Table 1

Summary statistics and maximum likelihood model parameters for gene regions. Ten individuals were sampled from each of the three populations, and the same individuals were sequenced for all genes. For nuclear loci, one or two sequences per individual was obtained via cloning of diploid genes. To investigate introgression, paired datasets for sympatric H. cydno and H. melpomene only from Panama (10 individuals each) were analysed using the IM Bayesian algorithm [18]; these are the IM dataset, and IM reduced datasets 1 and 2 – the latter have been purged of presumably recombinant sequences by deleting some individuals and by sampling from 5' or 3' regions of each gene (see methods). Complete alignment data in FASTA format and IM data file format are given in [2 ].

CoI/II

Tpi

Mpi

Ci


No. haplotypes sequenced overall

30

45

45

43

No. haplotypes IM dataset

20

31

27

12

No. haplotypes IM reduced dataset 1

20

31

26

12

No. haplotypes IM reduced dataset 2

20

31

26

12


No. of base pairs of finished sequence

1572

569

453

840

IM dataset

1571

419

315

660

IM reduced dataset 1

1571

245 (5')

315

95 (5')

IM reduced dataset 2

1571

245 (5')

315

495 (3')


Total no. variable sites

92

62

70

186

Variable sites in non-coding region

1

55

66

167

No. variable sites in coding region

91

7

4

19

No. variable sites by codon position (1st/2nd/3rd)

9/0/82

2/0/5

1/0/3

2/2/15

Recombination in IM dataset? (MP, MG, CP, MP+CP)

- - - -

+ - + -

- + - -

+ + + +

Maximum likelihood model selected

TrN+I+G

TrN+G

HKY+G

TrN+I+G

Proportion of invariable sites (I)

0.80

-

-

0.43

Gamma shape parameter (G)

0.90

0.22

0.44

0.75

Base composition

A

0.34

0.36

0.37

0.35

C

0.13

0.14

0.13

0.14

G

0.12

0.18

0.11

0.16

T

0.41

0.32

0.39

0.35

Relative substitution rates

A-C

1

1

1

1

A-G

13.58

1.43

1.50

1.54

A-T

1

1

1

1

C-G

1

1

1

1

C-T

35.7

3.6

1.50

2.95

G-T

1

1

1

1


Bull et al. BMC Biology 2006 4:11   doi:10.1186/1741-7007-4-11

Open Data