liu-AO 89
J. Q. Liu-AO 95
J. Q. Liu-AO 95
J. Q. Liu-AO 95
J. Q. Liu-AO 95
J. Q. Liu-AO 101
J. Q. Liu-AO 101
J. Q. Liu-AO 101
J. Q. Liu-AO 101
J. Q. Liu-AO 127
J. Q. Liu-AO 127
J. Q. Liu-AO 127
J. Q. Liu-AO 127
J. Q. Liu-AO 121
J. Q. Liu-AO 121
J. Q. Liu-AO 121
J. Q. Liu-2006290
J. Q. Liu-2006290
J. Q. Liu-2006290
J. Q. Liu-2006290
J. Q. Liu-2006290
J. Q. Liu-AO 157
J. Q. Liu-AO 157
J. Q. Liu-AO 157
J. Q. Liu-2006219
J. Q. Liu-2006219
J. Q. Liu-2006219
China: Shandan, GS
China: Zeku, QH
China: Zeku, QH
China: Zeku, QH
China: Zeku, QH
China: Zeku, QH
China: Yushu, QH
China: Yushu, QH
China: Yushu, QH
China: Yushu, QH
China: Yushu, QH
China: Yushu, QH
China: Yushu, QH
China: Yushu, QH
China: Yushu, QH
China: Yushu, QH
China: Yushu, QH
China: Dingqing, XZ
China: Dingqing, XZ
China: Dingqing, XZ
China: Dingqing, XZ
China: Leiwuqi, XZ
China: Leiwuqi, XZ
China: Leiwuqi, XZ
China: Ranwu, XZ
China: Ranwu, XZ
China: Ranwu, XZ
China: Ranwu, XZ
China: Ranwu, XZ
China: Dangxiong, XZ
China: Dangxiong, XZ
China: Dangxiong, XZ
China: Kangma, XZ
China: Kangma, XZ
China: Kangma, XZ
KM189103
KM189104
KM189105
KM189106
KM189107
KM189108
KM189109
KM189110
KM189111
KM189112
KM189113
KM189114
KM189115
KM189116
KM189117
KM189118
KM189119
KM189120
-
KM189034
KM189035
KM189036
KM189037
KM189038
KM189039
KM189040
KM189041
KM189042
KM189043
KM189044
KM189045
KM189046
KM189047
KM189048
KM189049
KM189050
KM189051
KM189052
KM189053
KM189054
KM189055
KM189056
KM189057
KM189058
KM189059
KM189060
KM189061
KM189062
KM189063
KM189064
KM189065
KM189066
KM189067
KM189068
Table S4 Details of the 60 sites used for ecological niche modeling
Population
Locality
Geographical position
Altitude
Voucher specimens
DP & NTP
Haiyan, QH
N 36°51.367’ E 101°03.252’
2950m
J. Q. Liu-AO 14
DP & NTP
Huangyuan, QH
N 36°39.920’ E 101°23.567’
2470-2520m
J. Q. Liu-AO 162
DP & NTP
QH Lake, QH
N 36°33.157’ E 100°43.757’
3210m
J. Q. Liu-AO 78
DP & NTP
Xining, QH
N 36°33.786’ E 101°54.361’
2210m
J. Q. Liu-AO 72
DP & NTP
Yushu, QH
N 31°51.329’ E 096°17.741’
3660m
J. Q. Liu-AO 103
DP
Huzhu, QH
N 37°03.029’ E 102°23.934’
2378m
J. Q. Liu-AO 01
DP
Ledu, QH
N 36°25.007’ E 102°46.160’
2560m
J. Q. Liu-AO 69
DP
Lintao, GS
N 35°23.327’ E 103°50.402’
1880m
J. Q. Liu-AO 66
DP
Tongren, QH
N 35°15.775’ E 101°52.997’
3170m
J. Q. Liu-AO 54
DP
Luqu, GS
N 34°35.576’ E 102°28.045’
3120m
J. Q. Liu-2006033
DP
Henan, QH
N 34°44.195’ E 101°18.090’
3600m
J. Q. Liu-AO 30
DP
Guoluo, QH
N 33°43.289’ E 100°48.921’
