We have initiated research to determine the genetic basis of a male wing polymorphism in the pea aphid Acyrthosiphon pisum (Hemiptera: Aphididae). Previous studies showed that this polymorphism is controlled by a single biallelic locus, which we name aphicarus (api), on the X chromosome. Our objectives were to confirm that api segregates as a polymorphism of a single gene on the X chromosome, and to obtain molecular markers flanking api that can be used as a starting point for high-resolution genetic and physical mapping of the target region, which will ultimately allow the cloning of api. We have established an F2 population segregating for api and have generated X-linked AFLP markers. The segregation pattern of api in the F2 population shows that the male wing polymorphism segregates as a polymorphism of a single gene, or set of closely linked genes on the X chromosome. Using a subset of 78 F2 males, we have constructed a linkage map of the chromosomal region encompassing api using seven AFLP markers. The map spans 74.1 cM and we have mapped api to an interval of 10 cM. In addition, we confirmed X linkage of our AFLP markers and api by using one X-linked marker developed in an earlier study. Our study presents the first mapping of a gene with known function in aphids, and the results indicate that target gene mapping in aphids is feasible.

Many polyphenisms are examples of adaptive phenotypic plasticity where a single genotype produces distinct phenotypes in response to environmental cues. Such alternative phenotypes occur as winged and wingless parthenogenetic females in the pea aphid (Acyrthosiphon pisum). However, the proportion of winged females produced in response to a given environmental cue varies between clonal genotypes. Winged and wingless phenotypes also occur in males of the sexual generation. In contrast to parthenogenetic females, wing production in males is environmentally insensitive and controlled by the sex-linked, biallelic locus, aphicarus (api). Hence, environmental or genetic cues induce development of winged and wingless phenotypes at different stages of the pea aphid life cycle. We have tested whether allelic variation at the api locus explains genetic variation in the propensity to produce winged females. We assayed clones from an F2 cross that were heterozygous or homozygous for alternative api alleles for their propensity to produce winged offspring. We found that clones with different api genotypes differed in their propensity to produce winged offspring. The results indicate genetic linkage of factors controlling the female wing polyphenism and male wing polymorphism. This finding is consistent with the hypothesis that genotype by environment interaction at the api locus explains genetic variation in the environmentally cued wing polyphenism.

Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.

Two invasive hemipteran adelgids cause widespread damage to North American conifers. Adelges tsugae (the hemlock woolly adelgid) has decimated Tsuga canadensis and Tsuga caroliniana (the Eastern and Carolina hemlocks, respectively). A. tsugae was introduced from East Asia and reproduces parthenogenetically in North America, where it can kill trees rapidly. A. abietis, introduced from Europe, makes pineapple galls on several North American spruce species, and weakens trees, increasing their susceptibility to other stresses. Broad-spectrum insecticides that are often used to control adelgid populations can have off-target impacts on beneficial insects and the development of more selective chemical treatments could improve control methods and minimize ecological damage. Whole genome sequencing was performed on both species to aid in development of targeted pest control solutions and improve species conservation. The assembled A. tsugae and A. abietis genomes are 231.71 Mbp and 290.39 Mbp, respectively, each consisting of nine chromosomes and both genomes are over 96% complete based on BUSCO assessment. Genome annotation identified 11,424 and 14,118 protein-coding genes in A. tsugae and A. abietis, respectively. Comparative analysis across 29 Hemipteran species and 14 arthropod outgroups identified 31,666 putative gene families. Gene family expansions in A. abietis included ABC transporters and carboxypeptidases involved in carbohydrate metabolism, while both species showed contractions in core histone families and oxidoreductase pathways. Gene family expansions in A. tsugae highlighted families associated with the regulation of cell differentiation and development (survival motor protein, SMN; juvenile hormone acid methyltransferase JHAMT) as well as those that may be involved in the suppression of plant immunity (clip domain serine protease-D, CLIPD; Endoplasmic reticulum aminopeptidase 1, ERAP1). Among the analyzed gene families, Nicotinic acetylcholine receptors (nAChRs) maintained consistent copy numbers and structural features across species, a finding particularly relevant given their role as targets for current forestry management insecticides. Detailed phylogenetic analysis of nAChR subunits across adelgids and other ecologically important insects revealed remarkable conservation in both sequence composition and predicted structural features, providing crucial insights for the development of more selective pest control strategies.

