Genes in parallel

Adaptation from genetic variation

One of the central themes of this blog, and indeed of evolutionary biology as a whole, is the notion that adaptation is often underpinned by genes. Genetic variation acts as the basis for natural selection to favour or disfavour traits: while this is directly through phenotypic traits (e.g. fur colour, morphology, behaviour), these traits are typically determined by a genetic component. In the early stages of adaptation, evolution can often be observed by changes in the frequency of genetic variants (alleles) within a species or population over time as natural selection acts, gradually leading to the observable (and sometimes dramatic) change in species over time.

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Crossing the Wires: why ‘genetic hardwiring’ is not the whole story

The age-old folly of ‘nature vs. nurture’

It should come as no surprise to any reader of The G-CAT that I’m a firm believer against the false dichotomy (and yes, I really do love that phrase) of “nature versus nurture.” Primarily, this is because the phrase gives the impression of some kind of counteracting balance between intrinsic (i.e. usually genetic) and extrinsic (i.e. usually environmental) factors and how they play a role in behaviour, ecology and evolution. While both are undoubtedly critical for adaptation by natural selection, posing this as a black-and-white split removes the possibility of interactive traits.

We know readily that fitness, the measure by which adaptation or maladaptation can be quantified, is the product of both the adaptive value of a certain trait and the environmental conditions said trait occurs in. A trait that might confer strong fitness in white environment may be very, very unfit in another. A classic example is fur colour in mammals: in a snowy environment, a white coat provides camouflage for predators and prey alike; in a rainforest environment, it’s like wearing one of those fluoro-coloured safety vests construction workers wear.

Genetics and environment interactions figure.jpg
The real Circle of Life. Not only do genes and the environment interact with one another, but genes may interact with other genes and environments may be complex and multi-faceted.

Genetically-encoded traits

In the “nature versus nurture” context, the ‘nature’ traits are often inherently assumed to be genetic. This is because genetic traits are intrinsic as a fundamental aspect of life, inheritable (and thus can be passed on and undergo evolution by natural selection) and define the important physiological traits that provide (or prevent) adaptation. Of course, not all of the genome encodes phenotypic traits at all, and even less relate to diagnosable and relevant traits for natural selection to act upon. In addition, there is a bit of an assumption that many physiological or behavioural traits are ‘hardwired’: that is, despite any influence of environment, genes will always produce a certain phenotype.

Adaptation from genetic variation.jpg
A very simplified example of adaptation from genetic variation. In this example, we have two different alleles of a single gene (orange and blue). Natural selection favours the blue allele so over time it increases in frequency. The difference between these two alleles is at least one base pair of DNA sequence; this often arises by mutation processes.

Despite how important the underlying genes are for the formation of proteins and definition of physiology, they are not omnipotent in that regard. In fact, many other factors can influence how genetic traits relate to phenotypic traits: we’ve discussed a number of these in minor detail previously. An example includes interactions across different genes: these can be due to physiological traits encoded by the cumulative presence and nature of many loci (as in quantitative trait loci and polygenic adaptation). Alternatively, one gene may translate to multiple different physiological characters if it shows pleiotropy.

Differential expression

One non-direct way genetic information can impact on the phenotype of an organism is through something we’ve briefly discussed before known as differential expression. This is based on the notion that different environmental pressures may affect the expression (that is, how a gene is translated into a protein) in alternative ways. This is a fundamental underpinning of what we call phenotypic plasticity: the concept that despite having the exact same (or very similar) genes and alleles, two clonal individuals can vary in different traits. The is related to the example of genetically-identical twins which are not necessarily physically identical; this could be due to environmental constraints on growth, behaviour or personality.

Brauer DE figure_cropped
An example of differential expression in wild populations of southern pygmy perch, courtesy of Brauer et al. (2017). In this figure, each column represents a single individual fish, with the phylogenetic tree and coloured boxes at the top indicating the different populations. Each row represents a different gene (this is a subset of 50 from a much larger dataset). The colour of each cell indicates whether the expression of that gene is expressed more (red) or less (blue) than average. As you can see, the different populations can clearly be seen within their expression profiles, with certain genes expressing more or less in certain populations.

From an evolutionary perspective, the ability to translate a single gene into multiple phenotypic traits has a strong advantage. It allows adaptation to new, novel environments without waiting for natural selection to favour adaptive mutations (or for new, adaptive alleles to become available from new mutation events). This might be a fundamental trait that determines which species can become invasive pests, for instance: the ability to establish and thrive in environments very different to their native habitat allows introduced species to quickly proliferate and spread. Even for species which we might not consider ‘invasive’ (i.e. they have naturally spread to new environments), phenotypic plasticity might allow them to very rapidly adapt and evolve into new ecological niches and could even underpin the early stages of the speciation process.

Epigenetics

Related to this alternative expression of genes is another relatively recent concept: that of epigenetics. In epigenetics, the expression and function of genes is controlled by chemical additions to the DNA which can make gene expression easier or more difficult, effectively promoting or silencing genes. Generally, the specific chemicals that are attached to the DNA are relatively (but not always) predictable in their effects: for example, the addition of a methyl group to the sequence is generally associated with the repression of the gene underlying it. How and where these epigenetic markers may in turn be affected by environmental conditions, creating a direct conduit between environmental (‘nurture’) and intrinsic genetic (‘nature’) aspects of evolution.

