1 Introduction

Fish are the most diverse group of vertebrates. They make up more than half of all known vertebrates, and they live in a wide variety of places—from oceans and freshwater rivers to the frozen polar regions and even harsh environments such as sulfur springs and sewage. The reason they thrive in so many different habitats is that they are highly adaptable. This ability helps them survive harsh conditions such as salinity changes, temperature fluctuations, and oxygen differences (Tobler et al., 2018; Wang and Guo, 2019; Shang et al., 2022). Their success in a wide range of environments reflects their extraordinary ability to adapt over time, driven by a complex genetic makeup. ​

Fish are found all over the world: in saltwater oceans, freshwater lakes, and even in harsh or rapidly changing habitats. This speaks to their great adaptability to the environments they live in. This flexibility is reflected in the diverse body shapes, body systems, and behaviors that fish have evolved to cope with local challenges. For example, they evolve to cope with salinity changes, temperature fluctuations, and exposure to toxins. These changes often occur quickly, and different species facing similar environmental pressures often evolve in similar ways (Reid et al., 2016; Wang and Guo, 2019; Velotta et al., 2022). Gobies are a clear example: their mitochondrial genes change to adapt to regions with different energy demands. Other fish have also seen similar changes when facing the same environmental pressures (Hill et al., 2019; Wang and Guo, 2019; Shang et al., 2022). ​

Studying the genes that help fish adapt to their environments is key to understanding how they respond to environmental pressures. This knowledge allows us to build better models to predict future changes, improve fisheries management, and support plans to maintain healthy fish populations. Central to these strategies is maintaining genetic diversity and adaptability in fish (Bernatchez, 2016; Wang and Guo, 2019). Studies of local adaptation, natural selection, and intrinsic genetic differences show that fish can remain adaptable even when their overall genetic diversity is low. This highlights the importance of genetic and epigenetic factors for the long-term survival and evolutionary capacity of fish (Bernatchez, 2016; Crotti et al., 2021).

This study will synthesize existing knowledge on the genetic mechanisms and evolutionary dynamics of ecological adaptation in fishes, explore the application of genomics, transcriptomics and epigenomics methods in adaptation to diverse and extreme environments, and integrate the research results of population genomics, comparative genomics and function in fishes to identify common patterns, unique mechanisms and emerging themes of fish adaptation. This study will provide an integrated framework that links genetic diversity, evolutionary processes and ecological outcomes, providing guidance for future research and practical applications in conservation and resource management.

2 Forms of Ecological Adaptation in Fish​

2.1 Body structure changes​

Fish grow different physical features to live in various homes. Some fish that can live both in water and on land develop special fins and stronger muscles to move around on land. Their eyes often stick out and are placed closer to each other. This makes their vision better in both air and water—which is really important for getting around and finding food. Some types of fish grow extra blood vessels in their breathing parts to take in oxygen from the air. They also have changes in their skin that stop them from drying out when they’re on land (Sayer, 2005). In water where there’s not much oxygen, fish might make their lips bigger or change the way their gills are shaped to help them breathe better (Braz-Mota and Almeida-Val, 2021).​

2.2 Internal system adjustments

In the face of harsh environments, fish will actively adjust their internal physiological mechanisms. The koi genus (Astronotus spp.) in the Amazon River basin is a typical example - they live in hypoxic waters and survive by strengthening anaerobic metabolism and increasing blood sugar and lactate concentrations. Some fish have evolved special breathing skills: modifying pharyngeal structures or swim bladders to breathe air, and a few have even grown real "lungs" (Braz-Mota and Almeida-Val, 2021). When shuttling between freshwater and saltwater, fish will regulate ion transport genes and hormone pathways related to ATPase to adapt to the switching of salt processing systems (Velotta et al., 2022). When responding to temperature fluctuations, they either gradually adjust their metabolic rhythm or reshape their internal mechanisms through long-term evolution to ensure vitality at different temperatures (Jutfelt, 2020). These physiological adjustments often originate from rapid genetic or epigenetic changes (Bernatchez, 2016; Wang and Guo, 2019).

2.3 Activity pattern changes

When environmental stress comes, fish often respond by adjusting their behavior. Fish in oxygen-deficient waters may float to the surface to breathe air (Braz-Mota and Almeida-Val, 2021). Fish that can move on land will change their behavior: hiding in the shade or becoming active at night to avoid dehydration and overheating (Sayer, 2005). Some fish also adapt to the local environment better by changing their foraging habits, choosing new habitats, or adjusting the timing of reproduction. These behavioral changes are often related to DNA differences, which may lead to species differentiation over time (Tobler et al., 2018). It is the combined effect of these behavioral strategies that allows fish to survive in various complex and harsh environments.

