Evolutionary genetic mechanisms of metabolic adaptation
When consumers experience selection for n-3 LC-PUFA synthesis, they can increase enzymatic activity with three different types of genetic processes: 1) gene copy number increases, 2) enzymatic activity changes by amino acid substitutions, and 3) regulatory mutations that increase transcription rates (Fig. 6). These three mechanisms differ in their effect sizes and pleiotropy (i.e., the number of phenotypic traits influenced by the gene). Copy number increases may have the strongest effects on metabolic processes like fatty acid synthesis (Loehlin and Carroll 2016; Loehlin et al. 2019), but are also likely to have pleiotropic effects on other metabolic processes. This is because an increase in copy number may affect expression in multiple tissues throughout different ontogenetic stages (developmental pleiotropy) and/or they may change the amounts of other organic compounds produced as by-products when enzymes are multifunctional (biochemical pleiotropy) (Fig. 6B). Pleiotropic changes may be neutral, favorable, or unfavorable with respect to fitness. For instance, because n-3 and n-6 fatty acids are elongated and desaturated via the same metabolic pathway (Fig. 4), increased fatty acid desaturase and/or elongase activity may result in increased production of both n-3 or n-6 LC-PUFA, depending on the relative availability of n-3 and n-6 precursors. Amino acid substitutions generally have even more pleiotropic effects than copy number increases (Carroll 2005), but their effect sizes are reported to be smaller in some cases (Loehlin et al. 2019). Regulatory mutations may have relatively strong effects (Loehlin et al. 2019) and enable tissue- or ontogenetic stage-specific expression, but may still be biochemically pleiotropic. Importantly, these three types of mutations often occur together. After gene duplication, these mutations can diverge in both functional amino acid sequences and expression patterns (Ohno 1970; Lynch 2007), becoming more specific (neo-functionalization) and thus reducing pleiotropic effects while still having strong effect sizes (Fig. 6C).
Examples of all three types of genetic mechanisms can be found within the evolution of fatty acid metabolism. Copy number variation in fatty acid desaturase (Fads ) genes is widely observed in vertebrates (Castro et al. 2012). For instance, Ishikawa et al. (2019) recently found that freshwater threespine stickleback have increased Fads2 copy number and thus greater capability to synthesize DHA, thereby overcoming the nutritional constraints of freshwater ecosystems. However, increased expression ofFads2 also results in increased production of n-6 LC-PUFA, such as ARA, in sticklebacks, thus demonstrating a biochemical pleiotropic effect (Ishikawa et al. 2019). In humans, regulatory mutations are known to underlie adaptation to low n-3 LC-PUFA diets (Fumagalli et al. 2015; Ye et al. 2017; Tucci et al. 2018). Derived alleles with higher Fads1 expression appear to have enabled humans to survive better on cultivated, land plant-derived, and n-3 LC-PUFA-deficient diets, allowing them to expand their distribution (Ameur et al. 2012; Fumagalli et al. 2015; Tucci et al. 2018). In contrast, human populations that consume n-3 LC-PUFA-rich diets with high amounts of fish and meat have the ancestral haplotypes (Amorin et al. 2017). Amino acid changes that alter enzymatic functions can also help consumers adapt to diets that vary in n-3 LC-PUFA content. For example, although zebrafish (Danio rerio ) have just one copy of Fads2 , they have high ∆5 and ∆6 desaturase activities as a result of amino acid changes (Hastings et al. 2001). Neo-functionalization following duplication appears to be a common genetic process (Ohno 1970; Zhang 2003). In fishes, for instance, the acquisition of ∆4 activity occurred in one copy of Fads2 after gene duplication (Li et al. 2010; Morais et al. 2012; Oboh et al. 2017). Further genetic analysis of variation in fatty acid metabolism across a greater diversity of taxa will help us to understand which mechanisms are the most prevalent and how mechanisms differ in their effect sizes and pleiotropy on fatty acid adaptive landscapes.