Andrew D. Austin

Increased congruence does not necessarily indicate increased phylogenetic accuracy-The behavior of the incongruence length difference test in mixed-model analyses

Comprehensive phylogenetic analyses utilize data from distinct sources, including nuclear, mitochondrial, and plastid molecular sequences and morphology. Such heterogeneous datasets are likely to require distinct models of analysis, given the different histories of mutational biases operating on these characters. The incongruence length difference (ILD) test is increasingly being used to arbitrate between competing models of phylogenetic analysis in cases where multiple data partitions have been collected. Our work suggests that the ILD test is unlikely to be an effective measure of congruence when two datasets differ markedly in size. We show that models that increase the contribution of one data partition over another are likely to increase congruence, as measured by this test. More alarmingly, for many bipartition comparisons, character congruence increases bimodally - either increasing or decreasing the contribution of one data partition will increase congruence - making it impossible to arrive at a single optimally congruent model of analysis.

Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of genome 'morphology'

Mitochondrial gene rearrangements are the latest tool in the arsenal of phylogeneticists for investigating historical relationships. They are complex molecular characters that may provide more reliable evidence of ancestry than comparative molecular data. Here we review the phylogenetic utility of mitochondrial gene rearrangements, and find that despite isolated incidences of convergence, derived gene order appears highly congruent with phylogenies produced from other sources of data. We calculate that the chance of two mitochondrial genomes sharing the same derived genome organisation is only 1/2664, but caution that this ignores the possibility that the (as yet uncharacterised) gene rearrangement mechanism may greatly increase the chance of convergence. Broader taxonomic surveys of mitochondrial genome organisation will lead to a more realistic indication of the historical incidence of convergence in genome organisation.

Characterization of 67 Mitochondrial tRNA Gene Rearrangements in the Hymenoptera Suggests That Mitochondrial tRNA Gene Position Is Selectively Neutral

We present entire sequences of two hymenopteran mitochondrial genomes and the major portion of three others. We combined these data with nine previously sequenced hymenopteran mitochondrial genomes. This allowed us to infer and analyze the evolution of the 67 mitochondrial gene rearrangements so far found in this order. All of these involve tRNA genes, whereas four also involve larger (protein-coding or ribosomal RNA) genes. We find that the vast majority of mitochondrial gene rearrangements are independently derived. A maximum of four of these rearrangements represent shared, derived organizations, whereas three are convergently derived. The remaining mitochondrial gene rearrangements represent new mitochondrial genome organizations. These data are consistent with the proposal that there are an enormous number of alternative mitochondrial genome organizations possible and that mitochondrial genome organization is, for the most part, selectively neutral. Nevertheless, some mitochondrial genes appear less mobile than others. Genes close to the noncoding region are generally more mobile but only marginally so. Some mitochondrial genes rearrange in a pattern consistent with the duplication/random loss model, but more mitochondrial genes move in a pattern inconsistent with this model. An increased rate of mitochondrial gene rearrangement is not tightly associated with the evolution of parasitism. Although parasitic lineages tend to have more mitochondrial gene rearrangements than nonparasitic lineages, there are exceptions (e.g., Orussus and Schlettererius). It is likely that only a small proportion of the total number of mitochondrial gene rearrangements that have occurred during the evolution of the Hymenoptera have been sampled in the present study.

The function of spider egg sacs in relation to parasitoids and predators, with special reference to the Australian fauna

The function of spider egg sacs is analysed as structures to reduce or prevent mortality by parasitoids and predators. The host relationships of the groups concerned are documented, with special reference to the Australian fauna. Many new records are presented and the biology of each group is discussed. Information presented supports the hypothesis that egg sacs are an effective barrier against scavenging predators (generalists), while coevolution between spiders and their specialized (highly adapted) parasitoids and predators is responsible for the specificity displayed by the latter two groups and the structural diversity evident of egg sacs.

Frequent mitochondrial gene rearrangements at the hymenopteran nad3-nad5 junction.

We characterized the organization of mitochondrial genes from a diverse range of hymenopterans. Of the 21 taxa characterized, 12 had distinct, derived organizations. Some rearrangements were consistent with the duplication–random loss mechanism, while others were not. Local inversions were relatively common, i.e., rearrangements characterized by the movement of genes from one mitochondrial strand to the other, opposite or close to their ancestral position. This type of rearrangement is inconsistent with the duplication/random loss model of mitochondrial gene rearrangement. Instead, they are best explained by the operation of recombination. Taxa with derived organizations were restricted to a single, monophyletic group of wasps, the Apocrita, which comprise about 90% of all hymenopterans.

INCREASED GENETIC DIVERSITY IN MITOCHONDRIAL GENES IS CORRELATED WITH THE EVOLUTION OF PARASITISM IN THE HYMENOPTERA

A higher AT content and rate of mtDNA sequence divergence was found in parasitic wasps (Apocrita) compared with nonparasitic wasps (Symphyta). The compositional bias was reflected in extreme codon bias for a cytochrome oxidase I protein coding gene fragment as well as in the types of amino acid substitutions that have occurred during the evolution of this gene fragment. In some instances, compositional bias influenced the definition of a conservative amino acid change. The increased rate of mtDNA sequence evolution probably arose during the early Jurassic, coincident with the first appearance of parasitic wasps in the fossil record. Our results suggest a causal link between the rate of sequence divergence and the parasitic lifestyle.

