In this blog post, we’ll examine, from the perspective of modern evolutionary biology, the role genes play in shaping phenotype and how their influence is understood in the context of interactions with the environment.
We use the biological term “gene” very frequently in everyday conversation. For example, there are countless expressions referring to genes, such as “genes for height,” “genes for academic success,” and “obesity genes.” Although we mention genes in so many different contexts, few people clearly understand what a gene actually is, how much it influences the phenotype, or whether genes are the only carriers of biological information. Let’s take a closer look at genes—which can be considered the foundation of life—from the perspective of evolutionary biology.
Even among biologists, few can provide a simple and clear explanation when asked, “What is a gene?” From a molecular biology perspective, a gene refers to a DNA sequence that contains the information necessary to produce functional RNA or proteins. In the past, only DNA strands that encode proteins were often considered genes, but today’s general definition includes genes that produce functional RNA as well. The genes we commonly refer to constitute only a portion of the total DNA, and not only the exons that encode proteins but also various regulatory regions that control expression play important roles. While definitions of genes vary among scholars, understanding them from an evolutionary perspective makes them easier to explain. For example, the eyeless gene in fruit flies induces eye formation during development. If the eyeless gene does not function normally, fruit flies develop without eyes, demonstrating that specific genes have a crucial influence on phenotype formation. Thus, a gene can be understood as a DNA sequence that directly or indirectly influences phenotype formation.
We now know that the essence of a gene is its DNA sequence. Genes play a crucial role in phenotype formation by regulating the production of proteins and functional RNAs, as well as the timing of their expression. However, there has long been ongoing debate regarding the extent to which genes determine phenotypes. Representative perspectives include the gene-centered view of evolution and the multilevel selection theory, which posits that selection acts not only at the gene level but also at the levels of the individual, the population, and the environment. In evolutionary biology today, while there is general agreement that gene selection plays a significant role, it is also widely accepted that interactions between the environment and various biological levels have a major influence on phenotypes and evolution.
Some scholars question the claim that genes alone determine the phenotype. They argue that genes shape the phenotype through interactions with the environment, which encompasses not only the ecological environment in which an individual lives but also the molecular environment within the cell. In other words, it is not genes alone that play a leading role; rather, both genes and the environment exert a significant influence on phenotype formation. This argument is supported by the fact that even identical twins, who share the same genes, can exhibit different phenotypes depending on their upbringing or lifestyle. However, such examples do not negate the importance of genes. While it is true that a phenotype is formed only when a specific gene is expressed in an appropriate environment, that phenotype cannot manifest if the gene itself is absent. Ultimately, while the phenotype is shaped through the interaction between genes and the environment, genes play an essential role in that process.
If we say that genes determine the phenotype, how can we understand the relationship between genes and the phenotype? Richard C. Lewontin proposed several response patterns to explain how the phenotype changes in response to genetic and environmental changes.
These can be broadly categorized into genetic determinism, environmental determinism, additive interaction, and non-additive interaction. Genetic determinism is the concept that a given genotype will always produce the same phenotype regardless of the environment, while environmental determinism is the concept that different genotypes will exhibit the same phenotype under identical environmental conditions. However, in actual living organisms, genes and the environment act in complex ways, so these extreme forms are rarely observed. Today, most biologists agree that both genes and the environment influence phenotype formation and continue to study the relative magnitude and mechanisms of these influences.
Additive interaction refers to cases where, even as the phenotypes of different genotypes change together in response to environmental changes, the difference between them remains constant. In contrast, non-additive interaction refers to cases where the relative advantage of different genotypes’ phenotypes can be reversed depending on the environment. LeWontin argued that while many people consider only additive interactions, non-additive interactions are also very important in nature. Changes in plant growth with altitude and changes in survival rates during fruit fly development due to temperature are frequently cited as examples of this. Based on the synthesis of research findings to date, it is difficult to generalize that a specific type of interaction is always dominant in all organisms. Depending on the species and trait, both additive and non-additive interactions can occur, and the current mainstream view is that phenotypes result from the complex interplay of genes and the environment.
Some scholars argue that genes do not have a sole influence on determining phenotypes, pointing out that genetic information is not confined to DNA alone. For example, in maternal effects, maternal proteins and RNA contained in the egg exert a significant influence on early development. Furthermore, epigenetic changes—such as chemical modifications of histone proteins or DNA methylation—regulate gene expression, and some of these changes are even passed on to the next generation during cell division. These phenomena demonstrate that the transmission of genetic information cannot be explained solely by DNA base sequences.
However, this does not negate the importance of genes. Even if environmental factors and epigenetic regulatory mechanisms exist to optimize gene expression during an organism’s development, the phenotype cannot be formed without the corresponding genes. Rather, the existence of genetic information and regulatory mechanisms at various levels demonstrates that the interaction between genes and regulatory systems is of paramount importance. For example, the Pax6 gene in vertebrates and the eyeless gene in fruit flies exhibit a very high degree of functional similarity from an evolutionary perspective; such cases clearly demonstrate how important the conservation and interaction of gene networks are during development.
Some scholars who criticize the gene-centric perspective argue that the environment and various biological levels must be considered together to understand the phenotype. In fact, modern biology is actively studying these interactions, and our understanding of phenotype formation is deepening thanks to advances in epigenetics, systems biology, and evolutionary developmental biology. Nevertheless, genes remain a key element in understanding biological phenomena, and research aimed at elucidating the interactions between genes and the environment will continue to develop as a major field of study in biology.