Identifying the genes underlying genetically complex traits is of fundamental importance for medicine, agriculture, and evolutionary biology. However, the level of resolution offered by traditional quantitative trait locus (QTL) mapping is usually coarse. We analyze here a trait closely related to fitness, ovariole number. Our initial interspecific mapping between Drosophila sechellia (8 ovarioles/ovary) and D. simulans (15 ovarioles/ovary) identified a major QTL on chromosome 3 and a minor QTL on chromosome 2. To refine the position of the major QTL, we selected 1038 additional recombinants in the region of interest using flanking morphological markers (selective phenotyping). This effort generated approximately one recombination event per gene and increased the mapping resolution by approximately seven times. Our study thus shows that using visible markers to select for recombinants can efficiently increase the resolution of QTL mapping. We resolved the major QTL into two epistatic QTL, QTL3a and QTL3b. QTL3a shows sign epistasis: it has opposite effects in two different genetic backgrounds, the presence vs. the absence of the QTL3b D. sechellia allele. This property of QTL3a allows us to reconstruct the probable order of fixation of the QTL alleles during evolution.

The reciprocal hemizygosity test is a straightforward genetic test that can positively identify genes that have evolved to contribute to a phenotypic difference between strains or between species. The test involves a comparison between hybrids that are genetically identical throughout the genome except at the test locus, which is rendered hemizygous for alternative alleles from the two parental strains. If the two reciprocal hemizygotes display different phenotypes, then the two parental alleles must have evolved. New methods for targeted mutagenesis will allow application of the reciprocal hemizygosity test in many organisms. This review discusses the principles, advantages, and limitations of the test.

Much diversity in animal morphology results from variation in the relative size of morphological traits. The scaling relationships, or allometries, that describe relative trait size can vary greatly in both intercept and slope among species or other animal groups. Yet within such groups, individuals typically exhibit low variation in relative trait size. This pattern of high intra- and low intergroup variation may result from natural selection for particular allometries, from developmental constraints restricting differential growth among traits, or both. Here we explore the relative roles of short-term developmental constraints and natural selection in the evolution of the intercept of the allometry between the forewing and hindwing of a butterfly. First, despite a strong genetic correlation between these two traits, we show that artificial selection perpendicular to the forewing-hindwing scaling relationship results in rapid evolution of the allometry intercept. This demonstrates an absence of developmental constraints limiting intercept evolution for this scaling relationship. Mating experiments in a natural environment revealed strong stabilizing selection favoring males with the wild-type allometry intercept over those with derived intercepts. Our results demonstrate that evolution of this component of the forewing-hindwing allometry is not limited by developmental constraints in the short term and that natural selection on allometry intercepts can be powerful.

Environmental changes can elicit alterations in the form, behavior and/or physiology of all species, and this developmental response to environment is known as phenotypic plasticity. Despite its ubiquity, the molecular basis for phenotypic plasticity is not fully understood. The pea aphid, Acyrthosiphon pisum, serves as a model for an extreme form of phenotypic plasticity, known as polyphenism. Changes in photoperiod stimulate a switch in female aphid reproductive mode from asexual to sexual reproduction over the course of one generation without changes in genotype. This reproductive polyphenism results in female aphids with ovaries of one of two types: sexual ovaries (producing haploid oocytes via meiosis), or asexual ovaries (producing identical diploid aphid clones via parthenogenesis). To better understand how aphid ovaries could produce different outputs, we surveyed the transcriptomes of sexual and asexual ovaries using RNA-seq. Among genes that exhibited greater than two-fold differences in gene expression between sexual and asexual ovaries, we identified several aubergine paralogs, which encode for germline-specific members of the Argonaute small RNA-binding protein family. The A. pisum genome contains eight aubergine paralogs and at least two piwi paralogs. We are currently comparing the expression patterns of these aphid aubergine paralogs between asexual and sexual aphid ovaries. Aubergine proteins in other species are thought to help suppress the activity of transposable elements, which are found in high quantities throughout the A. pisum genome. Together, these experiments will help elucidate a potential relationship between aubergine paralogs and aphid reproductive plasticity.

Ever since the integration of Mendelian genetics into evolutionary biology in the early 20th century, evolutionary geneticists have for the most part treated genes and mutations as generic entities. However, recent observations indicate that all genes are not equal in the eyes of evolution. Evolutionarily relevant mutations tend to accumulate in hotspot genes and at specific positions within genes. Genetic evolution is constrained by gene function, the structure of genetic networks, and population biology. The genetic basis of evolution may be predictable to some extent, and further understanding of this predictability requires incorporation of the specific functions and characteristics of genes into evolutionary theory.