Table S1 Description of the five topo-climatic factors used in the environmental association analyses of Arabidopsis halleri. All factors are available
at a resolution of 25 m and were interpolated and averaged from meteorological measurements collected over a 30-year period between 1961
and 1990 (Zimmermann & Kienast 1999).
Environmental factor Abbreviation Description
Unit
In this study correlated with
Precipitation
PRECYY
Yearly precipitation sum (rain and snow)
1/10 mm/yr Moisture index
Slope
SLP25
Slope
°
Aspect*
Solar radiation
SRADYY
Annual mean of daily global potential shortwave radiation
kJ/m2/day
Topographic position, topographic wetness index*
Site water balance
SWB
Temperature
TAVEYY
Annual average site water balance (= precipitation – evapotranspiration) 1/10 mm/yr Moisture index, topographic wetness index*
Altitude*, cloudiness, degree days, frost*, moisture index*,
Mean average annual temperature
1/100 °C
precipitation days, topographic position*, topographic wetness
index
* Negatively correlated factors.
Table S2 Average genome-wide FST of pairwise population comparisons in Arabidopsis halleri, and threshold for accepting strongly differentiated
SNPs. To take population structure into account, the thresholds have been adjusted by the pairwise neutral population genetic differentiation.
Comparison
Aha 09:11
Aha 09:19
Aha 09:21
Aha 09:31
Aha 11:19
Aha 11:21
Aha 11:31
Aha 19:21
Aha 19:31
Aha 21:31
Mean
mean FST
0.042
0.034
0.035
0.026
0.041
0.048
0.044
0.037
0.035
0.036
0.038
SNP FST threshold
0.555
0.547
0.548
0.539
0.554
0.561
0.557
0.550
0.548
0.549
0.545
Table S3 The 175 identified genes covering the highly differentiated SNPs that have at least one association with one or more of the five
environmental factors studied (see Table S1; Supporting information). Given are the gene IDs from TAIR10 (Lamesch et al. 2012), the
number of associations with environmental factors, and the putative gene function.
Gene ID
AT1G04510
AT1G05540
AT1G05700
AT1G06000
AT1G06170
AT1G06960
AT1G06970
AT1G09020
AT1G09190
AT1G09970
AT1G10380
AT1G11905
AT1G15050
AT1G16460
AT1G16540
AT1G20200
AT1G20500
AT1G24095
AT1G30290
AT1G30330
AT1G48090
AT1G52900
AT1G53050
AT1G53460
AT1G53470
Precipitation
(PRECYY)
Slope
(SLP25)
SNPs associated with
Radiation
Site water balance
(SRADYY)
(SWB)
2
1
3
1
1
Temperature
(TAVEYY)
8
1
2
1
1
1
1
7
6
3
2
1
1
2
1
4
5
1
1
10
1
2
4
2
2
1
1
Description
Pre-mRNA-processing factor 19
hypothetical protein
Leucine-rich repeat transmembrane protein kinase protein
UDP-glycosyltransferase-like protein
transcription factor bHLH89
RNA recognition motif-containing protein
cation/H(+) antiporter 14
sucrose nonfermenting 4-like protein
pentatricopeptide repeat-containing protein
leucine-rich receptor-like protein kinase
Putative membrane lipoprotein
B-cell receptor-associated protein 31-like protein
auxin-responsive protein IAA34
rhodanese homologue 2
Molybdenum cofactor sulfurase
26S proteasome regulatory subunit N3
4-coumarate--CoA ligase-like 4
Putative thiol-disulfide oxidoreductase DCC
PPR repeat domain-containing protein
auxin response factor 6
calcium-dependent lipid-binding-like protein
Toll-Interleukin-Resistance domain-containing protein
protein kinase-like protein
hypothetical protein
mechanosensitive channel of small conductance-like 4
AT1G53500
AT1G53520
AT1G60860
AT1G61240
AT1G64010
AT1G64070
AT1G64610
AT1G65730
AT1G68720
AT1G69720
AT1G78650
AT1G80560
AT1G80580
AT1G80660
AT1G80680
AT1G80690
AT1G80740
AT1G80750
AT2G17050
AT2G19600
1
14
AT2G19880
AT2G20960
AT2G20970
AT2G21500
AT2G21680
AT2G21770
AT2G21900
AT2G21950
AT2G21960
AT2G22070
AT2G22090
1
3
1
5
2
5
10
1
1
1
4
2
1
1
1
1
1
1
2
1
1
13
1
1
3
3
3
5
2
2
6
2
1
3
3
15
UDP-glucose 4,6-dehydratase
chalcone isomerase-like protein
ADP-ribosylation factor GTPase-activating protein AGD2
lysine ketoglutarate reductase trans-splicing related 1
serine protease inhibitor-like protein
