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Fruit flies (Tephritidae: Dacini) are a frugivorous insect group that exhibit high endemic diversity in the rainforests of Australia and the western Pacific. In this region, biogeography has been influenced by tectonic plate movements and cycles of isolation and re‐connection of landmasses and rainforest habitats during glacial periods. However, how such factors have influenced the speciation and historical dispersal of the regional Dacini is largely unknown. To address this, we use a dated phylogeny to reconstruct the biogeographical history of the tribe. We found the Dacini radiated eastward into the Pacific islands largely from sources in New Guinea. We also found evidence for historical dispersal from both Australia and New Guinea into New Caledonia, a pathway unique to this island compared with neighbouring islands. There was also evidence for multiple, bidirectional dispersal events between Papua New Guinea and Australia, likely facilitated by the cyclically exposed Torres Strait land bridge. Cape York in far northern Australia was likely the only entry point for species dispersing into Australia; there was no evidence for entry of flies into Australia directly from West Papua or Wallacea. Several lineages radiated after entering Australia, such as members of the Bactrocera dorsalis species group. Within Australia, speciation was not associated with the biogeographic barriers known to have impacted other rainforest fauna in eastern Australia. Overall, we demonstrate that isolation between islands and large landmasses is important in the evolution of the Australo‐Pacific Dacini, but the reason for their extensive radiation within Australia and Papua New Guinea remains unclear. [ABSTRACT FROM AUTHOR]

Larval feeding by the moth genus Ogmograptis (Bucculatricidae: Lepidoptera) creates one of the most iconic features of the Australian bush—the 'scribbles' found on smooth‐barked Eucalyptus. The taxonomic history of Ogmograptis has been challenging, with members of the genus being initially described in four different genera representing three different superfamilies. While prior phylogenetic analysis has placed Ogmograptis within the Bucculatricidae, these findings were not strongly supported and there was poor resolution of the early diverging, non‐Apoditrysia superfamilies that Ogmograptis has been assigned to by different authors. As a consequence, the unique larval biology of scribbly moths cannot yet be interpreted in an evolutionary context. Phylogenomic analysis of whole mitochondrial (mt) genome data for Ogmograptis, related non‐Apoditrysia and taxa representing the superfamily‐level diversity of the order strongly supports its placement within the Bucculatricidae, a monophyletic Gracillarioidea and a clade of Gracillarioidea + Yponomeutoidea that was sister to the Apoditrysia. The hypermetamorphic larval development in Ogmograptis can thus be interpreted as an elaboration of the ancestral pattern of the clade Gracillarioidea + Yponomeutoidea that has specialised for phellogen/callus feeding within the bark. The utility of mt genomes for deep‐level phylogenetic study of the Lepidoptera is reviewed against prior multi‐locus and nuclear phylogenomic datasets. Mt phylogenomic analyses are sensitive to analytical methods and the inclusion versus exclusion of high‐variability data partitions for deep‐level relationships, already shown to be uncertain by multi‐locus or nuclear phylogenomic analyses, in particular relationships between apoditrysian and obtectomeran superfamilies. While mt genomes are ideal for examining the relationships of rare, physically small or difficult to collect taxa such as Ogmograptis, due to the low technical hurdles to collecting whole genomes, continued attention to the analytical sensitivities of phylogenies that use this data source is needed to reliably advance our understanding of deep lepidopteran evolution. [ABSTRACT FROM AUTHOR]

A phylogenetic hypothesis for the lepidopteran superfamily Noctuoidea was inferred based on the complete mitochondrial (mt) genomes of 12 species (six newly sequenced). The monophyly of each noctuoid family in the latest classification was well supported. Novel and robust relationships were recovered at the family level, in contrast to previous analyses using nuclear genes. Erebidae was recovered as sister to (Nolidae + (Euteliidae + Noctuidae)), while Notodontidae was sister to all these taxa (the putatively basalmost lineage Oenosandridae was not included). In order to improve phylogenetic resolution using mt genomes, various analytical approaches were tested: Bayesian inference (BI) vs. maximum likelihood (ML), excluding vs. including RNA genes (rRNA or tRNA), and Gblocks treatment. The evolutionary signal within mt genomes had low sensitivity to analytical changes. Inference methods had the most significant influence. Inclusion of tRNAs positively increased the congruence of topologies, while inclusion of rRNAs resulted in a range of phylogenetic relationships varying depending on other analytical factors. The two Gblocks parameter settings had opposite effects on nodal support between the two inference methods. The relaxed parameter (GBRA) resulted in higher support values in BI analyses, while the strict parameter (GBDH) resulted in higher support values in ML analyses. [ABSTRACT FROM AUTHOR]

The termite genus Coptotermes (Rhinotermitidae) is found in Asia, Africa, Central/South America and Australia, with greatest diversity in Asia. Some Coptotermes species are amongst the world’s most damaging invasive termites, but the genus is also significant for containing the most sophisticated mound-building termites outside the family Termitidae. These mound-building Coptotermes occur only in Australia. Despite its economic and evolutionary significance, the biogeographic history of the genus has not been well investigated, nor has the evolution of the Australian mound-building species. We present here the first phylogeny of the Australian Coptotermes to include representatives from all described species. We combined our new data with previously generated data to estimate the first phylogeny to include representatives from all continents where the genus is found. We also present the first estimation of divergence dates during the evolution of the genus. We found the Australian Coptotermes to be monophyletic and most closely related to the Asian Coptotermes , with considerable genetic diversity in some Australian taxa possibly representing undescribed species. The Australian mound-building species did not form a monophyletic clade. Our ancestral state reconstruction analysis indicated that the ancestral Australian Coptotermes was likely to have been a tree nester, and that mound-building behaviour has arisen multiple times. The Australian Coptotermes were found to have diversified ∼13 million years ago, which plausibly matches with the narrowing of the Arafura Sea allowing Asian taxa to cross into Australia. The first diverging Coptotermes group was found to be African, casting doubt on the previously raised hypothesis that the genus has an Asian origin. [ABSTRACT FROM AUTHOR]

The author reflects on the methods to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research. Topics discussed include use of mitochondrial (mt) genome for systematic entomology, procedures and software used for insect mt genome annotation, and quality control steps used for new annotations.

Molecular and morphological data indicate that the pest thrips damaging Myoporum species in California and Hawai'i, Klambothrips myopori Mound and Morris, originated in Tasmania, Australia. This trans-Pacific dispersal presumably resulted from the international horticultural trade in Myoporum species. The data distinguish the pest from K. adelaideae sp.n. that induces leaf deformation on M. insulare along the coast of mainland Australia that is separated by ~300 km from Tasmania by the Bass Strait. K. myopori is more damaging to its non-native hosts in California and Hawai'i than to M. insulare in Tasmania, and further research is needed to determine if this is the result of release from its natural enemies. However, in certain areas of California, some Myoporum species are invasive weeds, and K. myopori may be considered an example of an accidental but beneficial introduction in this instance because of its detrimental impact on the plant species. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract: 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. [Copyright &y& Elsevier]

