Intron retention in the Drosophila melanogaster Rieske Iron Sulphur Protein gene generated a new protein

Genomes can encode a variety of proteins with unrelated architectures and activities. It is known that protein-coding genes of de novo origin have significantly contributed to this diversity. However, the molecular mechanisms and evolutionary processes behind these originations are still poorly understood. Here we show that the last 102 codons of a novel gene, Noble, assembled directly from non-coding DNA following an intronic deletion that induced alternative intron retention at the Drosophila melanogaster Rieske Iron Sulphur Protein (RFeSP) locus. A systematic analysis of the evolutionary processes behind the origin of Noble showed that its emergence was strongly biased by natural selection on and around the RFeSP locus. Noble mRNA is shown to encode a bona fide protein that lacks an iron sulphur domain and localizes to mitochondria. Together, these results demonstrate the generation of a novel protein at a naturally selected site.

Identification of a developmentally and hormonally regulated Delta-Class glutathione S-transferase in rice moth Corcyra cephalonica

Glutathione S-transferases (GSTs) are a large family of multifunctional enzymes, known for their role in cellular detoxification. Here we report a cytosolic GST with optimal activity at alkaline pH (8.3) from the visceral fat body of late-last instar (LLI) larvae of a lepidopteran insect rice moth Corcyra cephalonica. All previously known GSTs are active between pH 6.0 to 6.5. Purification and characterization revealed the Corcyra cephalonica GST (CcGST) as a 23-kDa protein. HPLC and 2D analysis showed a single isoform of the protein in the LLI visceral fat body. Degenerate primer based method identified a 701-nucleotide cDNA and the longest open reading frame contained 216 amino acids. Multiple sequence and structural alignment showed close similarity with delta-class GSTs. CcGST is present mainly in the fat body with highest activity at the late-last instar larval stage. Juvenile hormone (JH) negatively inhibits the CcGST activity both ex vivo and in vivo. We speculate that high expression and activity of CcGST in the fat body of the late-last instar larvae, when endogenous JH titer is low may have role in the insect post-embryonic development unrelated to their previously known function.

Pupal deposition and ecology of bat flies (Diptera: Streblidae): Trichobius sp. (caecus group) in a Mexican cave habitat

We studied the deposition of pupae of the winged bat fly Trichobius sp. (caecus group; Diptera), an ectoparasite of Natalus stramineus (Chiroptera, Natalidae), in a natural cave in Tamaulipas, Mexico. For the first time, we show a strong spatial segregation of populations of a streblid bat fly at different stages of development. Using molecular techniques we were able to match developmental stages to adults. Only 5 pupae were present in the main bat roosts. The overwhelming majority occurred exclusively in the bat flyway passages at a considerable distance from roosting bats. Pupal density corresponded positively with the average flight height of bats in the cave passage. Taken together, observations suggest that these ectoparasites must actively seek out their hosts by moving onto passing or roosting bats. The scarceness of pupae in the main roost may be dictated by environmental constraints for their development. The estimated population of viable pupae far exceeds the population of imagoes on the bats, and predation on adults by spiders is common.

Phylogeny and evolution of male genitalia within the praying mantis genus Tenodera (Mantodea:Mantidae)

The mantis genus Tenodera is composed of several species distributed across Africa, Asia and Australasia, along with recent human introductions to North America. Species of the genus are morphologically similar and utilise equivalent habitats across their distribution. Relationships among these species and the morphological characters used to diagnose them have never been formally tested, leaving authors to disagree as to the species composition of Tenodera. With DNA sequence data from five molecular loci and morphological characters from male genitalia, we reconstructed the phylogeny of Tenodera using multiple optimality criteria. All included species were found to be monophyletic in analyses of the combined data. Tenodera sinensis and T. bokiana were both supported as distinct species recovered in separate clades, resolving confusion as to their placement and classification. Our analysis identified a previously undescribed species of Tenodera collected in India, recovered as sister to T. aridifolia and T. sinensis, and exhibiting distinct male genital morphology. In light of the phylogeny, we characterise for the first time, and investigate the evolution of, the male genitalia, which allowed us to discover several transitions in structural forms. We also consider the connection of these transitions to sexual cannibalism and how this behaviour may have led to rapid evolution of the male genitalia.

