Supplementary Table 1 Sampling localities for accessions from the M. guttatus complex included in our genetic, phenotypic, and redundancy analyses. Accessions are ordered first by state/province from north to south, then alphabetically. AL = Alaska; BC =
British Columbia; WA = Washington; OR = Oregon; CA = California; ID = Idaho; NV = Nevada; CO = Colorado; AZ = Arizona
Species
M. arvensis
M. cupriphilus
M. guttatus
Accession ID State or Province Latitude (N) Longitude (W) Elevation (m) Annual/Perennial
CVP
NAP
POT
SEC
NKL
SKZ
TAY
WLD
AWP
LCU
RFA
BSP
BVG
FEV
IM
LIN
MAR
MED
RGR
S2G
SAG
SAM
SWC
BHI
BHT
CAV
CA
CA
CA
CA
BC
BC
BC
BC
WA
WA
WA
OR
OR
OR
OR
OR
OR
OR
OR
OR
OR
OR
OR
CA
CA
CA
38.372
38.752
37.925
37.915
50.358
48.782
49.299
49.898
48.495
47.495
46.631
43.712
43.059
44.400
44.401
45.136
43.479
37.809 -120.302
42.489
43.982
44.797
45.959
43.959
41.155
37.977
38.343
-123.055
-122.615
-122.609
-120.725
-126.930
-123.953
-125.292
-124.550
-122.702
-123.277
-123.230
-124.099
-123.571
-122.298
-122.150
-123.896
-123.294
-124.208
-123.096
-122.544
-123.680
-123.902
-123.890
-120.639
-122.485
224
335
622
297
96
125
59
286
22
230
83
13
476
490
1582
18
183
288
17
580
243
545
38
777
293
118
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A

Species
M. guttatus
Accession ID State or Province Latitude (N) Longitude (W) Elevation (m) Annual/Perennial
GCC
GTR
KLM
LON
LQH
OAE
PCR
RNC
SEX
SGS
SHO
SSR
STO
USK
CMF
KRR
AGG
ATT
BAM
CPB
GPT
PCL
SCC
TSG
CHR
GBS
HEC
MWV
OSW
CA
CA
CA
CA
CA
CA
CA
CA
CA
CA
CA
CA
CA
CA
CA
CA
BC
AL
BC
BC
BC
BC
BC
BC
WA
OR
OR
OR
OR
37.874
38.580
41.270
38.044
37.921
38.411
40.641
38.911
37.915
34.301
37.931
38.676
38.439
38.672
38.443
38.580
52.626
52.936
48.837
53.171
49.052
53.689
48.412
53.419
46.780
42.425
44.135
44.419
45.761
-120.434
-122.197
-123.606
-120.648
-120.717
-122.960
-123.892
-123.245
-120.725
-118.107
-120.733
-123.240
-122.940
-123.210
-122.974
-123.117
-131.422
-123.245
-125.144
-131.785
-125.722
-132.184
-124.012
-131.916
-121.779
-124.410
-124.123
-121.773
-123.983
392
144
227
512
279
280
702
314
297
1164
204
333
212
125
87
106
15
1200
3
10
0
5
1
17
1118
26
11
1215
0
P
P
P
P
P
P
P
A
A
A
A
A
P
P
P
P
P
P
A
A
A
A
A
A
A
A
A
A
A

Species Accession ID
ORO
SBC
SMO
STB
SVH
SWB
USB
WEV
WFM
YJS
ALL
BOB
BOG
DHS
SOL
CC
COT
EML
OTT
THR
ANR
BCB
BSR
BUL
CAB
CAN
DAV
GBM
MRR
State or Province Latitude (N) Longitude (W) Elevation (m) Annual/Perennial
CA
CA
CA
CA
CA
CA
CA
CA
ID
ID
NV
NV
NV
NV
NV
CO
CO
CO
OR
OR
CA
CA
CA
CA
CA
CA
CA
CA
CA
44.753
44.101
39.737
-124.057
-121.623
-123.631
36.063 -121.592
40.529 -124.163
34.921
39.359
36.069
37.025
41.379
38.456
35.273
36.484
38.323
37.891
41.616
39.036
39.832
35.423
44.710
44.951
39.006
48.529
41.924
41.051
40.051
38.986
38.839
39.007
-120.436
-123.817
-121.551
-122.218
-124.069
-123.141
-120.889
-121.196
-122.590
-122.635
-120.104
-123.690
-123.849
-120.789
-114.335
-114.584
-114.219
-124.451
-118.804
-119.029
-116.985
-106.948
-106.419
-107.040
76
1992
397
8
16
73
5
573
4
21
8
10
647
494
9
1408
4
11
108
1992
1656
2076
4
1308
1208
1597
3214
3517
3193
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P

