Conservation

Not that kind of native-ity: endemism and invasion of Australia

Sean Buckley1 Comment

The endemics of Australia

Australia is world-renowned for the abundant and bizarre species that inhabit this wonderful island continent. We have one of the highest numbers of unique species in the entire world (in the top few!): this is measured by what we call ‘endemism’. A species is considered endemic to a particular place or region if that it is the only place it occurs: it’s completely unique to that environment. In Australia, a whopping 87% of our mammals, 45% of our birds, 93% of our reptiles, 94% of our amphibians 24% of our fishes and 86% of our plants are endemic, making us a real biodiversity paradise! Some lists even label us as a ‘megadiverse country’, which sounds pretty awesome on paper. And although we traditionally haven’t been very good at looking after it, our array of species is a matter of some pride to Aussies.

Endemism map
A map representing the relative proportion of endemic species in Australia, generated through the Atlas of Living Australia. The colours range from no (white; 0% endemics) or little (blue) to high levels of endemism (red; 100% of species are endemic). As you can see, some biogeographic hotspots are clearly indicated (southwest WA, the east coast, the Kimberley ranges).

But the real question is: why are there so many endemics in Australia? What is so special about our country that lends to our unique flora and fauna? Although we naturally associate tropical regions with lush, vibrant and diverse life, most of Australia is complete desert. That said, most of our species are concentrated in the tropical regions of the country, particularly in the upper east coast and far north (the ‘Top End’).

There are a number of different factors which contribute to the high species diversity of Australia. Most notably is how isolated we are as a continent: Australia has been separated from most of the rest of the world for millions of years. In this time, the climate has varied dramatically as the island shifted northward, creating a variety of changing environments and unique ecological niches for species to specialise into. We refer to these species groups as ‘Gondwana relicts’, since their last ancestor with the rest of the world would have been distributed across the supercontinent Gondwana over 100 million years ago. These include marsupials, many birds groups (including ratites and megapodes), many fish groups and a plethora of others. A Gondwanan origin explains why they are only found within Australia, southern Africa and South America (the closest landmass that was also historically connected to Gondwana).

Early arrivals and naturalisation to the Australian ecosystem 

But not all of Australia’s species are so ancient and ingrained in the landscape. As Australia drifted northward and eventually collided with the Sunda plate (forming the mountain ranges across southeast Asia), many new species and groups managed to disperse into Australia. This includes the first indigenous people to colonise Australia, widely regarded as one of the oldest human civilisations and estimated to have arrived down under over 65 thousand years ago.

Eventually, this connection also brought with them one of our most iconic species; the dingo. Estimates of their arrival dates the migration at around 6 thousand years ago. As Australia’s only ‘native’ dog, there has been much debate about its status as an Australian icon. To call the dingo ‘native’ implies it’s always been there: but 6 thousand years is more than enough time to become ingrained within the ecosystem in a stable fashion. So, to balance the debate (and prevent the dingo from being labelled as an ‘invasive pest’ unfairly), we often refer to them as ‘naturalised’. This term helps us to disentangle modern-day pests, many of which our immensely destructive to the natural environment, from other species that have naturally migrated and integrated many years ago.

Patriotic dingo
Although it may not be a “true native”, the dingo will forever be a badge of our native species pride.

Invaders of the Australian continent

Of course, we can never ignore the direct impacts of humans on the ecosystem. Particularly with European settlement, another plethora of animals were introduced for the first time into Australia; these were predominantly livestock animals or hunting-related species (both as predators and prey). This includes the cane toad, widely regarded as one of the biggest errors in pest control on the planet.

When European settlers in the 1930s attempted to grow sugar cane in the far eastern part of the country, they found their crops decimated by a local beetle. In an effort to eradicate them, they brought over a species of cane toad, with the idea that they would control the beetle population and all would be well. Only, cane toads are particularly lazy and instead of targeting the cane beetles, they just thrived on all the other native invertebrates around. They’re also very resilient and adaptable (and highly toxic), so their numbers exploded and they’ve since spread across a large swathe of the country. Their toxic skin makes them fatal food objects for many native predators and they strongly compete against other similar native animals (such as our own amphibians). The cane toad introduction of 1935 is the poster child of how bad failed pest control can be.

