We found that intraspecific and interspecific genetic divergence overlaps for 7 of 13 species. Five of these species are not monophyletic. Several factors may explain species non-monophyly (Funk and Omland 2003), but incomplete
lineage sorting and imperfect taxonomy are probably among the most important for Gomphostilbiain Thailand. Simulium
asakoae and S. doisaketense are not monophyletic. One sample of each forms another lineage with 100% bootstrap
support. Deep divergence of this clade from the others suggests that it is a genetically distinct species.Simulium kuvangkadilokae is not monophyletic because it includes the sister species S. chumpornense; yet, these two species are
clearly differentiated morphologically. The geographic distributions of these species would seem to exclude the possibility of hybridization.Simulium kuvangkadilokaeis found in northeastern Thailand, whereas S. chumpornenseoccurs
in southern and western Thailand. The most likely explanation, therefore, is incomplete lineage sorting. Nonetheless,
imperfect taxonomy cannot be excluded because three haplotypes of S. kuvangkadilokae showed high genetic divergence (1.03%–4.43%). Imperfect taxonomy is also the reason for overlap of intraspecific and interspecific genetic
divergence inS. sheilae, which shows two deep-divergence lineages. One lineage is the sister of S. trangenseand another is the sister of this clade. Genetic differentiation between the two clades of S. sheilaeis high (8.69%–9.08%),
suggesting genetically distinct species. Overlap also occurs between intraspecific and interspecific sequence divergence
in three reciprocally monophyletic species (S. angulistylum, S. decuplum, and S. gombakense). This overlap might not affect the use of DNA barcoding for species identification, but it suggests the presence of additional diversity.