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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 [Additional file 2 ].

From: Polyphyly and gene flow between non-sibling Heliconius species

  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