Species
M. laciniatus
M. micranthus
M. nasutus
M. nudatus
M. pardalis
M. tilingii
Accession ID State or Province Latitude (N) Longitude (W) Elevation (m) Annual/Perennial
PGA
SCH
STR
PED
GB
TRT
CECL
DNK
PETL
SHL
SNB
TIGR
WLF
LGR
WSK
HCN
NFN
SBN
SF
BCR
MEN
MHA
SHI
SMC
SQP
GUN
DPP
BAG
RAN
CO
CO
CO
AZ
OR
OR
CA
CA
CA
CA
CA
CA
CA
CA
WA
OR
OR
OR
OR
CA
CA
CA
CA
CA
CA
CA
CA
WA
WA
38.964
39.018
39.025
32.711
37.136
37.716
37.309
37.085
37.056
37.145
37.042
37.812
37.842
39.140
45.754
42.547
45.241
45.261
45.262
37.823
37.809
37.340
39.877
36.062
36.565
38.752
37.661
48.873
47.010
-107.094
-107.035
-107.031
-110.628
-122.133
-119.705
-119.495
-119.218
-119.369
-119.306
-119.404
-119.506
-119.594
-123.286
-121.518
-123.502
-122.261
-121.033
-121.030
-120.258
-120.302
-121.657
-123.732
-121.554
-118.766
-122.615
-120.456
-121.688
-121.760
3259
3448
3377
727
1865
1479
1302
1880
1250
1603
1043
2584
2405
622
148
360
218
241
242
867
288
962
225
696
1965
335
94
1186
1354
A
A
A
A
A
A
A
A
A
P
P
A
A
A
A
A
A
A
P
P
P
P
A
A
A
A
A
A
A

Species Accession ID State or Province Latitude (N) Longitude (W) Elevation (m) Annual/Perennial
STV
TWN
ICE
LPI
LVR
SAB
SOP
WA
WA
OR
CA
CA
CA
CA
46.802
48.950
45.226
38.289
37.951
37.212
40.362
-121.714
-121.636
-117.268
-119.638
-119.226
-118.610
-120.510
1910
1594
2402
3167
2774
2793
1251
P
P
P
P
P
P
P

Supplementary Table 2 Primers for the 1 microsatellite and 15 intron-length polymorphic markers used in our genetic analyses. All primers are written 5’ to 3’. Positions given are based on the genome sequence for
M. guttatus IM62. PCR protocols are found in
Kelly and Willis (1998). LG = linkage group.
Marker LG Position Primer Sequences
DIV1 Inversion
MgSTS299 8
MgSTS675 8
MgSTS173 8
MgSTS059 8
MgSTS084 8
MgSTS278 8
MgSTS563 8
MgSTS069 8
Noninversion
MgSTS665 1
MgSTS617
MgSTS423
MgSTS571
2
6
8
1844602
2044482
2444182
2636431
2943772
3605725
3695076
3717111
5030756
2505570
4650184
8885823
F: CTTGATCTTCATGCTCACACG
F: TCGTTGGTGGAAATCAAAGC
F: GGCAATCTTCAACCTTTTCC
F: TTTCCGATTGGAGATTCGAC
F: CCACCGAAGAAGTTGAAACC
F: ACGTCAGCCCTTTGTACACC
R: GCCTTAATAGGACCCCCAAC
R: ACTCAGTTGTGCCAGTCACC
F: AAACTGGTGTGCTGAAAGAGC R: GCTTCCACCGTAAATTCTCC
F: GAGGAAGTGGGAGACGACAA R: CCTTCCAACGATCCAATCAT
F: CATTGCAAAGCGATTACCC
F: CGCCTTGGAAGAGTTAATCG
F: TCTGATCTCTCGAACCTCTCG
F: TGCTTTCTCTGCATCACTCG
MgSTS837 10 357023 F: AATGACGCACGATCTCTCG
MgSTS332 10 18598693 F: GTGGTGTGCAATTCATTATCC
MgSTS672 14 25799001 F: AATCAACCGCAATTCTGACC
AAT217 17 727542 F: ACCTGGACTACCATGTACCG
R: TAATCACATTCGGCAACTCG
R: CCGGATCCTTGTTGAGTAGC
R: AGGCTGGTGGCTTATCTTCC
R: ACTCCAGGAACGTTTGGATG
R: ATGCAAAGCCTGAAAAGTGC
R: ATCGTTGGATCTCGTTGTCC
R: ATCTAGCTCGCACCAACTCC
R: CTCTACCCCGGTTGTATTGC
R: GGAACCCCTATCATCACTTTCC
R: AAATTCATCACTGGACATTTCG
R: GGGAATTAATCCTCAACAAAGC
R: CCTTGAGTACGGCTTCTTCG