3500m
J. Q. Liu-AO 53
DP
Hongyuan, SC
N 33°00.880’ E 102°36.397’
3470m
J. Q. Liu-2006026
DP
Shiqu, SC
N 32°59.862’ E 098°20.369’
3970m
J. Q. Liu-AO 108
DP
Jiangda, XZ
N 31°26.607’ E 098°09.073’
3640m
J. Q. Liu-AO 117
DP
Ping’an, QH
N 36°38.717’ E 102°02.336’
2200m
J. Q. Liu-AO 70
DP
Gonghe, QH
N 35°57.803’ E 100°59.769’
2850m
J. Q. Liu-AO 77
NTP
Xinghai, QH
N 35°53.205’ E 099°40.588’
3760m
J. Q. Liu-AO 85
NTP
Xinghai, QH
N 35°44.433’ E 100°13.405’
3220m
J. Q. Liu-AO 82
NTP
Tongren, QH
N 35°22.337’ E 101°37.747’
2740m
J. Q. Liu-AO 25
NTP
Yuzhong, GS
N 35°46.796’ E 104°01.378’
2450m
J. Q. Liu-AO 67
NTP
Tongren, QH
N 35°42.662’ E 102°17.652’
3020m
J. Q. Liu-AO 23
NTP
Tongren, QH
N 35°35.598’ E 102°03.158’
2360m
J. Q. Liu-AO 56
NTP
Tongren, QH
N 35°26.772’ E 102°27.402’
3080m
J. Q. Liu-AO 62
NTP
Zeku, QH
N 35°16.497’ E 101°06.670’
3500m
J. Q. Liu-AO 41
NTP
Hezuo, GS
N 35°08.350’ E 102°51.059’
2650m
J. Q. Liu-2006039
NTP
Ningxiu, QH
N 35°07.752’ E 100°43.657’
3450m
J. Q. Liu-AO 43
NTP
Gonghe, QH
N 36°22.386’ E 100°23.673’
3490m
J. Q. Liu-AO 80
NTP
Aerjinshan, GS
N 38°33.254’ E 090°10.182’
3358m
J. Q. Liu-TB07121
NTP
Dangjinshan, GS
N 39°22.601’ E 094°19.511’
2930m
J. Q. Liu-TB07117
NTP
Yumen, GS
N 39°48.429’ E 097°17.189’
3361m
J. Q. Liu-TB07113
NTP
Delingha, QH
N 37°26.826’ E 097°20.282’
3310m
J. Q. Liu-AO 160
NTP
Dulan, QH
N 36°00.821’ E 097°53.443’
3050m
J. Q. Liu-AO 158
NTP
Dulan, QH
N 36°14.677’ E 098°06.370’
3250m
J. Q. Liu-AO 159
NTP
Wulan, QH
N 37°04.310’ E 098°52.464’
3470m
J. Q. Liu-AO 161
NTP
Ebo, QH
N 37°59.878’ E 100°45.921’
3223m
J. Q. Liu-AO 03
NTP
Shandan, GS
N 38°06.326’ E 101°33.209’
2612m
J. Q. Liu-TB07101
NTP
Wuwei, GS
N 37°12.218’ E 102°51.436’
2900m
J. Q. Liu-TB07099
NTP
Huangzhong, QH
N 36°30.434’ E 101°37.905’
2540m
J. Q. Liu-AO 75
STP
Yushu, QH
N 33°50.522’ E 097°10.601’
4020m
J. Q. Liu-AO 89
STP
Yushu, QH
N 32°51.782’ E 096°57.465’
3950m
J. Q. Liu-AO 106
STP
Yushu, QH
N 33°11.008’ E 097°23.636’
4010m
J. Q. Liu-AO 92
STP
Yushu, QH
N 33°00.198’ E 097°19.007’
3610m
J. Q. Liu-AO 95
STP
Yushu, QH
N 32°20.524’ E 096°25.850’
3680m
J. Q. Liu-AO 101
STP
Changdu, XZ
N 31°08.853’ E 097°01.170’
3630m
J. Q. Liu-AO 119
STP
Deqin, YN
N 28°27.626’ E 098°54.589’
3040m
J. Q. Liu-2006310
STP
Ranwu, XZ
N 29°30.292’ E 096°45.802’
3950m
J. Q. Liu-2006290
STP
Basu, XZ
N 30°11.523’ E 097°19.351’
4210m
J. Q. Liu-2006297
STP
Leiwuqi, XZ
N 31°12.321’ E 096°36.056’
3800m
J. Q. Liu-AO 121
STP
Leiwuqi, XZ
