Supplementary material.
Table S1. Reference strains and accession numbers used.
Reference strains
|
Genus/species
|
Host plant
|
Origin
|
dnaK
|
ITS
|
recA
|
glnII
|
atpD
|
USDA110
|
B. japonicum
|
Glycine max
|
USA
|
NC004463
|
AF338865
|
NC_004463
|
NC_004463
|
NC_004463
|
ARC403
|
B. japonicum
|
Lupinus albus
|
Egypt
|
AJ431134
|
|
|
|
|
USDA122
|
B. japonicum bv. glycinearum
|
Glycine max
|
USA
|
|
AF208503
|
AY591562
|
AY386777
|
AY653767
|
NC92
|
B. japonicum
|
Arachis hypogaea
|
USA
|
AJ431144
|
|
|
|
|
WM9
|
B. japonicum
|
Lupinus albus
|
Poland
|
AF222752
|
|
|
|
|
USDA3505
|
B. japonicum
|
Lupinus montanus
|
USA
|
AJ431150
|
|
|
|
|
ANU289
|
B. elkanii
|
Parasponia sp.
|
USA
|
AJ431133
|
|
|
|
|
USDA94
|
B. elkanii
|
Glycine max
|
USA
|
AY328393
|
AF338868
|
AY591569
|
AY59911
|
AY386759
|
USDA76
|
B. elkanii
|
Glycine max
|
USA
|
AJ431152
|
U35000
|
AY591568
|
AY599117
|
AY386758
|
CGA009
|
R. palustris
|
Non-symbiotic
|
|
|
AJ534609
|
|
|
|
BTA-1
|
B. canariense bv. genistearum
|
Chamaecytisus proliferus
|
Canary Islands, Spain
|
|
AY591553
|
AY591553
|
AY386765
|
AY386739
|
BC-C2
|
B. canariense bv. genistearum
|
Chamaecytisus proliferus
|
Canary Islands, Spain
|
AJ431135
|
AY386704
|
AY591541
|
AY386762
|
AY386736
|
BES-1
|
B. canariense bv. genistearum
|
Chamaecytisus proliferus
|
Canary Islands, Spain
|
|
AY386707
|
AY591548
|
AY386764
|
|
BES-2
|
B. canariense bv. genistearum
|
Chamaecytisus proliferus
|
Canary Islands, Spain
|
|
AY599096
|
AY591549
|
AY599109
|
AY653753
|
ISLU16
|
B. canariense bv. genistearum
|
Ornithopus sp.
|
Sevila, Spain
|
|
AY386712
|
|
|
|
BGA-1
|
B. japonicum bv. genistearum
|
Teline stenopetala
|
Canary Islands, Spain
|
|
AY386714
|
AY591558
|
AY386772
|
|
USDA6
|
B. liaoningense bv. glycinearum
|
Glycine max
|
Canary Islands, Spain
|
|
U69638
|
|
AF169582
|
|
LMG18230
|
B. liaoningense bv. glycinearum
|
Glycine max
|
China
|
|
AF345256
|
AY591564
|
AY386775
|
AY386752
|
CCBAU10071
|
B. yuanmingense
|
Lespedeza cuneata
|
Canary Islands, Spain
|
|
AY386734
|
AY591566
|
AY386780
|
|
LMG10690
|
|
|
Canary Islands, Spain
|
|
AJ534598
|
|
|
|
BRE-4
|
B. canariense bv. genistearum
|
Teline canariense
|
Canary Islands, Spain
|
|
|
AY591552
|
|
AY653755
|
BC-MAM1
|
B. canariense bv. genistearum
|
Chamaecytisus proliferus
|
Canary Islands, Spain
|
|
|
AY591546
|
AY386767
|
|
BC-MAM2
|
B. canariense bv. genistearum
|
Chamaecytisus proliferus
|
Morocco
|
|
|
|
|
AY653756
|
BC-MAM3
|
B. canariense bv. genistearum
|
Chamaecytisus proliferus
|
Morocco
|
|
AY386710
|
|
|
AY386768
|
BC-MAM5
|
B. canariense bv. genistearum
|
Chamaecytisus proliferus
|
Morocco
|
|
AY386711
|
AY591547
|
AY386769
|
|
BC-MAM6
|
B. canariense bv. genistearum
|
Chamaecytisus proliferus
|
Morocco
|
|
|
|
|
AY653757
|
BC-MAM8
|
B. canariense bv. genistearum
