Fish Out of Water: Uncovering the Mechanisms for Survival in Extreme Environments

Peter Gillespie ’25

Figure 1: Paralogs specialized for diapause were enriched over time with transcription factors to promote their expression in killifish that undergo diapause
Figure 2: Killifish embryos survive in ephemeral ponds, which go completely dry for roughly eight months a year

Most fish, when left without water, will simply not survive. However, research from Dr. Chi-Kuo Hu from Stony Brook University reveals how the embryos of the African turquoise killifish can survive eight-month long droughts in a dormant state known as diapause. Diapause is a state of suspended animation during which a fully developed killifish may temporarily halt its development. Dr. Hu and his team revealed that recent alterations to ancient paralogs, or duplicated gene pairs, in the species’ DNA have enabled the fish to survive these extremely harsh conditions.

The team first sought to determine the difference in gene expression during diapause as compared to normal development. They performed an Assay for Transposase-Accessible Chromatin (ATAC), which identified areas of chromatin that were free during diapause but not normal development. They then dated these paralogs by examining for their presence within other species. Paralogs shared with all other vertebrates and those present across all fish were considered very ancient, while paralogs present just in the killifish species were considered recent. To determine the paralogs’ relevance specifically to diapause, they compared their expression in the African turquoise killifish to other killifish species, some that do undergo diapause and others that do not.

Hu and his team identified more than 6,000 paralogs present in the African turquoise killifish during diapause but not during development. Comparison of these paralogs to other species revealed that the most ancient paralogs were specialized, and must have developed very recently within the past 18 million years. Analysis of paralog expression revealed that the killifish undergoing diapause had one gene in the paralog pair that was heavily active during diapause and another that was heavily active during normal development. However, in the killifish that do not undergo diapause, both genes in the paralog pair were active during development, suggesting a unique specialization of the paralog pair in the killifish undergoing diapause. Indeed, Dr. Hu and his team identified transcription factors on the specialized paralog pair that are the result of years of mutations and the insertion of transposable DNA. The genes identified function in the storage and breakdown of lipids, which may provide an energy source and protective antioxidative benefits during diapause. Determining the mechanism through which the killifish have developed diapause and identifying the ancient – and vastly shared – paralogs that allow them to do so are enormous strides in uncovering the secrets behind the killifish’s magnificent ability.

Works Cited: 

[1] P. Priya Singh, et al., Evolution of diapause in the african turquoise killifish by remodeling ancient gene regulatory landscape. Cold Spring Harbor bioRxiv, (2021).

[2] Image 1 retrieved from:

[3] Image 2 retrieved from:


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