TIR-NBS-LRR class disease resistance protein
WD40 domain-containing protein
putative metal-nicotianamine transporter YSL7
tRNA-specific adenosine deaminase
heme oxygenase 3
DNA-directed DNA polymerase
3-isopropylmalate dehydrogenase 2
ethylene-responsive transcription factor ERF084
H(+)-ATPase 9
suppressor of auxin resistance 3
PPPDE putative thiol peptidase family protein
putative DNA (cytosine-5)-methyltransferase CMT1
60S ribosomal protein L7-1
TIR-NBS-LRR class disease resistance protein
K(+) efflux antiporter 4
nucleotide-diphospho-sugar transferase domain-containing
protein
phospholipase-like protein (PEARLI 4) domain-containing protein
putative lipid binding protein
RING/U-box domain-containing protein
Kelch motif-containing protein
cellulose synthase A
putative WRKY transcription factor 59
F-box/kelch-repeat protein SKIP6
hypothetical protein
pentatricopeptide repeat-containing protein
UBP1 interacting protein 1a
AT2G22680
AT2G23350
AT2G23390
AT2G23460
AT2G23790
AT2G23810
AT2G24617
AT2G25410
AT2G28490
AT2G28890
AT2G29510
AT2G29760
AT2G30280
AT2G30290
AT2G30300
AT2G30590
AT2G30780
AT2G31060
AT2G31570
AT2G31620
AT2G32860
AT2G33010
AT2G33040
AT2G33150
AT2G33670
AT2G35140
AT2G35160
AT2G35800
AT2G36190
AT2G36330
AT2G36370
AT2G36910
2
31
1
1
3
3
5
1
1
3
2
2
1
14
3
4
2
1
1
2
1
8
11
2
8
1
2
6
1
2
6
1
11
2
52
1
12
1
6
C3HC4-type RING finger domain-containing protein
poly(A) binding protein 4
hypothetical protein
extra-large G-protein 1
hypothetical protein
tetraspanin8
hypothetical protein
RING-H2 finger protein ATL22
cupin domain-containing protein
putative protein phosphatase 2C 23
hypothetical protein
pentatricopeptide repeat-containing protein
RNA-directed DNA methylation 4
vacuolar-sorting receptor 2
major facilitator protein
WRKY DNA-binding protein 21
pentatricopeptide repeat-containing protein
elongation factor-like protein
glutathione peroxidase
putative cysteine-rich repeat secretory protein 10
beta glucosidase 33
Ubiquitin-associated (UBA) protein
ATP synthase subunit gamma
3-ketoacyl-CoA thiolase 2
MLO-like protein 5
DCD (Development and Cell Death) domain protein
histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5
mitochondrial substrate carrier family protein
beta-fructofuranosidase
hypothetical protein
ubiquitin-protein ligase
ABC transporter B family member 1
AT2G36950
AT2G37070
AT2G37110
AT2G38010
AT2G41460
7
16
7
AT2G41890
3
1
AT2G42330
AT2G42440
AT2G42450
AT2G42560
AT2G42570
AT2G42600
AT2G43255
AT2G43350
AT2G43370
AT2G47010
AT3G19040
AT3G19050
AT3G19220
AT3G19230
AT3G21480
AT3G22425
AT3G22430
AT3G24160
AT3G26100
AT3G26115
AT3G26120
AT3G26590
AT3G26890
AT3G27020
2
9
12
1
8
31
5
12
3
10
2
1
4
10
18
18
20
1
1
37
57
1
2
21
36
9
2
2
4
1
5
12
6
1
2
7
1
1
5
heavy-metal-associated domain-containing protein
hypothetical protein
PLAC8 domain-containing protein
neutral ceramidase
apurinic endonuclease-redox protein
curculin-like mannose-binding lectin fand PAN domaincontaining protein
GC-rich sequence DNA-binding factor-like protein with Tuftelin
interacting domain
LOB domain-containing protein 17
alpha/beta-hydrolase domain-containing protein
late embryogenesis abundant domain-containing protein
protein trichome birefringence-like 39
phosphoenolpyruvate carboxylase 2
hypothetical protein
putative glutathione peroxidase 3
U11/U12 small nuclear ribonucleoprotein 35 kDa protein
hypothetical protein
transcription initiation factor TFIID subunit 1-B
phragmoplast orienting kinesin 2
protein disulfide isomerase
leucine-rich repeat-containing protein
BRCT domain-containing DNA repair protein
Imidazoleglycerol-phosphate dehydratase 1
hypothetical protein
putative type 1 membrane protein
regulator of chromosome condensation repeat-containing
protein
Pyridoxal-5'-phosphate-dependent enzyme family protein
terminal EAR1-like 1
mate efflux domain-containing protein
hypothetical protein
putative metal-nicotianamine transporter YSL6