Research over the last two decades has significantly increased our understanding of the evolutionary position of the insects among other arthropods, and the relationships among the insect Orders. Many of these insights have been established through increasingly sophisticated analyses of DNA sequence data from a limited number of genes. Recent results have established the relationships of the Holometabola, but relationships among the hemimetabolous orders have been more difficult to elucidate. A strong consensus on the relationships among the Palaeoptera (Ephemeroptera and Odonata) and their relationship to the Neoptera has not emerged with all three possible resolutions supported by different data sets. While polyneopteran relationships generally have resisted significant resolution, it is now clear that termites, Isoptera, are nested within the cockroaches, Blattodea. The newly discovered order Mantophasmatodea is difficult to place with the balance of studies favouring Grylloblattodea as sister-group. While some studies have found the paraneopteran orders (Hemiptera, Thysanoptera, Phthiraptera and Psocoptera) monophyletic, evidence suggests that parasitic lice (Phthiraptera) have evolved from groups within the book and bark lice (Psocoptera), and may represent parallel evolutions of parasitism within two major louse groups. Within Holometabola, it is now clear that Hymenoptera are the sister to the other orders, that, in turn are divided into two clades, the Neuropteroidea (Coleoptera, Neuroptera and relatives) and the Mecopterida (Trichoptera, Lepidoptera, Diptera and their relatives). The enigmatic order Strepsiptera, the twisted wing insects, have now been placed firmly near Coleoptera, rejecting their close relationship to Diptera that was proposed some 15 years ago primarily based on ribosomal DNA data. Phylogenomic-scale analyses are just beginning to be focused on the relationships of the insect orders, and this is where we expect to see resolution of palaeopteran and polyneopteran relationships. Future research will benefit from greater coordination between intra and inter-ordinal analyses. This will maximise the opportunities for appropriate outgroup choice at the intraordinal level and provide the background knowledge for the interordinal analyses to span the maximum phylogenetic scope within groups. [ABSTRACT FROM AUTHOR]

Abstract: The ancestral genome composition in Onychophora (velvet worms) is unknown since only a single species of Peripatidae has been studied thus far, which shows a highly derived gene order with numerous translocated genes. Due to this lack of information from Onychophora, it is difficult to infer the ancestral mitochondrial gene arrangement patterns for Panarthropoda and Ecdysozoa. Hence, we analyzed the complete mitochondrial genome of the onychophoran Opisthopatus cinctipes, a representative of Peripatopsidae. Our data show that O. cinctipes possesses a highly conserved gene order, similar to that found in various arthropods. By comparing our results to those from different outgroups, we reconstruct the ancestral gene arrangement in Panarthropoda and Ecdysozoa. Our phylogenetic analysis of protein-coding gene sequences from 60 protostome species (including outgroups) provides some support for the sister group relationship of Onychophora and Arthropoda, which was not recovered by using a single species of Peripatidae, Epiperipatus biolleyi, in a previous study. A comparison of the strand-specific bias between onychophorans, arthropods, and a priapulid suggests that the peripatid E. biolleyi is less suitable for phylogenetic analyses of Ecdysozoa using mitochondrial genomic data than the peripatopsid O. cinctipes. [Copyright &y& Elsevier]

We present a mitochondrial (mt) genome phylogeny inferring relationships within Neuropterida (lacewings, alderflies and camel flies) and between Neuropterida and other holometabolous insect orders. Whole mt genomes were sequenced for Sialis hamata (Megaloptera: Sialidae), Ditaxis latistyla (Neuroptera: Mantispidae), Mongoloraphidia harmandi (Raphidioptera: Raphidiidae), Macrogyrus oblongus (Coleoptera: Gyrinidae), Rhopaea magnicornis (Coleoptera: Scarabaeidae), and Mordella atrata (Coleoptera: Mordellidae) and compared against representatives of other holometabolous orders in phylogenetic analyses. Additionally, we test the sensitivity of phylogenetic inferences to four analytical approaches: inclusion vs. exclusion of RNA genes, manual vs. algorithmic alignments, arbitrary vs. algorithmic approaches to excluding variable gene regions and how each approach interacts with phylogenetic inference methods (parsimony vs. Bayesian inference). Of these factors, phylogenetic inference method had the most influence on interordinal relationships. Bayesian analyses inferred topologies largely congruent with morphologically-based hypotheses of neuropterid relationships, a monophyletic Neuropterida whose sister group is Coleoptera. In contrast, parsimony analyses failed to support a monophyletic Neuropterida as Raphidioptera was the sister group of the entire Holometabola excluding Hymenoptera, and Neuroptera + Megaloptera is the sister group of Diptera, a relationship which has not previously been proposed based on either molecular or morphological data sets. These differences between analytical methods are due to the high among site rate heterogeneity found in insect mt genomes which is properly modelled by Bayesian methods but results in artifactual relationships under parsimony. Properly analysed, the mt genomic data set presented here is among the first molecular data to support traditional, morphology-based interpretations of relationships between the three neuropterid orders and their grouping with Coleoptera. [ABSTRACT FROM AUTHOR]

Abstract: We entirely sequenced two new hymenopteran mitochondrial genomes (Cephus cinctus and Orussus occidentalis), and a substantial portion of another three hymenopterans (Schlettererius cinctipes, Venturia canescens, and Enicospilus). We analyze them together with nine others reported in the literature. We establish that the rate of genetic divergence is two to three times higher among some Hymenoptera when compared with others, making this a group with both long and short phylogenetic branches. We then assessed the ability of a range of phylogenetic approaches to recover seven uncontroversial relationships, when lineages show markedly different rates of molecular evolution. This range encompassed maximum parsimony and Bayesian analysis of (i) amino acid data, (ii) nucleotide data, and (iii) nucleotide data excluding third codon positions. Unpartitioned analyses were compared with partitioned analyses, with the data partitioned by codon position (ribosomal genes were placed in a separate partition). These analyses indicated that partitioned, Bayesian analysis of nucleotide data, excluding 3rd codon positions, recovered more of the uncontroversial relationships than any other approach. These results suggest that the analysis of complete mitochondrial genome sequences holds promise for the resolution of hymenopteran superfamily relationships. [Copyright &y& Elsevier]

The Gondwanan relict oribatid mite family Crotoniidae contains the genera AustronothrusHammer, 1966, CrotoniaThorell, 1876 and HolonothrusWallwork, 1963. This family is of considerable interest biogeographically and also because the members of the family may have re-evolved sexuality from thelytokous parthenogenetic ancestors. Crotoniaand Holonothrusare speciose and widely distributed whereas Austronothrusis obscure, hitherto monospecific and known only from New Zealand. We revise Austronothrusand compare it with its better-known congeners. Two new species of Austronothrusare described from New Zealand, namely A. clarki, sp. nov., and A. flagellatus, sp. nov. The only previously known species, Austronothrus curvisetaHammer, 1966, is redescribed and the genus is redefined. The presence of male specimens of all species confirmed Austronothrusas a sexual genus, like its congeners. Secondary sexual characteristics within Austronothrusand Crotoniainclude significant differences in body size and proportion, as well as the lengths and shapes of various setae, predominantly those of the notogastral region. Because these characters are frequently used by taxonomists to separate and define species within the Crotoniidae, it is important that the sex of adult specimens be determined to avoid describing conspecific males and females as separate species. A phylogenetic analysis based on morphological characters shows the crotoniid genera nested within the Camisiidae, with Camisiavon Heyden, 1826 basal to the crotoniid clade of Austronothrus, Holonothrusand Crotonia, and with a clade of PlatynothrusBerlese, 1913, HeminothrusBerlese, 1913 and ParacamisiaOlszanowski & Norton, 2002 (Camisiidae) forming the sister clade of Camisia+Crotoniidae. Thus, Camisiidae is paraphyletic with respect to Crotoniidae. The family Crotoniidae is revised in light of the cladistic analysis, and relegated to subfamily rank. Three subfamilies are defined within the Camisiidae:Crotoniinae (containing Crotonia, Austronothrusand Holonothrus), Camisiinae (containing Camisia) and Heminothridae, subfam. nov. (containing Heminothrus, Platynothrusand NeonothrusForsslund, 1955). Nothrus maximusTrägårdh, 1901 belongs to the genus Platynothrusand is recombined. [ABSTRACT FROM AUTHOR]