A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles

Coleoptera is the most diverse group of insects with over 360,000 described species divided into four suborders: Adephaga, Archostemata, Myxophaga, and Polyphaga. In this study, we present six new complete mitochondrial genome (mtgenome) descriptions, including a representative of each suborder, and analyze the evolution of mtgenomes from a comparative framework using all available coleopteran mtgenomes. We propose a modification of atypical cox1 start codons based on sequence alignment to better reflect the conservation observed across species as well as findings of TTG start codons in other genes. We also analyze tRNA-Ser(AGN) anticodons, usually GCU in arthropods, and report a conserved UCU anticodon as a possible synapomorphy across Polyphaga. We further analyze the secondary structure of tRNA-Ser(AGN) and present a consensus structure and an updated covariance model that allows tRNAscan-SE (via the COVE software package) to locate and fold these atypical tRNAs with much greater consistency. We also report secondary structure predictions for both rRNA genes based on conserved stems. All six species of beetle have the same gene order as the ancestral insect. We report noncoding DNA regions, including a small gap region of about 20 bp between tRNA-Ser(UCN) and nad1 that is present in all six genomes, and present results of a base composition analysis.

Mitochondrial genome organization and phylogeny of two vespid wasps

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.

Head morphology of Caurinus (Boreidae, Mecoptera) and its phylogenetic implications

External and internal head structures of Caurinus dectes were examined and described in detail. The features are compared to conditions found in other groups of Antliophora. Caurinus is obviously crucial for the reconstruction of the mecopteran and antliophoran groundplan. It displays a remarkable series of plesiomorphic character states such as a complete clypeolabral suture, the presence of M. hypopharyngomandibularis (M. 13) and M. frontohypopharyngalis (M. 41), a subdivided clypeus, a short head without rostrum, a dorsal tentorial arm attached to the head capsule, the absence of a cranial dilator of the antenna, and large mandibles with a well developed apical tooth, two distinct subapical teeth, and a basal molar part. The first three plesiomorphic features render potential autapomorphies of Mecoptera in the traditional sense invalid. Autapomorphies of Caurinus are the distinctly flattened labrum, the absence of the labroepipharyngeal muscle, the very large size of M. 13, the strongly enlarged penultimate palpomeres, the partition of M. 41, the very strongly developed precerebral sucking chamber, strongly curved optic lobes, the presence of a large protocerebral extension in the genal region and deep posterior excavations of the protocerebrum. The maxillolabial plate, the absence of cardines as separate structures, the reduction of ocelli, and the origin of maxillary palp muscles on a median ridge or area of the maxillolabial plate are likely autapomorphies of Boreidae. Another potential autapomorphy of the family is the presence of longitudinal furrows on the mandibles. However, they are absent in Boreus. The thick strongly sclerotised, median ridge of the maxillolabial plate, the missing retractibility of the prementum, the absence of extrinsic labial muscles, and the presence of a median ridge on the prepharyngeal roof suggest a clade Boreus+Hesperoboreus. The origin of extrinsic maxillary muscles from the clypeus has probably evolved independently in Boreus and Hesperoboreus, and in Panorpa, respectively. The absence of M. craniolacinialis and the presence of a row of several subapical mandibular teeth are autapomorphies of Boreus. The presence of a specific intrinsic muscle of the salivary duct and a membranous galea enclosing the labrum and mandibular base are derived features shared by Boreidae and Pistillifera (galea absent in Nannochorista, Siphonaptera and Diptera). The loss of M. frontolabralis (M. 8) is a potential apomorphy of Mecoptera incl. Siphonaptera. A sister group relationship between Boreidae and Siphonaptera is not supported by characters of the adult head. Head structures of Siphonaptera are extremely modified in correlation with ectoparasitic habits.

