The phylogenetic characteristics of three different 28S rRNA gene regions in Encarsia (Insecta, Hymenoptera, Aphelinidae)

Two expansion segments of the large ribosomal subunit (28S-D2 and 28S-D3) and the ribosomal first internal transcribed spacer (ITS-1) were sequenced to investigate the potential of each region for defining species limits and for inferring phylogenetic relationships within the aphelinid genus Enearsi.a (Hymenoptera, Chalcidoidea). Alignment of the ITS-1 region was complicated by the presence of high levels of length polymorphism. Secondary-structure models of the ITS-I molecule are proposed which led to an improved alignment and the inclusion of some highly polymorphic sequences. The additional information obtained from the secondary-structure models can provide a justification for the exclusion of hypervariable regions from the phylogenetic analysis. The D3 region is the most conserved, ITS-I the most variable of the three gene regions investigated. Phylogenetic analyses suggest the D2 region to be most suitable not only for inferring relationships, but also for taxonomic and diagnostic purposes at species level. The ITS-I region is best suited for inferring relationships between closely related species or among populations of the same species. The combined analysis using all three regions led to a better tree and a reduced number of equally most parsimonious trees. (c) 2006 Gesellschaft fur Biologische Systematik. Published by Elsevier GmbH. All rights reserved.