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Background The mountain pine beetle, Dendroctonus ponderosae Hopkins, is the most serious insect pest of western North American pine forests. A recent outbreak destroyed more than 15 million hectares of pine forests, with major environmental effects on forest health, and economic effects on the forest industry. The outbreak has in part been driven by climate change, and will contribute to increased carbon emissions through decaying forests. Results We developed a genome sequence resource for the mountain pine beetle to better understand the unique aspects of this insect's biology. A draft de novo genome sequence was assembled from paired-end, short-read sequences from an individual field-collected male pupa, and scaffolded using mate-paired, short-read genomic sequences from pooled field-collected pupae, paired-end short-insert whole-transcriptome shotgun sequencing reads of mRNA from adult beetle tissues, and paired-end Sanger EST sequences from various life stages. We describe the cytochrome P450, glutathione S-transferase, and plant cell wall-degrading enzyme gene families important to the survival of the mountain pine beetle in its harsh and nutrient-poor host environment, and examine genome-wide single-nucleotide polymorphism variation. A horizontally transferred bacterial sucrose-6-phosphate hydrolase was evident in the genome, and its tissue-specific transcription suggests a functional role for this beetle. Conclusions Despite Coleoptera being the largest insect order with over 400,000 described species, including many agricultural and forest pest species, this is only the second genome sequence reported in Coleoptera, and will provide an important resource for the Curculionoidea and other insects.

A combination of polymerase-chain-reaction amplification and automated DNA sequencing was used to survey variation in a species complex of pest insects, the spruce budworms (Choristoneura fumiferana species group), and an outgroup species, C. rosaceana. We sequenced an mtDNA region of 1,573 bp that extends from the middle of cytochrome oxidase subunit I (COI) through tRNA leucine (UUR) to the end of cytochrome oxidase subunit II. In addition, we examined levels of intraspecific variation within a 470-bp region of the COI gene. Choristoneura fumiferana clearly represented the oldest lineage within its species group, with 2.7%-2.9% sequence divergence from the other species. In contrast, the four remaining species (C. pinus, C. biennis, C. occidentalis, and C. orae) had closely related or identical mtDNA, with < 1% divergence among most of their haplotypes. Despite its older lineage and widespread geographic distribution, C. fumiferana showed significantly lower intraspecific genetic diversity than did C. occidentalis. Choristoneura orae shared haplotypes with C. occidentalis and C. biennis, and species-level separation of these three species was not supported. Two divergent, uncommon haplotypes were also found in C. occidentalis and C. biennis. The divergent haplotype in C. biennis had an unusually high number of inferred amino acid replacements, suggesting selective differences between mitochondrial DNA haplotypes. Transition:transversion ratios in Choristoneura paralleled those found in Drosophila; transition:transversion ratios were highest in closely related sequences but decreased with increasing sequence divergence. Nucleotide composition showed an A+T bias that was near the high end of the range known for insects. This work illustrates the potential utility of direct DNA sequencing in assessing population structures, species limits, and phylogenetic relationships among organisms that have not previously been subjected to DNA analysis.

The water stricter species Limnoporus dissortis and L. notabilis hybridize across a broad zone in western Canada. Body length and alleles at four allozyme loci show a steep cline along the east slope of the Rocky Mountains in western Alberta, while in central British Columbia the parental phenotypes coexist without merging fully. One sex-linked locus shows little introgression, while there is apparently considerable gene flow at three autosomal loci. Although the hybrid zone has characteristics of a broad tension zone, the spatial distribution of introgression suggests that habitat patchiness and differential habitat associations of the two species also contribute to the pattern of hybridization. Asymmetry in interspecific mating success and incompatibilities of sex chromosomes with each other or with cytoplasmic factors appear to account for the occurrence of L. dissortis genotypes within the range of L. notabilis, and the lack of L. notabilis genotypes within the range of L. dissortis. The genetic structure of this hybrid zone supports the importance of sex-linked traits in maintaining the integrity of species, while its spatial structure suggests that extrinsic habitat features can combine with intrinsic genetic incompatibilities to produce complex hybrid interactions.