The phylogeny of termites (Dictyoptera: Isoptera) based on mitochondrial and nuclear markers: Implications for the evolution of the worker and pseudergate castes, and foraging behaviors

A phylogenetic hypothesis of termite relationships was inferred from DNA sequence data. Seven gene fragments (12S rDNA, 16S rDNA, 18S rDNA, 28S rDNA, cytochrome oxidase I, cytochrome oxidase II and cytochrome b) were sequenced for 40 termite exemplars, representing all termite families and 14 outgroups. Termites were found to be monophyletic with Mastotermes darwiniensis (Mastotermitidae) as sister group to the remainder of the termites. In this remainder, the family Kalotermitidae was sister group to other families. The families Kalotermitidae, Hodotermitidae and Termitidae were retrieved as monophyletic whereas the Termopsidae and Rhinotermitidae appeared paraphyletic. All of these results were very stable and supported with high bootstrap and Bremer values. The evolution of worker caste and foraging behavior were discussed according to the phylogenetic hypothesis. Our analyses suggested that both true workers and pseudergates ("false workers") were the result of at least two different origins. Our data support a traditional hypothesis of foraging behavior, in which the evolutionary transition from a one-piece type to a separate life type occurred through an intermediate behavioral form.

The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths

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.

Mitochondrial genomic comparisons of the subterranean termites from the Genus Reticulitermes (Insecta: Isoptera: Rhinotermitidae)

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.

The complete mitochondrial genome sequence of the Mormon cricket (Anabrus simplex: Tettigoniidae: Orthoptera) and an analysis of control region variability

The Anabrus simplex is a swarming plague orthopteran found in western North America. The genome is 15 766 bp in length and genome organization follows the ancestral insect gene arrangement. atp6 lacked any readily identifiable stop codon. Examination of mRNA secondary structure for this gene suggested a stem/loop-mediated mRNA post-transcriptional processing to liberate a mature atp6 mRNA with a complete stop codon produced by polyadenylation. Comparison of similar protein with protein gene boundaries in other insect species reveal a general mechanism for mRNA excision and provide further supporting evidence for post-transcriptional mRNA processing in mitochondrial genomes. The A + T-rich region, or control region, was sequenced for 55 A. simplex individuals from 12 different populations. Variance studies between these individuals show that the A + T-rich region contains significant phylogenetic signal to be used in population studies.

Phylogeny and biogeography of ice crawlers (Insecta: Grylloblattodea) based on six molecular loci: designating conservation status for Grylloblattodea species

Ice crawlers (Insecta: Grylloblattodea) are rarely encountered insects that consist of five genera representing 26 species from North America and Asia. Asian grylloblattids are the most diverse, but North American ice crawlers (genus Grylloblatta) are known for their adaptation to cold conditions. Phylogenetic relationships among grylloblattid species and genera are not known. Six genes were sampled in 35 individuals for 18S rRNA, 28S rRNA, histone 3, 12S rRNA, 16S rRNA, and cytochrome oxidase II from 21 populations of Grylloblatta, three populations from Japan (genus Galloisiana), and three populations from Russia (genus Grylloblattina). Phylogenetic analysis of these data with two mantophasmid outgroups in POY supported monophyletic genera, with Grylloblatta as sister to Grylloblattina. Grylloblatta was shown to contain two major lineages: a clade in Northern California and Oregon and a clade in Washington and Oregon. One new species and six candidate species are proposed. IUCN Red List Conservation Criteria were implemented to designate conservation status for each lineage.

Identification and phylogenetic analysis of Arsenophonus- and Photorhabdus-type bacteria from adult Hippoboscidae and Streblidae (Hippoboscoidea)

This is the first report of Arsenophonus- and Photorhabdus-type bacteria from Streblidae (bat flies) and Hippoboscidae (louse flies, keds). Strains were detected by means of polymerase chain reaction of 16S rDNA, and phylogenetic analysis determined the relationship of the obtained sequences to previously reported sequences in GenBank. Phylogenetic analysis by means of maximum parsimony revealed that all isolated Arsenophonus spp. 16S rDNA sequences formed a monophyletic sub-clade within other insect Arsenophonus spp., while the Photorhabdus spp. sequences are part of a monophyletic clade including Photorhabdus spp., Xenorhabdus spp. and Proteus spp.