N 30°57.976’ E 096°14.537’
4150m
J. Q. Liu-AO 126
STP
Dingqing, XZ
N 31°30.000’ E 095°23.000’
3770m
J. Q. Liu-AO 127
STP
Dingqing, XZ
N 31°18.364’ E 095°45.659’
3680m
J. Q. Liu-AO 128
STP
Dingqing, XZ
N 31°41.341’ E 095°01.492’
3860m
J. Q. Liu-AO 130
STP
Baqing, XZ
N 31°48.803’ E 093°44.462’
3970m
J. Q. Liu-AO 132
STP
Naqu, XZ
N 31°45.293’ E 092°46.547’
4220m
J. Q. Liu-AO 134
STP
Dangxiong, XZ
N 30°32.355’ E 091°07.669’
4310m
J. Q. Liu-AO 157
STP
Jiangzi, XZ
N 28°50.995’ E 089°55.043’
4300m
J. Q. Liu-AO 142
STP
Kangma, XZ
N 28°32.649’ E 089°42.990’
4430m
J. Q. Liu-2006219
STP
Jilong, XZ
N 28°48.806’ E 085°30.074’
4644m
J. Q. Liu-2007140
STP
Jilong, XZ
N 28°26.737’ E 085°14.864’
3026-4126m
J. Q. Liu-2007042
Note: DP, the diploid population; NTP, tetraploid populations in the northern QTP;
STP, tetraploid populations in the southern QTP; DP & NTP indicates that the
population has both cytotypes (from Cui et al., 2008).
Table S5 The 12 environmental variables used for ENM in this study
Environmental variable
Abbreviation
Mean Monthly Temperature Range
bio2
Isothermality
bio3
Temperature Annual Range
bio7
Mean Temperature of Wettest Quarter
bio8
Mean Temperature of Warmest Quarter
bio10
Mean Temperature of Coldest Quarter
bio11
Precipitation Seasonality
bio15
Precipitation of Wettest Quarter
bio16
Precipitation of Driest Quarter
bio17
Precipitation of Warmest Quarter
bio18
Altitude
alt
Table S6 Analysis of STRUCTURE output
lnP(D)Mean
lnP(D)SD
ΔK
Diploid and tetraploid
20
-6173.755
0.455925894
0
Mixed
2
20
-5233.805
0.131689427
4402.593374
Mixed
3
20
-4873.63
21.16820108
1.963295079
Mixed
4
20
-4526.06
5.497693296
22.81388634
Partially separate
5
20
-4301.11
75.99871121
1.790369834
Separate
6
20
-4129
85.09611903
1.86549195
Separate
7
20
-4021.91
66.05154208
2.118248804
Separate
8
20
-3941.69
103.6761857
1.764484523
Separate
9
20
-3803.72
134.9992577
1.901988606
Separate
10
20
-3674.65
132.5236761
-
Separate
K
RepTimes
1
Note: K, the number of clusters; RepTimes, repeat times of independent simulations
run for each value of K; lnP (D), the log likelihood of the observed genotype
distribution in K clusters that can be output by STRUCTURE simulation (Pritchard et
al., 2000); ΔK, an ad hoc quantity related to the second order rate of change of the log
probability of data with respect to K, this is a good predictor of the real value of K
(Evanno et al., 2005).
Table S7 ITS genotypes (H) and CHS genotypes (C) among the 28 populations
P.
