Molecular phylogeny and evolution in Calyptratae flies with an emphasis on the Oestridae

With some 23,000 named species, calyptrate flies (Diptera: Calyptratae), consisting of Hippoboscoidea, Oestroidea and the muscoid grade and representing 20% of dipteran diversity, make up the largest and most ecologically diverse clade within the schizophoran super-radiation.The Calyptratae are distributed worldwide, and exhibit enormously diverse life habits, especially for the larvae. The phylogeny of calyptrates is well resolved except for the Oestroidea, within which group the family-level relationships have only recently begun to emerge with reliable support, and biology of many subgroups are still missing. This thesis aims to construct calyptrate phylogeny using transcriptomic / mitogenomic data, suggest a suitable classification of key groups (i.e., Calliphoridae) and trace the evolutionary history of the diverse life habits of calyptrates. The major findings are described as follows.

By documenting mitogenomic data of two calyptrate species, we conducted phylogeneticanalyses of calyptrates using mitogenomes with the most comprehensive methodologies by then.This study indicates that, for calyptrate phylogeny reconstruction using mitogenomes, data partitioning and the inclusion of conserved tRNA genes have little effect, and that the 3rd -codon positions of protein-coding genes are not saturated and therefore should be included. The Oestroidea are nested within the paraphyletic muscoid grade, and relationships at the family level within Oestroidea are: {remaining Calliphoridae (Sarcophagidae (Oestridae, Pollenia + Tachinidae))}.

With newly documented mitogenomic data for one species and transcriptomic data for 25 sarcophagid species, we reconstructed the phylogeny of the Sarcophagidae, and the subfamilylevel relationship is consistently recovered as {Sarcophaginae, (Miltogramminae, Paramacronychinae)}. The Sarcophagidae and each subfamily are reconstructed as having originated and diversified in the New World. The ancestral larval feeding habit of all sarcophagids is estimated to be sarcosaprophagy, with larval food usage and feeding habits becoming specialized during the radiation of flesh flies. The kleptoparasitism of Miltogramminae is derived from sarcosaprophagy in buried vertebrate carrion.

Aiming at clarifying the phylogeny of the Calliphoridae, the main challenge in calyptrate phylogeny, we reconstructed the calyptrate phylogeny with transcriptomic data covering all calyptrate families and 10 out of 13 (formerly) recognized calliphorid subfamilies. After comprehensive analyses testing robustness of the topology, we confirmed that the typical metallic-coloured blowflies (Calliphorinae, Chrysomyinae and Luciliinae) have originated twice independently, and we hereby propose a re-classification of calliphorids sensu lato, keeping Calliphoridae to comprise Calliphorinae (including Melanomyinae) and Luciliinae, raising the remaining subfamilies (Ameniinae, Bengaliinae, Chrysomyinae and Helicoboscinae) to family rank.

Phylogeny of the mysterious stomach bot flies (Oestridae: Gasterophilinae) was constructed using extensive mitogenomic data for Cobboldia, Gyrostigma and six of the eight known species of Gasterophilus. Based on this phylogeny, we traced evolutionary history of several biological patterns for the first time for this group: (a) their host shifts from elephants to rhinoceroses and then from rhinoceroses to equids; (b) dispersal from the Afrotropical region into the Palaearctic and Oriental regions together with their hosts; (c) oviposition site originated on the host head area, and fecundity positively correlated with distance from host mouth; (d) 3rd -instar larvae originally attaching in the stomach, with other locations secondarily derived; and (e) enrichment of guanine and cytosine (GC) in the mitogenome as a possible adaptation to larvae living in the host digestive tract, combined with the need for a high evolutionary rate to cope with the fast evolution of their mammalian hosts.