The space for species: how spatial aspects influence speciation

Spatial and temporal factors of speciation

The processes driving genetic differentiation, and the progressive development of populations along the speciation continuum, are complex in nature and influenced by a number of factors. Generally, on The G-CAT we have considered the temporal aspects of these factors: how time much time is needed for genetic differentiation, how this might not be consistent across different populations or taxa, and how a history of environmental changes affect the evolution of populations and species. We’ve also touched on the spatial aspects of speciation and genetic differentiation before, but in significantly less detail.

To expand on this, we’re going to look at a few different models of how the spatial distribution of populations influences their divergence, and particularly how these factor into different processes of speciation.

What comes first, ecological or genetic divergence?

One key paradigm in understanding speciation is somewhat an analogy to the “chicken and the egg scenario”, albeit with ecological vs. genetic divergence. This concept is based on the idea that two aspects are key for determining the formation of new species: genetic differentiation of the populations in question, and ecological (or adaptive) changes that provide new ecological niches for species to inhabit. Without both, we might have new morphotypes or ecotypes of a singular species (in the case of ecological divergence without strong genetic divergence) or cryptic species (genetically distinct but ecologically identical species).

The order of these two processes have been in debate for some time, and different aspects of species and the environment can influence how (or if) these processes occur.

Different spatial models of speciation

Generally, when we consider the spatial models for speciation we divide these into distinct categories based on the physical distance of populations from one another. Although there is naturally a lot of grey area (as there is with almost everything in biological science), these broad concepts help us to define and determine how speciation is occurring in the wild.

Allopatric speciation

The simplest model is one we have described before called “allopatry”. In allopatry, populations are distributed distantly from one another, so that there are separated and isolated. A common way to imagine this is islands of populations separated by ocean of unsuitable habitat.

Allopatric speciation is considered one of the simplest and oldest models of speciation as the process is relatively straightforward. Geographic isolation of populations separates them from one another, meaning that gene flow is completely stopped and each population can evolve independently. Small changes in the genes of each population over time (e.g. due to different natural selection pressures) cause these populations to gradually diverge: eventually, this divergence will reach a point where the two populations would not be compatible (i.e. are reproductively isolated) and thus considered separate species.

Allopatry_example
The standard model of allopatric speciation, following an island model. 1) We start with a single population occupying a single island.  2) A rare dispersal event pushes some individuals onto a new island, forming a second population. Note that this doesn’t happen often enough to allow for consistent gene flow (i.e. the island was only colonised once). 3) Over time, these populations may accumulate independent genetic and ecological changes due to both natural selection and drift, and when they become so different that they are reproductively isolated they can be considered separate species.

Although relatively straightforward, one complex issue of allopatric speciation is providing evidence that hybridisation couldn’t happen if they reconnected, or if populations could be considered separate species if they could hybridise, but only under forced conditions (i.e. it is highly unlikely that the two ‘species’ would interact outside of experimental conditions).

Parapatric and peripatric speciation

A step closer in bringing populations geographically together in speciation is “parapatry” and “peripatry”. Parapatric populations are often geographically close together but not overlapping: generally, the edges of their distributions are touching but do not overlap one another. A good analogy would be to think of countries that share a common border. Parapatry can occur when a species is distributed across a broad area, but some form of narrow barrier cleaves the distribution in two: this can be the case across particular environmental gradients where two extremes are preferred over the middle.

The main difference between paraptry and allopatry is the allowance of a ‘hybrid zone’. This is the region between the two populations which may not be a complete isolating barrier (unlike the space between allopatric populations). The strength of the barrier (and thus the amount of hybridisation and gene flow across the two populations) is often determined by the strength of the selective pressure (e.g. how unfit hybrids are). Paraptry is expected to reduce the rate and likelihood of speciation occurring as some (even if reduced) gene flow across populations is reduces the amount of genetic differentiation between those populations: however, speciation can still occur.

Parapatric speciation across a thermocline.jpg
An example of parapatric species across an environment gradient (in this case, a temperature gradient along the ocean coastline). Left: We have two main species (red and green fish) which are adapted to either hotter or colder temperatures (red and green in the gradient), respectively. A small zone of overlap exists where hybrid fish (yellow) occur due to intermediate temperature. Right: How the temperature varies across the system, forming a steep gradient between hot and cold waters.

Related to this are peripatric populations. This differs from parapatry only slightly in that one population is an original ‘source’ population and the other is a ‘peripheral’ population. This can happen from a new population becoming founded from the source by a rare dispersal event, generating a new (but isolated) population which may diverge independently of the source. Alternatively, peripatric populations can be formed when the broad, original distribution of the species is reduced during a population contraction, and a remnant piece of the distribution becomes fragmented and ‘left behind’ in the process, isolated from the main body. Speciation can occur following similar processes of allopatric speciation if gene flow is entirely interrupted or paraptric if it is significantly reduced but still present.

