Generalized structure and evolution of ITS1 and ITS2 rDNA in black flies (Diptera: Simuliidae)

A sample of 15 Nearctic black fly species spread over five genera is used to perform the first systematic study of the internal transcribed spacer 1 (ITS1) from the nuclear rDNA transcription unit of Simuliidae. ITS1 from the Prosimuliini tribe is a conserved, repeat-free and highly structured sequence of about 490 nucleotides (nt), while Simuliini exhibit a medium-sized or short version, the latter minimally 95 nt long. All size versions possess a common 39 nt core made from eight short blocks interspersed among highly variable sequences. Conversely, that variability which generally excludes ITS1 from phylogenetic applications translates for many species into polymorphisms suggesting the general feasibility of ITS1-based population studies. We show in a parallel investigation that ITS2, the other rDNA transcribed spacer, is length-constrained around 270 nt and possesses a three-domain fold anchored by four conserved regions representing about 40% of the whole sequence. An alignment guided by this secondary structure leads to a phylogeny, derived through the GTR model, which convincingly displays the basal divergence between Simuliini and Prosimuliini. However, the poorer support of some intermediate nodes could indicate rapid divergence events within Simulium.