New stiletto flies in the genus Anabarhynchus Macquart (Diptera: Therevidae) from Kangaroo Island, South Australia.

Anabarhynchus Macquart 1848 is a species-rich genus of stiletto flies (Diptera: Therevidae) belonging to the subfamily Therevinae, with over 113 species described from Australia. These flies are diverse and abundant in Australia's eucalypt woodland and mallee habitats. Here we describe, diagnose and illustrate a further three new Anabarhynchus species in the genus as follows: A. aurantilateralis sp. nov. and A. halmaturinus sp. nov., and A. venabrunneis sp. nov., from Kangaroo Island. These new species bring the total number of described Australian species in the genus to 116, with 13 of these known to occur on Kangaroo Island.

Phylogenetics of Australasian gall flies (Diptera: Fergusoninidae): Evolutionary patterns of host-shifting and gall morphology.

This study investigated host-specificity and phylogenetic relationships in Australian galling flies, Fergusonina Malloch (Diptera: Fergusoninidae), in order to assess diversity and explore the evolutionary history of host plant affiliation and gall morphology. A DNA barcoding approach using COI data from 203 Fergusonina specimens from 5gall types on 56 host plant species indicated 85 presumptive fly species. These exhibited a high degree of host specificity; of the 40 species with multiple representatives, each fed only on a single host genus, 29 (72.5%) were strictly monophagous, and 11 (27.5%) were reared from multiple closely related hosts. COI variation within species was not correlated with either sample size or geographic distance. However variation was greater within oligophagous species, consistent with expectations of the initial stages of host-associated divergence during speciation. Phylogenetic analysis using both nuclear and mitochondrial genes revealed host genus-restricted clades but also clear evidence of multiple colonizations of both host plant genus and host species. With the exception of unilocular peagalls, evolution of gall type was somewhat constrained, but to a lesser degree than host plant association. Unilocular peagalls arose more often than any other gall type, were primarily located at the tips of the phylogeny, and did not form clades comprising more than a few species. For ecological reasons, species of this gall type are predicted to harbor substantially less genetic variation than others, possibly reducing evolutionary flexibility resulting in reduced diversification in unilocular gallers.

INSECT PHYLOGENOMICS. Response to Comment on "Phylogenomics resolves the timing and pattern of insect evolution".

Tong et al. comment on the accuracy of the dating analysis presented in our work on the phylogeny of insects and provide a reanalysis of our data. They replace log-normal priors with uniform priors and add a "roachoid" fossil as a calibration point. Although the reanalysis provides an interesting alternative viewpoint, we maintain that our choices were appropriate.

The evolution and biogeography of the austral horse fly tribe Scionini (Diptera: Tabanidae: Pangoniinae) inferred from multiple mitochondrial and nuclear genes.

Phylogenetic relationships within the Tabanidae are largely unknown, despite their considerable medical and ecological importance. The first robust phylogenetic hypothesis for the horse fly tribe Scionini is provided, completing the systematic placement of all tribes in the subfamily Pangoniinae. The Scionini consists of seven mostly southern hemisphere genera distributed in Australia, New Guinea, New Zealand and South America. A 5757 bp alignment of 6 genes, including mitochondrial (COI and COII), ribosomal (28S) and nuclear (AATS and CAD regions 1, 3 and 4) genes, was analysed for 176 taxa using both Bayesian and maximum likelihood approaches. Results indicate the Scionini are strongly monophyletic, with the exclusion of the only northern hemisphere genus Goniops. The South American genera Fidena, Pityocera and Scione were strongly monophyletic, corresponding to current morphology-based classification schemes. The most widespread genus Scaptia was paraphyletic and formed nine strongly supported monophyletic clades, each corresponding to either the current subgenera or several previously synonymised genera that should be formally resurrected. Molecular results also reveal a newly recognised genus endemic to New Zealand, formerly placed within Scaptia. Divergence time estimation was employed to assess the global biogeographical patterns in the Pangoniinae. These analyses demonstrated that the Scionini are a typical Gondwanan group whose diversification was influenced by the fragmentation of that ancient land mass. Furthermore, results indicate that the Scionini most likely originated in Australia and subsequently radiated to New Zealand and South American by both long distance dispersal and vicariance. The phylogenetic framework of the Scionini provided herein will be valuable for taxonomic revisions of the Tabanidae.

Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota.