We sequenced the entire mitochondrial genome of Abispa ephippium (Hymenoptera: Vespoidea: Vespidae: Eumeninae) and most of the mitochondrial genome of Polistes humilis synoecus (Hymenoptera: Vespoidea: Vespidae: Polistinae). The arrangement of genes differed between the two genomes and also differed slightly from that inferred to be ancestral for the Hymenoptera. The genome organization for both vespids is different from that of all other mitochondrial genomes previously reported. A number of tRNA gene rearrangements were identified that represent potential synapomorphies for a subset of the Vespidae. Analysis of all available hymenopteran mitochondrial genome sequences recovered an uncontroversial phylogeny, one consistent with analyses of other types of data. [ABSTRACT FROM AUTHOR]

Abstract: The entire mitochondrial genome of the tobacco hornworm, Manduca sexta (Lepidoptera: Spinghidae) was sequenced — a circular molecular 15516 bp in size. The arrangement of the protein coding genes (PCGs) was the same as that found in the ancestral insect, however Manduca possessed the derived tRNA arrangement of CR-M-I-Q which has been found in all Lepidoptera sequenced to date. Additionally, Manduca, like all lepidopteran mt genomes, has numerous large intergenic spacer regions and microsatellite-like repeat regions. Nucleotide composition is highly A+T biased, and the lepidopterans have the second most biased nucleotide composition of the insect orders after Hymenoptera. Secondary structural features of the PCGs identified in other Lepidoptera were present but highly modified by the presence of microsatellite-like repeat regions which may significantly alter their function in the post-transcriptional modification of pre-mRNAs. Secondary structure models of the ribosomal RNA genes of Manduca are presented and are similar to those proposed for other insect orders. Conserved regions were identified within non-translated spacer regions which correspond to sites for the origin and termination of replication and transcription. Comparisons of gene variability across the order suggest that the mitochondrial genes most frequently used in phylogenetic analysis of the Lepidoptera, cox1 and cox2, are amongst the least variable genes in the genome and phylogenetic resolution could be improved by using alternative, higher variability genes such as nad2, nad3, nad4 and nad5. [Copyright &y& Elsevier]

Mitochondrial (mt) genome rearrangement has generally been studied with respect to the phenomenon itself, focusing on their phylogenetic distribution and causal mechanisms. Rearrangements have additional significance through effects on substitution, transcription, and mRNA processing. Lice are an ideal group in which to study the interactions between rearrangements and these factors due to the heightened rearrangement rate within this group. The entire mt genome of the screamer louse Bothriometopus was sequenced and compared to previously sequenced louse genomes. The mt genome is 15,564 bp, circular, and all genes are encoded on the same strand. The gene arrangement differs radically from both other louse species and the ancestral insect. Nucleotide composition is A+T biased, but there is no skew which may be due to reversal of replication direction or a transcriptional effect. Bothriometopus has both tRNA duplication and concerted evolution which has not been observed previously. Eleven of the 13 protein-coding genes have 3′ end stem-loop structures which may allow mRNA processing without flanking tRNAs and so facilitate gene rearrangements. There are five candidate control regions capable of forming stem-loop structures. Two are structurally more similar to the control regions of other insect species than those of other lice. Analyses of Bothriometopus demonstrate that louse mt genomes, in addition to being extensively rearranged, differ significantly from most insect species in nucleotide composition biases, tRNA evolution, protein-coding gene structures and putative signaling sites such as the control region. These may be either a cause or a consequence of gene rearrangements. [ABSTRACT FROM AUTHOR]

Termites of the genus Reticulitermes are some of the most significant pests of structural timber and tree farming in the northern hemisphere, causing losses in the billions of dollars annually because of direct damage and termite control costs. This group has been frequently targeted for population genetic, phylogenetic, and species limit studies, most of which use mitochondrial (mt) genes; however, only a small fraction of the genome has been sequenced. The entire mt genome was sequenced for the eastern North American members of Reticulitermes: R. flavipes, R. santonensis, R. virginicus, and R. hageni. The mt genome has the same gene content and organization as that found in most insect species; however, the nucleotide composition and skew are highly biased (AT% low, strong A- and C-skew). Both the protein-coding and transfer RNA genes show high absolute levels of nucleotide substitution, suggesting that the high rates of mutation within Reticulitermes inferred from analyses of single mt genes are a general characteristic of the entire mt genome. The AT-rich or control region has a remarkable structure not previously observed in insect mt genomes. The majority of the control region is made up of 2 sets of repeat units, typically with 2 full and 1 partial copies of both the A (or small; 186 bp) and B (or large; 552 bp) repeats. The partial repeat units overlap by 36 bp. The size, location, and degree of overlap for the partial repeat units correspond to highly conserved stem/loop structures within the repeat units, suggesting that these structures are involved in the replication-mediated processes that govern repeat-unit evolution within mt genomes. Finally, molecular variation within the mt gene regions was compared with previous regions used in molecular diagnostics or phylogenetics of Reticulitermes. High numbers of single nucleotide polymorphisms were found in each of the mt genes, and some of the highest variability was found in gene regions that have not previously been investigated in this group. The whole mt genome sequence can thus be used to predict useful regions for future investigation. [ABSTRACT FROM AUTHOR]

Mitochondrial genomes provide a promising new tool for understanding deep-level insect phylogenetics, but have yet to be evaluated for their ability to resolve intraordinal relationships. We tested the utility of mitochondrial genome data for the resolution of relationships within Diptera, the insect order for which the most data are available. We sequenced an additional three genomes, from a syrphid, nemestrinid and tabanid, representing three additional dipteran clades, ‘aschiza’, non-heteroneuran muscomorpha and ‘basal brachyceran’, respectively. We assessed the influence of optimality criteria, gene inclusion/exclusion, data recoding and partitioning strategies on topology and nodal support within Diptera. Our consensus phylogeny of Diptera was largely consistent with previous phylogenetic hypotheses of the order, except that we did not recover a monophyletic Muscomorpha (Nesmestrinidae grouped with Tabanidae) or Acalyptratae (Drosophilidae grouped with Calliphoridae). The results were very robust to optimality criteria, as parsimony, likelihood and Bayesian approaches yielded very similar topologies, although nodal support varied. The addition of ribosomal and transfer RNA genes to the protein coding genes traditionally used in mitochondrial genome phylogenies improved the resolution and support, contrary to previous suggestions that these genes would evolve too quickly or prove too difficult to align to provide phylogenetic signal at deep nodes. Strategies to recode data, aimed at reducing homoplasy, resulted in a decrease in tree resolution and branch support. Bayesian analyses were highly sensitive to partitioning strategy: biologically realistic partitions into codon groups produced the best results. The implications of this study for dipteran systematics and the effective approaches to using mitochondrial genome data are discussed. Mitochondrial genomes resolve intraordinal relationships within Diptera accurately over very wide time ranges (1–200 million years ago) and genetic distances, suggesting that this may be an excellent data source for deep-level studies within other, less studied, insect orders. [ABSTRACT FROM AUTHOR]

