Supplemental Table 1. Coordinates of seven sequenced gene regions on Muller’s C of D. pseudoobscura.

Gene / bp / Scaffold / Begin / End / Map Begin / Map End / Distance / Ori
en / 377 / Contig3295_Contig8282 / 157,054 / 157,430 / 4,578,323 / 4,578,699 / 3,985,503 / -
exu1 / 357 / Contig3342_Contig5418 / 1,493,205 / 1,493,561 / 8,564,203 / 8,564,559 / 2,311,494 / +
eve / 374 / Contig3083_Contig4177 / 818,191 / 818,564 / 10,876,054 / 10,876,427 / 62,030 / -
Mef2 / 381 / Contig3083_Contig4177 / 880,585 / 880,979 / 10,938,458 / 10,938,842 / 961,655 / +
Amy1 / 427 / Contig2000_Contig6534 / 659,535 / 659,957 / 11,900,498 / 11,900,920 / 2,950,080 / -
vg / 489 / Contig3531_Contig5436 / 2,791,902 / 2,792,390 / 14,851,001 / 14,851,516 / 1,803,163 / +
F6 / 431 / Contig1714_Contig4288 / 30,039 / 30,469 / 16,654,680 / 16,655,110 / 1,271,508 / +

bp, length of the sequenced segment in the Arrowhead background; Scaffold, scaffold that contains the listed gene from the Freeze 1 assembly of the D. pseudoobscura genome (Human Genome Sequencing Center 2003); Begin and End, coordinates of the sequenced gene in the scaffold; Map Begin and End, coordinates of the gene on the ultrascaffold for Muller’s element C (GenBank Accession number CM000071); Distance, number of base pairs to the next gene on the Arrowhead background; Ori, orientation of the gene.

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Supplemental Table 2. Length of the cytogenetic subsections of Muller’s C in D. pseudoobscura

Sect / Length / Gene No. / Sect / Length / Gene No. / Sect / Length / Gene No.
63E / 365,681 / 28 / 69B / 183,296 / 35 / 75C / 383,605 / 54
64A / 352,434 / 35 / 69C / 321,925 / 49 / 76A / 298,327 / 34
64B / 319,283 / 41 / 69D / 245,454 / 11 / 76B / 248,745 / 36
64C / 472,718 / 33 / 69E / 246,531 / 21 / 76C / 200,741 / 11
65A / 240,059 / 18 / 70A / 500,237 / 43 / 77A / 348,745 / 28
65B / 521,788 / 74 / 70B / 441,084 / 38 / 77B / 359,640 / 31
65C / 621,925 / 70 / 70C / 394,370 / 57 / 78A / 387,154 / 44
65D / 309,761 / 36 / 70D / 203,770 / 14 / 78B / 421,225 / 48
66A / 258,500 / 25 / 71A / 293,782 / 46 / 78C / 304,648 / 15
66B / 322,937 / 38 / 71B / 266,855 / 33 / 79A / 383,939 / 55
66C / 322,810 / 42 / 71C / 91,338 / 2 / 79B / 269,501 / 58
66D / 426,588 / 54 / 72A / 354,010 / 6 / 79C / 233,114 / 34
67A / 272,097 / 12 / 72B / 478,715 / 47 / 79D / 244,702 / 15
67B / 234,575 / 34 / 72C / 360,028 / 47 / 80A / 250,783 / 15
67C / 303,762 / 24 / 73A / 282,930 / 29 / 80B / 239,547 / 34
67D / 265,822 / 51 / 73B / 321,523 / 22 / 80C / 259,612 / 24
67E / 220,586 / 10 / 73C / 363,673 / 39 / 81A / 344,402 / 29
68A / 384,693 / 33 / 74A / 217,036 / 40 / 81B / 306,897 / 30
68B / 285,628 / 28 / 74B / 250,763 / 32 / 81C / 241,824 / 16
68C / 483,283 / 68 / 74C / 111,641 / 25 / 81D / 178,596 / 13
68D / 362,872 / 36 / 75A / 213,380 / 8
69A / 154,865 / 16 / 75B / 430,262 / 25

Sect, cytological subsection on Muller’s element C in D. pseudoobscura; Length, number of nucleotides estimated to be within the cytological subsection; Gene No., number of genes estimated to be within the cytological subsection.

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Supplemental Table 3. Maximum heterozygosity observed for ten gene arrangement combinations in D. pseudoobscura. Data from Anderson et al. (1991).

