Table S1. Population sample names and latitudes from the east coasts of Australia and the US. The
two “tropical” and two “temperate” populations on each continent are in bold. “n” refers to the
sample size for the RFLP cline analysis.
Continent
Australia
Australia
Australia
Australia
Australia
Australia
Australia
Australia
Australia
Population Name
Cooktown
Cairns
Cardwell
Red Rock
Tuncury
Sydney
Yarra Valley
Miller’s Orchard
Sorell
United States
United States
United States
United States
United States
United States
United States
Rocky Ridge
Biscay Farms
Terhune Orchards
Solebury Orchards
Raleigh
Robert is Here Orchard
Fruit&Spice Park
Latitude
15.48
16.91
18.26
29.98
32,18
33.96
37.66
41.24
42.77
n
9
10
10
10
6
10
10
9
9
44.01
43.05
40.35
40.21
35.47
25.28
25.50
15
14
17
16
15
15
19
Table S2. Genes associated with chromatin that overlap significant windows from tiling array
analysis (Turner et al. In review).
Gene
Aus?/US? Chr Gene Location
HERC2
Y/N
X
CG2995 Y/N
glu
Y/N
X
2L
chd1
Y/N
2L
CG7420 Y/N
2L
chm
Y/Y
2L
ssrp
Y/N
2R
Mi-2
Y/N
3L
Bj1
Y/N
3L
CG9153 Y/Y
3L
trx
Y/N
3R
tara
Y/Y
3R
HP1c
Y/N
3R
trr
Y/N
X
Mes-4
Y/N
3R
dwg
Y/N
X
msl3
Y/N
3L
2020315420224924
102829-110847
1672954616734301
29796972987677
15008301502903
74124537422389
1931496119316595
1981588619844050
59042065906720
12952101303860
1008908010112623
1204937112088024
1857135018572327
17374631745931
2375870423763571
25838562586215
70971577099470
Associated
window
20,213,33720,218,718
85,735-104,334
16,731,31716,737,494
2,982,4962,986,379
1,502,7791,507,146
7,410,8977,416,684
19,311,72019,315,687
19,816,83519,818,616
5,904,6985,909,853
1,291,9811,300,882
10,110,44010,117,537
12,086,01612,087,006
18,565,43518,571,487
1738978-1742532
Window #genes
Gene
size
/window centered?
5381
1
Y
18,600
6177
3
2
N
Y
3883
1
Y
4367
1
N
5787
2
Y
3967
2
Y/N
1781
1
Y
5155
2
Y/N
8901
3
N
7097
3
N
990
1
N
6053
4
N
3554
1
Y
2376338923768901
2580241-2584214
5512
2
N
3973
3
N
7,096,0477,101,391
5344
3
Y
Table S3. See Excel file.
Table S4. Report of primer pairs used to generate sequence data used to generate Table 2 and all
chm figures and tables.
Gene Regions (Corresponding to Table 2, except chm--see below)
region
Forward primer (5’-3’)
chd1
1
CATTCGCAGCCAGCCGCATCTT
2
CTGCAGTGGCGGGAGGGAGTG
3
GTCGCCCACGCTGCTCTACTTCC
glu
2
CGGTTCGTACGCGGTCATCTTCAA
3
GATGGTGGCGCTTATGATTATGTC
4
CATCCCACGCCCAGCAACCAG
ssrp
1
AGTCCGCCTGCGAAACACATACGA
2
GGGGCATCATGTCCAGAACCT
3
CTGTCGCCTCCGCCGCCACTA
4
TGCCCGAAAAACAAATGATGACTT
Mi-2
1
ATGCCGCCGATTGGTGAGTATTTC
2
GCCGGTCCGCTCGTGAATG
3
TCCTGGCAGTGGGTGAAAA
HERC
1
AGCCCACCTCCGCCACACTTCCTT
2
CCCAATGGTCGCGCCCTTTCTTC
3
TCAATTGACGGGCGAGGTTCTACG
trr
1
GCCAGACGCGCAATCAAACCT
2
CTACGCCCTCGCTCTCCACCAG
3
TTTTTGGCCCGCGTTTGATAAGT
chm region
(Peaks corresponding to Figure 1)
peak1
CAGCTGCCGCATCAACAACA
peak2
TTGAGTTGGCGGCGAATGAGATAC
peak3
GCCGGAGAAGTAGCAAGTCAAACC
peak4
AAGCCAAAATCAAGCGAAACCAAT
peak5
AAGGCGAACTACTGGCTGGGT
peak6
CAGCGATCGGCCAACAACAACAC
peak7a
CAGCGATCGGCCAACAACAACAC
peak7b
CTGCCGATGTGGATGGATGT
peak8
CCCACCCCATTTCCCCTCATCTTT
peak9
GCCCGCGGATCCCTTTGAATAC
peak10
CGGACAGAAACGACCCATCAC
Reverse primer
GGCCCCACCTCCC
TGACGGGTCTAG
CTGGCTTCCTTTG
GCGCACCAAATC
TGTAGGCCACTTG
TAAGGAGAAGCG
CCAGAGGCCCAC
AACGCCCACCAG
ACGCCTAAAGAT
CGCTGCAGGCCC
CGACGCCGTAGC
ACCAGTGCGGCT
TTGTGTAAGCCGC
CCGCCAACGCCG
CAGCGATGGCAT
GATTCGCCAGGC
GCCCACTGTAGCC
ATGCGACGATTCC
AAAGGCGAAACC
TCCGGTCGACGTC
ATGCGGATGGGG
GGGCTGCGGGCG
GCAGCCCCCAAG
TACGCTCGGCTTG
GCAGGCGGGCAG
GCAGGCGGGCAG
TCGTTCGCGCCGC
CTGCCGCCGTCGC
CACTTTTTGCGTT
GTCCTGCCCGCCA
Table S5. Frequencies of 2-site haplotypes (amino acid variant and genotyped clinal SNP). Note
that these two sites exhibit strong evidence of differentiation, further supporting the inference from
D’ estimates (D’=1 for all regions) that on each continent, the arginine/proline amino acid
polymorphism is clinal.
Australia
US
Tropical
Temperate
G-C
0.31
0.07
G-T
0.25
0.86
C-C
0.44
0.07
C-T
0
0
Tropical
Temperate
G-C
0.26
0.8
G-A
0
0
C-A
0.66
0.2
C-C
0
0
Figure S1. Multi-species alignment of the portion of coding sequence carrying the 3’ amino acid
variant between tropical and temperate chm alleles. Note that the “tropical variant” actually occurs
at a frequency of 0.43 and 0.47 in the tropical regions of Australia and the US, respectively, and at
0.08 and0.06 in the temperate regions of Australia and US.
Figure S2. Multi-species alignment of the portion of coding sequence carrying the 3’ amino acid
variant between tropical and temperate chm alleles. Note that the “tropical variant” actually occurs
at a frequency of 0.47 and 0.69 in the tropical regions of Australia and the US, respectively, and at
0.0.08 and 0.2 in the temperate regions of Australia and US.