An analysis of the relationships of the major arthropod groups was undertaken using mitochondrial genome data to examine the hypotheses that Hexapoda is polyphyletic and that Collembola is more closely related to branchiopod crustaceans than insects. We sought to examine the sensitivity of this relationship to outgroup choice, data treatment, gene choice and optimality criteria used in the phylogenetic analysis of mitochondrial genome data. Additionally we sequenced the mitochondrial genome of an archaeognathan,Nesomachilis australica, to improve taxon selection in the apterygote insects, a group poorly represented in previous mitochondrial phylogenies. The sister group of the Collembola was rarely resolved in our analyses with a significant level of support. The use of different outgroups (myriapods, nematodes, or annelids + mollusks) resulted in many different placements of Collembola. The way in which the dataset was coded for analysis (DNA, DNA with the exclusion of third codon position and as amino acids) also had marked affects on tree topology. We found that nodal support was spread evenly throughout the 13 mitochondrial genes and the exclusion of genes resulted in significantly less resolution in the inferred trees. Optimality criteria had a much lesser effect on topology than the preceding factors; parsimony and Bayesian trees for a given data set and treatment were quite similar. We therefore conclude that the relationships of the extant arthropod groups as inferred by mitochondrial genomes are highly vulnerable to outgroup choice, data treatment and gene choice, and no consistent alternative hypothesis of Collembola's relationships is supported. Pending the resolution of these identified problems with the application of mitogenomic data to basal arthropod relationships, it is difficult to justify the rejection of hexapod monophyly, which is well supported on morphological grounds.© The Willi Hennig Society 2004. [ABSTRACT FROM AUTHOR]

• Comparative study at taxonomic order level of rearrangement and the Hexapoda mitogenome evolution. • We found that each Hexapoda order has a particular mitochondrial rearrangement dynamic. • Inversions/translocations are the most frequent rearrangements in the Hexapoda mitochondrial genome. • The most rearranged orders are Phthiraptera, Thysanoptera, Protura and Hymenoptera. • This is the First report of convergences between mitogenome architectures within Hexapoda. The evolution of the Hexapoda mitochondrial genome has been the focus of several genetic and evolutionary studies over the last decades. However, they have concentrated on certain taxonomic orders of economic or health importance. The recent increase of mitochondrial genomes sequencing of diverse taxonomic orders generates an important opportunity to clarify the evolution of this group of organisms. However, there is no comparative study that investigates the evolution of the Hexapoda mitochondrial genome. In order to verify the level of rearrangement and the mitochondrial genome evolution, we performed a comparative genomic analysis of the Hexapoda mitochondrial genome available in the NCBI database. Using a combination of bioinformatics methods to carefully examine the mitochondrial gene rearrangements in 1198 Hexapoda species belonging to 32 taxonomic orders, we determined that there is a great variation in the rate of rearrangement by gene and by taxonomic order. A higher rate of genetic reassortment is observed in Phthiraptera, Thysanoptera, Protura, and Hymenoptera; compared to other taxonomic orders. Twenty-four events of convergence in the genetic order between different taxonomic orders were determined, most of them not previously reported; which proves the great evolutionary dynamics within Hexapoda. [ABSTRACT FROM AUTHOR]

The mitochondrial genomes (mitogenomes) of bilaterian animals are highly conserved structures that usually consist of a single circular chromosome. However, several species of parasitic lice (Insecta: Phthiraptera) possess fragmented mitogenomes, where the mitochondrial genes are present on separate, circular chromosomes. Nevertheless, the extent, causes, and consequences of this structural variation remain poorly understood. Here, we combined new and existing data to better understand the evolution of mitogenome fragmentation in major groups of parasitic lice. We found strong evidence that fragmented mitogenomes evolved many times within parasitic lice and that the level of fragmentation is highly variable, including examples of heteroplasmic arrangements. We also found a significant association between mitochondrial fragmentation and signatures of relaxed selection. Mitochondrial fragmentation was also associated with changes to a lower AT%, possibly due to differences in mutation biases. Together, our results provide a significant advance in understanding the process of mitogenome fragmentation and provide an important perspective on mitochondrial evolution in eukaryotes. Multiple independent origins of fragmented mitochondrial genome evolution in parasitic lice provide insights into eukaryotic mitochondrial evolution. [ABSTRACT FROM AUTHOR]

Vermileonidae (wormlions) comprises 61 described species in 12 genera and is one of the oddest and most rarely collected dipteran families. Larvae of Vermileonidae are famous for their pitfall prey behaviour, whereas the adults are rarely seen. Here we report, for the first time, the complete mitochondrial genome from members of Vermileonidae. Phylogenetic reconstruction based on a representative sampling of the order reveals new insights into relationships between the Vermileonidae and other members of lower brachyceran flies. A sister-group relationship between Vermileonidae and Xylophagidae is supported, and the higher-level clade relationships are Tabanomorpha + (Muscomorpha + (Xylophagomorpha + Stratiomyomorpha)). Combining mitochondrial genome data with a morphological phylogeny, geographical distribution and geological history, we propose that the Vermileonidae originated in India during the Middle Jurassic, spreading to Africa via land bridges during the Late Jurassic, to the Palaearctic after the collision of India with Laurasia in the Late Oligocene, and to the Nearctic in the Early Miocene, via either North Atlantic or Beringian land bridges. Wet forested regions have proved to be barriers to their dispersal, explaining their absence from Central Africa, South America and eastern North America. [ABSTRACT FROM AUTHOR]

The monogeneric family Fergusoninidae consists of gall-forming flies that, together with Fergusobia (Tylenchida: Neotylenchidae) nematodes, form the only known mutualistic association between insects and nematodes. In this study, the entire 16,000 bp mitochondrial genome of Fergusonina taylori Nelson and Yeates was sequenced. The circular genome contains one encoding region including 27 genes and one non-coding A++T-rich region. The arrangement of the protein-coding, ribosomal RNA (rRNA) and transfer RNA (tRNA) genes was the same as that found in the ancestral insect. Nucleotide composition is highly A++T biased. All of the protein initiation codons are ATN, except for nad1 which begins with TTT. All 22 tRNA anticodons of F. taylori match those observed in Drosophila yakuba, and all form the typical cloverleaf structure except for tRNA-Ser (AGN) which lacks a dihydrouridine (DHU) arm. Secondary structural features of the rRNA genes of Fergusonina are similar to those proposed for other insects, with minor modifications. The mitochondrial genome of Fergusonina presented here may prove valuable for resolving the sister group to the Fergusoninidae, and expands the available mtDNA data sources for acalyptrates overall. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome of the tarnished plant bug,Lygus lineolaris,comprised 17,027 bp. The genome contained 13 protein coding regions, 22 tRNA genes and 2 ribosomal RNA genes. The gene arrangement corresponded to the common order found among insect mtDNAs which was considered to be the ancestral arrangement. The protein coding genes started with ATN and stopped with TAA or TAG. The nucleotide distribution was 76.0% A + T. The control region contained two repeat regions, one was 24 bp and the other was 161 bp. The Genbank accession for the completeL. lineolarismt genome is EU401991. [ABSTRACT FROM AUTHOR]