Peripatric distributions.jpg
The two main ways peripatric species can form. Left: The dispersal method. In this example, there is a central ‘source’ population (orange birds on the main island), which holds most of the distribution. However, occasionally (more frequently than in the allopatric example above) birds can disperse over to the smaller island, forming a (mostly) independent secondary population. If the gene flow between this population and the central population doesn’t overwhelm the divergence between the two populations (due to selection and drift), then a new species (blue birds) can form despite the gene flow. Right: The range contraction method. In this example, we start with a single widespread population (blue lizards) which has a rapid reduction in its range. However, during this contraction one population is separated from the main body (i.e. as a refugia), which may also be a precursor of peripatric speciation.

Sympatric (ecological) speciation

On the other end of the distribution spectrum, the two diverging populations undergoing speciation may actually have completely overlapping distributions. In this case, we refer to these populations as “sympatric”, and the possibility of sympatric speciation has been a highly debated topic in evolutionary biology for some time. One central argument rears its head against the possibility of sympatric speciation, in that if populations are co-occurring but not yet independent species, then gene flow should (theoretically) occur across the populations and prevent divergence.

It is in sympatric speciation that we see the opposite order of ecological and genetic divergence happen. Because of this, the process is often referred to as “ecological speciation”, where individual populations adapt to different niches within the same area, isolating themselves from one another by limiting their occurrence and tolerances. As the two populations are restricted from one another by some kind of ecological constraint, they genetically diverge over time and speciation can occur.

This can be tricky to visualise, so let’s invent an example. Say we have a tropical island, which is occupied by one bird species. This bird prefers to eat the large native fruit of the island, although there is another fruit tree which produces smaller fruits. However, there’s only so much space and eventually there are too many birds for the number of large fruit trees available. So, some birds are pushed to eat the smaller fruit, and adapt to a different diet, changing physiology over time to better acquire their new food and obtain nutrients. This shift in ecological niche causes the two populations to become genetically separated as small-fruit-eating-birds interact more with other small-fruit-eating-birds than large-fruit-eating-birds. Over time, these divergences in genetics and ecology causes the two populations to form reproductively isolated species despite occupying the same island.

Ecological sympatric speciation
A diagram of the ecological speciation example given above. Note that ecological divergence occurs first, with some birds of the original species shifting to the new food source (‘ecological niche’) which then leads to speciation. An important requirement for this is that gene flow is somehow (even if not totally) impeded by the ecological divergence: this could be due to birds preferring to mate exclusively with other birds that share the same food type; different breeding seasons associated with food resources; or other isolating mechanisms.

Although this might sound like a simplified example (and it is, no doubt) of sympatric speciation, it’s a basic summary of how we ended up with so many species of Darwin’s finches (and why they are a great model for the process of evolution by natural selection).

The complexity of speciation

As you can see, the processes and context driving speciation are complex to unravel and many factors play a role in the transition from population to species. Understanding the factors that drive the formation of new species is critical to understanding not just how evolution works, but also in how new diversity is generated and maintained across the globe (and how that might change in the future).

 

What’s the (allele) frequency, Kenneth?

Allele frequency

A number of times before on The G-CAT, we’ve discussed the idea of using the frequency of different genetic variants (alleles) within a particular population or species to test a number of different questions about evolution, ecology and conservation. These are all based on the central notion that certain forces of nature will alter the distribution and frequency of alleles within and across populations, and that these patterns are somewhat predictable in how they change.

One particular distinction we need to make early here is the difference between allele frequency and allele identity. In these analyses, often we are working with the same alleles (i.e. particular variants) across our populations, it’s just that each of these populations may possess these particular alleles in different frequencies. For example, one population may have an allele (let’s call it Allele A) very rarely – maybe only 10% of individuals in that population possess it – but in another population it’s very common and perhaps 80% of individuals have it. This is a different level of differentiation than comparing how different alleles mutate (as in the coalescent) or how these mutations accumulate over time (like in many phylogenetic-based analyses).

Allele freq vs identity figure.jpg
An example of the difference between allele frequency and identity. In this example (and many of the figures that follow in this post), the circle denote different populations, within which there are individuals which possess either an A gene (blue) or a B gene. Left: If we compared Populations 1 and 2, we can see that they both have A and B alleles. However, these alleles vary in their frequency within each population, with an equal balance of A and B in Pop 1 and a much higher frequency of B in Pop 2. Right: However, when we compared Pop 3 and 4, we can see that not only do they vary in frequencies, they vary in the presence of alleles, with one allele in each population but not the other.

