SummaryThe phylogenetic position of amphioxus, together with its relatively simple and evolutionarily conserved morphology and genome structure, has led to its use as a model for studies of vertebrate evolution. In particular, the recent development of technical approaches, as well as access to the complete amphioxus genome sequence, has provided the community with tools with which to study the invertebrate-chordate to vertebrate transition. Here, we present this animal model, discussing its life cycle, the model species studied and the experimental techniques that it is amenable to. We also summarize the major findings made using amphioxus that have informed us about the evolution of vertebrate traits.Key words: Cephalochordates, Vertebrate evolution, Branchiostoma, Amphioxus, Lancelet Introduction Amphioxus (also called lancelets or cephalochordates) form one of the three chordate subphyla, along with urochordates (see Glossary, Box 1) and vertebrates (Schubert et al., 2006) (Fig. 1A). They form a small group comprising about 35 species (Poss and Boschung, 1996). The number of genera within the cephalochordate subphylum has long been debated, but recent molecular phylogenetic studies show that cephalochordates are divided into three genera (Kon et al., 2007) (Fig. 1B): Branchiostoma, Epigonichthys and Asymmetron.Described for the first time in 1774 (Pallas, 1774), lancelets were classified as molluscs and were called Limax lanceolatus. Later, in 1834, they were renamed as Branchiostoma lubricus (Costa, 1834) and classified as animals closely related to vertebrates. The first to use the name Amphioxus was William Yarrell, who named them Amphioxus lanceolatus and for the first time described their notochord (see Glossary, Box 1), the defining morphological trait of chordates (Yarrell, 1836). After these initial studies, and until the beginning of the 20th century, amphioxus was considered to be a vertebrate. A consensus was then reached whereby amphioxus were considered to be the closest living relatives of vertebrates, with urochordates representing the most basally divergent chordate lineage. These evolutionary relationships were based on morphological characteristics and on some molecular studies of rRNA genes (Winchell et al., 2002). However, in 2006, based on large molecular data set analyses, it was established that cephalochordates represent the most basally divergent lineage of chordates, being the sister group of urochordates and vertebrates (Bourlat et al., 2006; Delsuc et al., 2006) (Fig. 1A).The adult anatomy of amphioxus is vertebrate-like, but simpler. Amphioxus possess typical chordate characters, such as a dorsal hollow neural tube and notochord, a ventral gut and a perforated pharynx with gill slits, segmented axial muscles and gonads, a postanal tail, a pronephric kidney, and homologues of the thyroid gland and adenohypophysis (the endostyle and pre-oral pit, respectively) ( Fig. 2A). However, they lack typical vertebrate-specific structures, such as paired sensory organs (image-forming eye...