Despite the broad adoption of multispecies coalescent (MSC) methods for nuclear phylogenomics, they have yet to be applied to mitochondrial (mt) genomic data. As the potential sources of phylogenomic bias that MSC methods can address, such as incomplete lineage sorting, horizontal gene transfer and gene tree heterogeneity, have been found in mt genomic data, these approaches may improve the accuracy of phylogenetic inference with these data. In the present study, we examined the behaviour of MSC methods in reconstructing the phylogeny of Lepidoptera (butterflies and moths), a group for which mt genomic data are known to have strong resolving power. Traditional concatenation methods of analysing mt genomes for Lepidoptera infer topologies highly congruent with those generated from independent nuclear datasets. Individual mt gene trees performed poorly in recovering consensus relationships at deep levels (i.e. superfamily monophyly and inter‐relationships) and only moderately well for shallow relationships (i.e. within Papilionoidea). In contrast, MSC analyses with ASTRAL performed strongly with almost complete concordance to both concatenated mt genome analyses and independent nuclear analyses at both deep and shallow phylogenetic scales. Outgroup choice had a limited impact on tree accuracy, with even phylogenetically distant outgroups still resulting in topologies highly congruent with results from nuclear datasets, although MSC analyses appeared to be marginally more affected by outgroup choice than concatenation analyses. In general, discordance between concatenation and MSC analyses was found at nodes whose resolution varied between previous nuclear phylogenomic studies. The sensitivity of individual relationships to analysis with MSC vs concatenation can thus be used to test the robustness of phylogenetic hypotheses. For insect phylogenetics, MSC is a reliable inference method for mt genomic data and is thus a useful complement to the already widely used concatenation approaches. [ABSTRACT FROM AUTHOR]

The complete mitogenome sequence of the flea, Jellisonia amadoi (Siphonaptera: Ceratophyllidae), was sequenced. The 17,031 bp long genome has the standard metazoan complement of 37 genes, in the insect ancestral genome arrangement. The very large (2338 bp) A + T rich region is marked by two macro-repeats and multiple microsatellite and homopolymer regions. The protein-coding, rRNA and tRNA genes are all highly similar to homologues in related insect orders - similar length, few indels and high proportion of invariant sites. Sequencing of a flea mitogenome provides data for one of the last three insect orders from which data were lacking and provides further proof that parasitic life histories alone do not cause aberrant mitogenomes. [ABSTRACT FROM AUTHOR]

Prior to this study, complete mitochondrial genomes from Order Thysanoptera were restricted to a single family, the Thripidae, resulting in a biased view of their evolution. Here we present the sequences for the mitochondrial genomes of four additional thrips species, adding three extra families and an additional subfamily, thus greatly improving taxonomic coverage. Thrips mitochondrial genomes are marked by high rates of gene rearrangement, duplications of the control region and tRNA mutations. Derived features of mitochondrial tRNAs in thrips include gene duplications, anticodon mutations, loss of secondary structures and high gene translocation rates. Duplicated control regions are found in the Aeolothripidae and the 'core' Thripinae clade but do not appear to promote gene rearrangement as previously proposed. Phylogenetic analysis of thrips mitochondrial sequence data supports the monophyly of two suborders, a sister-group relationship between Stenurothripidae and Thripidae, and suggests a novel set of relationships between thripid genera. Ancestral state reconstructions indicate that genome rearrangements are common, with just eight gene blocks conserved between any thrips species and the ancestral insect mitochondrial genome. Conversely, 71 derived rearrangements are shared between at least two species, and 24 of these are unambiguous synapomorphies for clades identified by phylogenetic analysis. While the reconstructed sequence of genome rearrangements among the protein-coding and ribosomal RNA genes could be inferred across the phylogeny, direct inference of phylogeny from rearrangement data in MLGO resulted in a highly discordant set of relationships inconsistent with both sequence-based phylogenies and previous morphological analysis. Given the demonstrated rates of genomic evolution within thrips, extensive sampling is needed to fully understand these phenomena across the order. [ABSTRACT FROM AUTHOR]

The evolution of dung beetles remains contentious with two hypotheses reflecting Cretaceous and Paleogene origins driven by different methods. We explore biogeographic evidence and phylogeographic origins against vicariance and dispersal scenarios that attribute to the four elements of the Australian fauna using a multi-gene approach. Maximum-likelihood and Bayesian analyses supported the Australasian clade, composed of almost all Australian, New Caledonian and New Zealand endemic genera (to the exclusion of Boletoscapter). Two Australian lineages with east-west splits and few lineages with restricted, non-overlapping distrbution were identified, and biogeography models provided evidence that vicariance and founder event speciation are important processes in the diversification of Australasian scarabaeines. Our phylogenetic results are largely congruent with a mid-Cretaceous origin of the Australasian clade, the tectonic history of Gondwanaland and climatic history of the Australian continent, and provide compelling evidence that Australian dung beetles are a relictual fauna whose history is linked to mesic zone fragmentation. [ABSTRACT FROM AUTHOR]

Stromatium Audinet‐Serville 1834 is considered to be one of the most economically important genera of Cerambycidae. Three species of this genus, Stromatium barbatum (Fabricius), Stromatium longicorne (Newman 1842) and Stromatium auratum (Böber 1793), are able to develop to maturity in seasoned timber and are distributed worldwide due to human commerce. We clarified here the status of wild populations of Stromatium in Australia. Stromatium darwinense Jin & Weir sp. nov. is described from the Northern Territory in Australia, based on evidence from morphological characters and mtDNA barcode sequences (421 bp fragment of COI). The new species is morphologically very similar to S. longicorne, which is native to Christmas Island but not to mainland Australia. We redescribe S. barbatum and S. longicorne, the introductions of which still remain high risks for Australian biosecurity. [ABSTRACT FROM AUTHOR]

Approximately 2500 fly species comprise the Sarcophagidae family worldwide. The complete mitochondrial genome of the carrion-breeding, forensically important Sarcophaga impatiens Walker (Diptera: Sarcophagidae) from Australia was sequenced. The 15,169 bp circular genome contains the 37 genes found in a typical Metazoan genome: 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. It also contains one non-coding A++T-rich region. The arrangement of the genes was the same as that found in the ancestral insect. All the protein initiation codons are ATN, except for cox1 that begins with TCG (encoding S). The 22 tRNA anticodons of S. impatiens are consistent with those observed in Drosophila yakuba, and all form the typical cloverleaf structure, except for tRNA-Ser(AGN) that lacks the DHU arm. The mitochondrial genome of Sarcophaga presented will be valuable for resolving phylogenetic relationships within the family Sarcophagidae and the order Diptera, and could be used to identify favourable genetic markers for species identifications for forensic purposes. [ABSTRACT FROM AUTHOR]