3 Genetic Mechanisms Underlying Fish Ecological Adaptation

3.1 Genetic foundations of adaptive characteristics

Fish adapt to their environment through subtle adjustments of multiple genes and significant changes in key traits. When coping with salinity differences, genes that regulate water and salt in the body are often relied upon, such as V-type, Ca²⁺, and Na⁺/K⁺-ATPase genes. Many fish facing similar challenges often make similar choices in these genes (Velotta et al., 2022). Even small changes in eye pigment genes can come in handy when adapting to different light conditions. Such changes occur frequently in unrelated species, suggesting that this is a common adaptive path (Hill et al., 2019). Large changes in DNA are also critical, such as the flipping of chromosome segments. In the case of Coilia nasus, such structural changes help them to gain a foothold in freshwater by adjusting genes related to energy consumption, growth, and salt processing (Zong et al., 2020). In the genome of Atlantic herring, changes in both coding and noncoding regions help them adapt to new habitats and reproductive opportunities. These beneficial changes tend to cluster in regions that have been preserved by natural selection (Barrio et al., 2016).

3.2 Molecular processes in environmental adaptation

To survive in harsh environments, fish have a variety of molecular means. Killifish living in polluted waters have evolved different ways to resist toxins, and each population survives with unique versions of genes (Reid et al., 2016). Fish in high-altitude areas, such as the Tibetan species, have undergone some changes in their genes to help them cope with low oxygen, generate energy, and maintain body temperature. These changes often involve genes in the body's oxygen response system (Yang et al., 2014; Zhou et al., 2023). Epigenetic changes are getting more attention - such as adding marks to DNA or adjusting the proteins that package DNA, which can convey useful traits without changing the DNA code (Abdelnour et al., 2024). Other changes after RNA production, such as m6A methylation, are also involved in regulating how genes function under stress (Ahi and Singh, 2024).

3.3 Genomic approaches for studying adaptive evolution​

New ways of reading DNA have completely changed how we study adaptation. Looking at the whole genome helps find genetic changes and structural shifts (like flipped chromosome parts) that let fish adapt to local conditions even when genes are mixing between groups (Barth et al., 2017; Kess et al., 2020; Zong et al., 2020). Comparing entire genomes and the sets of active genes in different fish shows that genes with important jobs evolve faster. Better mapping methods show that many traits that help with adaptation are controlled by many genes working together (Barrio et al., 2016; Wang and Guo, 2019; Zong et al., 2020). These discoveries show that the genetic differences already present in a group of fish let them adapt quickly to changes in their environment (Nelson and Cresko, 2017).

4 Evolutionary Processes in Fish Adaptation

4.1 Selective pressures and adaptation

Environmental factors have a profound influence on the shaping of fish traits that allow them to survive in different environments. Fish populations often evolve favorable traits that are compatible with their habitats to improve their chances of survival. Field observations and genetic data provide support for this phenomenon. These changes are often not the result of a major mutation, but the result of countless subtle genetic adjustments accumulated over time (Bernatchez, 2016). Challenges such as predation threats, food scarcity, and extreme climates may prompt different fishes—even distantly related ones—to evolve similar traits (Hill et al., 2019; Wang and Guo, 2019; Jacobs et al., 2020). Human activities, such as overfishing, can also increase environmental pressures, which can rapidly change fish growth rhythms, reproductive patterns, and even adaptive strategies in the food chain (Therkildsen et al., 2019; Perälä and Kuparinen, 2020).

4.2 Genetic exchange and population adaptation​

The movement of genes between different fish groups shapes how they change to fit their surroundings. It can bring in helpful genetic differences, but it might also make groups become more alike. Changes in how chromosomes are arranged help keep good gene combinations that aid survival, even when genes mix between groups. This is especially true for fish that live in fresh water (Thorstensen et al., 2021). Fish that move from place to place have trouble with their genes mixing as much because people have changed the waterways. This affects how well they can adapt (Tamario et al., 2019). Sometimes, good genes that help with things like living in polluted areas get passed between different groups or even species. This shows another way fish can evolve (Oziolor et al., 2019).​

4.3 Random genetic changes and hybridization

In small or isolated fish populations, random changes in genes can have significant effects. Such variation may weaken their ability to adapt. Even so, some fish populations can still retain enough beneficial differences through DNA or other non-genetic means to maintain adaptive flexibility (Bernatchez, 2016). Reproduction between different fish populations or species can bring them new genes. However, this genetic mixing may also lead to the loss of local-specific traits or reduce survival (Oziolor et al., 2019). Ultimately, the future direction of these fish in a changing environment depends on the combined effects of factors such as random variation, genetic mixing, and natural selection.

