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Fig. 3. NEXUS files used for the genealogy estimations of Heliconius erato and Heliconius melpomene at the nuclear loci Mannose phosphate isomerase (Mpi) and Triose phosphate isomerase (Tpi). Alignments were generated by using CLUSTAL W (Thompson, J., Higgins, D. & Gibson, T. [1994] Nucleic Acids Res. 22, 4673–4680) and adjusted by eye. Simple sequence repeat (microsatellite) regions were observed in all alignments. Two alignments in particular (Mpi for the H. erato/himera group, and Tpi for the H. melpomene/cydno group), were characterized by extensive regions of repetitive DNA sequences. These included simple poly-A/T sequences, short dinucleotide or trinucleotide repeats, and imperfect repeats of longer units. Additionally, more complex repetitive sequence was particularly characteristic of Mpi in the H. erato/himera alignment. Such regions of DNA sequence are known to undergo a different mode of molecular evolution, replication slippage, although this process is less likely with shorter lengths of repeat sequence (Schlötterer, C. & Tautz, D. [1992] Nucleic Acids Res. 20, 211–215). Nonetheless, if such regions displayed length variation across the alignment, they were excluded from further analyses.