1. Major global horticultural and food security tephritid fruit fly pests, Bactrocera papayae (papaya fruit fly) and B. invadens (invasive fruit fly), were synonymised with B. dorsalis (Oriental fruit fly) by Schutze et al. (2015a) based on extensive integrative taxonomic evidence from multiple sources. This synonymy was peer reviewed by eight independent experts. 2. Drew & Romig (2016) withdrew B. papayae and B. invadens from synonymy based on opinion drawn primarily from disparate geographical distribution, morphological, and host use information. This reversal was not subjected to peer review. 3. We consider the withdrawal from synonymy as invalid due to significant errors and misrepresentations of the literature provided in the arguments of Drew & Romig (2016) that we propose would not have withstood peer scrutiny. 4. This case reflects a broader issue of individual taxonomic authorities using opinion to challenge extensive evidence generated via scientific hypothesis-testing methods by discipline specialists. 5. We recommend that taxonomic acts not subjected to peer review, especially of pest species, be actively discouraged by the broader scientific and regulatory community. [ABSTRACT FROM AUTHOR]

Sequencing high molecular weight (HMW) DNA with long-read and linked-read technologies has promoted a major increase in more complete genome sequences for nonmodel organisms. Sequencing approaches that rely on HMW DNA have been limited to larger organisms or pools of multiple individuals, but recent advances have allowed for sequencing from individuals of small-bodied organisms. Here, we use HMW DNA sequencing with PacBio long reads and TELL-Seq linked reads to assemble and annotate the genome from a single individual feather louse (Brueelia nebulosa) from a European Starling (Sturnus vulgaris). We assembled a genome with a relatively high scaffold N50 (637 kb) and with BUSCO scores (96.1%) comparable to louse genomes assembled from pooled individuals. We annotated a number of genes (10,938) similar to the human louse (Pediculus humanus) genome. Additionally, calling phased variants revealed that the Brueelia genome is more heterozygous (~1%) then expected for a highly obligate and dispersal-limited parasite. We also assembled and annotated the mitochondrial genome and primary endosymbiont (Sodalis) genome from the individual louse, which showed evidence for heteroplasmy in the mitogenome and a reduced genome size in the endosymbiont compared to its free-living relative. Our study is a valuable demonstration of the capability to obtain high-quality genomes from individual small, nonmodel organisms. Applying this approach to other organisms could greatly increase our understanding of the diversity and evolution of individual genomes. [ABSTRACT FROM AUTHOR]

Aim The Australian Coptotermes (Family: Rhinotermitidae) are a small monophyletic group of termites, some of which build mounds. In this study, we construct predicted distributions based on environmental data (niche models) for all Australian species of Coptotermes to test whether specific environmental factors have contributed to the evolution of mound-building behaviour and whether the degree of niche similarity and degree of phylogenetic similarity are correlated. Location The Australian mainland, including the known native ranges of all Australian species of Coptotermes. Methods We estimated the phylogenetic relationships between the species of Australian Coptotermes. We then generated and compared environmental niche models in a phylogenetic framework for all study species to test niche conservation. Our analyses were based on location data from our own sampling and from the Atlas of Living Australia, genetic data from a previous study of Australian Coptotermes, and environmental data from WorldClim and ASRIS. Results We found that no environmental variable differed consistently between mound-building and non-mound-building taxa and that the differences in niches between pairs of Australian species of Coptotermes are uncorrelated with time since divergence. The environmental tolerances of the Australian Coptotermes termites are more restricted by rainfall than they are by soil or temperature. Main conclusions Our results show that mound-building behaviour has not necessarily evolved in response to similar abiotic conditions. Our results are consistent with ecological speciation leading to niche divergence since Coptotermes first arrived in Australia ~12.5 million years ago. [ABSTRACT FROM AUTHOR]

Integrative taxonomy, including molecular, morphological, distributional and biological data, is applied in a review of the taxonomy of the Australian species of the pest termite genus Coptotermes. The validity of the previously described species is discussed, and two new species, Coptotermes nanus, sp. nov. and Coptotermes cooloola, sp. nov., are described from the Kimberley region of Western Australia and south-east Queensland respectively. Their delimitation is based on morphological and distributional data, and the results of generalised mixed Yule-coalescent analysis of mitochondrial DNA sequence data. Images of the external view of the two new species are provided, as well as a key, based on soldier characters, for all Australian species of Coptotermes. [ABSTRACT FROM AUTHOR]

With over 60 000 described species in approximately 5800 genera, weevils ( Curculionoidea) represent one of the most diverse and species-rich superfamilies of eukaryotes on the planet. Recent attempts to resolve the phylogeny of family-group taxa in weevils using morphological, molecular or combined data sets have produced vastly different patterns of relationships, particularly within the largest family, Curculionidae. Here we present an estimation of the phylogeny of Australian weevils and of the divergence dates of the major lineages based on a multi-gene data set (28S, 16S and COI) spanning ∼3.5 kbp of DNA sequence. We assess its topological similarities to, and differences from, other recently published phylogenetic trees, particularly in relation to taxon sampling and relative diversity of the lineages, and we discuss the implications for weevil systematics. Our results, derived from a different set of taxa that has different combination of loci and different fossil calibration points, recover a number of relationships and age estimates that are congruent with those obtained by other recent weevil phylogeny estimates, indicating that we are beginning to recognise the major monophyletic lineages and reconstruct the major diversification events within Curculionoidea. Resolution of natural groups within families (e.g. subfamilies and tribes) however remains poor, even for studies with the largest volume of sequence data (whole mitochondrial genome analyses), evidently largely due to deficient taxon sampling. Although taxon sampling is known to be one of the most critical determinants of accurate phylogenetic reconstruction, it is rarely addressed in phylogenetic assessments. Our case study of weevils highlights not only its importance, but also the fact that it is very difficult to achieve comprehensive representative sampling in hyperdiverse lineages because of their sheer taxic diversity. Doubts concerning the monophyly of many subordinate lineages exacerbate this problem, restricting the use of exemplar approaches to taxon sampling. The value of comparing different data sets and analyses for assessing systematic relationships is often overlooked, even despite the presence of many conflicting results in previous phylogenetic hypotheses. A summary of relationships recovered relative to taxon sampling and methodological differences between different phylogenetic reconstructions provides an important stepping-stone in understanding the diversification of weevils. [ABSTRACT FROM AUTHOR]

Sepsid flies (Diptera: Sepsidae) are important model insects for sexual selection research. In order to develop mitochondrial (mt) genome data for this significant group, we sequenced the first complete mt genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997. The circular 15,878 bp mt genome is typical of Diptera, containing all 37 genes usually present in bilaterian animals. We discovered inaccurate annotations of fly mt genomes previously deposited on GenBank and thus re-annotated all published mt genomes of Cyclorrhapha. These re-annotations were based on comparative analysis of homologous genes, and provide a statistical analysis of start and stop codon positions. We further detected two 18 bp of conserved intergenic sequences from tRNAGlu-tRNAPhe and ND1-tRNASer(UCN) across Cyclorrhapha, which are the mtTERM binding site motifs. Additionally, we compared automated annotation software MITOS with hand annotation method. Phylogenetic trees based on the mt genome data from Cyclorrhapha were inferred by Maximum-likelihood and Bayesian methods, strongly supported a close relationship between Sepsidae and the Tephritoidea. [ABSTRACT FROM AUTHOR]

The article focuses on a framework of DNA barcoding that incorporates the multispecies coalescent and mentions that there are currently three approaches that delimit species with a consideration of the multispecies coalescent including Brownie, SpedeSTEM and BPP. Topics discussed include test database that contains 428 specimens of sarcophagine flies, alignment of nucleotide sequences and gene analysis with each gene as a separate partition.

