Intron positions and near intron pairs

The relatively rare changes of spliceosomal intron positions have been used both for the estimation of intron evolution and phylogenetic relationships, however with variable success. A specific subset of changes at intron positions is here introduced as a novel phylogenetic marker, termed near intron pair (NIP). It is defined here as a pair of mutually-exclusive intron presences at two (different) orthologous sequence positions in close proximity. The idea that NIPs are powerful characters is based on the assumption that both very small exons and multiple gains at the same position are rare. The results of several studies briefly summarized in this chapter demonstrate the successful usage of the NIP character to reconstruct the tree of life and to deliver new insights into mechanisms of intron gain. In a first NIP-based application the phylogenetic position of major orders of holometabolic insects was evaluated supporting Hymenoptera as resulting from their basal split, in agreement with other studies, but contradicting the previously established view. As part of the genome paper describing a new species of twisted-wing parasites (Strepsiptera), the NIP method was applied to help to resolve the phylogenetic position of them within holometabolic insects. However, a NIP-based reconstruction of the metazoan tree covering a broad selection of representative species also identified some weaknesses of the NIP approach that may suffer e.g. from alignment/ortholog prediction artifacts (also depending on the depth of range of taxa) and long-branch attraction (unequal evolutionary rates of intron gain/loss; maximum parsimony based analysis). In a further study, the identification of NIPs within the genus Drosophila could be used to characterize recent intron gain events that apparently involved several cases of intron sliding and tandem exon duplication. Summarizing, the NIP marker could be established as a novel phylogenetic character, in particular dedicated to complementarily explore the wealth of genome data for phylogenetic purposes and to help to resolve open questions of intron evolution.