Non-adaptive (neutral) uses

Testing neutral structure

Arguably one of the most standard uses of allele frequency data is the determination of population structure, one which more avid The G-CAT readers will be familiar with. This is based on the idea that populations that are isolated from one another are less likely to share alleles (and thus have similar frequencies of those alleles) than populations that are connected. This is because gene flow across two populations helps to homogenise the frequency of alleles within those populations, by either diluting common alleles or spreading rarer ones (in general). There are a number of programs that use allele frequency data to assess population structure, but one of the most common ones is STRUCTURE.

Gene flow homogeneity figure
An example of how gene flow across populations homogenises allele frequencies. We start with two initial populations (and from above), which have very different allele frequencies. Hybridising individuals across the two populations means some alleles move from Pop 1 and Pop 2 into the hybrid population: which alleles moves is random (the smaller circles). Because of this, the resultant hybrid population has an allele frequency somewhere in between the two source populations: think of like mixing red and blue cordial and getting a purple drink.

 

Simple YPP structure figure.jpg
An example of a Structure plot which long-term The G-CAT readers may be familiar with. This is taken from Brauer et al. (2013), where the authors studied the population structure of the Yarra pygmy perch. Each small column represents a single individual, with the colours representing how well the alleles of that individual fit a particular genetic population (each population has one colour). The numbers and broader columns refer to different ‘localities’ (different from populations) where individuals were sourced. This shows clear strong population structure across the 4 main groups, except for in Locality 6 where there is a mixture of Eastern and Merri/Curdies alleles.

Determining genetic bottlenecks and demographic change

Other neutral aspects of population identity and history can be studied using allele frequency data. One big component of understanding population history in particular is determining how the population size has changed over time, and relating this to bottleneck events or expansion periods. Although there are a number of different approaches to this, which span many types of analyses (e.g. also coalescent methods), allele frequency data is particularly suited to determining changes in the recent past (hundreds of generations, as opposed to thousands of generations ago). This is because we expect that, during a bottleneck event, it is statistically more likely for rare alleles (i.e. those with low frequency) in the population to be lost due to strong genetic drift: because of this, the population coming out of the bottleneck event should have an excess of more frequent alleles compared to a non-bottlenecked population. We can determine if this is the case with tests such as the heterozygosity excess, M-ratio or mode shift tests.

Genetic drift and allele freq figure
A diagram of how allele frequencies change in genetic bottlenecks due to genetic drift. Left: Large circles again denote a population (although across different sequential times), with smaller circle denoting which alleles survive into the next generation (indicated by the coloured arrows). We start with an initial ‘large’ population of 8, which is reduced down to 4 and 2 in respective future times. Each time the population contracts, only a select number of alleles (or individuals) ‘survive’: assuming no natural selection is in process, this is totally random from the available gene pool. Right: We can see that over time, the frequencies of alleles A and B shift dramatically, leading to the ‘extinction’ of Allele B due to genetic drift. This is because it is the less frequent allele of the two, and in the smaller population size has much less chance of randomly ‘surviving’ the purge of the genetic bottleneck. 

Adaptive (selective) uses

Testing different types of selection

We’ve also discussed previously about how different types of natural selection can alter the distribution of allele frequency within a population. There are a number of different predictions we can make based on the selective force and the overall population. For understanding particular alleles that are under strong selective pressure (i.e. are either strongly adaptive or maladaptive), we often test for alleles which have a frequency that strongly deviates from the ‘neutral’ background pattern of the population. These are called ‘outlier loci’, and the fact that their frequency is much more different from the average across the genome is attributed to natural selection placing strong pressure on either maintaining or removing that allele.

Other selective tests are based on the idea of correlating the frequency of alleles with a particular selective environmental pressure, such as temperature or precipitation. In this case, we expect that alleles under selection will vary in relation to the environmental variable. For example, if a particular allele confers a selective benefit under hotter temperatures, we would expect that allele to be more common in populations that occur in hotter climates and rarer in populations that occur in colder climates. This is referred to as a ‘genotype-environment association test’ and is a good way to detect polymorphic selection (i.e. when multiple alleles contribute to a change in a single phenotypic trait).

Genotype by environment figure.jpg
An example of how the frequency of alleles might vary under natural selection in correlation to the environment. In this example, the blue allele A is adaptive and under positive selection in the more intense environment, and thus increases in frequency at higher values. Contrastingly, the red allele B is maladaptive in these environments and decreases in frequency. For comparison, the black allele shows how the frequency of a neutral (non-adaptive or maladaptive) allele doesn’t vary with the environment, as it plays no role in natural selection.