DSC_0867_small
This guy here, he’s a bastard. Spotted in my parent’s backyard in Ipswich, QLD. Source: me, with spite.

But is native always better?

History tells a very stark tale about the poor native animals and the ravenous, rampaging pest species. Because of this, it is a widely adopted philosophical viewpoint that ‘native is always best’. And while I don’t disagree with the sentiment (of course we need to preserve our native wildlife, and not the massively overabundant pests), there are rare examples where nature is a little more complicated. In Australia, this is exemplified in the noisy miner.

The noisy miner is a small bird which, much like its name implies, is incredibly noisy and aggressive. It’s highly abundant, found predominantly throughout urban and suburban areas, and seems to dominate the habitat. It does this by bullying out other bird species from nesting grounds, creating a monopoly on the resource to the exclusion of many other species (even larger ones such as crows and magpies). Despite being native, it seems to have thrived on human alteration of the landscape and is a serious threat to the survival and longevity of many other species. If we thought of it solely under the ‘nature is best’ paradigm, we would dismiss the noisy miner as ‘doing what it should be.’ The truth is really more of a philosophical debate: is it natural to let the noisy miner outcompete many other natives, possibly resulting in their extinction? Or is it only because of human interference (and thus is our responsibility to fix) that the noisy miner is doing so well in the first place? It’s not a simple question to answer, although the latter seems to be incredibly important.

Noisy miner harassing currawong
An example of the aggressive behaviour of the noisy miner (top), swooping down on a pied currawong (bottom). Despite the size differences, noisy miners will frequently attempt to harass and scare off other larger birds. Image source: Bird Ecology Study Group website.

The amazing biodiversity of Australia is a badge of honour we should wear with patriotic pride. Conservation efforts of our endemic fauna are severely limited by a lack of funding and resources, and despite a general acceptance of the importance of diverse ecosystems we remain relatively ineffective at preserving it. Understanding and connecting with our native wildlife, whilst finding methods to control invasive species, is key to conserving our wonderful ecosystems.

Why we should always pander to diversity

Sean Buckley5 Comments

Diversity in the natural world

‘Diversity’ is a term that gets used a lot these days, albeit usually in reference to social changes and structures. However, diversity is not merely a human construct and reflects an extremely important aspect of the natural world at a variety of levels. From the smallest genes to the biggest ecosystems, diversity is a trait that confers a massive range of benefits to individuals, populations, species and even the entire globe. Let’s dissect this diversity down at different scales and see how beneficial it can be.

Hierarchy of diversity
The generalised hierarchy at life, with diversity being an important component of each tier. At the smallest tier, genes underpin all life. The collection of genetic diversity is often summarised into a population (as a single cohesive genetic unit). Several populations can be pooled together into a single (usually) cohesive species. Different species are then components of a larger community (which in turn are components of a broader ecosystem).

Genetic diversity

At the smallest scale in the hierarchy of genetic differentiation, we have the genes themselves. It is a well-established concept that having a diversity of genetic variants (alleles) within a population or species is critical to their future adaptation, evolution and persistance. This is because different alleles will have different benefits (or costs) depending on the environmental pressure that influences them; natural selection might favour one allele over another at one time, but a different one as the pressure changes. Having a higher number of alleles within the population or species means that there is a greater chance at least a few individuals will possess an adaptive gene with the changing environment (which we know can be quite rapid and very, very strong). The diversity serves as a ‘buffer’ against extinction; evolution by natural selection functions best when there are many options to choose from.

Without this diversity, species run the risk of having no adaptive genes at the ready to deal with a selective pressure. Either a new adaptive gene must mutate (or come about in other ways, such as through gene flow from another population or species) or the population/species will suffer and potentially go extinct. As strong selection causes the species to dwindle, it enters what is referred to as the ‘extinction vortex’. Without genetic diversity, they can’t adapt: thus, more individuals die off, causing more genetic diversity to be lost from the population. This pattern is a vicious cycle which can inevitably destroy species (without serious intervention).

