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 / Population Name / Latitude / nAustralia / Cooktown / 15.48 / 9
Australia / Cairns / 16.91 / 10
Australia / Cardwell / 18.26 / 10
Australia / Red Rock / 29.98 / 10
Australia / Tuncury / 32,18 / 6
Australia / Sydney / 33.96 / 10
Australia / Yarra Valley / 37.66 / 10
Australia /
Miller’s Orchard
/ 41.24 / 9Australia / Sorell / 42.77 / 9
United States / Rocky Ridge / 44.01 / 15
United States / Biscay Farms / 43.05 / 14
United States / Terhune Orchards / 40.35 / 17
United States / Solebury Orchards / 40.21 / 16
United States / Raleigh / 35.47 / 15
United States / Robert is Here Orchard / 25.28 / 15
United States / Fruit&Spice Park / 25.50 / 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 / Associated window / Window size / #genes /window / Gene centered?HERC2 / Y/N / X / 20203154-20224924 / 20,213,337-20,218,718 / 5381 / 1 / Y
CG2995 / Y/N / X / 102829-110847 / 85,735-104,334 / 18,600 / 3 / N
glu / Y/N / 2L / 16729546-16734301 / 16,731,317-16,737,494 / 6177 / 2 / Y
chd1 / Y/N / 2L / 2979697-2987677 / 2,982,496-2,986,379 / 3883 / 1 / Y
CG7420 / Y/N / 2L / 1500830-1502903 / 1,502,779-1,507,146 / 4367 / 1 / N
chm / Y/Y / 2L / 7412453-7422389 / 7,410,897-7,416,684 / 5787 / 2 / Y
ssrp / Y/N / 2R / 19314961-19316595 / 19,311,720-19,315,687 / 3967 / 2 / Y/N
Mi-2 / Y/N / 3L / 19815886-19844050 / 19,816,835-19,818,616 / 1781 / 1 / Y
Bj1 / Y/N / 3L / 5904206-5906720 / 5,904,698-5,909,853 / 5155 / 2 / Y/N
CG9153 / Y/Y / 3L / 1295210-1303860 / 1,291,981-1,300,882 / 8901 / 3 / N
trx / Y/N / 3R / 10089080-10112623 / 10,110,440-10,117,537 / 7097 / 3 / N
tara / Y/Y / 3R / 12049371-12088024 / 12,086,016-12,087,006 / 990 / 1 / N
HP1c / Y/N / 3R / 18571350-18572327 / 18,565,435-18,571,487 / 6053 / 4 / N
trr / Y/N / X / 1737463-1745931 / 1738978-1742532 / 3554 / 1 / Y
Mes-4 / Y/N / 3R / 23758704-23763571 / 23763389-23768901 / 5512 / 2 / N
dwg / Y/N / X / 2583856-2586215 / 2580241-2584214 / 3973 / 3 / N
msl3 / Y/N / 3L / 7097157-7099470 / 7,096,047-7,101,391 / 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’) / Reverse primer (5’-3’)
chd1 / 1 / CATTCGCAGCCAGCCGCATCTT / GGCCCCACCTCCCCATCTACA
2 / CTGCAGTGGCGGGAGGGAGTG / TGACGGGTCTAGTGGCAGTGATTC
3 / GTCGCCCACGCTGCTCTACTTCC / CTGGCTTCCTTTGCAATCCTAACA
glu / 2 / CGGTTCGTACGCGGTCATCTTCAA / GCGCACCAAATCCTTCCACATCCA
3 / GATGGTGGCGCTTATGATTATGTC / TGTAGGCCACTTGCTCGCTTAGA
4 / CATCCCACGCCCAGCAACCAG / TAAGGAGAAGCGCCGCAAGGAGTC
ssrp / 1 / AGTCCGCCTGCGAAACACATACGA / CCAGAGGCCCACGGACAGGATAAG
2 / GGGGCATCATGTCCAGAACCT / AACGCCCACCAGAAGCTCCTCAGA
3 / CTGTCGCCTCCGCCGCCACTA / ACGCCTAAAGATGACCGAGCAGAA
4 / TGCCCGAAAAACAAATGATGACTT / CGCTGCAGGCCCTCTCGTTCC
Mi-2 / 1 / ATGCCGCCGATTGGTGAGTATTTC / CGACGCCGTAGCCTTTGTGGA
2 / GCCGGTCCGCTCGTGAATG / ACCAGTGCGGCTCCCAGTCC
3 / TCCTGGCAGTGGGTGAAAA / TTGTGTAAGCCGCGAATAGAAG
HERC / 1 / AGCCCACCTCCGCCACACTTCCTT / CCGCCAACGCCGTCACCAACTT
2 / CCCAATGGTCGCGCCCTTTCTTC / CAGCGATGGCATGTGCGAGTGAT
3 / TCAATTGACGGGCGAGGTTCTACG / GATTCGCCAGGCTGCCAAGGTCTC
trr / 1 / GCCAGACGCGCAATCAAACCT / GCCCACTGTAGCCAATTCGTATCC
2 / CTACGCCCTCGCTCTCCACCAG / ATGCGACGATTCCCCTTCCAGTTA
3 / TTTTTGGCCCGCGTTTGATAAGT / AAAGGCGAAACCCGAAAGAGTAGC
chm region / (Peaks corresponding to Figure 1)
peak1 / CAGCTGCCGCATCAACAACA / TCCGGTCGACGTCCTGGTAAT
peak2 / TTGAGTTGGCGGCGAATGAGATAC / ATGCGGATGGGGTTGAAGGTC
peak3 / GCCGGAGAAGTAGCAAGTCAAACC / GGGCTGCGGGCGTATCTCTGTA
peak4 / AAGCCAAAATCAAGCGAAACCAAT / GCAGCCCCCAAGAAACAGAACC
peak5 / AAGGCGAACTACTGGCTGGGT / TACGCTCGGCTTGGGTTTATC
peak6 / CAGCGATCGGCCAACAACAACAC / GCAGGCGGGCAGCATCGTC
peak7a / CAGCGATCGGCCAACAACAACAC / GCAGGCGGGCAGCATCGTC
peak7b / CTGCCGATGTGGATGGATGT / TCGTTCGCGCCGCTTGTTTCT
peak8 / CCCACCCCATTTCCCCTCATCTTT / CTGCCGCCGTCGCTGTCG
peak9 / GCCCGCGGATCCCTTTGAATAC / CACTTTTTGCGTTGCCACAC
peak10 / CGGACAGAAACGACCCATCAC / GTCCTGCCCGCCAACTACAA
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.
G-C / G-T / C-C / C-TAustralia / Tropical / 0.31 / 0.25 / 0.44 / 0
Temperate / 0.07 / 0.86 / 0.07 / 0
G-C / G-A / C-A / C-C
US / Tropical / 0.26 / 0 / 0.66 / 0
Temperate / 0.8 / 0 / 0.2 / 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.