Madagascar is home to numerous endemic species and lineages, but the processes that have contributed to its endangered diversity are still poorly understood. Evidence is accumulating to demonstrate the importance of Tertiary dispersal across varying distances of oceanic barriers, supplementing vicariance relationships dating back to the Cretaceous, but these hypotheses remain tentative in the absence of well-supported phylogenies. In the Papilio demoleus group of swallowtail butterflies, three of the five recognized species are restricted to Madagascar, whereas the remaining two species range across the Afrotropical zone and southern Asia plus Australia. We reconstructed phylogenetic relationships for all species in the P. demoleus group, as well as 11 outgroup Papilio species, using 60 morphological characters and about 4 kb of nucleotide sequences from two mitochondrial (cytochrome oxidase I and II) and two nuclear (wg and EF-1alpha) genes. Of the three endemic Malagasy species, the two that are formally listed as endangered or at risk represented the most basal divergences in the group, while the more common third endemic was clearly related to African P. demodocus. The fifth species, P. demoleus, showed little differentiation across southern Asia, but showed divergence from its subspecies sthenelus in Australia. Dispersal-vicariance analysis using cladograms derived from morphology and three independent genes indicated a Malagasy diversification of lime swallowtails in the middle Miocene. Thus, diversification processes on the island of Madagascar may have contributed to the origin of common butterflies that now occur throughout much of the Old World tropical and subtemperate regions. An alternative hypothesis, that Madagascar is a refuge for ancient lineages resulting from successive colonizations from Africa, is less parsimonious and does not explain the relatively low continental diversity of the group.

Insect larvae found on a corpse can be used for estimating postmortem intervals. Here, we describe a molecular method for rapid identification of these insects. Specific insect DNA fragments were amplified using the polymerase chain reaction (PCR), followed by direct DNA sequencing of the amplification products. We sequenced 2300 base pairs of mitochondrial DNA from each of three blowfly species: Phormia regina, Phaenicia sericata and Lucilia illustris. All three species are important in forensic entomology. We found 118 nucleotide differences between the L. illustris and P. sericata sequences, 186 between L. illustris and P. regina, and 192 between P. sericata and P. regina. Based on these abundant DNA sequence differences, we can unambiguously identify the immature larval stages of these insects. These DNA sequence differences were also used to predict species-specific, diagnostic restriction sites in the amplified DNA, and these predictions were verified by digestion with nine restriction enzymes. The DNA sequences reported here encode the mitochondrial COI, COII and tRNA-leucine genes.

We assess the potential of complete coding sequences of the mitochondrial cytochrome oxidase genes (COI and COII) and the intervening tRNA-Leucine gene for use in mosquito higher-level systematics, and apply this data to an outstanding question: the phylogenetic affinities of Toxorhynchites. Traditionally placed in its own subfamily and regarded as sister group to Culicinae, recent morphological data instead have suggested that this distinctive genus belongs well within the Culicinae. Published molecular systematic studies seemingly conflict with this new morphological data or are ambiguous. The mitochondrial gene data that we present show good potential for elucidating suprageneric relationships in Culicidae, and strongly support the placement of Toxorhynchites well within the Culicinae. Reexamination of published data sets suggests that there is no substantive conflict among data sets on this issue.

Phycitinae are a morphologically and ecologically diverse group of Lepidoptera with numerous pest species. Establishment of a stable classification system for the subfamily has been challenging due to complex evolutionary patterns in adult morphological structures and difficult species identifications. Currently, Carl Heinrich's dual system, published in 1956, serves as the main reference point for tribal classification, but its inherent ambiguity and geographic constraints have meant that no system is widely accepted for the subfamily. Here we present the first molecular phylogeny of the Phycitinae, based on two independent gene regions (cytochrome oxidase I and elongation factor 1 alpha). We use this molecular phylogeny to examine evolutionary trends in four key morphological structures (hind wing venation, male antennae, male maxillary palpi and male abdomen 8 modifications for pheromone dispersion) and determine their phylogenetic utility. Our results indicate two major groups of genera in t...