Extinction vortex
A very dramatic representation of the extinction vortex.

For this reason, captive breeding programs aim to maintain as much of the genetic diversity of the original population as possible. This reduces the probability of entering a downward extinction spiral from inbreeding depression and helps to maintain populations into the future (both the captive one and the wild population when we reintroduce individuals into the wild).

“Population”  diversity

Because genetic diversity is critically important for species survival, we must also try to preserve the diversity of the entire gene pool of a species. This means conserving highly genetically differentiated populations within a species as a priority, as they may be the only ones that possess the necessary adaptive genes to save the rest of the species. This adaptive genetic variation can then be introduced into other populations in genetic rescue programs and serve as a means to semi-naturally allow the species to evolve. Evolutionarily-significant units (ESUs) are one measure of the invaluable nature of genetically unique populations.

Although many more traditional conservationists strongly believe that ESUs should be managed entirely independently of one another (to preserve their evolutionary ‘pedigree’ and prevent the risk of outbreeding depression), it has been suggested that the benefit of genetic rescue in many cases significantly outweighs this risk of outbreeding depression. For some species, this really is an act of rescue: they are at the edge of extinction, and if we do nothing we condemn them to die out.

Introducing genetic material across populations (or even species!) can generate new functional genes that allow the recipient species to adapt to selective pressures. This might sound very strange, and could be extremely rare, but examples of adaptive genetic material in one species originating from another species through hybridisation do exist in nature. For example, the black coat of wolves is a highly adaptive trait in some populations and is encoded for by the Melanocortin 1 receptor (Mc1r) gene. However, the specific mutation in Mc1r gene that generates the black coat colour actually first originated in domestic dogs; when wild wolves and domestic dogs interbred, this mutation was transferred into the wolf gene pool. Natural selection strongly favoured this new variant, and it very rapidly underwent strong positive selection. Thus, the adaptiveness of black wolves is thanks to a domestic dog mutation!

Species diversity

At a higher level of the hierarchy, the diversity of species within a particular community or ecosystem has been shown to be important for the health and stability of said community. Every species, however small or seemingly unimpressive, plays a role in the greater ecosystem balance, through interactions with other species (e.g. as predator, as prey, as competitor) and the abiotic environment. While some species are known to have very strong impacts on the immediate ecosystem (often dubbed ‘keystone species’, such as apex predators), all species have some influence on the world around them (we’re especially good at it).

Species interactions flowchart

The overall health and stability of an ecosystem, as well as the benefits it can provide to all living things (including humans) is largely determined by the diversity of species. For example, ‘habitat engineers’ are types of species that, by altering the physical environment around them (such as to build a home), directly provide new habitat for other species. They are a fundamental underpinning of many incredibly vibrant ecosystems; think of what a reef system would look like if there were no corals in it. There’d be no anemones growing colourfully; no fish to live in them; no sharks to feed on these non-existent fish. This is just one example of a complex ecosystem that truly relies on its inhabiting species to function.

Ecosystem jenga
Much like Jenga, taking out one block (a species) could cause the entire stack (the ecosystem) to collapse in on itself. Even if it stands up, however, the system will still be weaker without the full diversity to support it.

Protecting our diversity

Diversity is not just a social construct and is an important phenomenon in nature, at a variety of different levels. Preserving the full diversity of life, from genetic diversity within populations and species to full species diversity within ecosystems, is critical to maintaining healthy and robust natural systems. The more diversity we have at each level of this hierarchy, the greater robustness and security we will have in the future.

Surviving the Real-World Apocalypse

Sean Buckley2 Comments

The changing world

Climate change seems to be the centrefold of a large amount of scientific research and media attention, and rightly so: it has the capacity to affect every living organism on the planet. It’s our duty as curators and residents of Earth to be responsible for our influences on the global environmental stage. While a significant part of this involves determining causes and solutions to our contributions to climate change, we also need to know how extensive the effects will be: for example, how can we predict how well species will do in the future?

