The Bad and the Ugly of evolution: an introduction to maladaptation

Adaptation and natural selection

Adaptation via natural selection is one of the most fundamental components of understanding evolution. It describes how species can continually evolve new, innovative traits and produce the wondrous diversity of the natural world. This process is inevitably underpinned by particular heritable traits often linked to particular genetic variants (alleles). Remember that the underlying genetic trait (the allele) is referred to as the genotype; the physical outcomes of that allele (i.e. how it changes the physiological, behaviour or ecology of the organism) is the phenotype; and the scale of the benefit of possessing that trait is referred to as its fitness. Under the normal process of natural selection, phenotypes which increase fitness are selected for, which results in a shift in genotypes underpinning it.

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Rebuilding the genomic architecture of evolution

Beyond mutations in the genome

Although genetic variation is, in itself, often considered to be one of the fundamental underpinnings of adaptation by natural selection, it can appear through a number of different forms. Typically, we think of genetic variation in terms of individual mutations at a single site (referred to as ‘single nucleotide polymorphisms’, or SNPs), which may vary in frequency across a population or species in response to selective pressures. However, we’ve also discussed some other types of genetic-related variation within The G-CAT before, such as differential gene expression or epigenetic markers.

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What’s yours is mine: evolution by adaptive introgression

Gene flow and introgression

Genetic variation remains a key component of not only understanding the process and history of evolution, but also for allowing evolution to continue into the future. This is the basis of the concept of ‘evolutionary potential’ – the available variation within a population or species which may enable them to adapt to new environmental stressors as they occur. With the looming threat of contemporary climate change and environmental transformations by humanity, predicting and supporting evolutionary potential across the diversity of life is critical for conserving the stability of our biosphere.

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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)!

You’re perfect, you’re beautiful, you look like a model (species)

What is a ‘model’?

There are quite literally millions of species on Earth, ranging from the smallest of microbes to the largest of mammals. In fact, there are so many that we don’t actually have a good count on the sheer number of species and can only estimate it based on the species we actually know about. Unsurprisingly, then, the number of species vastly outweighs the number of people that research them, especially considering the sheer volumes of different aspects of species, evolution, conservation and their changes we could possibly study.

Species on Earth estimate figure
Some estimations on the number of eukaryotic species (i.e. not including things like bacteria), with the number of known species in blue and the predicted number of total species on Earth in purpleSource: Census of Marine Life.

This is partly where the concept of a ‘model’ comes into it: it’s much easier to pick a particular species to study as a target, and use the information from it to apply to other scenarios. Most people would be familiar with the concept based on medical research: the ‘lab rat’ (or mouse). The common house mouse (Mus musculus) and the brown rat (Rattus norvegicus) are some of the most widely used models for understanding the impact of particular biochemical compounds on physiology and are often used as the testing phase of medical developments before human trials.

So, why are mice used as a ‘model’? What actually constitutes a ‘model’, rather than just a ‘relatively-well-research-species’? Well, there are a number of traits that might make certain species ideal subjects for understanding key concepts in evolution, biology, medicine and ecology. For example, mice are often used in medical research given their (relative) similar genetic, physiological and behavioural characteristics to humans. They’re also relatively short-lived and readily breed, making them ideal to observe the more long-term effects of medical drugs or intergenerational impacts. Other species used as models primarily in medicine include nematodes (Caenorhabditis elegans), pigs (Sus scrofa domesticus), and guinea pigs (Cavia porcellus).

The diversity of models

There are a wide variety and number of different model species, based on the type of research most relevant to them (and how well it can be applied to other species). Even with evolution and conservation-based research, which can often focus on more obscure or cryptic species, there are several key species that have widely been applied as models for our understanding of the evolutionary process. Let’s take a look at a few examples for evolution and conservation.

Drosophila

It would be remiss of me to not mention one of the most significant contributors to our understanding of the genetic underpinning of adaptation and speciation, the humble fruit fly (Drosophila melanogaster, among other species). The ability to rapidly produce new generations (with large numbers of offspring with very short generation time), small fully-sequenced genome, and physiological variation means that observing both phenotypic and genotypic changes over generations due to ‘natural’ (or ‘experimental’) selection are possible. In fact, Drosphilia spp. were key in demonstrating the formation of a new species under laboratory conditions, providing empirical evidence for the process of natural selection leading to speciation (despite some creationist claims that this has never happened).