AT3G28315
AT3G28960
AT3G48010
AT3G49250
AT3G51390
AT3G51410
AT3G51470
AT3G51480
AT3G51490
AT3G51570
2
2
12
2
1
10
1
23
4
11
AT3G51740
AT3G51770
AT3G51850
AT3G51860
AT3G56430
AT3G56590
AT3G61750
AT3G61760
AT4G00550
AT4G00570
AT4G02010
AT4G09040
AT4G09160
AT4G10120
AT4G14220
AT4G17650
AT4G20230
AT4G21070
AT4G21450
AT4G31520
2
1
3
1
2
6
1
3
1
1
27
1
1
1
5
1
1
9
3
1
7
4
11
5
1
4
pseudo
Transmembrane amino acid transporter family protein
cyclic nucleotide gated channel
protein defective in meristem silencing 3
putative S-acyltransferase
hypothetical protein
putative protein phosphatase 2C 47
glutamate receptor 3.6
monosaccharide-sensing protein 3
TIR-NBS-LRR class disease resistance protein
probably inactive leucine-rich repeat receptor-like protein kinase
IMK2
tetratricopeptide repeat (TPR)-containing protein
calcium-dependent protein kinase 13
vacuolar cation/proton exchanger 3
hypothetical protein
hydroxyproline-rich glycoprotein family protein
Cytochrome b561/ferric reductase transmembrane with DOMON
related domain
dynamin-related protein 1B
digalactosyldiacylglycerol synthase 2
malate dehydrogenase (decarboxylating)
protein kinase family protein
RNA recognition motif-containing protein
patellin-5
sucrose-phosphate synthase
E3 ubiquitin-protein ligase RHF1A
Polyketide cyclase / dehydrase and lipid transport protein
terpene cyclase, C1 domain-containing protein
protein BREAST CANCER SUSCEPTIBILITY 1-like protein
vesicle-associated membrane family protein
SDA1 family protein
AT5G03570
AT5G07130
AT5G11720
AT5G12210
AT5G13160
AT5G14570
AT5G14950
AT5G15340
AT5G15440
AT5G15450
AT5G37530
AT5G42800
AT5G43420
AT5G43430
AT5G43650
AT5G46270
AT5G47210
AT5G48170
AT5G48360
AT5G56680
AT5G56790
AT5G56810
AT5G62230
AT5G63000
AT5G63140
AT5G67230
AT5G67500
No annotation
(various genes)
4
2
1
1
2
1
1
1
2
1
1
10
4
1
2
7
7
4
1
1
1
1
1
6
10
9
4
1
6
7
1
1
3
7
6
26
3
protein iron regulated 2
laccase 13
alpha-glucosidase
RAB geranylgeranyl transferase beta subunit 1
serine/threonine-protein kinase PBS1
high affinity nitrate transporter 2.7
alpha-mannosidase II
pentatricopeptide repeat-containing protein
EID1-like F-box protein 1
casein lytic proteinase B3
Rossmann-fold NAD(P)-binding domain-containing protein
dihydroflavonol-4-reductase
RING-H2 finger protein ATL16
Electron transfer flavoprotein subunit beta
transcription factor bHLH92
Disease resistance protein (TIR-NBS-LRR class) family protein
hyaluronan / mRNA binding-like protein
F-box protein SNE
formin-like protein 9
asparaginyl-tRNA synthetase, cytoplasmic 1
protein kinase family protein
putative F-box/FBD/LRR-repeat protein
LRR receptor-like serine/threonine-protein kinase ERL1
Mitochondrial import inner membrane translocase subunit
Tim17/Tim22/Tim23 family protein
purple acid phosphatase 29
glycosyl transferase family 43 protein
voltage dependent anion channel 2
Figure S1: Results for the three candidate genes LOS5/ABA3 (a,d,g), GPX3 (b,e,f) and ATGLR 3.6 (c,f,i). (a,b,c) represent pairwise FST values from
highly differentiated sliding windows (lines) and SNPs (open circles). The bold dotted line at 0.038 indicates the mean FST across all SNPs
and the dotted line at 0.47 represents the 99.9% quantile threshold for strongly differentiated sliding windows. (d,e,f) show correlations
between pairwise population differences in FST, and site water balance (d, e) or solar radiation (f). rPMT represents the correlation coefficient of the
partial Mantel test. (g,h,i) display linear regressions between major allele frequencies and site water balance (g, h) or solar radiation (i).
References
Lamesch P, Berardini TZ, Li D, et al. (2012) The Arabidopsis information resource (TAIR): improved gene annotation and new tools. Nucleic
Acids Research 40, D1202-D1210.
Zimmermann NE, Kienast F (1999) Predictive mapping of alpine grasslands in Switzerland: species versus community approach. Journal of
Vegetation Science 10, 469-482.