Predicting the effect of climate change on all of the world’s biodiversity is an immense task. Climate change itself is a complicated system, and causes diverse, interconnected and complex alterations to both global and local climate. Adding on top of this, though, is that climate affects different species in different ways; where some species might be sensitive to some climatic variables (such as rainfall, available sunlight, seasonality), others may be more tolerant to the same factors. But all living things share some requirements, so surely there must be some consistency in their responses to climate change, right?

Apocalypse 2
Lucky for Mr Fish here, he’s responding to a (very dramatic) climate change much, much better than his bird counterpart.

How predictable are species responses to climate change?

Well, evidence would surprisingly suggest not. Many species, even closely related ones, can show very different responses to the exact same climatic pressures or biogeographical events. There are a number of different traits that might affect a species’ ability to adapt, particularly their adaptive genetic diversity (which underpins ‘adaptive potential’). Thus, we need good information of a variety of genetic, physiological and life history traits to be able to make predictions about how likely a species is to adapt and respond to future (and current) climate changes.

Although this can be hard to study in species of high extinction risk (getting a good number of samples is always an issue…), traditional phylogeographic methods might help us to make some comparisons. See, although the modern Earth is rapidly changing (undoubtedly influenced by human society), the climate of the globe has always varied to some degree. There has always been some tumultuousness in the climate and specific Earth history events like volcano eruptions, sea-level changes, or glaciation periods (‘ice ages’) have had diverse effects on organisms globally.

Using comparative phylogeography to predict species responses

One tool for looking at how different species have, in the past, responded to the same biogeographical force is the domain of ‘comparative phylogeography’. Phylogeography itself is something we have discussed before: the ‘comparative’ aspect simply means comparing (with complex statistical methods) these patterns across different and often unrelated species to see how universal (‘congruent’) or unique (‘incongruent’) these patterns are among species. The more broadly we look at the species community in the region, the more we can observe widespread effects of any given environmental or geographical event: if we only look at fish, for example, we might not to be able to infer what response mammals, birds or invertebrates have had to our given event. Sometimes this still meets the scale we wish to focus; other times, we want to see how all the species of an area have been affected.

Actual island diagram
An (very busy) example of different species responses to a single environmental event. In this example, we have three species (a fish, a lizard, and a bird) all living on the same island. In the middle of the island, there is a small mountain range (A). At this point in time, all three species are connected across the whole island; fish can travel via lakes and wetlands (green arrows), lizards can travel across the land (blue arrow) and birds can fly anywhere. However, as the mountain range grows with tectonic movements, the waterways are altered and the north and south are disconnected (B). The fish species is now split into two evolutionarily separate groups (green and gold), while lizards and birds are not. As the range expands further, however, the dispersal route for lizards is cut off, causing them to eventually also become separated into blue and black groups (C). Birds, however, have no problems flying over the mountain range and remain one unified and connected orange group over time (D). Thus, each species has a different response to the formation of the mountain range.
Evol history of island diagram
The phylogenetic history of the three different species in the above example. As you can see, each lineage has a slightly different pattern; birds show no divergences at all, whereas the timing of the lizard and fish N/S splits are different (i.e. temporally incongruent).

Typically, comparative phylogeographic studies have looked at the neutral components of species’ evolution (as is the realm of traditional phylogeography). This includes studying the size of populations over time, how well connected they are and were, what their spatial patterns are and how these relate to the environment. Comparing all of these patterns across species can allow us to start painting a fuller picture of the history of biota in a region. In this way, we can start to see exactly which species have shown what responses and start to relate these to the characteristics that allowed them to respond in that certain way (and including adaptation in our studies). So, what kinds of traits are important?

What traits matter? Who wins?