Carrion-breeding Sarcophagidae (Diptera) can be used to estimate the post-mortem interval in forensic cases. Difficulties with accurate morphological identifications at any life stage and a lack of documented thermobiological profiles have limited their current usefulness. The molecular-based approach of DNA barcoding, which utilises a 648-bp fragment of the mitochondrial cytochrome oxidase subunit I gene, was evaluated in a pilot study for discrimination between 16 Australian sarcophagids. The current study comprehensively evaluated barcoding for a larger taxon set of 588 Australian sarcophagids. In total, 39 of the 84 known Australian species were represented by 580 specimens, which includes 92% of potentially forensically important species. A further eight specimens could not be identified, but were included nonetheless as six unidentifiable taxa. A neighbour-joining tree was generated and nucleotide sequence divergences were calculated. All species except Sarcophaga (Fergusonimyia) bancroftorum, known for high morphological variability, were resolved as monophyletic (99.2% of cases), with bootstrap support of 100. Excluding S. bancroftorum, the mean intraspecific and interspecific variation ranged from 1.12% and 2.81-11.23%, respectively, allowing for species discrimination. DNA barcoding was therefore validated as a suitable method for molecular identification of Australian Sarcophagidae, which will aid in the implementation of this fauna in forensic entomology. [ABSTRACT FROM AUTHOR]

Abstract: The phylogeny of Onychophora (velvet worms) is unresolved and even the monophyly of the two major onychophoran subgroups, Peripatidae and Peripatopsidae, is uncertain. Previous studies of complete mitochondrial genomes from two onychophoran species revealed two strikingly different gene arrangement patterns from highly conserved in a representative of Peripatopsidae to highly derived in a species of Peripatidae, suggesting that these data might be informative for clarifying the onychophoran phylogeny. In order to assess the diversity of mitochondrial genomes among onychophorans, we analyzed the complete mitochondrial genome of Metaperipatus inae, a second representative of Peripatopsidae from Chile. Compared to the proposed ancestral gene order in Onychophora, the mitochondrial genome of M. inae shows dramatic rearrangements, although all protein-coding and ribosomal RNA genes are encoded on the same strands as in the ancestral peripatopsid genome. The retained strand affiliation of all protein-coding and ribosomal RNA genes and the occurrence of three control regions and several pseudo-genes suggest that the derived mitochondrial gene arrangement pattern in M. inae evolved by partial genome duplications, followed by a subsequent loss of redundant genes. Our findings, thus, confirm the diversity of the mitochondrial gene arrangement patterns among onychophorans and support their utility for clarifying the phylogeography of Onychophora, in particular of the Peripatopsidae species from South Africa and Chile. [Copyright &y& Elsevier]

The ability to generate large molecular datasets for phylogenetic studies benefits biologists, but such data expansion introduces numerous analytical problems. A typical molecular phylogenetic study implicitly assumes that sequences evolve under stationary, reversible and homogeneous conditions, but this assumption is often violated in real datasets. When an analysis of large molecular datasets results in unexpected relationships, it often reflects violation of phylogenetic assumptions, rather than a correct phylogeny. Molecular evolutionary phenomena such as base compositional heterogeneity and among-site rate variation are known to affect phylogenetic inference, resulting in incorrect phylogenetic relationships. The ability of methods to overcome such bias has not been measured on real and complex datasets. We investigated how base compositional heterogeneity and among-site rate variation affect phylogenetic inference in the context of a mitochondrial genome phylogeny of the insect order Coleoptera. We show statistically that our dataset is affected by base compositional heterogeneity regardless of how the data are partitioned or recoded. Among-site rate variation is shown by comparing topologies generated using models of evolution with and without a rate variation parameter in a Bayesian framework. When compared for their effectiveness in dealing with systematic bias, standard phylogenetic methods tend to perform poorly, and parsimony without any data transformation performs worst. Two methods designed specifically to overcome systematic bias, LogDet and a Bayesian method implementing variable composition vectors, can overcome some level of base compositional heterogeneity, but are still affected by among-site rate variation. A large degree of variation in both noise and phylogenetic signal among all three codon positions is observed. We caution and argue that more data exploration is imperative, especially when many genes are included in an analysis. [ABSTRACT FROM AUTHOR]

Many published phylogenies are based on methods that assume equal nucleotide composition among taxa. Studies have shown, however, that this assumption is often not accurate, particularly in divergent lineages. Nonstationary sequence evolution, when taxa in different lineages evolve in different ways, can lead to unequal nucleotide composition. This can cause inference methods to fail and phylogenies to be inaccurate. Recent advancements in phylogenetic theory have proposed new models of nonstationary sequence evolution; these models often outperform equivalent stationary models. A variety of new phylogenetic software implementing such models has been developed, but the studies employing the new methodology are still few. We discovered convergence of nucleotide composition within mitochondrial genomes of the insect order Coleoptera (beetles). We found variation in base content both among species and among genes in the genome. To this data set, we have applied a broad range of phylogenetic methods, including some traditional stationary models of evolution and all the more recent nonstationary models. We compare 8 inference methods applied to the same data set. Although the more commonly used methods universally fail to recover established clades, we find that some of the newer software packages are more appropriate for data of this nature. The software packages p4, PHASE, and nhPhyML were able to overcome the systematic bias in our data set, but parsimony, MrBayes, NJ, LogDet, and PhyloBayes were not. [ABSTRACT FROM PUBLISHER]

Abstract: The phylogenetic utility of mitochondrial genomes (mtgenomes) is examined using the framework of a preliminary phylogeny of Orthoptera. This study presents five newly sequenced genomes from four orthopteran families. While all ensiferan and polyneopteran taxa retain the ancestral gene order, all caeliferan lineages including the newly sequenced caeliferan species contain a tRNA rearrangement from the insect ground plan tRNALys(K)–tRNAAsp(D) swapping to tRNAAsp (D)–tRNALys (K) confirming that this rearrangement is a possible molecular synapomorphy for this suborder. The phylogenetic signal in mtgenomes is rigorously examined under the analytical regimens of parsimony, maximum likelihood and Bayesian inference, along with how gene inclusion/exclusion, data recoding, gap coding, and different partitioning schemes influence the phylogenetic reconstruction. When all available data are analyzed simultaneously, the monophyly of Orthoptera and its two suborders, Caelifera and Ensifera, are consistently recovered in the context of our taxon sampling, regardless of the optimality criteria. When protein-coding genes are analyzed as a single partition, nearly identical topology to the combined analyses is recovered, suggesting that much of the signals of the mtgenome come from the protein-coding genes. Transfer and ribosomal RNAs perform poorly when analyzed individually, but contribute signal when analyzed in combination with the protein-coding genes. Inclusion of third codon position of the protein-coding genes does not negatively affect the phylogenetic reconstruction when all genes are analyzed together, whereas recoding of the protein-coding genes into amino acid sequences introduces artificial resolution. Over-partitioning in a Bayesian framework appears to have a negative effect in achieving convergence. Our findings suggest that the best phylogenetic inferences are made when all available nucleotide data from the mtgenome are analyzed simultaneously, and that the mtgenome data can resolve over a wide time scale from the Permian (∼260MYA) to the Tertiary (∼50MYA). [Copyright &y& Elsevier]

