A mitochondrial genome phylogeny of termites (Blattodea: Termitoidae) : robust support for interfamilial relationships and molecular synapomorphies define major clades

Despite their ecological significance as decomposers and their evolutionary significance as the most speciose eusocial insect group outside the Hymenoptera, termite (Blattodea: Termitoidae or Isoptera) evolutionary relationships have yet to be well resolved. Previous morphological and molecular analyses strongly conflict at the family level and are marked by poor support for backbone nodes. A mitochondrial (mt) genome phylogeny of termites was produced to test relationships between the recognised termite families, improve nodal support and test the phylogenetic utility of rare genomic changes found in the termite mt genome. Complete mt genomes were sequenced for 7 of the 9 extant termite families with additional representatives of each of the two most speciose families Rhinotermitidae (3 of 7 subfamilies) and Termitidae (3 of 8 subfamilies). The mt genome of the well supported sister group of termites, the subsocial cockroach Cryptocercus, was also sequenced. A highly supported tree of termite relationships was produced by all analytical methods and data treatment approaches, however the relationship of the termites + Cryptocercus clade to other cockroach lineages was highly affected by the strong nucleotide compositional bias found in termites relative to other dictyopterans. The phylogeny supports previously proposed suprafamilial termite lineages, the Euisoptera and Neoisoptera, a later derived Kalotermitidae as sister group of the Neoisoptera and a monophyletic clade of dampwood (Stolotermitidae, Archotermopsidae) and harvester termites (Hodotermitidae). In contrast to previous termite phylogenetic studies, nodal supports were very high for family-level relationships within termites. Two rare genomic changes in the mt genome control region were found to be molecular synapomorphies for major clades. An elongated stem-loop structure defined the clade Polyphagidae + (Cryptocercus + termites), and a further series of compensatory base changes in this stem loop is synapomorphic for the Neoisoptera. The complicated repeat structures first identified in Reticulitermes, composed of short (A-type) and long (B-type repeats) defines the clade Heterotermitinae + Termitidae, while the secondary loss of A-type repeats is synapomorphic for the non-macrotermitine Termitidae.

Piecing together an integrative taxonomic puzzle: microsatellite, wing shape and aedeagus length analyses of Bactrocera dorsalis s.l. (Diptera: Tephritidae) find no evidence of multiple lineages in a proposed contact zone along the Thai/Malay Peninsula

Bactrocera dorsalis (Hendel) and B. papayae Drew & Hancock represent a closely related sibling species pair for which the biological species limits are unclear; i.e., it is uncertain if they are truely two biological species, or one biological species which has been incorrectly taxonomically split. The geographic ranges of the two taxa are thought to abut or overlap on or around the Isthmus of Kra, a recognised biogeographic barrier located on the narrowest portion of the Thai Peninsula. We collected fresh material of B. dorsalis sensu lato (i.e., B. dorsalis sensu stricto + B. papayae) in a north-south transect down the Thai Peninsula, from areas regarded as being exclusively B. dorsalis s.s., across the Kra Isthmus, and into regions regarded as exclusively B. papayae. We carried out microsatellite analyses and took measurements of male genitalia and wing shape. Both the latter morphological tests have been used previously to separate these two taxa. No significant population structuring was found in the microsatellite analysis and results were consistent with an interpretation of one, predominantly panmictic population. Both morphological datasets showed consistent, clinal variation along the transect, with no evidence for disjunction. No evidence in any tests supported historical vicariance driven by the Isthmus of Kra, and none of the three datasets supported the current taxonomy of two species. Rather, within and across the area of range overlap or abutment between the two species, only continuous morphological and genetic variation was recorded. Recognition that morphological traits previously used to separate these taxa are continuous, and that there is no genetic evidence for population segregation in the region of suspected species overlap, is consistent with a growing body of literature that reports no evidence of biological differentiation between these taxa.

Evidence of unique genotypes of Beak and feather disease virus in Southern Africa

Psittacine beak and feather disease (PBFD), caused by Beak and feather disease virus (BFDV), is the most significant infectious disease in psittacines. PBFD is thought to have originated in Australia but is now found worldwide; in Africa, it threatens the survival of the indigenous endangered Cape parrot and the vulnerable black-cheeked lovebird. We investigated the genetic diversity of putative BFDVs from southern Africa. Feathers and heparinized blood samples were collected from 27 birds representing 9 psittacine species, all showing clinical signs of PBFD. DNA extracted from these samples was used for PCR amplification of the putative BFDV coat protein (CP) gene. The nucleotide sequences of the CP genes of 19 unique BFDV isolates were determined and compared with the 24 previously described sequences of BFDV isolates from Australasia and America. Phylogenetic analysis revealed eight BFDV lineages, with the southern African isolates representing at least three distinctly unique genotypes; 10 complete genome sequences were determined, representing at least one of every distinct lineage. The nucleotide diversity of the southern African isolates was calculated to be 6.4% and is comparable to that found in Australia and New Zealand. BFDVs in southern Africa have, however, diverged substantially from viruses found in other parts of the world, as the average distance between the southern African isolates and BFDV isolates from Australia ranged from 8.3 to 10.8%. In addition to point mutations, recombination was found to contribute substantially to the level of genetic variation among BFDVs, with evidence of recombination in all but one of the genomes analyzed.

