Advancing biology through a deeper understanding of zebrafish ecology and evolution

Abstract

Over the last two decades, the zebrafish has joined the ranks of premier model organisms for biomedical research, with a full suite of tools and genomic resources. Yet we still know comparatively little about its natural history. Here I review what is known about the natural history of the zebrafish, where significant gaps in our knowledge remain, and how a fuller appreciation of this organism's ecology and behavior, population genetics, and phylogeny can inform a variety of research endeavors.

Keywords: behavior; ecology; evolutionary biology; genomics; phylogeny; pigment pattern; population genetics; sex determination; the natural history of model organisms; zebrafish.

Figure 1.. Zebrafish and their geographic range.

(A) Historic and more recent sites where zebrafish have been reported in India, Nepal, Bangladesh and possibly Myanmar (Spence et al., 2006; Engeszer et al., 2007b; Spence et al., 2008; Whiteley et al., 2011; Arunachalam et al., 2013). (B) Zebrafish from several populations in northeastern India (Engeszer et al., 2007b). The upper two fish are males and the lower two fish are females; males tend to have a slightly yellow cast ventrally. (C) A group of zebrafish (a single fish is highlighted with the arrow) in a stream-side pool in Meghalaya, India, north of Bangladesh. Scale bar: 5 mm (B). Image credits: D Parichy. DOI: http://dx.doi.org/10.7554/eLife.05635.002

Figure 2.. Zebrafish habitat and co-occurring species.

(A–F) Zebrafish are found in streams both pristine (A) and shared with people (B, D, E), in ephemeral pools at stream margins (F; a close-up of Figure 1C), and in man-made bodies of water (C). (G–K) Many fish might compete with zebrafish at one or more of its life stages, including E. danricus (G), D. dangila (juvenile; H), Oryzias (I), Aplocheilus panchax (J), and P. shalynius (K). (L–O) Among potential predators are Mastecembalus (L), Channa (M), Xenentodon (top) and Barilius (N), and Notopterus (O). For details see Engeszer et al. (2007b). Scale bars: 5 mm (G–M); 5 cm (N, O). Image credits: D Parichy. DOI: http://dx.doi.org/10.7554/eLife.05635.003

Figure 3.. Zebrafish relatives and phylogeny.

(A) Examples of Danio pigment patterns, including spotted and striped morphs of D. kyathit. (B) Adult male of the miniaturized species Danionella dracula. (C) Larval D. tinwini (3 days post-fertilization), illustrating a typical Danio early larval pigment pattern. (D) Relationships within Danio (redrawn from: McCluskey and Postlethwait, 2015). (E) Relationships within Danioninae (simplified and redrawn from: Tang et al., 2010). Branch lengths in D and E are arbitrary. Scale bars: 5 mm (A, B); 0.5 mm (C). Image credits: D Parichy. DOI: http://dx.doi.org/10.7554/eLife.05635.004