Supplementary Table 3 Missing alleles for M. guttatus sp. – indicates number of accessions with missing data.
M. arvensis
M. guttatus
M. nasutus
M. nudatus
M. pardalis
M. tilingii
M. cupriphilus
perennials
M. laciniatus
M. micranthus
M. guttatus annuals
Inversion markers
278 59 69
–
–
–
–
–
–
– – 1
3
–
1
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
84
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
173 299 563 675
– – – –
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
M. arvensis
M. cupriphilus
M. guttatus
M. guttatus
M. laciniatus
M. micranthus
M. nasutus
M. nudatus
M. tilingii annuals perennials
M. pardalis
217 332 423 571 617 665 672 837
–
–
2
2
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
Non inversion markers
–
–
–
2
–
–
–
–
–
–
–
–
–
1
–
–
–
–
1
–
–
–
2
1
–
–
1
–
–
–
–
–
–
2
–
–
–
–
–
–
–
–
1
1
1
–
–
–
–
–
–
–
1
1
–
–
–
–
–
–

Supplementary Table 4 Genetic diversity indices for each locus for members of the M. guttatus sp. complex and for M. guttatus annuals and perennials. N a
= Number of alleles; H e
= expected heterozygosity; H o
= observed heterozygosity; F
IS
= inbreeding coefficient; Inv = inverted region; NI = non-inverted region. Indices are given with standard error. Indices for which the inversion markers exhibit lower diversity than the noninversion markers are in bold. NA = insufficient data.
Taxon Inv Locus
M. guttatus annuals
M. guttatus perennials
299
173
563
84
M. guttatus all accessions 69
278
675
59
299
173
563
84
69
278
675
59
299
173
563
84
69
278
675
59
N a
38
38
19
6
18
11
9
19
12
21
15
7
18
7
10
15
16
31
24
9
24
12
13
26
H o
0.421
0.421
0.421
0.263
0.395
0.395
0.211
0.421
0.227
0.405
0.267
0.364
0.333
0.222
0.244
0.341
0.317
0.413
0.337
0.317
0.361
0.301
0.229
0.378
H e
0.883
0.928
0.872
0.759
0.897
0.800
0.765
0.889
0.830
0.902
0.877
0.791
0.893
0.613
0.724
0.759
0.885
0.938
0.896
0.792
0.914
0.779
0.770
0.850
F
IS
0.522
0.551
0.517
0.653
0.560
0.506
0.725
0.526
0.723
0.551
0.692
0.540
0.627
0.637
0.662
0.551
0.642
0.560
0.624
0.600
0.605
0.613
0.703
0.555