Epigenetic_mechanisms.jpg
A diagram of different epigenetic factors and the mechanisms by which they control gene expression. Source: Wikipedia.

Typically, these epigenetic ‘marks’ (chemical additions to the DNA) are erased and reset during fertilisation: the epigenetic marks on the parental gametes are removed, and new marks are made on the fertilised embryo. However, it has been shown that this removal process is not 100% effective, and in fact some marks are clearly passed down from parent to offspring. This means that these marks are heritable, and could allow them to evolve similarly to full DNA mutations.

The discovery of epigenetic markers and their influence on gene expression has opened up the possibility of understanding heritable traits which don’t appear to be clearly determined by genetics alone. For example, research into epigenetics suggest that heritable major depressive disorder (MDD) may be controlled by the expression of genes, rather than from specific alleles or genetic variants themselves. This is likely true for a number of traits for which the association to genotype is not entirely clear.

Epigenetic adaptation?

From an evolutionary standpoint again, epigenetics can similarly influence the ‘bang for a buck’ of particular genes. Being able to translate a single gene into many different forms, and for this to be linked to environmental conditions, allows organisms to adapt to a variety of new circumstances without the need for specific adaptive genes to be available. Following this logic, epigenetic variation might be critically important for species with naturally (or unnaturally) low genetic diversity to adapt into the future and survive in an ever-changing world. Thus, epigenetic information might paint a more optimistic outlook for the future: although genetic variation is, without a doubt, one of the most fundamental aspects of adaptability, even horrendously genetically depleted populations and species might still be able to be saved with the right epigenetic diversity.

Epigenetic cats example
A relatively simplified example of adaptation from epigenetic variation. In this example, we have a species of cat; the ‘default’ cat has non-tufted ears and an orange coat. These two traits are controlled by the expression of Genes A and B, respectively: in the top cat, neither gene is expressed. However, when this cat is placed into different environments, the different genes are “switched on” by epigenetic factors (the green markers). In a rainforest environment, the dark foliage makes darker coat colour more adaptive; switching on Gene B allows this to happen. Conversely, in a desert environment switching on Gene A causes the cat to develop tufts on its ears, which makes it more effective at hunting prey hiding in the sands. Note that in both circumstances, the underlying genetic sequence (indicated by the colours in the DNA) is identical: only the expression of those genes change.

 

Epigenetic research, especially from an ecological/evolutionary perspective, is a very new field. Our understanding of how epigenetic factors translate into adaptability, the relative performance of epigenetic vs. genetic diversity in driving adaptability, and how limited heritability plays a role in adaptation is currently limited. As with many avenues of research, further studies in different contexts, experiments and scopes will reveal further this exciting new aspect of evolutionary and conservation genetics. In short: watch this space! And remember, ‘nature is nurture’ (and vice versa)!

The many genetic faces of adaptation

The transition from genotype to phenotype

While evolutionary genetics studies often focus on the underlying genetic architecture of species and populations to understand their evolution, we know that natural selection acts directly on physical characteristics. We call these the phenotype; by studying changes in the genes that determine these traits (the genotype), we can take a nuanced approach at studying adaptation. However, our ability to look at genetic changes and relate these to a clear phenotypic trait, and how and why that trait is under natural selection, can be a difficult task.

One gene for one trait

The simplest (and most widely used) models of understanding the genetic basis of adaptation assume that a single genotype codes for a single phenotypic trait. This means that changes in a single gene (such as outliers that we have identified in our analyses) create changes in a particular physical trait that is under a selective pressure in the environment. This is a useful model because it is statistically tractable to be able to identify few specific genes of very large effect within our genomic datasets and directly relate these to a trait: adding more complexity exponentially increases the difficulty in detecting patterns (at both the genotypic and phenotypic level).

Single locus figure
An example of a single gene coding for a single phenotypic trait. In this example, the different combination of alleles of the one gene determines the colour of the cat.

Many genes for one trait: polygenic adaptation

Unfortunately, nature is not always convenient and recent findings suggest that the overwhelming majority of the genetics of adaptation operate under what is called ‘polygenic adaptation’. As the name suggestions, under this scenario changes (even very small ones) in many different genes combine together to have a large effect on a particular phenotypic trait. Given the often very small magnitude of the genetic changes, it can be extremely difficult to separate adaptive changes in genes from neutral changes due to genetic drift. Likewise, trying to understand how these different genes all combine into a single functional trait is almost impossible, especially for non-model species.

Polygenic adaptation is often seen for traits which are clearly heritable, but don’t show a single underlying gene responsible. Previously, we’ve covered this with the heritability of height: this is one of many examples of ‘quantitative trait loci’ (QTLs). Changes in one QTL (a single gene) causes a small quantitative change in a particular trait; the combined effect of different QTLs together can ‘add up’ (or counteract one another) to result in the final phenotype value.