The integration of phylogenetics, phylogeography and palaeoenvironmental studies is providing major insights into the historical forces that have shaped the Earth's biomes. Yet our present view is biased towards arctic and temperate/tropical forest regions, with very little focus on the extensive arid regions of the planet. The Australian arid zone is one of the largest desert landform systems in the world, with a unique, diverse and relatively well-studied biota. With foci on palaeoenvironmental and molecular data, we here review what is known about the assembly and maintenance of this biome in the context of its physical history, and in comparison with other mesic biomes. Aridification of Australia began in the Mid-Miocene, around 15 million years, but fully arid landforms in central Australia appeared much later, around 1-4 million years. Dated molecular phylogenies of diverse taxa show the deepest divergences of arid-adapted taxa from the Mid-Miocene, consistent with the onset of desiccation. There is evidence of arid-adapted taxa evolving from mesic-adapted ancestors, and also of speciation within the arid zone. There is no evidence for an increase in speciation rate during the Pleistocene, and most arid-zone species lineages date to the Pliocene or earlier. The last 0.8 million years have seen major fluctuations of the arid zone, with large areas covered by mobile sand dunes during glacial maxima. Some large, vagile taxa show patterns of recent expansion and migration throughout the arid zone, in parallel with the ice sheet-imposed range shifts in Northern Hemisphere taxa. Yet other taxa show high lineage diversity and strong phylogeographical structure, indicating persistence in multiple localised refugia over several glacial maxima. Similar to the Northern Hemisphere, Pleistocene range shifts have produced suture zones, creating the opportunity for diversification and speciation through hybridisation, polyploidy and parthenogenesis. This review highlights the opportunities that development of arid conditions provides for rapid and diverse evolutionary radiations, and re-enforces the emerging view that Pleistocene environmental change can have diverse impacts on genetic structure and diversity in different biomes. There is a clear need for more detailed and targeted phylogeographical studies of Australia's arid biota and we suggest a framework and a set of a priori hypotheses by which to proceed.

Amplification of DNA from preserved specimens shows blowflies were preadapted for the rapid evolution of insecticide resistance.

Mutations of esterase 3 confer two forms of organophosphate resistance on contemporary Australasian Lucilia cuprina. One form, called diazinon resistance, is slightly more effective against commonly used insecticides and is now more prevalent than the other form, called malathion resistance. We report here that the single amino acid replacement associated with diazinon resistance and two replacements associated with malathion resistance also occur in esterase 3 in the sibling species Lucilia sericata, suggesting convergent evolution around a finite set of resistance options. We also find parallels between the species in the geographic distributions of the polymorphisms: In both cases, the diazinon-resistance change is absent or rare outside Australasia where insecticide pressure is lower, whereas the changes associated with malathion resistance are widespread. Furthermore, PCR analysis of pinned specimens of Australasian L. cuprina collected before the release of organophosphate insecticides reveals no cases of the diazinon-resistance change but several cases of those associated with malathion resistance. Thus, the early outbreak of resistance in this species can be explained by the preexistence of mutant alleles encoding malathion resistance. The pinned specimen analysis also shows much higher genetic diversity at the locus before organophosphate use, suggesting that the subsequent sweep of diazinon resistance in Australasia has compromised the scope for the locus to respond further to the ongoing challenge of the insecticides.

Molecular phylogeny and biogeography of the dung beetle genus Temnoplectron Westwood (Scarabaeidae: Scarabaeinae) from Australia's wet tropics.

The landscape of the Australian Wet Tropics can be described as "islands" of montane rainforest surrounded by warmer or more xeric habitats. Historical glaciation cycles have caused expansion and contraction of these rainforest "islands" leading to consistent patterns of genetic divergence within species of vertebrates. To explore whether this dynamic history has promoted speciation in endemic and diverse groups of insects, we used a combination of mtDNA sequencing and morphological characters to estimate relationships and the tempo of divergence among Australian representatives of the dung beetle genus Temnoplectron. This phylogenetic hypothesis shares a number of well-supported clades with a previously published phylogenetic hypothesis based on morphological data, though statistical support for several nodes is weak. Sister species relationships well-supported in both tree topologies, and a tree obtained by combining the two data sets, suggest that speciation has mostly been allopatric. We identify a number of speciation barriers, which coincide with phylogeographic breaks found in vertebrate species. Large sequence divergences between species emphasize that speciation events are ancient (pre-Pleistocene). The flightless, rainforest species appear to have speciated rapidly, but also in the distant past.

Phylogeny of the syrphoidea (Diptera) inferred from mtDNA sequences and morphology with particular reference to classification of the pipunculidae (Diptera).

Sequence data from 420 bp of mitochondrial 12s ribosomal DNA and 490 bp of 16s rDNA were analyzed for 27 species of Syrphoidea (Diptera) and two outgroup taxa. Morphological data for the Pipunculidae were combined with the pipunculid molecular data set. A partition homogeneity test on these data sets revealed no significant incongruence. The pipunculid phylogeny from molecular data closely resembles the published phylogeny based on morphology, with differences only with respect to the Nephrocerinae. There is very strong support for the monophyly of the Pipunculinae and the Chalarinae. The Nephrocerinae are hypothesized to be paraphyletic. Within the Syrphidae, there is support for a monophyletic Syrphinae and Microdontinae, but the Eristalinae are paraphyletic. More data are needed to resolve the eristaline phylogeny.

Higher-level phylogeny of the Therevidae (Diptera: insecta) based on 28S ribosomal and elongation factor-1 alpha gene sequences.