5 Case Studies of Fish Ecological Adaptation

5.1 Survival strategies in extreme habitats

Fish in extreme environments have evolved a set of sophisticated survival methods. In the oxygen-deficient waters of the Amazon Basin, cichlid fish such as Astronotus have many unique skills: surfacing to breathe, modifying the structure of their gills, producing energy in an anaerobic environment, and a few even grow lungs to breathe air directly (Braz-Mota and Almeida-Val, 2021). The same is true for Mexican guppies (Poecilia mexicana) living in toxic springs containing hydrogen sulfide. In order to survive in a highly toxic environment, their appearance, behavior, and even physiological functions have changed. These changes often block mating with other populations, giving rise to new species. These examples provide us with excellent materials to reveal the mystery of rapid species variation and differentiation (Tobler et al., 2018). DNA studies have shown that these survival traits often evolve along the same path, whether between different species or within the same group (Wang and Guo, 2019).

5.2 Adaptive mechanisms in migratory species​

Fish that move around a lot, like Atlantic herring and cod, have changes that help them live in specific areas even though their groups mix a lot. Looking at the herring’s genes has found many small differences that are linked to moving between different environments (like from the ocean to slightly salty water) and when they have babies. These helpful changes involve both the parts of genes that make proteins and the parts that control how genes work. They’re often grouped together in blocks or in big flipped sections of chromosomes, kept that way by the environment (Barrio et al., 2016; Pettersson et al., 2019). Atlantic cod that live in fjords show similar patterns. A big flip in one of their chromosomes keeps the genes that help them live in different salt levels, even though genes are still mixing with cod from the open sea (Barth et al., 2017). These examples show how the way genes are arranged helps fish that move around a lot to adapt.​

5.3 Human-influenced adaptation scenarios

Human activities—climate warming, habitat modification, species protection measures, etc.—are quietly reshaping the evolutionary trajectory of fish. Fishing communities are also actively adapting: moving fishing grounds, expanding livelihoods, and trying new resource management models (Galappaththi et al., 2021). In Scotland, dam construction and water flow changes threaten the survival of native European whitefish. To protect the species, some individuals were moved to undisturbed lakes to form safe refuge populations (Figure 1). Although the genetic diversity of these whitefish has decreased, they still show characteristics shaped by natural selection and DNA modification, which help them to establish themselves in their new homes (Crotti et al., 2021). These cases clearly show that natural forces and human activities are intertwined and have a profound impact on the process of fish adapting to the contemporary world.

Figure 1 Figure 1 Map indicating the location of the source and refuge populations of European whitefish in Scotland, with a simplified representative fish shown (Adopted from Crotti et al., 2021) Image caption: Populations from the Eck system are represented by circles, and populations from the Lomond system are represented by triangles. Source populations are in grey and refuge populations are in colour (Adopted from Crotti et al., 2021)

6 Practical Applications and Conservation Implications of Fish Adaptation Studies

6.1 Conservation strategies and habitat rehabilitation

Studying the environmental adaptation mechanisms of fish can help us identify populations with beneficial traits. These findings can be used to develop targeted conservation measures and restore damaged habitats. The field of conservation physiology provides guidance for conservation actions for endangered species and key areas by observing signals and behaviors in fish to monitor the status of populations and habitats. Combining genetic data with detailed physiological functions of fish to build models can more accurately predict how fish will respond to future changes, making restoration plans more effective. The application of new technologies such as biotelemetry and environmental DNA testing allows people to track fish and understand their health status without disturbing them, so managers can take timely countermeasures. In addition, it is extremely important to retain the diverse combination of genes and traits that help fish adapt to local survival - it is these genes and traits that make it easier for populations to survive when faced with pressure and achieve long-term survival (McKenzie et al., 2016; Wang et al., 2020; Yao et al., 2022).

