Adaption to extreme environments: a perspective from fish genomics
Fishes exhibit greater species diversity than any other group of vertebrates. They are found in most bodies of water, including those that pose extreme challenges, such as sulfide springs, rivers contaminated with heavy metals and organic pollutants, and caves without light. Adaptation to these extreme environments usually occurs rapidly, which has stimulated much interest in uncovering the genetic basis of such rapid adaptation. Since the sequencing of the zebrafish genome in 2001, rapid development of high-throughput sequencing technology has facilitated the additional sequencing of ~ 210 ray-finned fish genomes to date. As a result of this wealth of resources, much attention has been focused on the genetic basis of adaptation in fishes, particularly in extreme environments. The goal of this review is to summarize recent advances in fish genomics, with a specific focus on the use of genomic data to understand the genetic basis of adaptation to extreme environments in fishes. The results highlight that fishes often adapt to extreme environments through phenotypic and physiological changes that have a confirmed or inferred genetic basis. Moreover, such changes are usually rapid and repeated when parallel adaptation to similar extreme environments occurs. Specifically, parallel genetic changes are usually observed at both the intra- and interspecific level. The advances in fish genomics provide the opportunity to understand how evolutionary changes feed back into ecosystems that are facing extreme environmental changes, as well as to advance our understanding of the repeatability and predictability of evolutionary response (of fishes) to extreme environmental changes.
KeywordsAdaptation Comparative genomics Extreme environment Parallelism Population genomics
This work was supported by CAS Pioneer Hundred Talents Program, the Second Tibetan Plateau Scientific Expedition and Research (STEP) program (Grant No. 2019QZKK0501), and the National Natural Science Foundation of China (Grant No. 31672273) to B.G.
- Engel AS (2007) Observations on the biodiversity of sulfidic karst habitats. J Cave Karst Stud 69:187–206Google Scholar
- Kavembe GD, Meyer A, Wood CM (2016a) Fish populations in East African saline lakes. In: Schagerl M (ed) Soda Lakes of East Africa. Springer, Berlin, pp 227–257Google Scholar
- Laverty G, Skadhauge E (2015) Hypersaline environments. In: Riesch R, Tobler M, Plath M (eds) Extremophile fishes: ecology, evolution and physiology of teleosts in extreme environments, 1st edn. Springer, Heidelberg, New York, London, pp 85–106Google Scholar
- Levin LA (2005) Ecology of cold seep sediments: interactions of fauna with flow, chemistry and microbes. In: Gibson RN, Atkinson RJA, Gordon JDM (eds) Oceanography and marine biology. CRC Press, Boca Raton, pp 11–56Google Scholar
- Li Z, Guo B, Li J, He S, Chen Y (2008) Bayesian mixed models and divergence time estimation of Chinese cavefishes (Cyprinidae: Sinocyclocheilus). Chin Sci Bull 53:2342–2352Google Scholar
- Plath M, Tobler M, Riesch RD (2015) Extremophile fishes: an introduction. In: Riesch R, Tobler M, Plath M (eds) Extremophile fishes. Springer, Berlin, pp 1–7Google Scholar
- Smith CR, Baco AR (2003) Ecology of whale falls at the deep-sea floor. Oceanog Mar Biol 41:311–354Google Scholar
- Van Dover C (2000) The ecology of deep-sea hydrothermal vents. Princeton University Press, PrincetonGoogle Scholar
- Wood CM (2011) An introduction to metals in fish physiology and toxicology. In: Wood CM, Farrell AP, Brauner CJ (eds) Fish physiology: homeostasis and toxicology of essential metals, 1st edn, vol 31A. Academic Press, London, pp 1–51Google Scholar
- Wright PA, Wood CM (1985) An analysis of branchial ammonia excretion in the freshwater rainbow trout: effects of environmental pH change and sodium uptake blockade. J Exp Biol 114:329–353Google Scholar
- Zhao Y, Zhang C (2009) Endemic fishes of Sinocyclocheilus (Cypriniformes: Cyprinidae) in China—species diversity, cave adaptation, systematics and zoogeography. Science Press, HendersonGoogle Scholar