Often, we find that life history traits of an organism better dictates how they will respond to a certain pressure than other factors such as phylogeny (e.g. one group does not always do better than another). Instead, individual species with certain physical characteristics might handle the pressure better than others. For example, a fish, bird and snake that are all able to tolerate higher temperatures than other fish, birds or snakes in that region are more likely to survive a drought. In this case, none of the groups (fish, birds or snakes) inherently do better than the other two groups. Thus, it can be hard to predict how a large swathe of species will respond to any given environmental change, unless we understand the physical characteristics of every species.

Climate change risk flowchart
A generalised framework of various factors, and their interactions, on the vulnerability of species under current and future climate changes by Williams et al. 2018. The schematic includes genetic, ecological, physical and environmental factors and how these can interact with one another to alleviate or exacerbate the risk of extinction.

We can also see that other physiological or ecological traits, such as climatic preferences and tolerance thresholds, can be critical for adapting to climatic pressures. Naturally, the genetic diversity of species is also an important component underlying their ability to adapt to these new selective pressures and to survive into the future. Trying to incorporate all of these factors into a projected model can be difficult, but with more data of higher quality we can start to make more refined predictions. But by understanding how particular traits influence how well a species may adapt to a changing climate, as well as knowing the what traits different species have, might just be the key to predicting who wins and who dies in the real-world Game of Thrones.

Fantastic Genes and Where to Find Them

Sean Buckley10 Comments

The genetics of adaptation

Adaptation and evolution by natural selection remains one of the most significant research questions in many disciplines of biology, and this is undoubtedly true for molecular ecology. While traditional evolutionary studies have been based on the physiological aspects of organisms and how this relates to their evolution, such as how these traits improve their fitness, the genetic component of adaptation is still somewhat elusive for many species and traits.

Hunting for adaptive genes in the genome

We’ve previously looked at the two main categories of genetic variation: neutral and adaptive. Although we’ve focused predominantly on the neutral components of the genome, and the types of questions about demographic history, geographic influences and the effect of genetic drift, they cannot tell us (directly) about the process of adaptation and natural selective changes in species. To look at this area, we’d have to focus on adaptive variation instead; that is, genes (or other related genetic markers) which directly influence the ability of a species to adapt and evolve. These are directly under natural selection, either positively (‘selected for’) or negatively (‘selected against’).

Given how complex organisms, the environment and genomes can be, it can be difficult to determine exactly what is a real (i.e. strong) selective pressure, how this is influenced by the physical characteristics of the organism (the ‘phenotype’) and which genes are fundamental to the process (the ‘genotype’). Even determining the relevant genes can be difficult; how do we find the needle-like adaptive genes in a genomic haystack?

Magnifying glass figure
If only it were this easy.

There’s a variety of different methods we can use to find adaptive genetic variation, each with particular drawbacks and strengths. Many of these are based on tests of the frequency of alleles, rather than on the exact genetic changes themselves; adaptation works more often by favouring one variant over another rather than completely removing the less-adaptive variant (this would be called ‘fixation’). So measuring the frequency of different alleles is a central component of many analyses.

FST outlier tests

One of the most classical examples is called an ‘FST outlier test’. This can be a bit complicated without understanding what FST is actually measures: in short terms, it’s a statistical measure of ‘population differentiation due to genetic structure’. The FST value of one particular population can determine how genetically similar it is to another. An FST value of 1 implies that the two populations are as genetically different as they could possibly be, whilst an FST value of 0 implies that they are genetically identical populations.

Generally, FST reflects neutral genetic structure: it gives a background of how, on average, different are two populations. However, if we know what the average amount of genetic differentiation should be for a neutral DNA marker, then we would predict that adaptive markers are significantly different. This is because a gene under selection should be more directly pushed towards or away from one variant (allele) than another, and much more strongly than the neutral variation would predict. Thus, the alleles that are way more or less frequent than the average pattern we might assume are under selection. This is the basis of the FST outlier test; by comparing two or more populations (using FST), and looking at the distribution of allele frequencies, we can pick out a few alleles that vary from the average pattern and suggest that they are under selection (i.e. are adaptive).