Location
ITS (H)
CHS (C)
1
Huzhu, QH
H1,H2
C1,C2,C3
2
Ledu, QH
H1,H2
C4,C5,C6
3
Xining,QH
H1,H2
C7,C8,C9
4
Haiyan,QH
H3;H3,H4
C10,C11
5
Lintao,GS
H5
C12,C13;C13,C14
6
Luqu,GS
H6
C15,C16
7
Tongren,QH
H7
C16,C17,C18
8
Guoluo,QH
H7
C10,C19,C20;C19,C21,C22
9
Hongyuan,SC
H8
C23,C24
10
Shiqu,SC
H9; H10,H11
C10,C25;C25,C26;C20,C27,C28
11
Jiangda,XZ
H12,H13;H14,H15
C29;C30,C31
12
Yushu,QH
H16,H17
C32
13
Lixian,SC
H18,H19
C33,C34,C35,C36,C37
14
Aerjinshan,GS
H20
C38,C39,C40,C41,C42
15
Dangjinshan,GS
H20
C38,C43,C44,C45
16
Yumen,GS
H20
C41,C46,C47,C48,C49
17
Delingha,QH
H3,H21
C20,C49,C50,C51,C52,C53
18
Xinghai,QH
H22,H23
C46,C54,C55,C56,C57
19
Shandan,GS
H24,H25
C40,C58,C59,C60,C61
20
Zeku,QH
H26,H27
C16,C26,C46,C62,C63
21
Yushu,QH
H28,H29
C20,C50,C64
22
Yushu,QH
H7,H30
C16,C64,C65,C66
23
Yushu,QH
H31,H32
C66,C67,C68,C69
24
Dingqing,XZ
H31,H33
C13,C20,C36,C70
25
Leiwuqi,XZ
H28,H31
C20,C36,C71
26
Ranwu,XZ
H12,H13
C20,C36,C71,C72,C73
27
Dangxiong,XZ
H28,H31
C36,C69,C74
28
Kangma,XZ
H31,H34
C36,C69,C75
Fig. S1 Principal Co-ordinate Analysis (PCoA) plot based on a matrix of Jaccard
distances among 157 individuals using NTSYS-PC 2.0. All the individuals could
be identified within seven groups, which correspond to the output of the Structure
analysis when K=6: the tetraploid populations clustered into three groups, STP
(populations in southern QTP), ETP (populations in eastern QTP) and NTP
(populations in northern QTP); the diploid populations readily clustered into five
groups and DP-2 was intermixed with NTP.
Fig. S2 ITS phylogenetic relationships of sampled Allium przewalskianum in the
present study using Bayesian, ML and MP analyses. All analyses were performed
according to the methods outlined in the main paper. We used Allium ovalifolium,
Allium eduardii and Allium mongolicum as outgroups. All newly obtained ITS
sequences were deposited in GenBank (accessions KC189069–KC189120). We
recovered 34 genotypes from 28 populations (Table S7). The ML tree and the MP
tree were congruent with the 50% major consensus tree obtained from Bayesian
analysis (shown in this Fig., under the GTR+I+G model) and had a similar
topology. The support values are given above the branches (Left: posterior
probabilities of Bayesian analysis; Middle: bootstrap values of
maximum-parsimony and Right: bootstrap values of maximum-likelihood). These
analyses based on the nuclear ITS sequences suggest that all sampled diploid and
tetraploid individuals of A. przewalskianum can be grouped into five lineages,
A-E.
Fig. S3 CHS phylogenetic relationships of sampled Allium przewalskianum in the
present study using Bayesian, ML and MP analyses. All analyses were performed
according to the methods outlined in the main paper. We used Allium cepa as the
outgroup. All newly obtained CHS sequences were deposited in GenBank
(accession numbers KC188957–KC189068). We recovered 75 genotypes from 28
populations (Table S7). The ML tree and the MP tree were congruent with the
50% major consensus tree obtained from Bayesian analysis (shown in this Fig.,
under the GTR+I+G model) and had a similar topology with respect to the main
branches. The support values are given above the branches (Left: posterior
probabilities of Bayesian analysis; Middle: bootstrap values of
maximum-parsimony and Right: bootstrap values of maximum-likelihood). These
analyses based on the nuclear CHS sequences also suggest that all sampled
diploid and tetraploid individuals of A. przewalskianum can be grouped into five
lineages, I-V.
References:
Cui, X. K., Ao, C. Q., Zhang, Q., Chen, L. T., & Liu, J. Q. (2008). Diploid and
tetraploid distribution of Allium przewalskianum Regel. (Liliaceae) in the
Qinghai-Tibetan Plateau and adjacent regions. Caryologia, 61, 192–200.
Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters of
individuals using the software STRUCTURE: a simulation study. Molecular
Ecology, 14, 2611–2620.
Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population
structure using multilocus genotype data. Genetics, 155, 945–959.
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