6.2 Sustainable fishery practices and resource management

Understanding how fish respond to different environmental conditions is central to smart fisheries planning, especially as climate change and human activities continue to alter the natural environment. By identifying genetic patterns that confer survival advantages, scientists can develop fishing rules, select appropriate management areas, and design sustainable fishing plans that respect local adaptations of fish. New climate-resilient fisheries management systems that incorporate knowledge of ecology and fish physiology can help maintain healthy fish populations, but such systems have not yet been fully implemented in many areas (Bryndum-Buchholz et al., 2021; Galappaththi et al., 2021; Woods et al., 2021). Practical tools such as environmental DNA and genetic testing provide simple and cost-effective ways to examine species diversity, observe the dynamics of fish populations, track their adaptation, and provide a basis for policy making (Oosting et al., 2019; Wang et al., 2020; Yao et al., 2022). Identifying fish that are less resilient could help identify which populations need to be saved first and lead to action plans to reduce damage — which would benefit both aquatic life and the people who depend on these resources (Galappaththi et al., 2021; Woods et al., 2021; Bossier et al., 2025).

7 Future Prospects and Research Directions​

7.1 Enhancing aquaculture through adaptation research​

Learning about how fish change at the genetic and body function levels is getting more useful for developing fish farming. Studies that look at genetic differences, traits that work well in local areas, and how helpful features are kept can provide information for programs that choose which fish to breed. These programs try to create fish that grow faster, can fight off diseases better, and handle stress from the environment. Keeping the genetic differences in fish groups while saving their good traits helps avoid problems like reduced health from breeding different groups and makes sure fish farming can keep producing well for a long time. Future work should bring together the study of group genetics, how fish work in their environment, and breeding science. This will help make farmed fish both better at producing and better at fitting into their environment.​

7.2 Forecasting climate change responses in fish populations

To understand how fish respond to climate change, we need to examine multiple aspects of their biology – their genes, physiological functions, behavioral patterns, and how they survive in their habitats. These aspects are often interconnected and influence each other. Research shows that it is necessary to consider the synergy of different stressors, how traits are passed on to future generations, and how current genetic and epigenetic characteristics help fish adapt to the environment (Bernatchez, 2016). Predictive models that integrate physiological traits, energy use patterns, and genetic details are essential to determine whether fish populations can survive under future climate conditions (Villéger et al., 2017; Petitjean et al., 2019; Coll et al., 2020; Andersson et al., 2023). Scientists are increasingly concerned about the limits of fish adaptation to rapid changes in their surroundings, especially when human activities bring additional pressures (Galappaththi et al., 2021; Woods et al., 2021).

7.3 Advancing research through multi-omics integration

Combining different types of research data—such as DNA, RNA, protein, and epigenetic studies (i.e., “multi-omics”)—with evolutionary and ecological models has opened up new areas for researchers to explore. These approaches help identify key genes, reveal how genetic and non-genetic factors jointly shape adaptation, and predict how fish may change in new environments (Bernatchez, 2016; Wang and Guo, 2019; Hemmer-Hansen et al., 2014). The combination of large-scale genetic sequencing and advanced computational models can deepen the understanding of the mechanisms of fish adaptation. This knowledge can enhance fishery management and support the protection of aquatic biodiversity.

8 Concluding Remarks

Fish adaptability results from the synergy of different biological systems at the genetic, physiological, and behavioral levels. Small genetic adjustments (such as the replacement of a single amino acid) work together with larger DNA changes to help fish cope with harsh conditions such as saltwater environments, oxygen deprivation, and light differences. These changes affect the range of fish and may drive the emergence of new species over time.

Natural selection acts on both existing genetic differences and new mutations. This often leads to quick evolutionary changes, and sometimes unrelated species facing similar environmental pressures develop in similar ways. Other evolutionary forces—like genes moving between groups, random genetic shifts, and crossbreeding—also play a role in adaptation. They affect the variety of traits and the patterns of genetic differences. Modern genomic studies show that the parts of genes that make proteins, the elements that control genes, and structural changes (like flipped chromosome sections) all work together to help fish adapt to their environment. This is true even when groups of fish keep exchanging genes by moving around.​

Future research should focus on three core directions: (1) comparing multiple species to explore common adaptation patterns; (2) tracking the diachronic changes in the genes of wild fish populations; and (3) integrating genetic, physiological, and environmental research methods. These measures can deepen the understanding of the evolutionary process of fish and provide support for the development of more comprehensive species protection, fishery management, and aquatic habitat maintenance plans. Combining these research paths can better predict the response of fish to the continuous changes in their surrounding environment and provide guidance for the intelligent management of freshwater and marine resources.

Acknowledgments

We would like to thank Ms. Han continuous support throughout the development of this study.

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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