M. arvensis
M. laciniatus
M. nasutus
M. tilingii
563
84
69
278
675
59
299
173
563
84
69
278
675
59
299
173
563
84
69
278
675
59
299
173
563
84
69
278
675
59
299
173
3
4
4
5
6
5
9
8
6
2
4
5
8
6
4
5
4
4
2
1
2
2
1
1
2
1
3
4
3
2
4
3
0.222
0.444
0.167
0.417
0.250
0.083
0.000
0.000
0.295
0.083
0.111
0.333
0.444
0.000
0.333
0.222
0.111
0.889
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.111
0.333
0.222
0.000
0.222
0.222
0.728
0.852
0.719
0.451
0.361
0.538
0.583
0.292
0.308
0.601
0.772
0.796
0.765
0.494
0.809
0.741
0.500
0.673
0.000
0.000
0.444
0.000
0.000
0.000
0.444
0.444
0.475
0.599
0.494
0.370
0.636
0.204
0.766
0.443
0.550
1.000
0.650
-0.091
NA
NA
1.000
NA
1.000
NA
1.000
1.000
0.695
0.478
0.768
0.077
0.308
0.845
1.000
1.000
0.435
0.861
0.856
0.581
0.419
1.000
0.588
0.700
0.778
-0.321

Taxon NI Locus
M. guttatus annuals
M. guttatus perennials
665
423
571
332
M. guttatus all accessions 217
837
672
217
837
672
617
665
423
571
217
837
672
617
M. arvensis
617
665
423
571
332
217
837
672
617
665
423
571
N a
14
26
24
25
26
31
17
7
24
19
24
22
25
10
8
13
34
30
29
34
35
19
1
3
2
11
1
3
4
2
H o
0.528
0.405
0.447
0.541
0.237
0.421
0.474
0.279
0.205
0.395
0.535
0.279
0.326
0.273
0.111
0.380
0.296
0.420
0.538
0.259
0.370
0.378
0.157
0.000
0.000
0.000
0.333
0.000
0.667
0.000
H e
0.858
0.934
0.928
0.942
0.929
0.948
0.859
0.813
0.941
0.890
0.932
0.917
0.895
0.778
0.400
0.842
0.945
0.919
0.943
0.938
0.935
0.833
0.487
0.000
0.667
0.000
0.611
0.444
0.667
0.444
F
IS
0.385
0.566
0.518
0.426
0.745
0.556
0.449
0.657
0.783
0.556
0.426
0.696
0.636
0.649
0.722
0.549
0.687
0.543
0.430
0.724
0.604
0.546
0.678
NA
1.000
NA
0.455
1.000
0.000
1.000

M. laciniatus
M. nasutus
M. tilingii
423
571
332
217
837
672
617
665
423
571
332
332
217
837
672
617
665
423
571
332
217
837
672
617
665
7
6
7
3
4
6
3
7
6
11
10
5
7
3
5
1
4
7
5
3
5
5
1
4
7
0.083
0.250
0.083
0.444
0.000
0.667
0.556
0.444
0.111
0.667
0.000
0.000
0.222
0.000
0.125
0.222
0.333
0.000
0.333
0.000
0.167
0.083
0.083
0.364
0.500
0.358
0.569
0.392
0.710
0.741
0.895
0.883
0.802
0.772
0.796
0.370
0.000
0.568
0.815
0.758
0.673
0.710
0.494
0.623
0.000
0.635
0.767
0.344
0.587
0.764
0.767
0.561
0.788
0.374
1.000
0.255
0.371
0.446
0.856
0.163
1.000
NA
0.609
1.000
0.835
0.670
0.530
1.000
0.465
NA
0.738
0.891
0.758
0.380
0.345

Supplementary Table 5 Results of stepwise forward selection of variables for inclusion in RDA. CV = coefficient of variation. Mean diurnal range = mean of monthly (max temp – min temp). Temperature annual range = max temperature warmest month – min temperature coldest month. Isothermality = (mean diurnal range/temperature annual range)* 100. Temperature Seasonality (standard deviation *100). * p

0.050, ** p

0.010, *** p

0.001.
Model AIC
Noninversion
Mean temperature coldest quarter + Mean temperature driest quarter
+ Min. temperature coldest month + Temperature annual range
+ Temperature seasonality
+ Precipitation CV
+ Mean temperature warmest quarter
+ Annual mean temperature
+ Isothermality
+ Annual precipitation
+ Precipitation coldest quarter
+ Precipitation wettest quarter
+ Precipitation wettest month
+ Precipitation warmest quarter
+ Precipitation driest month
+ Mean diurnal range (Mean of monthly (max temp - min temp))
+ Precipitation driest quarter
+ Mean temperature wettest quarter
+ Maximum temperature warmest month
Inversion
Minimum temperature coldest month + Precipitation wettest month
+Precipitation wettest quarter + Precipitation warmest quarter
+ Precipitation CV + Isothermality
+ Precipitation driest month
121.23*
121.99
121.98
122.11
122.13
122.19
122.17
122.18
122.24
122.25
122.27
122.36
122.38
122.58
121.23
132.91**
133.56