|
Chamaecytisus proliferus
|
Morocco
|
|
|
AY653746
|
|
AY653758
|
BC-MAM9
|
B. canariense bv. genistearum
|
Chamaecytisus proliferus
|
Morocco
|
|
|
|
|
AY653759
|
BC-MAM12
|
B. canariense bv. genistearum
|
Chamaecytisus proliferus
|
Morocco
|
|
|
|
|
AY653760
|
BC0-1
|
B. canariense bv. genistearum
|
Adenocarpus foliolosus
|
Canary Islands, Spain
|
|
|
AY591550
|
|
AY653754
|
BC-P5
|
B. canariense bv. genistearum
|
Chamaecytisus proliferus
|
Canary Islands, Spain
|
|
|
AY591542
|
|
|
BC-P22
|
B. canariense bv. genistearum
|
Chamaecytisus proliferus
|
Canary Islands, Spain
|
|
AY386706
|
AY591545
|
AY386766
|
|
BC-P24
|
B. canariense bv. genistearum
|
Chamaecytisus proliferus
|
Canary Islands, Spain
|
|
|
|
|
AY653752
|
USDA 62
|
Bradyrhizobium japonicum
|
Glycine max
|
USA
|
|
AF271642
|
|
|
|
USDA 92
|
B. japonicum bv. glycinearum
|
Glycine max
|
USA
|
|
AF293382
|
|
|
|
Blup MR1
|
B. japonicum bv. genistearum
|
Lupinus polyphylus
|
Germany
|
|
AY386717
|
|
|
|
FN13
|
B. japonicum bv. genistearum
|
Lupinus montanus
|
Mexico
|
|
AY386716
|
|
|
|
LMG 4271
|
Bradyrhizobium japonicum
|
|
|
|
AJ279307
|
|
|
|
LMG 21987
|
Bradyrhizobium betae
|
Non-symbiotic
|
Spain
|
|
AJ631967
|
|
|
|
LMG 6136
|
Bradyrhizobium japonicum
|
Glycine max
|
USA
|
|
AJ534589
|
|
|
|
LMG 11955
|
Bradyrhizobium genosp. V
|
Faidherbia albida
|
Senegal
|
|
AJ534590
|
|
|
|
LMG 11957
|
Bradyrhizobium genosp. V
|
Faidherbia albida
|
Senegal
|
|
AJ534591
|
|
|
|
LMG 10691
|
Bradyrhizobium genosp. IX
|
Faidherbia albida
|
Senegal
|
|
AJ534600
|
|
|
|
LMG 10690
|
Bradyrhizobium genosp. IX
|
Faidherbia albida
|
Senegal
|
|
AJ534598
|
|
|
|
LMG 15178
|
Bradyrhizobium genosp. VII
|
Tephrosia purpurea
|
Senegal
|
|
AJ534604
|
|
|
|
LMG 11706
|
Bradyrhizobium genosp. X
|
Faidherbia albida
|
Senegal
|
|
AJ534593
|
|
|
|
LMG 15261
|
Bradyrhizobium genosp. XI
|
Crotalaria glauccoïdes
|
Senegal
|
|
AJ534596
|
|
|
|
LMG 4265
|
Bradyrhizobium japonicum
|
|
|
|
AJ279306
|
|
|
|
LMG 6134
|
B. elkanii
|
Glycine max
|
|
|
AJ279308
|
|
|
|
LMG 12186
|
Bradyrhizobium genosp. VI
|
Aeschynomene sensitiva
|
Senegal
|
|
AJ534585
|
|
|
|
LMTR28
|
B. yuanmingense
|
Phaseolus lunatus
|
Peru
|
|
AY599094
|
|
|
|
BC-C1
|
B. genosp. alpha bv. genistearum
|
Chamaecytisus proliferus
|
Canary Islands, Spain
|
|
AY386703
|
|
|
|
Nep1
|
B. japonicum bv. glycinearum
|
Glycine max
|
Nepal
|
|
AY386718
|
|
|
|
BC-MK6
|
Bradyrhizobium genosp. beta
|
Chamaecytisus proliferus
|
Morocco
|
|
AY386722
|
|
|
|
BC-MK1
|
Bradyrhizobium genosp. beta
|
Chamaecytisus proliferus
|
Morocco
|
|
AY386721
|
|
|
|
BC-P6
|
Bradyrhizobium genosp. beta
|
Chamaecytisus proliferus
|
Canary Islands, Spain
|
|
AY599097
|
|
|
|
STATISTICAL TESTS:
1) Tests of congruence of tree topologies using Shimodaira-Hasegawa (SH) test implemented in PAUP.