Subterranean archipelago in the Australian arid zone: mitochondrial DNA phylogeography of amphipods from central Western Australia

In 1998, a unique subterranean ecosystem was discovered in numerous isolated calcrete (carbonate) aquifers in the arid Yilgarn region of Western Australia. Previous morphological and genetic analyses of a subterranean water beetle fauna suggest that calcrete aquifers are equivalent to closed island habitats that have been isolated for millions of years. We tested this hypothesis further by phylogeographic analyses of subterranean amphipods (Crangonyctoidea: Paramelitidae and Hyalidae) using mitochondrial DNA sequence data derived from the cytochrome oxidase I gene. Phylogenetic analyses and population genetic analyses (samova) provided strong evidence for the existence of at least 16 crangonyctoid and six hyalid divergent mitochondrial lineages, each restricted in their distribution to a single calcrete aquifer, in support of the ‘subterranean island (archipelago) hypothesis’ and extending its scope to include entirely water respiring invertebrates. Sequence divergence estimates between proximate calcrete populations suggest that calcretes have been isolated at least since the Pliocene, coinciding with a major aridity phase that led to the intermittent drying of surface water. The distribution of calcretes along palaeodrainage channels and on either side of drainage divides, have had less influence on the overall phylogeographic structure of populations, with evidence that ancestral crangonyctoid and hyalid species moved between catchments multiple times prior to their isolation within calcretes. At least two potential modes of evolution may account for the diversity of subterranean amphipod populations: dispersal/vicariance of stygobitic species or colonization of calcretes by surface species and independent evolution of stygobitic characteristics.

Comparison of preservation techniques for DNA extraction from hymenopterous insects.

Two species of parasitic wasp, Venturia canescens and Leptomastix dactylopii, were killed and preserved by various methods used for Hymenoptera and in mass‐collecting devices. Total genomic DNA was subsequently extracted and a 524 bp fragment of the mitochondrial 16s ribosomal RNA gene amplified by PCR. Results for these techniques were compared with that for fresh material and museum specimens. Material from ‐80°C, 100% ethanol, air‐drying in a desiccator, and critical‐point dried from alcohol all yielded good results after short and long‐term storage, as did specimens from ethylene glycol but not formalin (the latter two being commonly used in pitfall and flight intercept traps). Specimens killed in ethyl acetate vapour and air‐dried yielded very degraded DNA which did not successfully PCR. The use of this killing agent is a likely reason for previous reports of inconsistent results obtained from museum specimens, and the now widespread use of critical‐point drying of wasps and other insects from alcohol is advocated as a potential source of DNA from rare taxa.

Evolutionary relationships among the Braconidae (Hymenoptera: Ichneumonoidea) inferred from partial 16S rDNA gene sequences.

Phylogenetic relationships among the Braconidae were examined using homologous 16S rDNA gene sequence data. Analyses recovered the few well‐supported relationships evident in this family from morphological analyses, viz the monophyly of the microgastroid complex of subfamilies, the monophyly of the cyclostome complex of subfamilies (=braconoids), a sister‐group relationship between the Alysiinae and Opiinae, and a close relationship between the Helconinae and Blacinae. With respect to the braconoid complex of subfamilies, a sister‐group relationship was recovered between Aphidiinae and Mesostoinae, and a clade composed of Gnamptodontinae + Histeromerinae + Rhyssalinae + Aphidiinae +Mesostoinae was also recovered. The Doryctinae and Rogadinae sensu lato (s.l.) were generally not resolved as monophyletic. With respect to the helconoid complex of subfamilies, a sister‐group relationship was recovered between Sigalphinae and Agathidinae, whereas Neoneurinae fell out among other helconoid subfamilies. Other relationships among the helconoid subfamilies were unclear from these analyses. With respect to the microgastroid complex of subfamilies, our data conform to morphological estimates, recovering ((Microgastrinae+Miracinae)+Cardiochilinae)+Cheloninae. The topology of our trees suggests that the cyclostome subfamilies are a natural derived group, inferring that endoparasitism (not ectoparasitism) is the ancestral state for the Braconidae, unless all of the ectoparasitic ancestors of the helconoid+microgastroid subfamilies are now extinct.

Molecular phylogeny of the apocritan wasps: the Proctotrupomorpha and Evaniomorpha

Phylogenetic relationships among the apocritan wasps were investigated using comparative sequence data from the mitochondrial 16S rRNA gene. The gene fragment contained three length polymorphic regions. Relationships that were not sensitive to the alignment procedure are discussed, but should be considered as preliminary only. Maximum parsimony analysis recovered the Evaniomorpha (sensu Rasnitsyn, 1988) as a monophyletic group, with the pattern of relationships Ceraphronoidea + (Evanioidea + [Megalyroidea + Trigonalyoidea]). The Proctotrupomorpha (sensu Rasnitsyn, 1988) were also recovered as a monophyletic group, while the Proctotrupoidea were recovered as paraphyletic. The Proctotrupoidea were only monophyletic if the Platygastroidea and Chalcidoidea were included (i.e. Proctotrupomorpha). Relationships of the Proctotrupomorpha that were supported by this analysis included Diapriidae + (Platygastroidea + Chalcidoidea), and the Vanhorniidae falling inside the Proctotrupidae. However, resolution of other relationships within the Proctotrupomorpha was less reliable, as indicated by low decay indices and low bootstrap proportions. Similarly, the placement of the Cynipoidea relative to the other apocritan lineages was also not recovered confidently.