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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.