There are a few significant drawbacks for FST outlier tests. One of the most major ones is that genetic drift can also produce a large number of outliers; in a small population, for example, one allele might be fixed (has a frequency of 1, with no alternative allele in the population) simply because there is not enough diversity or population size to sustain more alleles. Even if this particular allele was extremely detrimental, it’d still appear to be favoured by natural selection just because of drift.

Drift leading to outliers diagram
An example of genetic drift leading to outliers, featuring our friends the cat population. Top row: Two cat populations, one small (left; n = 5) and one large (middle, n = 12) show little genetic differentiation between them (right; each triangle represents a single gene or locus; the ‘colour’ gene is marked in green). The average (‘neutral’) pattern of differentiation is shown by the dashed line. Much like in our original example, one cat in the small population is horrifically struck by lightning and dies (RIP again). Now when we compare the frequency of the alleles of the two populations (bottom), we see that (because a green cat died), the ‘colour’ locus has shifted away from the general trend (right) and is now an outlier. Thus, genetic drift in the ‘colour’ gene gives the illusion of a selective loci (even though natural selection didn’t cause the change, since colour does not relate to how likely a cat is to be struck by lightning).

Secondly, the cut-off for a ‘significant’ vs. ‘relatively different but possibly not under selection’ can be a bit arbitrary; some genes that are under weak selection can go undetected. Furthermore, recent studies have shown a growing appreciation for polygenic adaptation, where tiny changes in allele frequencies of many different genes combine together to cause strong evolutionary changes. For example, despite the clear heritable nature of height (tall people often have tall children), there is no clear ‘height’ gene: instead, it appears that hundreds of genes are potentially very minor height contributors.

Polygenic height figure final
In this example, we have one tall parent (top) who produces two offspring; one who is tall (left) and one who isn’t (right). In order to understand what genetic factors are contributing to their height differences, we compare their genetics (right; each dot represents a single locus). Although there aren’t any particular loci that look massively different between the two, the cumulative effect of tiny differences (the green triangles) together make one person taller than the other. There are no clear outliers, but many (poly) different genes (genic) acting together.

Genotype-environment associations

To overcome these biases, sometimes we might take a more methodological approach called ‘genotype-environment association’. This analysis differs in that we select what we think our selective pressures are: often environmental characteristics such as rainfall, temperature, habitat type or altitude. We then take two types of measures per individual organism: the genotype, through DNA sequencing, and the relevant environmental values for that organisms’ location. We repeat this over the full distribution of the species, taking a good number of samples per population and making sure we capture the full variation in the environment. Then we perform a correlation-type analysis, which seeks to see if there’s a connection or trend between any particular alleles and any environmental variables. The most relevant variables are often pulled out of the environmental dataset and focused on to reduce noise in the data.

The main benefit of GEA over FST outlier tests is that it’s unlikely to be as strongly influenced by genetic drift. Unless (coincidentally) populations are drifting at the same genes in the same pattern as the environment, the analysis is unlikely to falsely pick it up. However, it can still be confounded by neutral population structure; if one population randomly has a lot of unique alleles or variation, and also occurs in a somewhat unique environment, it can bias the correlation. Furthermore, GEA is limited by the accuracy and relevance of the environmental variables chosen; if we pick only a few, or miss the most important ones for the species, we won’t be able to detect a large number of very relevant (and likely very selective) genes. This is a universal problem in model-based approaches and not just limited to GEA analysis.

New spells to find adaptive genes?

It seems likely that with increasing datasets and better analytical platforms, many more types of analysis will be developed to delve deeper into the adaptive aspects of the genome. With whole-genome sequencing starting to become a reality for non-model species, better annotation of current genomes and a steadily increasing database of functional genes, the ability of researchers to investigate evolution and adaptation at the genomic level is also increasing.

Drifting or driving: directionality in evolution

Sean Buckley26 Comments

How random is evolution?

