Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick–host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host ‘questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.

Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. M. sexta larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine. We report the sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages. The Msex_1.0 genome assembly resulted in a total genome size of 419.4 Mbp. Repetitive sequences accounted for 25.8% of the assembled genome. The official gene set is comprised of 15,451 protein-coding genes, of which 2498 were manually curated. Extensive RNA-seq data from many tissues and developmental stages were used to improve gene models and for insights into gene expression patterns. Genome wide synteny analysis indicated a high level of macrosynteny in the Lepidoptera. Annotation and analyses were carried out for gene families involved in a wide spectrum of biological processes, including apoptosis, vacuole sorting, growth and development, structures of exoskeleton, egg shells, and muscle, vision, chemosensation, ion channels, signal transduction, neuropeptide signaling, neurotransmitter synthesis and transport, nicotine tolerance, lipid metabolism, and immunity. This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects.

79Genetic variation is the fuel of evolution. However, analyzing evolutionary dynamics in 80 natural populations is challenging, sequencing of entire populations remains costly and 81 comprehensive sampling logistically difficult.

Chemoreception is the most important sense for the survival and reproduction of most animal species. In insects, the principal proteins involved in the recognition of chemical cues comprise moderately sized, multigene families. These families include (i) odorant‐binding (OBPs) and chemosensory (CSPs) proteins, which are involved in peripheral olfactory processing; (ii) the chemoreceptor super‐family, formed by the olfactory (OR) and gustatory (GR) receptors; and (iii) the ionotropic receptors (IR), a variant class of ionotropic glutamate receptors (iGluR). Recent comparative genomic analyses of fully sequenced arthropod genomes support the birth‐and‐death model as the major evolutionary mechanism in determining the chemosensory repertoire size, and provide evidence of adaptive changes fostered by ecological shifts that might influence the current size of chemosensory families. These studies also advocate for the origin of olfactory gene families with the evolution of terrestriality in insects. Key Concepts: The chemosensory system mediates the detection of food, predators and mates, eliciting feeding behaviours and innate sexual and reproductive responses. In arthropods, the most important proteins involved in the recognition of chemical cues comprise moderately sized multigene families. The chemosensory system of arthropods relies on transmembrane receptors (OR, GR and IR gene families) and small globular proteins (OBP and CSP families). The number of chemosensory genes is similar across the Drosophila genus, with little variation in the gene number among species. New OBP and CSP genes appear by gene duplication in extant chromosomal clusters, and diverge independently from each other. An unexpectedly high number of gene gains and losses occurred in the evolution of chemosensory families during the 40–60 Myr of divergence of the Drosophila genus. The chemosensory families in insects evolve under a birth‐and‐death process, with lineage‐specific family size expansions and contractions at large time scale. The selective constraints on chemosensory genes have varied over the evolution of the Drosophila genus, with some cases of positive selection. Random genomic drift, assisted by eventual adaptation processes, is the principal determinant of the chemosensory family size of arthropods.