Taxonomic (species identity) uses

At one end of the spectrum of allele frequencies, we can also test for what we call ‘fixed differences’ between populations. An allele is considered ‘fixed’ it is the only allele for that locus in the population (i.e. has a frequency of 1), whilst the alternative allele (which may exist in other populations) has a frequency of 0. Expanding on this, ‘fixed differences’ occur when one population has Allele A fixed and another population has Allele B fixed: thus, the two populations have as different allele frequencies (for that one locus, anyway) as possible.

Fixed differences are sometimes used as a type of diagnostic trait for species. This means that each ‘species’ has genetic variants that are not shared at all with its closest relative species, and that these variants are so strongly under selection that there is no diversity at those loci. Often, fixed differences are considered a level above populations that differ by allelic frequency only as these alleles are considered ‘diagnostic’ for each species.

Fixed differences figure.jpg
An example of the difference between fixed differences and allelic frequency differences. In this example, we have 5 cats from 3 different species, sequencing a particular target gene. Within this gene, there are three possible alleles: T, A or G respectively. You’ll quickly notice that the allele is both unique to Species A and is present in all cats of that species (i.e. is fixed). This is a fixed difference between Species A and the other two. Alleles and G, however, are present in both Species B and C, and thus are not fixed differences even if they have different frequencies.

Intrapopulation (relatedness) uses

Allele frequency-based methods are even used in determining relatedness between individuals. While it might seem intuitive to just check whether individuals share the same alleles (and are thus related), it can be hard to distinguish between whether they are genetically similar due to direct inheritance or whether the entire population is just ‘naturally’ similar, especially at a particular locus. This is the distinction between ‘identical-by-descent’, where alleles that are similar across individuals have recently been inherited from a similar ancestor (e.g. a parent or grandparent) or ‘identical-by-state’, where alleles are similar just by chance. The latter doesn’t contribute or determine relatedness as all individuals (whether they are directly related or not) within a population may be similar.

To distinguish between the two, we often use the overall frequency of alleles in a population as a basis for determining how likely two individuals share an allele by random chance. If alleles which are relatively rare in the overall population are shared by two individuals, we expect that this similarity is due to family structure rather than population history. By factoring this into our relatedness estimates we can get a more accurate overview of how likely two individuals are to be related using genetic information.

The wild world of allele frequency

Despite appearances, this is just a brief foray into the many applications of allele frequency data in evolution, ecology and conservation studies. There are a plethora of different programs and methods that can utilise this information to address a variety of scientific questions and refine our investigations.

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.

The MolEcol Toolbox: Species Distribution Modelling

Where on Earth are species?

Understanding the spatial distribution of species is a critical component for many different aspects of biological studies. Particularly for conservation, the biogeography of regions is a determinant factor for designating and managing biodiversity hotspots and management units. Or understanding the biogeographical mechanisms that have shaped modern biodiversity may allow us to understand how species will change under future climate change scenarios, and how their distributions will (and have) shift(ed).

Typically, the maximum distribution of species is based on their ecological tolerances: that is, the most extreme environments they can tolerate and proliferate within. Of course, there are a huge number of other factors on top of just natural environment which can shape species distributions, particularly related to human-induced environmental changes (or introducing new species as invasive pests, which we seem to be good at). But exactly where species are and why they occur there are intrinsically linked to the adaptive characteristics of species relative to their environment.

Species distribution modelling

The connection of a species distribution with innate environmental tolerances is the background for a type of analysis we call species distribution modelling (SDM) or environmental niche modelling (ENM). Species distribution modelling seeks to correlate the locations where a species occurs with the local environment around those sites to predict where the species should occur. This is an effective tool for trying to understand the distribution of species that might be tricky to study so thoroughly in the wild; either because they are hard to catch, live in very remote areas, or because they are highly threatened. There are a number of different algorithms and data types that will work with SDM, and there is always ongoing debate about ‘best practices’ in modelling techniques.

SDM method.jpg
The generalised pipeline of SDM, taken from Svenning et al. (2011). By correlating species occurrence data (bottom left) with environmental data (top left), we can develop a model that describes how the species is distributed based on environmental limitations (top right). From here, we can choose to validate the model with other methods (top and bottom centre) or see how the distribution might change with different environmental changes (e.g. bottom right).

A basic how-to on running SDM

The first major component that is needed for SDM is the occurrence data. Some methods will work with presence-only data: that is, a map of GPS coordinates which describes where that species has been found. Others work with presence-absence data, which may require including sites of known non-occurrence. This is an important aspect as the non-occurring sites defines the environment beyond the tolerance threshold of the species: however, it’s very likely that we haven’t sampled every location where they occur, and there will be some GPS co-ordinates that appear to be absent of our species where they actually occur. There are some different analytical techniques which can account for uneven sampling across the real distribution of the species, but they can get very technical.