Often, we like to think of evolution fairly anthropomorphically; as if natural selection actively decides what is, and what isn’t, best for the evolution of a species (or population). Of course, there’s not some explicit Evolution God who decrees how a species should evolve, and in reality, evolution reflects a more probabilistic system. Traits that give a species a better chance of reproducing or surviving, and can be inherited by the offspring, will over time become more and more dominant within the species; contrastingly, traits that do the opposite will be ‘weeded out’ of the gene pool as maladaptive organisms die off or are outcompeted by more ‘fit’ individuals. The fitness value of a trait can be determined from how much the frequency of that trait varies over time.

So, if natural selection is just probabilistic, does this mean evolution is totally random? Is it just that traits are selected based on what just happens to survive and reproduce in nature, or are there more direct mechanisms involved? Well, it turns out both processes are important to some degree. But to get into it, we have to explain the difference between genetic drift and natural selection (we’re assuming here that our particular trait is genetically determined).  

Allele frequency over time diagram
The (statistical) overview of natural selection. In this example, we have two different traits in a population; the blue X and the red O. Our starting population is 20 individuals (N), with 10 of each trait (a 1:1 ratio, or 50% frequency of each). We’re going to assume that, because the blue X is favoured by natural selection, it doubles in frequency each generation (i.e. one individual with the blue X has two offspring with one blue X each). The red O is neither here nor there and is stable over time (one red O produces one red O in the next generation). So, going from Gen 1 to Gen 2, we have twice as many blue Xs (Nt) as we did previously, changing the overall frequency of the traits (highlighted in yellow). Because populations probably don’t exponentially increase every generation, we’ll cut it back down to our original total of 20, but at the same ratios (Np). Over time, we can see that the population gradually accumulates more blue Xs relative to red Os, and by Gen 5 the red O is extinct. Thus, the blue X has evolved!

When we consider the genetic variation within a species to be our focal trait, we can tell that different parts of the genome might be more related with natural selection than others. This makes sense; some mutations in the genome will directly change a trait (like fur colour) which might have a selective benefit or detriment, while others might not change anything physically or change traits that are neither here-nor-there under natural selection (like nose shape in people, for example). We can distinguish between these two by talking about adaptive or neutral variation; adaptive variation has a direct link to natural selection whilst neutral variation is predominantly the product of genetic drift. Depending on our research questions, we might focus on one type of variation over the other, but both are important components of evolution as a whole.

Genetic drift

Genetic drift is considered the random, selectively ‘neutral’ changes in the frequencies of different traits (alleles) over time, due to completely random effects such as random mutations or random loss of alleles. This results in the neutral variation we can observe in the gene pool of the species. Changes in allele frequencies can happen due to entirely stochastic events. If, by chance, all of the individuals with the blue fur variant of a gene are struck by lightning and die, the blue fur allele would end up with a frequency of 0 i.e. go extinct. That’s not to say the blue fur ‘predisposed’ the individuals to be struck be lightning (we assume here, anyway), so it’s not like it was ‘targeted against’ by natural selection (see the bottom figure for this example).

Because neutral variation appears under a totally random, probabilistic model, the mathematical basis of it (such as the rate at which mutations appear) has been well documented and is the foundation of many of the statistical aspects of molecular ecology. Much of our ability to detect which genes are under selection is by seeing how much the frequencies of alleles of that gene vary from the neutral model: if one allele is way more frequent than you’d expect by random genetic drift, then you’d say that it’s likely being ‘pushed’ by something: natural selection.

Manhattan plot example
A Manhattan plot, which measures the level of genetic differentiation between two different groups across the genome. The x-axis shows the length of the genome, in this example colour-coded by the specific chromosome of the sequence, while the y-axis shows the level of differentiation between the two groups being studied. The dots represent certain spots (loci, singular locus) in the genome, with the level of differentiation (Fst) measured for that locus in one group vs that locus in the other group. The dotted line represents the ‘average differentiation’: i.e. how different you’d expect the two groups to be by chance. Anything about that line is significantly different between the two groups, either because of drift or natural selection. This plot has been slightly adapted from Axelsson et al. (2013), who were studying domestication in dogs by comparing the genetic architecture of wild wolves versus domestic dogs. In this example we can see that certain regions of the genome are clearly different between dogs and wolves (circled); when the authors looked at the genes within those blocks, they found that many were related to behavioural changes (nervous system), competitive breeding (sperm-egg recognition) and interestingly, starch digestion. This last category suggests that adaptation to an omnivorous diet (likely human food waste) was key in the domestication process.

