Systematics and evolution of the Australian Dacini (Diptera: Tephritidae) Melissa Starkie BAppSc/BBus, BSc(Hons) Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy 2020 School of Biology and Environmental Science Science and Engineering Faculty Queensland University of Technology i Keywords Dacini, systematics, phylogenetics, biogeography, Australia, Pacific, taxonomy, Tephritidae. ii Abstract The Dacini fruit flies (Diptera: Tephritidae) are a widely distributed clade that occupy tropical and subtropical forests across Africa, South-east Asia, Australia, and the Pacific. While there are existing systematic studies on this group, the Australian and Pacific fauna have been under-sampled and deeper evolutionary questions neglected. This study produces a molecular phylogenetic reconstruction based on targeted sampling of the Australian and Pacific Dacini in order to investigate biogeographic, systematic and evolutionary questions about the tribe. The overarching aim of this thesis was to produce a Dacini phylogenetic tree and apply this tree to evolutionary, taxonomic and biogeographical questions concerning the group. The main aims of each chapter were to: (i) employ a targeted sampling method to expand the taxonomic and geographic collections available for analysis (Chapter 2); (ii) produce a multi-locus molecular phylogenetic tree (Chapter 3) and then, (iii) use this tree to investigate phylogenetic signal of the traits: male lure response and host breadth (Chapter 3); (iv) evaluate the ability of morphological character traits to resolve phylogenetic relationships (Chapter 4); (v) investigate the influence of biogeography in the Australian and Pacific region on divergence of the regional Dacini (Chapter 5); (vi) investigate basal lineages and inform a taxonomic review of the Bactrocera aglaiae species group (Chapter 6); and (vii) reconcile new genetic data with previous taxonomic relationships (based on morphology) in a taxonomic review of the Bactrocera tryoni species group (Chapter 7). In Chapter 2, species were sampled along the east coast of Australia, using a combination of male lures, protein baits and fruit rearing in order to expand existing collections. Over 8600 specimens were collected during this study. New geographic distributions are recorded for five species, new lure responses are recorded for three species, a new species is described based on morphology. Chapter 3 utilised 144 described species from Australia, the Pacific, and South-east Asia for a phylogenetic reconstruction of the tribe Dacini. The Bactrocera aglaiae species group was resolved as the oldest Bactrocera clade sampled in this study, distributed in northern Australia and Papua New Guinea. Consistent with other molecular phylogenies of the Dacini, there was poor agreement between systematic placement of species in the phylogeny and their morphologically based taxonomic iii placement at the subgeneric and species complex levels. Divergence time estimates provided dates that were younger than the only previously dated phylogeny of this group, with the tribe estimated as diverging from its most recent common ancestor 43 million years ago. Ancestral trait reconstruction and tests for phylogenetic signal revealed that male lure response exhibits strong phylogenetic signal across the tree. Host diet breadth also exhibited phylogenetic signal, but was not as strong. My phylogeny, like others before it, found poor alignment between Dacini systematic placements based on molecular data versus morphological data. Chapter 4 evaluated colour patterns and structural characters that are typically used in descriptions and diagnosis of Dacini species for their utility in phylogenetic reconstruction. When compared against datasets that contained only molecular data, the AU test found there was no significant improvement to the resolution of the tree when morphological characters were added to a molecular dataset. When morphological characters were used to reconstruct a phylogeny alone, species were not able to be resolved at the generic or species levels in a way congruent with current systematic understanding of the group. Chapter 5 utilised the dated phylogeny from Chapter 3 to investigate divergence pathways. The analysis found that regional Dacini species moved eastward into the Pacific from Papua New Guinea and Australia, and that there was no westward movement of species back into those regions. There was evidence of multiple incursions via the Torres Strait land bridge into and out of Australia and Papua New Guinea, both in deeper and more recent evolutionary time. Within Australia, species have moved westward into the Northern Territory and southward out of north Queensland. There is no evidence, given the present-day distributions of fruit flies, that biogeographical land barriers have played a significant role in fruit fly speciation within Australia. In Chapter 6 a taxonomic review of the Bactrocera aglaiae species group is provided. This included resolution of discrepancies between the descriptions of the holotype, and previous descriptions based on paratypes. Within the review, new species descriptions and identification of variation was provided. In addition, likelihood mapping tests confirmed the clade as the oldest Bactrocera clade. iv The systematics of the Bactrocera tryoni species complex, which contains several of Australia’s most important fruit fly pest species, was investigated in detail in Chapter 7 of the thesis based on paraphyly of species in the phylogeny produced in Chapter 3. Utilising a reduced genome source of SNP data, sequence data and morphological observations, it was found that the traditional concept of the complex as containing four species (B. tryoni, B. neohumeralis, B. aquilonis and B. melas) needed to be enlarged to include B. ustulata, B. erubescentis, B. mutabilis and B. curvipennis. Further B. humilis (a taxa morphologically very similar to B. tryoni) and B. melas showed no genetic evidence consistent with them being true species. To accommodate the extra species, the B. tryoni complex was taxonomically redefined as a species group, B. tryoni was redescribed, and B. humilis and B. melas were synonymised with B. tryoni. The potential for unrecognised cryptic species, morphologically similar to B. tryoni and B. neohumeralis, existing within the group is discussed. Chapter 8 presents my final thoughts for the future of Dacini taxonomy and systematics. I recommend subgeneric groups be removed from use in Dacini taxonomy due to their lack of utility. In addition, using the term ‘species group’ instead of ‘species complex’ is also recommended based on the confusion this has caused other taxonomists. A case study using the B. frauenfeldi species complex is provided as an example of how results from each chapter can be used to investigate difficult species groups. Finally, I conclude by acknowledging this thesis has developed a comprehensive dataset which is a good starting point for any investigation of key species groups, trait analysis and large-scale biogeographic analyses. v Table of Contents Keywords .................................................................................................................. ii Abstract .................................................................................................................... iii List of Figures ........................................................................................................ xiii List of Tables ........................................................................................................ xxii Statement of authorship ....................................................................................... xxvi Acknowledgements ............................................................................................ xxvii Chapter 1: Introduction ................................................................................................ 1 1.1. General Introduction .......................................................................................... 1 1.2. The Dacini ......................................................................................................... 2 1.2.1. Distribution ................................................................................................. 3 1.2.2. Biology ........................................................................................................ 4 1.2.3. Current taxonomy and phylogenetic understanding of the Dacini tribe ..... 6 1.2.1. The Unified Species Concept .................................................................... 12 1.2.5. Morphology in phylogenetics ................................................................... 12 1.2.6. Current use of molecular phylogenies ...................................................... 15 1.2.7. Biogeography ............................................................................................ 17 1.3. Thesis aims and structure ................................................................................ 18 Chapter 2: Collections and new records ..................................................................... 21 2.1. Introduction ..................................................................................................... 21 2.2. Materials and methods ..................................................................................... 21 2.2.1. Trapping locations and rationale ............................................................... 21