+ Precipitation driest quarter
+ Mean diurnal range
+ Mean temperature driest quarter
+ Maximum temperature warmest month
+ Temperature annual range
+ Mean temperature wettest quarter
+ Annual precipitation
+ Mean temperature warmest quarter
+ Annual mean temperature
+ Precipitation coldest quarter
+ Mean temperature coldest quarter
+ Temperature seasonality
133.63
133.63
133.83
133.79
133.83
133.99
133.95
133.98
134.01
134.02
134.02
133.98

Appendix 1
We conducted a redundancy analysis (RDA) to determine whether variation in morphology and flowering time was correlated with variation in noninversion and inversion markers. We selected variables by first performing a RDA with stepwise forward addition of the morphological variables and flowering time and assessing their significance using AIC. We retained any variables that explained significant portions of genomic variation for full RDA and partial RDA
(the latter where the annual/perennial status of M. guttatus accessions was held constant). We found that one variable (height in cm) was correlated with noninversion variation and one variable (diameter between the first and second true leaves) was correlated with inversion variation (Supplementary Table 6). In a full RDA, we found that annual/perennial status was significantly associated with both noninversion and inversion marker variation. Height was significantly correlated with noninversion variation and diameter between first and second true leaves and significantly correlated with inversion variation (Supplementary Table 7); these correlations did not change in a partial RDA where annual/perennial status was held constant.

Supplementary Table 6 Results of stepwise forward selection of morphological variables and flowering time for inclusion in RDA. * p

0.050, ** p

0.010, *** p

0.001.
Model AIC
Noninversion
Height (cm)
Flowering time post germination (days)
Length of first leaf (mm)
Width of first leaf (mm)
Length of first flower (mm)
Length of second internode (mm)
Number of pairs of leaves upon flowering
Width of first flower (mm)
Diameter btw 1 st
and 2 nd
true leaves (mm)
Presence of anthocyanin calyx spots
Inversion
Diameter btw 1 st
and 2 nd
true leaves (mm)
Length of first flower (mm)
Width of first flower (mm)
Flowering time post germination (days)
Number of pairs of leaves upon flowering
Presence of anthocyanin calyx spots
Length of second internode (mm)
Length of first leaf (mm)
Height (cm)
Width of first leaf (mm)
104.98**
105.62
105.65
105.76
105.75
105.80
105.97
106.01
106.28
107.01
117.43**
118.12
118.26
118.21
118.24
119.19
118.33
118.43
118.46
118.52

Supplementary Table 7 Results of redundancy analysis testing for associations between morphology variables and variation in the inversion and non-inversion markers within M. guttatus . All terms remain significant when annual/perennial status is held constant. Significance assessed with a minimum of 1,000 permutations: * p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001.
% variance P
Inversion
Annual/Perennial 23.25 0.001***
Diameter btw 1 st
and 2 nd
true leaves 18.63 0.001***
Noninversion
Annual/Perennial
Height (cm)
12.78
20.22
0.022*
0.001**

Appendix 2
We investigated whether F
ST
and allelic variation in the DIV1 inversion markers could be a function of distance to the breakpoints. Plots of F
ST
and number of alleles (N a
) of inversion markers with respect to their position on linkage group 8 show little evidence of an association
(Supplementary Figures 1 and 2). There is no significant correlation between F
ST
and distance to the leftmost breakpoint (as determined by recent mapping experiments (Friedman, unpublished data) ( r = 0.19, p = 0.68; Spearman rank correlation coefficient). Similarly, there is no signficiant correlation between number of alleles and distance to the leftmost breakpoint. ( r = -0.13, p =
0.78; Spearman rank correlation coefficient). Since F
ST
can be impacted by the heterozygosity of the individual markers, and since we have so few markers, this analysis should be interpreted with caution. This question would be better addressed with genomic sequence data.

Supplementary Figure 1

Supplementary Figure 2