Trees were compared one by one with each other for each marker, on restricted datasets of 13 strains for which all markers sequences were available (USDA94, USDA76, USDA110, WSM2150, WSM2154, WSM2157, WSM471, WSM2150, 3S16, BC-C2, WU425, 4S16 and 1S20). Trees used for the test were generated by Maximum Likelihood, using a gamma distribution of site substitutions, with 2 types of substitutions and estimating base frequencies.
Values shown indicate the probability than 2 trees exhibit the same topology. If P<0.05 (5%), the hypothesis that the trees have the same topology is rejected.
|
recA
|
atpD
|
dnaK
|
glnII
|
ITS
|
recA
|
-
|
0.110
|
0.022
|
0.007
|
0.026
|
atpD
|
|
-
|
0.176
|
0.008
|
0.147
|
dnaK
|
|
|
-
|
0.140
|
0.373
|
glnII
|
|
|
|
-
|
0.210
|
ITS
|
|
|
|
|
-
|
Bold values indicate values greater than 5% between two trees topologies, meaning the topologies are statistically congruent using the SH test.
In conclusion, topology congruence of trees was found on nearly all trees, except glnII and recA trees that did show significant incongruence with others trees.
2) Partition-homogeneity or ILD test (Incongruence Length Difference) (using PAUP)
Calculation of incongruence used to measure character congruence, allow a direct comparison of data partitions by separating the incongruence into between-, and within-data set incongruence. Rather than limiting the study of incongruence to a small number of data partitions that were then combined, a randomisation procedure (sometimes termed the ILD test) was used to divide the combined data into a large number of sets of the same size and number as the original data partitions (Farris et al., 1995). If the data partitions are significantly incongruent at the 95% significance level, then less than 5% of the randomly divided data sets should have trees with lengths longer than the original data partitions. PAUP* includes the Partition Homogeneity Test (PHT), which performs the ILD test with branch swapping, and has been used to test the significance of character congruence.
A partition of all markers (dnaK, recA, atpD, glnII, ITS) was made for 11 strains for which sequences were available. These strains are USDA94, USDA76, USDA110, WSM2150, WSM2154, WSM2157, WSM471, WSM2150, 3S16, BC-C2 and WU425. Strains 4S16 and 1S20 were excluded as their phylogenetic position differed in several trees and recombination was detected in several markers. Tests were performed under parsimony criteria.
Partition used: “ABCDE”
A: recA (position 1-485)
B: atpD (position 486-968)
C: dnaK (969-1246)
D: glnII (1247-1840)
E: ITS (1841-2708)
Number of repetition used (Nrep) was 1000.
P values obtained indicate homogeneity (or not) in the partition. A P value >5% indicates homogeneity in the phylogenetical signal between the markers used in the partition.
Partition P value
ABCDE 0.015
ABCD 0.031
BCDE 0.001
ABCE 0.001
ABC 0.136 (recA-atpD-dnaK)
ABD 0.018
BCD 0.060 (atpD-dnaK-glnII)
ACD 0.030
ACE 0.001
ADE 0.001
CDE 0.002
AB 0.1500 (recA-atpD)
AC 0.1950 (recA-dnaK)
AE 0.002
AD 0.023
BC 0.424 (atpD-dnaK)
BD 0.049
BE 0.001
CD 0.479 (dnaK-glnII)
CE 0.002
DE 0.029
Homogeneity could be found in small partitions of two to three markers, but not when including four or all markers. |