Summary: The bacterium Rickettsia is found widely in phytophagous insects and often exerts profound effects on the phenotype and fitness of its hosts. Here, we decrypt a new, independent, phylogenetically ancient Torix Rickettsia endosymbiont found constantly in a laboratory line of an economically important insect Asia II 7, a putative species of the Bemisia tabaci whitefly complex (Hemiptera: Aleyrodidae), and occasionally in field whitefly populations. This new Rickettsia distributes throughout the body of its whitefly host. Genetically, compared to Rickettsia_bellii_MEAM1 found earlier in whiteflies, the new Rickettsia species has more gene families and pathways, which may be important factors in shaping specific symbiotic relationships. We propose the name 'Candidatus Rickettsia_Torix_Bemisia_tabaci (RiTBt)' for this new endosymbiont associated with whiteflies. Comparative genomic analyses indicate that RiTBi may be a relatively recent intruder in whiteflies given its low abundance in the field and relatively larger genome compared to Rickettsia_bellii_MEAM1. [ABSTRACT FROM AUTHOR]

Accurate species‐level identifications underpin many aspects of basic and applied biology; however, identifications can be hampered by a lack of discriminating morphological characters, taxonomic expertise or time. Molecular approaches, such as DNA "barcoding" of the cytochrome c oxidase (COI) gene, are argued to overcome these issues. However, nuclear encoding of mitochondrial genes (numts) and poor amplification success of suboptimally preserved specimens can lead to erroneous identifications. One insect group for which these molecular and morphological problems are significant are the dacine fruit flies (Diptera: Tephritidae: Dacini). We addressed these issues associated with COI barcoding in the dacines by first assessing several "universal" COI primers against public mitochondrial genome and numt sequences for dacine taxa. We then modified a set of four primers that more closely matched true dacine COI sequence and amplified two overlapping portions of the COI barcode region. Our new primers were tested alongside universal primers on a selection of dacine species, including both fresh preserved and decades‐old dry specimens. Additionally, Bactrocera tryoni mitochondrial and nuclear genomes were compared to identify putative numts. Four numt clades were identified, three of which were amplified using existing universal primers. In contrast, our new primers preferentially amplified the "true" mitochondrial COI barcode in all dacine species tested. The new primers also successfully amplified partial barcodes from dry specimens for which full length barcodes were unobtainable. Thus we recommend these new primers be incorporated into the suites of primers used by diagnosticians and quarantine labs for the accurate identification of dacine species. [ABSTRACT FROM AUTHOR]

• Denser mitogenome sampling solved higher-level relationships of Plecoptera. • Plecoptera is sister-group to a clade composed of all other Polyneoptera orders. • The divergence between the suborders was the Pangaea origin. Phylogenetic analysis based on mitochondrial genomic data from 25 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera (stoneflies). The monophyly of both currently recognized suborders was strongly supported, concordant with previous molecular analyses of Plecoptera. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae + Diamphipnoidae and Austroperlidae + Gripopterygidae; consistent with relationships proposed based on morphology. The largely northern hemisphere suborder Arctoperlaria also divided into two groups, Euholognatha and Systellognatha, each composed of the five families traditionally assigned to each infraorder (the placement Scopuridae by mt genome data remains untested at this time). Within Euholognatha, strong support for the clade Nemouridae + Notonemouridae confirmed the northern origin of the currently southern hemisphere restricted Notonemouridae. Other family level relationships within the Arctoperlaria differ from those recovered by previous morphology and molecular based analyses. A fossil-calibrated divergence estimation suggests the formation of two suborders dates back to the Jurassic (181 Ma), with subsequent diversification of most stonefly families during the Cretaceous. This result confirms the hypothesis that initial divergence between the suborders was driven by the breakup of the supercontinent Pangaea into Laurasia and Gondwanaland (commencing 200 Ma and complete by 150 Ma). [ABSTRACT FROM AUTHOR]

Development of novel molecular methods for accurate and economical identification of species has become critical both for pure biological research and for a wide range of applied areas. The most widely used current molecular diagnostic tool, the mitochondrial cytochrome c oxidase subunit 1 gene (COI), the so‐called DNA barcode, has been highly criticised and is known to be ineffective at distinguishing species in many groups. Alternative markers are needed to circumvent these issues and provide diagnosticians with a greater range of tools for making accurate identifications. To address this, we describe here a novel analytical workflow for diagnostic marker development that utilises near‐genomic‐scale data to search for potential informative loci. The workflow takes advantage of orthologous gene databases, in combination with tests of phylogenetic resolution, and benchmarking of nucleotide variation against COI, to determine putative loci that might outperform COI. We use transcriptomes of 14 tephritid fruit flies and especially the taxonomically complex genus Bactrocera, as a case study. Of 1646 orthologues searched, our workflow retained a total of five loci following our conservative filtering strategy. One locus, POP4, had strong potential as a novel diagnostic marker for Bactrocera fruit flies. POP4 discriminates most species in the training set of taxa, but like COI fails to separate the sibling species Bactrocera tryoni and Bactrocera neohumeralis. Further validation of this potential new marker against a broader taxonomic sample is ongoing. We advocate that this simple and efficient workflow is, with minor modification, customisable for diagnostic development in almost any taxonomic group. [ABSTRACT FROM AUTHOR]

Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid orders (Psocodea, Thysanoptera, and Hemiptera) is strongly supported, as are most relationships among suborders and families. Thysanoptera (thrips) is strongly supported as sister to Hemiptera. However, as in a recent large-scale analysis sampling all insect orders, trees from our data matrices support Psocodea (bark lice and parasitic lice) as the sister group to the holometabolous insects (those with complete metamorphosis). In contrast, four-cluster likelihood mapping of these data does not support this result. A molecular dating analysis using 23 fossil calibration points suggests hemipteroid insects began diversifying before the Carboniferous, over 365 million years ago. We also explore implications for understanding the timing of diversification, the evolution of morphological traits, and the evolution of mitochondrial genome organization. These results provide a phylogenetic framework for future studies of the group. [ABSTRACT FROM AUTHOR]

Interactions between DNA and proteins located in the cell nucleus play an important role in controlling physiological processes by specifying, augmenting and regulating context-specific transcription events. Chromatin immunoprecipitation (ChIP) is a widely used methodology to study DNA-protein interactions and has been successfully used in various cell types for over three decades. More recently, by combining ChIP with genomic screening technologies and Next Generation Sequencing (e.g. ChIP-seq), it has become possible to profile DNA-protein interactions (including covalent histone modifications) across entire genomes. However, the applicability of ChIP-chip and ChIP-seq has rarely been extended to non-model species because of a number of technical challenges. Here we report a method that can be used to identify genome wide covalent histone modifications in a group of non-model fruit fly species (Diptera: Tephritidae). The method was developed by testing and refining protocols that have been used in model organisms, including Drosophila melanogaster. We demonstrate that this method is suitable for a group of economically important pest fruit fly species, viz., Bactrocera dorsalis, Ceratitis capitata, Zeugodacus cucurbitae and Bactrocera tryoni. We also report an example ChIP-seq dataset for B. tryoni, providing evidence for histone modifications in the genome of a tephritid fruit fly for the first time. Since tephritids are major agricultural pests globally, this methodology will be a valuable resource to study taxa-specific evolutionary questions and to assist with pest management. It also provides a basis for researchers working with other non-model species to undertake genome wide DNA-protein interaction studies. [ABSTRACT FROM AUTHOR]