Therevidae (stilleto flies) are a little-known family of asiloid brachyceran Diptera (Insecta). Separate and combined phylogenetic analyses of 1200 bases of the 28S ribosomal DNA and 1100 bases of elongation factor-1alpha were used to infer phylogenetic relationships within the family. The position of the enigmatic taxon Apsilocephala Kröber is evaluated in light of the molecular evidence. In all analyses, molecular data strongly support the monophyly of Therevidae, excluding Apsilocephala, and the division of Therevidae into two main clades corresponding to a previous classification of the family into the subfamilies Phycinae and Therevinae. Despite strong support for some relationships within these groups, relationships at the base of the two main clades are weakly supported. Short branch lengths for Australasian clades at the base of the Therevinae may represent a rapid radiation of therevids in Australia.

Congruence and controversy: toward a higher-level phylogeny of Diptera.

The order Diptera (true flies) is one of the most species-rich and ecologically diverse clades of insects. The order probably arose in the Permian, and the main lineages of flies were present in the Triassic. A novel recent proposal suggests that Strepsiptera are the sister-order to Diptera. Within Diptera, evidence is convincing for the monophyly of Culicomorpha, Blephariceromorpha, and Tipulomorpha but weak for the monophyly of the other basal infraorders and for the relationships among them. The lower Diptera (Nematocera) is paraphyletic with respect to Brachycera, and morphological evidence suggests the sister-group of Brachycera lies in the Psychodomorpha. Recent analyses suggest Tipulomorpha are closer to the base of Brachycera than to the base of Diptera. Brachycera are undoubtedly monophyletic, but relationships between the basal lineages of this group are poorly understood. The monophyly of Stratiomyomorpha, Xylophagomorpha, Tabanomorpha, and Muscomorpha is well supported. Eremoneura, and its constituent clades Empidoidea and Cyclorrhapha, are monophyletic. The sister-group of Eremoneura is likely to be part or all of Asiloidea. Several viewpoints on the homology of the male genitalia of eremoneuran flies are discussed. Phylogenetic analyses suggest that lower Cyclorrhapha (Aschiza) are paraphyletic; however, schizophoran monophyly is well supported. The monophyly of Acalyptratae is not well-founded and the relationships between acalyptrate superfamilies remain obscure. Recent advances document the monophyly of the families of Calyptratae and the relationships among them. Areas critical to future advances in understanding dipteran phylogeny include the relationships among the basal infraorders of Diptera and Brachycera and the relationships between the superfamilies of acalyptrates. Progress in dipteran phylogenetics will accelerate with the exploration of novel data sources and the formulation of hypotheses in an explicitly quantitative framework.

DNA profiling resolves the limited importance of flower colour in defining varieties of Lantana camara.

Randomly amplified polymorphic DNA (RAPD), successfully used to establish flower colour, is of limited importance in characterising weedy varieties of Lantana camara. Initially the internal transcribed spacer 1 (ITS1) region was sequenced for common pink and common pink-edged red varieties of L. camara from Australia and L. urticofolia from the neotropics. This proved unhelpful in differentiating varieties due to a lack of variation and the hybrid origin of L. camara, necessitating the utilisation of DNA profiling techniques. Unweighted pair group method arithmetic average (UPGMA) analysis of RAPD data demonstrated that geographical proximity contributes more significantly to genetic relatedness than flower colour. Analysis of molecular variance (AMOVA) likewise demonstrated that geography accounts for a relatively large variance component. These data indicate that the use of flower colour as a primary identification tool needs to be reevaluated. The use of RAPD may prove useful in characterising the weedy varieties of lantana present in Australia and the South Pacific. Since biological control efforts are being hindered by the inadequacy of current morphological taxonomy, it is expected that DNA profiling will underpin continuing studies on the management and control of L. camara.

GROUNDPLANS AND EXEMPLARS: PATHS TO THE TREE OF LIFE.

- During cladistic analysis of a diverse higher taxon it is impractical to code every species as a separate terminal. In such cases, workers proceed in one of two distinct ways: (1) examine a number of member species in order to deduce groundplan character states of the higher group before the analysis is begun, here called the intuitive method, or (2), code a number of real species belonging to the group as terminals in the analysis, called the exemplar method. Both methods have the same aim, to estimate the groundplan of the higher taxon concerned. Both groundplan estimation methods will lead to identical results when the character in question has the same state in all members of the terminal group, however when the character has two or more states, the two methods may give different results. The precise methods employed in the intuitive approach have not been articulated in the literature, but possible techniques may result in non-parsimonious ancestral state assignments, even in simple cases. Groundplan estimation in the exemplar method is an extension of parsimony. The exemplar method allows groundplan state/s at internal nodes to be calculated during tree search. In many cases the exemplar method assigns a number of possible states to the groundplan, and the state assignment is therefore equivocal. This is not a deficiency of the method but reflects the notion that the parsimony criterion alone cannot always distinguish a single state present in a hypothetical ancestor. The optimal choice of exemplars required to estimate the groundplan most efficiently is discussed under a simple and common hypothesis of character transformation. For complex character distributions up to three exemplars may be required, each from a separate lineage of the group close to its hypothetical common ancestral node.