Zebrafish (Danio rerio) are small shoaling cyprinid fish native to the flood plains of the Indian subcontinent. The natural range of D. rerio is centered around the Ganges and Brahmaputra river basins in north-eastern India, Bangladesh, and Nepal, although in the past specimens have also been collected in the Indus, Cauvery, Pennar, Godavari, and Mahanadi river basins. There are also reports of occurrences from the Krishna river basin and the states of Rajasthan, Gujarat, and Andra Pradesh (river basins draining into the Arabian Sea) as well as northern Myanmar and Sri Lanka, but locality details are lacking. Although details of the distribution are unclear, D. rerio may be widely distributed in shallow, slow-flowing waters on the Indian subcontinent. Based on results from several studies, D. rerio occur in shallow water bodies with visibility to a depth of approximately 30 cm, frequently in unshaded locations with aquatic vegetation and a silty substratum. They are most commonly encountered in shallow ponds and standing water bodies, often connected to rice cultivation. Where they are found, they tend to be among the most abundant fish species. (Spence et al. 2008 and references therein)
Danio rerio are omnivorous, feeding primarily on zooplankton and insects, although phytoplankton, filamentous algae and vascular plant material, spores and invertebrate eggs, fish scales, arachnids, detritus, sand, and mud have also been reported from gut content analyses (Spence et al. 2008 and references therein).
The ‘‘leopard’’ danio, which displays a spotted color pattern rather than stripes, was originally thought to be a separate species, described as Brachydanio frankei (at one time, small Danio species with short dorsal fins and a reduced lateral line, including the species now known as Danio rerio, were segregated from the larger Danio species and placed in Brachydanio). However, neither molecular nor morphological analyses have differentiated between the two forms and hybrids have been shown to produce fertile progeny. The leopard danio is now known to be a spontaneous mutation of the wild-type D. rerio color pattern, with homozygotes displaying a spotted pattern and heterozygotes having a disrupted stripe pattern. Another aquarium variant is the ‘‘longfin’’ D. rerio, which is a dominant mutation resulting in elongated fins. The commonly used wild-type strain, TL (Tübingen long-fin) displays both the ‘‘leopard’’ and ‘‘longfin’’ mutations. (Spence et al. 2008 and references therein)
For many decades, D. rerio has been both a very popular aquarium fish and an important research model in several fields of biology (notably, toxicology and developmental biology; see, e.g., Creaser 1934). The development of D. rerio as a model organism for modern biological investigation began with the pioneering work of George Streisinger and colleagues at the University of Oregon (Streisinger et al. 1981; Briggs 2002), who recognized many of the virtues of D. rerio for research. Streisinger developed methods to produce homozygous strains by using genetically inactivated sperm, performed the first mutagenesis studies, and established that complementation methods (in which heterozygous mutant fish are paired) could be used to assign mutations to genetic complementation groups. Subsequently, the use and importance of D. rerio in biological research has exploded and diversified to the point that these fish are extremely important vertebrate models in an extraordinary array of research fields, although they have continued to play a major role in neorobiology (see review by Runkwitz et al. 2011; Vascotto et al. 1997).
A number of features make D. rerio tractable for experimental manipulation. It is a small, robust fish, so large numbers can be kept easily and cheaply in the laboratory, where it breeds all year round. Females can spawn every 2 to 3 days and a single clutch may contain several hundred eggs. Generation time is short (for a vertebrate), typically 3 to 4 months, making it suitable for selection experiments. Danio rerio eggs are large relative to other fish (0.7 mm in diameter at fertilization) and optically transparent, the yolk being sequestered into a separate cell. Furthermore, fertilization is external so live embryos are accessible to manipulation and can be monitored through all developmental stages under a dissecting microscope. Development is rapid, with precursors to all major organs developing within 36 h, and larvae display food seeking and active avoidance behaviors within five days after fertilization, i.e. 2 to 3 days after hatching. The large-scale random mutagenesis screens of D. rerio were the first to be conducted in a vertebrate. Danio rerio used for mutagenesis and screening are from lines that have been inbred for many generations in order to maintain a stable genetic background. Mutagenesis screens have now generated many thousands of mutations and have led to the identification of hundreds of genes controlling vertebrate development (Rinkwitz et al. 2011 report that as of their writing there was information on embryonic and larval expression of over 12,000 genes and just under 1000 mutant phenotypes). As a vertebrate, D. rerio has special value as a model of human disease and for the screening of therapeutic drugs (Chakraborty et al. 2009) and is often more tractable for genetic and embryological manipulation and cost effective than other vertebrate models such as mice. Hundreds of labs around the world now routinely use D. rerio in both basic and applied research, leading to the creation of a centralized online resource for this research community (http://zfin.org). Some researchers have even used D. rerio to investigate the genetic basis of vertebrate behavior (see, e.g., Miklósi and Andrew 2006; Norton and Bally-Cuif 2010). (Spence et al. 2008 and references therein) The D. rerio genome has now been largely sequenced (see http://www.sanger.ac.uk/Projects/D_rerio/), making it an even more valuable research organism.
Laale (1977) reviewed the D. rerio literature to date, with a focus on physiology. Wixon (2000) provides an overview of the current state of knowledge and resources for the study of D. rerio. Although D. rerio is extremely well studied as a lab organism, the ecology and behavior of these fish in the wild has been far less well studied. Spence et al. (2008) reviewed the ecology and behavior of D. rerio (see also McClure et al. 2006; Spence et al. 2006; Engeszer et al. 2007), as well as its taxonomic history, morphology, and many other aspects of its biology.