Edited_koala_data.jpg
An example of species (occurrence only) locality data (with >72,000 records) for the koala (Phascolarctos cinereus) across Australia, taken from the Atlas of Living Australia. Carefully checking the locality data is important, as visual inspection clearly shows records where koalas are not native: they might have been recorded from an introduced individual, given incorrect GPS coordinates or incorrectly identified (red circles).

The second major component is our environmental data. Typically, we want to include environmental data for the types of variables that are likely to constrain the distribution of our species: often temperature and precipitation variables are included, as these two largely predict habitat types. However, it can also be important to include non-climatic variables such as topography (e.g. elevation, slope) in our model to help constrain our predictions to a more reasonable area. It is also important to test for correlation between our variables, as using many variables which are highly correlated may ‘overfit’ the model and underestimate the range of the distribution by placing an unrealistic number of restrictions on the model.

Enviro_maps.jpg
An example of some of the environmental data/maps we might choose to include in a species distribution model, obtained from the Atlas of Living AustraliaA) Mean annual temperature. B) Mean annual precipitation. C) Elevation. D) Weighted distance to nearest waterbody (e.g. rivers, lakes, streams).

Our SDM analysis of choice (e.g. MaxEnt) will then use various algorithms to build a model which best correlates where the species occurs with the environmental variables at those sites. The model tries to create a set of environmental conditions that best encapsulate the occurrence sites whilst excluding the non-occurrence sites from the prediction. From the final model, we can evaluate how strong the effect of each of our variables is on the distribution of the species, and also how well our overall model predicts the locality data.

Projecting our SDM into the past and the future

One reason to use SDM is the ability to project distributions onto alternative environments based on the correlative model. For example, if we have historic data (say, from the last glacial maximum, 21,000 years ago), we can use our predictions of how the species responds to climatic variables and compare that to the environment back then to see how the distribution would have shifted. Similarly, if we have predictions for future climates based on climate change models, we can try and predict how species distributions may shift in the future (an important part of conservation management, naturally).

 

Correct LGM projection example.png
An example of projecting a species distribution model back in time (in this case, to the Last Glacial Maximum 21,000 years ago), taken from Pelletier et al. (2016). On the left is the contemporary distribution of each species; on the right the historic projection. The study focused on three different species of American salamanders and how they had evolved and responded to historic climate change. This figure clearly shows how the distribution of the species have changed over time, particularly how the top two species have significantly reduced in distribution in modern times.

 

Species distribution modelling continues to be a useful tool for conservation and evolution studies, and improvements in analytical algorithms, available environmental data and increased sampling of species will similarly improve SDM. Particularly, improvements in environmental projections from both the distant past and future will improve our ability to understand and predict how species will change, and have changed, with climatic changes

Rescuing the damselfish in distress: rescue or depression?

Conservation management

Managing and conserving threatened and endangered species in the wild is a difficult process. There are a large number of possible threats, outcomes, and it’s often not clear which of these (or how many of these) are at play at any one given time. Thankfully, there are also a large number of possible conservation tools that we might be able to use to protect, bolster and restore species at risk.

Using genetics in conservation

Naturally, we’re going to take a look at the more genetics-orientated aspects of conservation management. We’ve discussed many times the various angles and approaches we can take using large-scale genetic data, some of which include:
• studying the evolutionary history and adaptive potential of species
• developing breeding programs using estimates of relatedness to increase genetic diversity
identifying and describing new species for government legislation
• identifying biodiversity hotspots and focus areas for conservation
• identifying population boundaries for effective management/translocations

Genetics flowchart.jpg
An example of just some of the conservation applications of genetics research that we’ve talked about previously on The G-CAT.

This last point is a particularly interesting one, and an area of conservation research where genetics is used very often. Most definitions of a ‘population’ within a species rely on using genetic data and analysis (such as Fst) to provide a statistical value of how different groups of organisms are within said species. Ignoring some of the philosophical issues with the concept of a population versus a species due to the ‘speciation continuum’ (read more about that here), populations are often interpreted as a way to cluster the range of a species into separate units for conservation management. In fact, the most commonly referred to terms for population structure and levels are evolutionarily-significant units (ESUs), which are defined as a single genetically connected group of organisms that share an evolutionary history that is distinct from other populations; and management units (MUs), which may not have the same degree of separation but are still definably different with enough genetic data.

Hierarchy of structure.jpg
A diagram of the hierarchy of structure within a species. Remember that ESUs, by definition, should be evolutionary different from one another (i.e. adaptively divergent) whilst MUs are not necessarily divergent to the same degree.