Height QTL
An example of polygenic quantitative trait loci. In this example, height is partially coded for by a total of ten different genes: the dominant form of each gene (Capitals, green) provides more height whereas the recessive form (lowercase, red) doesn’t. The cumulative total of these components determines how tall the person is: the person on the far right was very unlucky and got 0/10 height bonuses and so is the shortest. Progressively from left to right, some genes are contributing to the taller height of the people, with the far right person standing tall with the ultimate 10/10 pro-height genes. For reference, height is actually likely to be coded for by thousands of genes, not 10.

The mechanisms which underlie polygenic adaptation can be more complex than simple addition, too. Individual genes might cause phenotypic changes which interact with other phenotypes (and their underlying genotypes) to create a network of changes. We call these interactions ‘epistasis’, where changes in one gene can cause a flow-on effect of changes in other genes based on how their resultant phenotypes interact. We can see this in metabolic pathways: given that a series of proteins are often used in succession within pathways, a change in any single protein in the process could affect every other protein in the pathway. Of course, knowing the exact proteins coded for every gene, including their physical structure, and how each of those proteins could interact with other proteins is an immense task. Similar to QTLs, this is usually limited to model species which have a large history of research on these specific areas to back up the study. However, some molecular ecology studies are starting to dive into this area by identifying pathways that are under selection instead of individual genes, to give a broader picture of the overall traits that are underlying adaptation.

Labrador epistasis figure
My favourite example of epistasis on coat colour in labradors. Two genes together determine the colour of the coat, with strong interactions between them. The first gene (E/e) determines whether or not the underlying coat gene (B/b) is masked or not: two recessive alleles of the first gene (ee) completely blocks Gene 2 and causes the coat to become golden regardless of the second gene genotype (much like my beloved late childhood pet pictured, Sunny). If the first gene has at least one dominant allele, then the second gene is allowed to express itself. Possessing a dominant allele (BB or Bb) leads to a black lab; possessing two recessive alleles (bb) makes a choc lab!
Labrador epistasis table
The possible combinations of genotypes for the two above genes and the resultant coat colour (indicated by the box colour).

One gene for many traits: pleiotropy and differential gene expression

In contrast to polygenic traits, changes in a single gene can also potentially alter multiple phenotypic traits simultaneously. This is referred to as ‘pleiotropy’ and can happen if a gene has multiple different functions within an organism; one particular protein might be a component of several different systems depending on where it is found or how it is arranged. A clear example of pleiotropy is in albino animals: the most common form of albinism is the result of possessing two recessive alleles of a single gene (TYR). The result of this is the absence of the enzyme tyrosinase in the organism, a critical component in the production of melanin. The flow-on phenotypic effects from the recessive gene most obviously cause a lack of pigmentation of the skin (whitening) and eyes (which appear pink), but also other physiological changes such as light sensitivity or total blindness (due to changes in the iris). Albinism has even been attributed to behavioural changes in wild field mice.

Albinism pleiotropy
A very simplified diagram of how one genotype (the albino version of the TYR gene) can lead to a large number of phenotypic changes via pleiotropy (although many are naturally physiologically connected).

Because pleiotropic genes code for several different phenotypic traits, natural selection can be a little more complicated. If some resultant traits are selected against, but others are selected for, it can be difficult for evolution to ‘resolve’ the balance between the two. The overall fitness of the gene is thus dependent on the balance of positive and negative fitness of the different traits, which will determine whether the gene is positively or negatively selected (much like a cost-benefit scenario). Alternatively, some traits which are selectively neutral (i.e. don’t directly provide fitness benefits) may be indirectly selected for if another phenotype of the same underlying gene is selected for.

Multiple phenotypes from a single ‘gene’ can also arise by alternate splicing: when a gene is transcribed from the DNA sequence into the protein, the non-coding intron sections within the gene are removed. However, exactly which introns are removed and how the different coding exons are arranged in the final protein sequence can give rise to multiple different protein structures, each with potentially different functions. Thus, a single overarching gene can lead to many different functional proteins. The role of alternate splicing in adaptation and evolution is a rarely explored area of research and its importance is relatively unknown.

Non-genes for traits: epigenetics

This gets more complicated if we consider ‘non-genetic’ aspects underlying the phenotype in what we call ‘epigenetics’. The phrase literally translates as ‘on top of genes’ and refers to chemical attachments to the DNA which control the expression of genes by allowing or resisting the transcription process. Epigenetics is a relatively new area of research, although studies have started to delve into the role of epigenetic changes in facilitating adaptation and evolution. Although epigenetics is still a relatively new research topic, future research into the relationship between epigenetic changes and adaptive potential might provide more detailed insight into how adaptation occurs in the wild (and might provide a mechanism for adaptation for species with low genetic diversity)!

 

The different interactions between genotypes, phenotypes and fitness, as well as their complex potential outcomes, inevitably complicates any study of evolution. However, these are important aspects of the adaptation process and to discard them as irrelevant will not doubt reduce our ability to examine and determine evolutionary processes in the wild.