Natural selection

Contrastingly to genetic drift, natural selection is when particular traits are directly favoured (or unfavoured) in the environmental context of the population; natural selection is very specific to both the actual trait and how the trait works. A trait is only selected for if it conveys some kind of fitness benefit to the individual; in evolutionary genetics terms, this means it allows the individual to have more offspring or to survive better (usually).

While this might be true for a trait in a certain environment, in another it might be irrelevant or even have the reverse effect. Let’s again consider white fur as our trait under selection. In an arctic environment, white fur might be selected for because it helps the animal to camouflage against the snow to avoid predators or catch prey (and therefore increase survivability). However, in a dense rainforest, white fur would stand out starkly against the shadowy greenery of the foliage and thus make the animal a target, making it more likely to be taken by a predator or avoided by prey (thus decreasing survivability). Thus, fitness is very context-specific.

Who wins? Drift or selection?

So, which is mightier, the pen (drift) or the sword (selection)? Well, it depends on a large number of different factors such as mutation rate, the importance of the trait under selection, and even the size of the population. This last one might seem a little different to the other two, but it’s critically important to which process governs the evolution of the species.

In very small populations, we expect genetic drift to be the stronger process. Natural selection is often comparatively weaker because small populations have less genetic variation for it to act upon; there are less choices for gene variants that might be more beneficial than others. In severe cases, many of the traits are probably very maladaptive, but there’s just no better variant to be selected for; look at the plethora of physiological problems in the cheetah for some examples.

Genetic drift, however, doesn’t really care if there’s “good” or “bad” variation, since it’s totally random. That said, it tends to be stronger in smaller populations because a small, random change in the number or frequency of alleles can have a huge effect on the overall gene pool. Let’s say you have 5 cats in your species; they’re nearly extinct, and probably have very low genetic diversity. If one cat suddenly dies, you’ve lost 20% of your species (and up to that percentage of your genetic variation). However, if you had 500 cats in your species, and one died, you’d lose only <0.2% of your genetic variation and the gene pool would barely even notice. The same applies to random mutations, or if one unlucky cat doesn’t get to breed because it can’t find a mate, or any other random, non-selective reason. One way we can think of this is as ‘random error’ with evolution; even a perfectly adapted organism might not pass on its genes if it is really unlucky. A bigger sample size (i.e. more individuals) means this will have less impact on the total dataset (i.e. the species), though.

Drift in small pops
The effect of genetic drift on small populations. In this example, we have two very similar populations of cats, each with three different alleles (black, blue and green) in similar frequencies across the populations. The major difference is the size of the population; the left is much smaller (5 cats) compared to the right (20 cats). If one cat randomly dies from a bolt of lightning (RIP), and assuming that the colour of the cat has no effect on the likelihood of being struck by lightning (i.e. is not under natural selection), then the outcome of this event is entirely due to genetic drift. In this case, the left population has lost 1/5th of its population size and 1/3rd of its total genetic diversity thanks to the death of the genetically unique blue cat (He will be missed) whereas the right population has only really lost 1/20th of its size and no changes in total diversity (it’ll recover).

Both genetic drift and natural selection are important components of evolution, and together shape the overall patterns of evolution for any given species on the planet. The two processes can even feed into one another; random mutations (drift) might become the genetic basis of new selective traits (natural selection) if the environment changes to suit the new variation. Therefore, to ignore one in favour of the other would fail to capture the full breadth of the processes which ultimately shape and determine the evolution of all species on Earth, and thus the formation of the diversity of life.