This can lead to a particular paradigm of conservation management: keeping everything separate and pure is ‘best practice’. The logic is that, as these different groups have evolved slightly differently from one another (although there is often a lot of grey area about ‘differently enough’), mixing these groups together is a bad idea. Particularly, this is relevant when we consider translocations (“it’s never acceptable to move an organism from one ESU into another”) and captive breeding programs (“it’s never acceptable to breed two organisms together from different ESUs”). So, why not? Why does it matter if they’re a little different?

Outbreeding depression

Well, the classic reasoning is based on a concept called ‘outbreeding depression’. We’ve mentioned outbreeding depression before, and it is a key concept kept in mind when developing conservation programs. The simplest explanation for outbreeding depression is that evolution, through the strict process of natural selection, has pushed particularly populations to evolve certain genetic variants for a certain selective pressure. These can vary across populations, and it may mean that populations are locally adapted to a specific set of environmental conditions, with the specific set of genetic variants that best allow them to do this.

However, when you mix in the genetic variants that have evolved in a different population, by introducing a foreign individual and allowing them to breed, you essentially ‘tarnish’ the ‘pure’ gene pool of that population with what could be very bad (maladaptive) genes. The hybrid offspring of ‘native’ and this foreign individual will be less adaptive than their ‘pure native’ counterparts, and the overall adaptiveness of the population will decrease as those new variants spread (depending on the number introduced, and how negative those variants are).

Outbreeding depression example figure.jpg
An example of how outbreeding depression can affect a species. The original red fish population is not doing well- it is of conservation concern, and has very little genetic diversity (only the blue gene in this example). So, we decide to introduce new genetic diversity by adding in green fish, which have the orange gene. However, the mixture of the two genes and the maladaptive nature of the orange gene actually makes the situation worse, with the offspring showing less fitness than their preceding generations.

You might be familiar with inbreeding depression, which is based on the loss of genetic diversity from having too similar individuals breeding together to produce very genetically ‘weak’ offspring through inbreeding. Outbreeding depression could be thought of as the opposite extreme; breeding too different individuals introduced too many ‘bad’ alleles into the population, diluting the ‘good’ alleles.

Inbreeding vs outbreeding figure.jpg
An overly simplistic representation of how inbreeding and outbreeding depression can reduce overall fitness of a species. In inbreeding depression, the lack of genetic diversity due to related individuals breeding with one another makes them at risk of being unable to adapt to new pressures. Contrastingly, adding in new genes from external populations which aren’t fit for the target population can also reduce overall fitness by ‘diluting’ natural, adaptive allele frequencies in the population.

Genetic rescue

It might sound awfully purist to only preserve the local genetic diversity, and to assume that any new variants could be bad and tarnish the gene pool. And, surprisingly enough, this is an area of great debate within conservation genetics.

The counterpart to the outbreeding depression concerns is the idea of genetic rescue. For populations with already severely depleted gene pools, lacking the genetic variation to be able to adapt to new pressures (such as contemporary climate change), the situation seems incredibly dire. One way to introduce new variation, which might be the basis of new adaptation, bringing in individuals from another population of the same species can provide the necessary genetic diversity to help that population bounce back.

Genetic rescue example figure.jpg
An example of genetic rescue. This circumstance is identical to the one above, with the key difference being in the fitness of the introduced gene. The orange gene in this example is actually beneficial to the target population: by providing a new, adaptive allele for natural selection to act upon, overall fitness is increased for the red fish population.

The balance

So, what’s the balance between the two? Is introducing new genetic variation a bad idea, and going to lead to outbreeding depression; or a good idea, and lead to genetic rescue? Of course, many of the details surrounding the translocation of new genetic material is important: how different are the populations? How different are the environments (i.e. natural selection) between them? How well will the target population take up new individuals and genes?

Overall, however, the more recent and well-supported conclusion is that fears regarding outbreeding depression are often strongly exaggerated. Bad alleles that have been introduced into a population can be rapidly purged by natural selection, and the likelihood of a strongly maladaptive allele spreading throughout the population is unlikely. Secondly, given the lack of genetic diversity in the target population, most that need the genetic rescue are so badly maladaptive as it is (due to genetic drift and lack of available adaptive alleles) that introducing new variants is unlikely to make the situation much worse.

Purging and genetic rescue figure.jpg
An example of how introducing maladaptive alleles might not necessarily lead to decreased fitness. In this example, we again start with our low diversity red fish population, with only one allele (AA). To help boost genetic diversity, we introduce orange fish (with the TT allele) and green fish (with the GG allele) into the population. However, the TT allele is not very adaptive in this new environment, and individuals with the TT gene quickly die out (i.e. be ‘purged’). Individual with the GG gene, however, do well, and continue to integrate into the red population. Over time, these two variants will mix together as the two populations hybridise and overall fitness will increase for the population.

