Doctor of Philosophy
School of Biological Sciences
Mao, Meng, Mitochondrial genomes and their utility for the recovery of phylogeny in the Hymenoptera, Doctor of Philosophy thesis, School of Biological Sciences, University of Wollongong, 2014. http://ro.uow.edu.au/theses/4206
The Hymenoptera, comprising of sawflies, wasps, bees and ants, is the third largest order of insects. It contains more than 155,000 described species, placed into two traditional suborders (Symphyta and Apocrita). Many hymenopteran species play important roles in biological control, ecosystems and production of commercial products. Unfortunately, higher-level relationships of the Hymenoptera, particularly within the highly diverse parasitic lineages, remain unresolved in both morphological and molecular studies.
The mitochondrial (mt) genome sequence is becoming a powerful tool for reconstructing phylogenetic relationships. In addition, mt gene rearrangements also provide useful phylogenetic information. However, deficient representation of a broad range of lineages restricts the evolutionary utility of the mt genome in the Hymenoptera. For the four infraorders of the Apocrita, the Aculeata and Ichneumonomorpha are reasonably sampled. By contrast, the Evaniomorpha and Proctotrupomorpha are poorly represented. Therefore, this PhD research was focussed on increasing our understanding of mt genomes of the Hymenoptera and their utility for the recovery of the higher-level phylogeny by extending the taxonomic range of available mt genome sequences.
Eleven new mt genomes for representatives of four evaniomorph and four proctotrupomorph superfamilies were determined. Several gene rearrangements were detected in each of the eleven mt genomes when compared with the ancestral positions. In particular, protein-coding or rRNA gene rearrangements were identified in six mt genomes. Mt genome organizations were also compared within the Evaniomorpha and Proctotrupomorpha. The results showed that there were no shared, derived gene rearrangements at the family level, indicating that the frequency of gene rearrangements of these groups is too high to be useful for assessing relationships between families. By contrast, comparison of mt genome organizations within the subfamily Scelioninae suggested that gene rearrangements have much potential as phylogenetic markers at the subfamily level. The large number of gene rearrangements identified in this study also facilitated the investigation of gene rearrangement mechanisms. Direct and indirect evidence that supports the notion that recombination is an important aspect of the gene rearrangement mechanism was identified. Most importantly, the end products of recombination were detected (minicircles), in a megaspilid wasp Conostigmus sp., which provided support for the link between recombination and mt gene rearrangement. Furthermore, a model of recombination which is important for our understanding of mtDNA evolution was developed.
The first mt genome phylogeny of the Apocrita with a complete representation of superfamilies (excluding Mymmaromatoidea) was reconstructed. The influence of inclusion/exclusion of 3rd codon positions, alignment approaches, partition schemes and phylogenetic approaches on topology and nodal support within the Hymenoptera was assessed. The results showed that the topologies were sensitive to the variation of dataset and analytical approach. However, some robust and highly supported relationships were recovered: the Ichneumonomorpha was monophyletic; the Trigonalyoidea + Megalyroidea and the Diaprioidea + Chalcidoidea were consistently recovered; the Cynipoidea was generally recovered as the sister group to the Diaprioidea + Chalcidoidea. In addition, the monophyletic Aculeata and Proctotrupomorpha were recovered in some analyses. Further phylogenetic analysis of the Hymenoptera will rely on increased sampling of both taxa and sequence data.