Drosophila speciation experiment
A simplified summary of the speciation experiment in Drosophila, starting with a single species and resulting in two reproductively isolated species based on mating and food preference. Source: Ilmari Karonen, adapted from here.

Darwin’s finches

The original model of evolution could be argued to be Darwin’s finches, as the formed part of the empirical basis of Charles Darwin’s work on the theory of evolution by natural selection. This is because the different species demonstrate very distinct and obvious changes in morphology related to a particular diet (e.g. the physiological consequences of natural selection), spread across an archipelago in a clear demonstration of a natural experiment. Thus, they remain the original example of adaptive radiation and are fundamental components of the theory of evolution by natural selection. However, surprisingly, Darwin’s finches are somewhat overshadowed in modern research by other species in terms of the amount of available data.

Darwin's finches drawings
Some of Darwin’s early drawings of the morphological differences in Galapagos finch beaks, which lead to the formulation of the theory of evolution by natural selection.

Zebra finches

Even as far as birds go, one species clearly outshines the rest in terms of research. The zebra finch is one of the most highly researched vertebrate species, particularly as a model of song learning and behaviour in birds but also as a genetic model. The full genome of the zebra finch was the second bird to ever be sequenced (the first being a chicken), and remains one of the more detailed and annotated genomes in birds. Because of this, the zebra finch genome is often used as a reference for other studies on the genetics of bird species, especially when trying to understand the function of genetic changes or genes under selection.

Zebra finches.jpg
A pair of (very cute) model zebra finches. Source: Michael Lawton via Smithsonian.com.

 

Fishes

Fish are (perhaps surprisingly) also relatively well research in terms of evolutionary studies, largely due to their ancient origins and highly diverse nature, with many different species across the globe. They also often demonstrate very rapid and strong bouts of divergence, such as the cichlid fish species of African lakes which demonstrate how new species can rapidly form when introduced to new and variable environments. The cichlids have become the poster child of adaptive radiation in fishes much in the same way that Darwin’s finches highlighted this trend in birds. Another group of fish species used as a model for similar aspects of speciation, adaptive divergence and rapid evolutionary change are the three-spine and nine-spine stickleback species, which inhabit a variety of marine, estuarine and freshwater environments. Thus, studies on the genetic changes across these different morphotypes is a key in understanding how adaptation to new environments occur in nature (particularly the relatively common transition into different water types in fishes).

cichlid diversity figure
The sheer diversity of species and form makes African cichlids an ideal model for testing hypotheses and theories about the process of evolution and adaptive radiation. Figure sourced from Brawand et al. (2014) in Nature.

Zebra fish

More similar to the medical context of lab rats is the zebrafish (ironically, zebra themselves are not considered a model species). Zebrafish are often used as models for understanding embryology and the development of the body in early formation given the rapid speed at which embryonic development occurs and the transparent body of embryos (which makes it easier to detect morphological changes during embryogenesis).

Zebrafish embryo
The transparent nature of zebrafish embryos make them ideal for studying the development of organisms in early stages. Source: yourgenome.org.

Using information from model species for non-models

While the relevance of information collected from model species to other non-model species depends on the similarity in traits of the two species, our understanding of broad concepts such as evolutionary process, biochemical pathways and physiological developments have significantly improved due to model species. Applying theories and concepts from better understood organisms to less researched ones allows us to produce better research much faster by cutting out some of the initial investigative work on the underlying processes. Thus, model species remain fundamental to medical advancement and evolutionary theory.

That said, in an ideal world all species would have the same level of research and resources as our model species. In this sense, we must continue to strive to understand and research the diversity of life on Earth, to better understand the world in which we live. Full genomes are progressively being sequenced for more and more species, and there are a number of excellent projects that are aiming to sequence at least one genome for all species of different taxonomic groups (e.g. birds, bats, fish). As the data improves for our non-model species, our understanding of evolution, conservation management and medical research will similarly improve.