That said, outbreeding depression is not an entirely trivial concept and there are always limitations in genetic rescue procedures. For example, it would be considered a bad idea to mix two different species together and make hybrids, since the difference between two species, compared to two populations, can be a lot stronger and not necessarily a very ‘natural’ process (whereas populations can mix and disjoin relatively regularly).

The reality of conservation management

Conservation science is, at its core, a crisis discipline. It exists solely as an emergency response to the rapid extinction of species and loss of biodiversity across the globe. The time spent trying to evaluate the risk of outbreeding depression – instead of immediately developing genetic rescue programs – can cause species to tick over to the afterlife before we get a clear answer. Although careful consideration and analysis is a requirement of any good conservation program, preventing action due to almost paranoid fear is not a luxury endangered species can afford.

Origination of adaptation: the old and the new (genes)

Adaptation is arguably the most critical biological process in the evolution of species. The process of evolution by natural selection is the cornerstone of evolutionary biology (and indeed, all of contemporary biology!) and adaptation remains fundamental to the process. We know that adaptation is based on the idea that some genetic variants are ‘better’ adapted than others, and thus are unequally shared across a population. But where does this genetic variation come from?

The accumulation of new genetic variation

The classic way for new genetic variants to appear is often thought of as mutation: changes in a single base in the DNA are caused by various external processes such as chemical, physical or environmental influences (such as the sci-fi classics like UV rays or toxic chemicals). Although these forms of mutations happen very rarely and certainly don’t have the same effects comic books would leave you to believe, new mutations can occur relatively rapidly depending on the characteristics of the species. However, the most common way for new mutations to occur is actually part of the DNA replication process: copying DNA is not always perfect and even though the relevant proteins essentially run a spellcheck, sometimes the copy is not 100% perfect and new mutations occur.

Adaptation of mutation figure
An example of how adaptation can occur from a new mutation. In this example, we have one gene (TTXTT), with initial only one allele (variant), TTATT. In the second generation (row), a mutation occurs in one individual which creates a new, second allele: TTGTT. This allele is favoured over the TTATT allele, and in the next generation it’s frequency increases as the alternative allele frequency decreases (the pattern is shown in the frequency values on the right side).

It is important to remember that only mutations that are present in the reproductive cells (sperm and eggs) can be inherited and passed on, and thus be a source for adaptation. Mutations in other tissues of the body, such as within the skin, are not spread across the entire body of the subject and thus aren’t passed on to offspring.

Standing genetic variation

Alternatively, genetic variation might already be present within a species or population. This is more likely if population sizes are large and populations are well connected and interbreeding. We refer to this diverse initial gene pool as ‘standing genetic variation’: that is, the amount of genetic variation within the population or species before the selective pressure requiring adaptation. Standing genetic variation can be thought of as the ‘diversity of choices’ for natural selection to act upon: the variants are readily available, and if a good choice exists it will be favoured by natural selection and become more widespread within the population or species (i.e. evolve).

Adaptation of standing variation figure.jpg
A slightly more complex example of how adaptation can occur from standing variation, this time with two different genes. One codes for fur colour, with two different alleles: GCATA codes for orange fur, and GCGTA codes for grey fur. The other gene codes for ear tufts, with TTCCT coding for tufts and TCCCT coding for no tufts. Natural selection favours both orange fur and tufted ears, and cats with these traits reproduce more frequently than those without (see graph below). These cats probably look familiar.
Graph of standing variation.jpg
The frequency of all four alleles (i.e. either allele for both genes) over the generations in the above figure. Clearly, we can see how adaptation rapidly favours orange fur and tufted ears over grey fur and non-tufted ears with the shifts in frequencies over the different alleles.

We’ve discussed standing genetic variation before on The G-CAT, but often in a different light (and phrasing). For example, when we’ve talked about founder effect: that is, when a population is formed from only a few different individuals which causes it to be very genetically depauperate. In populations under strong founder effect, there is very little standing genetic variation for natural selection to act upon. This has long been an enigma for many pest species: how have they managed to proliferate so widely when they often originate from so few individuals and lack genetic diversity?

Adaptive variation

Adaptation may not require new genetic variants to be generated from mutation. If there are a large number of alleles within the gene pool to start with, then natural selection may favour one of those variants over others and allow adaptation to start immediately. Compared to the rate at which new mutations occur, are potentially corrected for in DNA repair, are potentially erased by genetic drift, and then put under selective pressure, adaptation from standing genetic variation can occur very quickly.

Rate of adaptation figure.jpg
A rough example of the speed of adaptation depending on how the adaptive allele originated: whether it was already present (in the form of standing variation), or whether it was created by a new mutation. As one would expect, there is a significant lag delay in adaptation in the mutation scenario, based on the time it takes for said adaptive mutation to be created through relatively random processes. Thus, a positively selected allele from standing variation can allow a species to adapt much faster than waiting for a positive mutation to occur.

