From a total of 53 individuals analysed from the Indian Ocean islands (24), Southeast Asia (14), East (6) and West (9) Pacific Islands, sequencing of the 16s rRNA partial fragment revealed three haplotypes, belonging to two strongly differentiated lineages, and with a remarkable geographic structure. Southern Asian (Myanmar, Malaysia and Luzon, Philippines) and Indian Ocean islands individuals exhibited the same haplotype, with around 10% sequence divergence from the ‘Pacific lineage’, which harbours two closely related haplotypes (Fig. 2).
There were 55 variable positions, 53 of them diagnostic for the two clades, including four indels of variable (1-10 bp) size. In every case alignment was unambiguous and no ‘gappy’ region was excluded from the analysis. GenBank sequences from Madagascar and Mauritius had considerable 5’ or 3’ missing data regions, thus restricting the comparable fragment size including all sequences to 334 bp. As they were identical to all other Indian Ocean islands samples for the available sequence fragment (in total 418 bp for DQ857338/Madagascar; 495 bp for DQ270549/Mauritius; and 499bp for AY517559/Mauritius), they were excluded from the haplotype network construction, so that all the differences within the full length of the sequenced fragment could be represented.