Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.

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.

A major fraction of the diversity of insects is parasitic, as herbivores, parasitoids or vertebrate ectopara sites. Understanding this diversity requires information on the origin of parasitism in various insect groups. Parasitic lice (Phthiraptera) are the only major group of insects in which all members are permanent parasites of birds or mammals. Lice are classified into a single order but are thought to be closely related to, or derived from, book lice and bark lice (Psocoptera). Here, we use sequences of the nuclear 18S rDNA gene to investigate the relationships among Phthiraptera and Psocoptera and to identify the origins of parasitism in this group (termed Psocodea). Maximum-likelihood (ML), Bayesian ML and parsimony analyses of these data indicate that lice are embedded within the psocopteran infraorder Nanopsocetae, making the order Psocoptera paraphyletic (i.e. does not contain all descendants of a single common ancestor). Furthermore, one family of Psocoptera, Liposcelididae, is identified as the sister taxon to the louse suborder Amblycera, making parasitic lice (Phthiraptera) a polyphyletic order (i.e. descended from two separate ancestors). We infer from these results that parasitism of vertebrates arose twice independently within Psocodea, once in the common ancestor of Amblycera and once in the common ancestor of all other parasitic lice.

An approximate description of the zone of influence around the propagation path for a surface wave is provided by investigating the Fresnel zones for the frequency range of interest. The influence zone about surface wave paths, over which surface waves are coherent in phase, is identified as approximately one-third of the width of the first Fresnel zone. A technique called Fresnel-area ray tracing (FRT) for surface waves has been used to estimate this region around the ray path for each frequency. The FRT technique is developed by combining two standard ray tracing methods, i.e. kinematic ray tracing (KRT) and dynamic ray tracing (DRT). To obtain the exact Fresnel area in a laterally heterogeneous structure would require the solution of a large number of KRT equations. In contrast, the FRT approach requires just a few ray tracing calculations. In the first step, the trajectory of the surface wave is computed by solving the KRT system for the phase-velocity distribution at the required frequency. In the next step, the behaviour of rays in the zone surrounding the KRT path is calculated by solving the DRT system twice; once from the source to the receiver and once more from the receiver to the source along the same trajectory. Finally, combining the solutions of these ray tracing systems using paraxial ray theory, the Fresnel area around a central ray can be estimated. Using FRT, stationary-phase fields can be constructed around a central ray path in a laterally heterogeneous structure. The influence zone around the ray path is then estimated from the stationary-phase function with simple assumptions concerning the perturbed wavefield. The estimate of the influence zone can be efficiently calculated in laterally heterogeneous structure by using the FRT technique, and allows an extension of current methods of surface wave analysis, which have commonly been based on geometrical ray theory and on the approximation of great-circle propagation. This approach allows the treatment of finite-width rays as well as deviations in propagation from the great circle induced by moderate lateral heterogeneity as revealed by recent tomography models. Such finite-width rays should be of major benefit in enhancing ray-based surface wave tomography