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Table 1 ω values estimated from transcriptome and BAC sequences of putative genes in HmYb

From: Signatures of selection in loci governing major colour patterns in Heliconius butterflies and related species

     Pairwise 4
G#1 Putative gene name Total bps2 Lineage-based3 H. m. malletiv. H. m. cythera H. erato v. H. melpomene H. eratov. H. numata H. numatav. H. melpomene mean
     bps ω N5 S6 Bps ω N5 S6 bps ω N5 S6 bps ω N5 S6 ωs
4 Trehalase 1B 1921 0.112 528 0.143 4 8 1740 0.110 48 147 1740 0.110 46 135 1740 0.165 21 35 0.132
6 Trehalase 1A 1776 0.076 1773 0.049 4 21 1773 0.081 31 108 1773 0.086 33 113 1773 0.096 9 29 0.078
7 B9 protein 570               567 0.122 6 13 0.122
8 hypothetical 2235 0.060      2232 0.057 18 167 2232 0.055 17 158 2232 0.099 9 46 0.070
10 WD repeat domain 1038 0.172 1035 0.302 2 2 1035 0.195 30 52 1035 0.211 27 45 1035 0.124 7 22 0.208
11 CG18292 351 0.024 351 0.047 1 6 351 0.011 1 30 351 0.027 2 24 351 0.053 1 5 0.035
12 CG2519 3129 0.071      3129 0.068 48 264 3129 0.080 51 240 3129 0.069 11 64 0.072
13 Unkempt 1812 0.047      1812 0.048 15 103 1812 0.031 10 103 1812 0.059 10 64 0.046
14 Histone H3 408 0.000 408 0 0 0 408 0 0 0 408 0 0 11 408 0 0 0 0
15 hypothetical 408 0.141 408 0.152 1 2 408 0.163 15 24 408 0.135 14 23 408 0.279 3 3 0.182
16 hypothetical 819 0.207      819 0.199 38 62 819 0.190 36 62 819 0.339 13 14 0.243
17 RecQ helicase 1896 0.100 912 0.171 2 3 1896 0.086 29 87 1896 0.095 35 91 1896 0.163 15 20 0.129
18 sorting nexin 1056 0.168      1053 0.188 28 67 1053 0.167 27 69 1053 0.076 2 12 0.144
19 BmSuc2 1491 0.072      1491 0.083 35 152 1491 0.086 37 153 1491 0.036 4 40 0.068
20 CG5796 621 0.115 681 0 0 2 621 0.073 13 61 621 0.157 13 25 621 0.098 4 10 0.082
21 hypothetical 945 0.388 945 0.492 9 4 945 0.409 86 54 945 0.369 69 36 945 0.457 29 14 0.432
22 Enoyl-CoA hydratase 891 0.055 891 0.149 4 8 891 0.049 7 43 891 0.077 10 45 891 0.421 11 8 0.174
23 ATP Binding 288   288 0.139 1 2 288 0.158 12 18          0.149
24 LRR 1419 0.200 1419 0.4058 3 2 1419 0.192 72 82 1419 0.176 68 86 1419 0.504 30 16 0.319
25 Fizzy-like 1179 0.456 1179 0.474 9 7 1179 0.533 57 38 1179 0.567 67 40 1179 0.347 21 20 0.480
  Average   0.191   0.168     0.142     0.137     0.231    0.167
  1. 1G#: Unique gene number used in original annotation and in the BAC walk in Fig. 2. Here truncated from original format "HM000..."
  2. 2Total bps: total length, in basepairs, of the annotated gene.
  3. 3Lineage-based: Heliconius lineage-based background ω estimates ('branch model = 0' in CODEML) using BAC sequences of three species (H. melpomene, H. erato, H. numata). Entire length of each gene was used for this analysis.
  4. 4Pairwise: Results of pairwise analyses (YN00 in PAML) between two H. melpomene races and between three Heliconius species are presented. The number of changes between two sequences for each gene was calculated by taking the product of the substitution rate per site (d N and d S ) and the number of sites (N or S bases). Bps indicate the length of the nucleotide sequences used for each pairwise analysis.
  5. 5N: N*dN or the number of nonsynonymous changes
  6. 6S: S*dS or the number of synonymous changes
  7. Bold formatting indicates genes with ω > 0.19 (average background ω value from lineage wide analyses). ω values were not estimated for base changes of three or fewer.