Introduction

Insecta consists of 29 living orders that are not equivalent by any criteria except taxonomic rank (Davis et al. 2010). Insects demonstrate the greatest biodiversity, accounting for over half of all described eukaryotes, approximately 1 million described species (Grimaldi and Engel 2005) and a global total of anywhere between 5 and 10 million species (Gaston 1991; Raven and Yeates 2007). Although lower-end estimates of species numbers are more likely (Mora et al. 2011), around two-thirds of all insects probably remain to be discovered and described (May 2010), vastly outnumbering the total diversity of other better-studied taxonomic groups like vertebrates and vascular plants. The importance of insects for stable ecosystem functioning also cannot be understated. For example, insects are responsible for the breakdown of organic material, animal and human remains, removal of waste, aeration and turnover of soil, and the vital task of pollination for flowering plants. They also include important predators that control numbers of other pest invertebrates or weed plants, and are an essential food source for many birds, fish, reptiles and amphibians. Understanding the impressive numerical and ecological diversity of insects has long been recognized as an important research goal. To achieve this, it is vital to clarify the evolutionary history and ancestral attributes of lineages. Here we will (1) take stock of our current understanding of insect systematics and the role molecular phylogenetics has played, (2) review the taxonomic diversity of transcriptomes and whole genomes in Insecta and its current bias, (3) discuss the ways that NGS technologies can be used to study insect evolution, and (4) propose strategies for selecting future insects to sequence, for example to maximize genomic diversity and resolve important phylogenetic questions that remain in the field of insect systematics.

Systematics of insects and outstanding questions

In recent years of arthropod research, evidence in favour of a close affinity between hexapods (Insecta, Collembola, Protura and Diplura) and crustaceans has strengthened (Edgecombe 2010; Giribet and Edgecombe 2012; Trautwein et al. 2012; von Reumont et al. 2012). Major arthropod lineages like Myriapoda and Chelicerata are now typically considered more distant relatives than various ‘Crustacea’, and velvet worms are considered the sister-group to Arthropoda as a whole (Campbell et al. 2011, Fig 2.1). There has been some evidence that Hexapoda may be polyphyletic, or mutually paraphyletic with respect to Crustacea (Nardi et al. 2003; Cook et al. 2005).