Four new avian mitochondrial genomes help get to basic evolutionary questions in the late cretaceous

Good phylogenetic trees are required to test hypotheses about evolutionary processes. We report four new avian mitochondrial genomes, which together with an improved method of phylogenetic analysis for vertebrate mt genomes give results for three questions in avian evolution. The new mt genomes are: magpie goose (Anseranas semipalmata), an owl (morepork, Ninox novaeseelandiae); a basal passerine (rifleman, or New Zealand wren, Acanthisitta chloris); and a parrot (kakapo or owl-parrot, Strigops habroptilus). The magpie goose provides an important new calibration point for avian evolution because the well-studied Presbyornis fossils are on the lineage to ducks and geese, after the separation of the magpie goose. We find, as with other animal mitochondrial genomes, that RY-coding is helpful in adjusting for biases between pyrimidines and between purines. When RY-coding is used at third positions of the codon, the root occurs between paleognath and neognath birds (as expected from morphological and nuclear data). In addition, passerines form a relatively old group in Neoaves, and many modern avian lineages diverged during the Cretaceous. Although many aspects of the avian tree are stable, additional taxon sampling is required.

A description of the Mei2-like protein family; structure, phylogenetic distribution and biological context

The Schizosaccharomyces pombe Mei2 gene encodes an RNA recognition motif (RRM) protein that stimulates meiosis upon binding a specific non-coding RNA and subsequent accumulation in a “mei2-dot” in the nucleus. We present here the first systematic characterization of the family of proteins with characteristic Mei2-like amino acid sequences. Mei2-like proteins are an ancient eukaryotic protein family with three identifiable RRMs. The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is the most highly conserved of the three RRMs. RRM3 also contains conserved sequence elements at its C-terminus not found in other RRM domains. Single copy Mei2-like genes are present in some fungi, in alveolates such as Paramecium and in the early branching eukaryote Entamoeba histolytica, while plants contain small families of Mei2-like genes. While the C-terminal RRM is highly conserved between plants and fungi, indicating conservation of molecular mechanisms, plant Mei2-like genes have changed biological context to regulate various aspects of developmental pattern formation.

A phylogenetic analysis and taxonomic revision of the oribatid mite family Malaconothridae (Acari: Oribatida), with new species of Tyrphonothrus and Malaconothrus from Australia

Hitherto, the Malaconothridae contained Malaconothrus Berlese, 1904 and Trimalaconothrus Berlese, 1916, defined by the possession of one pre-tarsal claw (monodactyly) or by three claws (tridactyly) respectively. However, monodactyly is a convergent apomorphy within the Oribatida and an unreliable character for a classification. Therefore we undertook a phylogenetic analysis of 102 species as the basis for a taxonomic review of the Malaconothridae. We identified two major clades, equivalent to the genera Tyrphonothrus Knülle, 1957 and Malaconothrus. These genera are redefined. Trimala-conothrus becomes the junior subjective synonym of Malaconothrus. Some 42 species of Trimalaconothrus are recom-bined to Malaconothrus and 15 species to Tyrphonothrus. Homonyms created by the recombinations are rectified. The replacement name M. hammerae nom. nov. is proposed for M. angulatus Hammer, 1958, the junior homonym of M. an-gulatus (Willmann, 1931) and the replacement name M. luxtoni nom. nov. is proposed for M. scutatus Luxton, 1987, the junior homonym of M. scutatus Mihelč ič, 1959. Trimalaconothrus iteratus Subías, 2004 is an unnecessary replacement name and is a junior objective synonym of Malaconothrus longirostrum (Hammer 1966). Malaconothrus praeoccupatus Subías, 2004 is a junior objective synonym of M. machadoi Balogh & Mahunka, 1969. Malaconothrus obsessus (Subías, 2004), an unnecessary replacement name for Trimalaconothrus albulus Hammer 1966 sensu Tseng 1982, becomes an available name for what is in fact a previously-undescribed species of Malaconothrus. We describe four new species of Tyrphonothrus: T. gnammaensis sp. nov. from Western Australia, T. gringai sp. nov. and T. maritimus sp. nov. from New South Wales, and T. taylori sp. nov. from Queensland. We describe six new species of Malaconothrus: M. beecroftensis sp. nov., M. darwini sp. nov. M. gundungurra sp. nov. and M. knuellei sp. nov. from New South Wales, M. jowettae sp. nov. from Norfolk Island, and M. talaitae sp. nov. from Victoria.