Arr1 / Arr2 / Population / Year / Sample Size / Heterozygosity / Conversion Tracts
AR / PP / Capitan, Hondo, Ruidoso, Lincoln, NM / 1969 / 376 / 0.414 / 1
AR / ST / Methow, WA / 1972 / 320 / 0.417 / 0
AR / CH / Keen Camp, CA / 1939-40 / 4,368 / 0.210 / 2
AR / TL / Spray, OR / 1981-82 / 185 / 0.231 / 5
PP / ST / Placerville, Camino, and Apple Hill, CA / 1957 / 300 / 0.137 / 0
PP / CH / Keen Camp, CA / 1955-56 / 1,838 / 0.034 / 6
PP / TL / Muggins Gulch, CO / 1969 / 410 / 0.122 / 3
ST / CH / Keen Camp, CA / 1948 / 571 / 0.318 / 6
ST / TL / St. Helena, CA / 1963 / 362 / 0.236 / 1
CH / TL / Santa Barbara, CA / 1981 / 312 / 0.174 / 1

Arr1, gene arrangement 1; Arr2, gene arrangement 2. The maximum heterozygosity is estimated from the gene arrangement frequencies and assumes that the chromosomes within the local population are in Hardy-Weinberg equilibrium.

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Supplemental Table 4. Estimates of net nucleotide divergence (dA ± SE) at seven loci between different gene arrangements in D. pseudoobscura.

Arr1 / Arr2 / en / exu1 / eve / Mef2 / Amy1 / vg / F6
AR / PP / 0.005 ± 0.002 / 0.000 ± 0.000 / 0.006 ± 0.003 / 0.005 ± 0.012 / 0.009 ± 0.004 / 0.053 ± 0.012 / 0.001 ± 0.000
AR / ST / 0.000 ± 0.000 / 0.001 ± 0.000 / 0.003 ± 0.003 / 0.001 ± 0.001 / 0.014 ± 0.005 / 0.034 ± 0.009 / 0.000 ± 0.000
AR / CH / 0.002 ± 0.001 / 0.001 ± 0.000 / 0.003 ± 0.001 / 0.006 ± 0.014 / 0.011 ± 0.005 / 0.077 ± 0.015 / 0.018 ± 0.006
AR / TL / 0.005 ± 0.002 / 0.000 ± 0.000 / 0.004 ± 0.003 / 0.006 ± 0.016 / 0.021 ± 0.006 / 0.079 ± 0.014 / 0.015 ± 0.005
PP / ST / 0.007 ± 0.003 / 0.001 ± 0.000 / 0.004 ± 0.002 / 0.005 ± 0.010 / 0.010 ± 0.005 / 0.027 ± 0.008 / 0.000 ± 0.000
PP / CH / 0.007 ± 0.003 / 0.002 ± 0.001 / 0.009 ± 0.003 / 0.008 ± 0.024 / 0.009 ± 0.004 / 0.066 ± 0.013 / 0.019 ± 0.006
PP / TL / 0.015 ± 0.005 / 0.000 ± 0.000 / 0.006 ± 0.003 / 0.000 ± 0.001 / 0.017 ± 0.006 / 0.040 ± 0.010 / 0.015 ± 0.005
ST / CH / 0.003 ± 0.001 / 0.001 ± 0.001 / 0.009 ± 0.004 / 0.005 ± 0.011 / 0.008 ± 0.004 / 0.063 ± 0.013 / 0.019 ± 0.006
ST / TL / 0.002 ± 0.001 / 0.001 ± 0.000 / 0.008 ± 0.004 / 0.006 ± 0.015 / 0.016 ± 0.005 / 0.061 ± 0.013 / 0.015 ± 0.005
CH / TL / 0.006 ± 0.003 / 0.001 ± 0.001 / 0.005 ± 0.003 / 0.009 ± 0.029 / 0.013 ± 0.004 / 0.024 ± 0.007 / 0.011 ± 0.004

Arr1, gene arrangement 1; Arr2, gene arrangement 2. These estimates exclude sequences with an inferred gene conversion tract. Underlined estimates of dA indicate comparisons where gene conversions tracts were detected within the locus.

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Literature Cited

Anderson, W. W., J. Arnold, D. G. Baldwin, A. T. Beckenbach, C. J. Brown et al., 1991 Four decades of inversion polymorphism in Drosophila pseudoobscura. Proceedings of the National Academy of Sciences USA 88: 10367-10371.

Human Genome Sequencing Center, 2003 Drosophila Genome Project, July 12, 2003.

Supplemental Figure Legend

Supplemental Figure 1. Hypothetical gene conversion events in a locus across five gene arrangements of D. pseudoobscura. The five gene arrangements are: AR, Arrowhead; PP, Pikes Peak; ST, Standard; CH, Chiricahua; and TL, Tree Line. The boxes in the diagram represent the polymorphic nucleotides within 30 strains of D. pseudoobscura that carry one of five gene arrangements as well as the one strain of the outgroup species D. miranda. Each column represents a segregating site within the locus. The white squares indicate the nucleotide observed in the outgroup species D. miranda. The derived nucleotide within each segregating site is represented with one of four boxes (black, gray, black dot, and white dot). Example 1 indicates a case where a gene conversion event within Chiricahua would be detected with comparisons to either the Standard or Pikes Peak arrangements. Example 2 shows a case where two Pikes Peak strains share the same gene conversion event that would be detected with comparisons to either the Chiricahua or Treeline arrangements.

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