Multi-gene phylogenetic analysis of south-east Asian pest members of the Bactrocera dorsalis species complex (Diptera: Tephritidae) does not support current taxonomy

Bactrocera dorsalis sensu stricto, B. papayae, B. philippinensis and B. carambolae are serious pest fruit fly species of the B. dorsalis complex that predominantly occur in south-east Asia and the Pacific. Identifying molecular diagnostics has proven problematic for these four taxa, a situation that cofounds biosecurity and quarantine efforts and which may be the result of at least some of these taxa representing the same biological species. We therefore conducted a phylogenetic study of these four species (and closely related outgroup taxa) based on the individuals collected from a wide geographic range; sequencing six loci (cox1, nad4-3′, CAD, period, ITS1, ITS2) for approximately 20 individuals from each of 16 sample sites. Data were analysed within maximum likelihood and Bayesian phylogenetic frameworks for individual loci and concatenated data sets for which we applied multiple monophyly and species delimitation tests. Species monophyly was measured by clade support, posterior probability or bootstrap resampling for Bayesian and likelihood analyses respectively, Rosenberg's reciprocal monophyly measure, P(AB), Rodrigo's (P(RD)) and the genealogical sorting index, gsi. We specifically tested whether there was phylogenetic support for the four 'ingroup' pest species using a data set of multiple individuals sampled from a number of populations. Based on our combined data set, Bactrocera carambolae emerges as a distinct monophyletic clade, whereas B. dorsalis s.s., B. papayae and B. philippinensis are unresolved. These data add to the growing body of evidence that B. dorsalis s.s., B. papayae and B. philippinensis are the same biological species, which poses consequences for quarantine, trade and pest management.

Insect mitochondrial genomics : implications for evolution and phylogeny

The mitochondrial (mt) genome is, to date, the most extensively studied genomic system in insects, outnumbering nuclear genomes tenfold and representing all orders versus very few. Phylogenomic analysis methods have been tested extensively, identifying compositional bias and rate variation, both within and between lineages, as the principal issues confronting accurate analyses. Major studies at both inter- and intraordinal levels have contributed to our understanding of phylogenetic relationships within many groups. Genome rearrangements are an additional data type for defining relationships, with rearrangement synapomorphies identified across multiple orders and at many different taxonomic levels. Hymenoptera and Psocodea have greatly elevated rates of rearrangement offering both opportunities and pitfalls for identifying rearrangement synapomorphies in each group. Finally, insects are model systems for studying aberrant mt genomes, including truncated tRNAs and multichromosomal genomes. Greater integration of nuclear and mt genomic studies is necessary to further our understanding of insect genomic evolution.

A molecular phylogeny of the checkered beetles and a description of Epiclininae a new subfamily (Coleoptera: Cleroidea: Cleridae)

We provide the first molecular phylogeny of the clerid lineage (Coleoptera: Cleridae, Thanerocleridae) within the superfamily Cleroidea to examine the two most recently-proposed hypotheses of higher-level classification. Phylogenetic relationships of checkered beetles were inferred from approximately ~5,000nt of both nuclear and mitochondrial rDNA (28S, 16S, and 12S) and the mitochondrial protein-coding gene COI. A worldwide sample of ~70 genera representing almost a quarter of generic diversity of the clerid lineage was included and phylogenies were reconstructed using Bayesian and Maximum Likelihood approaches. Results support the monophyly of many proposed subfamilies but were not entirely congruent with either current classification system. The subfamilial relationships within the Cleridae are resolved with support for three main lineages. Tillinae are supported as the sister group to all other subfamilies within the Cleridae, whereas Thaneroclerinae, Korynetinae and a new subfamily formally described here, Epiclininae subf. n, form a sister group to Clerinae + Hydnocerinae.

Pleistocene climate fluctuations influence phylogeographical patterns in Melomys cervinipes across the mesic forests of eastern Australia

Aim Our aim was to clarify the lineage-level relationships for Melomys cervinipes and its close relatives and investigate whether the patterns of divergence observed for these wet-forest-restricted mammals may be associated with recognized biogeographical barriers. Location Mesic closed forest along the east coast of Australia, from north Queensland to mid-eastern New South Wales. Methods To enable rigorous phylogenetic reconstruction, divergence-date estimation and phylogeographical inference, we analysed DNA sequence and microsatellite data from 307 specimens across the complete distribution of M. cervinipes (45 localities). Results Three divergent genetic lineages were found within M. cervinipes, corresponding to geographically delineated northern, central and southern clades. Additionally, a fourth lineage, comprising M. rubicola and M. capensis, was identified and was most closely related to the northern M. cervinipes lineage. Secondary contact of the northern and central lineages was identified at one locality to the north of the Burdekin Gap. Main conclusions Contemporary processes of repeated habitat fragmentation and contraction, local extinction events and subsequent re-expansion across both small and large areas, coupled with the historical influence of the Brisbane Valley Barrier, the St Lawrence Gap and the Burdekin Gap, have contributed to the present phylogeographical structure within M. cervinipes. Our study highlights the need to sample close to the periphery of putative biogeographical barriers or risk missing vital phylogeographical information that may significantly alter the interpretation of biogeographical hypotheses.