Conserving genetic variation

Given the adaptive potential provided by maintaining a good amount of standing genetic variation, it is imperative to conserve genetic diversity within populations in conservation efforts. This is why we often equate genetic diversity with ‘adaptive potential’ of species, although the exact amount of genetic diversity required for adaptive potential depends on a large number of other factors. Clearly, in some instances species show the ability to adapt to new pressures or novel environments even without a large amount of standing genetic variation.

It is important to remember that standing genetic variation consists of two types: neutral genetic diversity, which is not necessarily under selection at the time, and adaptive genetic diversity, which is directly under selection (although this can be either for or against the given variant). However, currently neutral genetic variants may become adaptive variants in the future if selective pressures change: although those different variants aren’t necessarily beneficial or detrimental at the moment, that may change in the future. Thus, conserving both types of genetic diversity is important for the survivability and longevity of populations under conservation programs.

Other types of adaptation

Although genetic diversity is clearly critically important for adaptive potential, alternative mechanisms for adaptation also exist. One of these relies less on the actual genetic variants being different, but rather how individual genes are used. This can happen in a few different ways, but mostly commonly this is through alternative splicing: when a gene is being ‘read’ and a protein is produced, different parts of the gene can be used (and in different order) to make a completely different protein.

Alternate splicing figure.jpg
An extreme example of alternate splicing of one gene. We start with a single gene, composed of 5 (AE) main gene elements (exons). Different environmental pressures (like fire risk, flooding, cold weather or predators, for example) cause the organism to use different combinations of these exons to make different proteins (right side; AD). Actual alternate splicing is not usually this straight-forward (one gene doesn’t conveniently split into four forms depending on the threat), but the process is generally the same.

Believe it or not, we’ve sort of discussed the effects of alternative splicing before. Phenotypic plasticity occurs when a single organism can have very different physiological traits depending on the environment: even though the genes are the same, they are utilised in different ways to make a different body shape. This is how some species can look incredibly different when they live in different places even if they’re genetically very similar. That said, for the vast majority of species maintaining good levels of genetic diversity is critical for the survivability of said species.

It takes (at least) two: coevoultion and species interactions

The environmental context of adaptation

We’ve talked many times before about how species evolve in response to some kind of environmental pressure, which favours (or disfavours) certain traits within that species. Over time, this drives changes in the frequencies of species traits and alters the overall average phenotype of that species (sometimes slowly, sometimes rapidly).

While we usually talk about the environment in terms of abiotic conditions such as temperature or climate, biotic factors are equally important: that is, the parts of the environment which are themselves also alive. Because of this, changes in one species can have profound repercussions on other species linked within the ecosystem. Thus, the evolution of one species is intrinsically linked to the evolution of other relevant species within the ecosystem: often, these connected evolutionary pathways battle with one another as each one changes. Let’s take a look at a few different examples of how evolution of one species may impact the evolution of another.

Predator-prey coevolution

One of the most obvious ways the evolution of two different species can interact is in predator and prey relationships. Naturally, prey species evolve to be able to defend themselves from predators in various ways, such as crypsis (e.g. camouflage), toxicity or behavioural changes (such as nocturnalism or group herding). Contrastingly, predators will evolve new and improved methods for detecting and hunting prey, such as enhanced senses, venom and stealth (through soft-padded feet, for example).

There are millions of possible examples of predator-prey coevolution that could be used as examples here, based on the continual drive for one species to get the upper hand over the other. But one that comes to mind is of a creature that I learnt about while on holiday in Scandinavia: the pine marten, and how it affects squirrels.

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This photo is one that I took whilst on a lunch break at a bakery in the Norwegian mountains, of a small critter running among the rocks by the lakeside. Not sure exactly what species it was, I asked the tour director who excitedly told me that it was a pine marten. After doing a bit of research on them (and trying to figure out what the difference between a pine marten, a stoat, and a weasel is), I’ve discovered that it’s actually more likely to be a stoat than a pine marten, based on size and colour. But pine martens are still an intriguing species in their own right (and also found in Norway, so the confusion is understandable).

The pine marten is a species in the mustelid family, along with otters, weasels, stoats, and wolverines. Like many mustelids, they are carnivorous mammals which feed on a variety of different prey items like rodents, small birds and insects. One of the more abundant species that they prey upon are squirrels: both red squirrels and grey squirrels are potential food for the cute yet savage pine marten.

However, within the distribution of pine martens (across much of Europe), red squirrels are the native species and grey squirrels are invasive, originating from North America. Because of the long-lasting relationship between red squirrels and pine martens, they’ve co-evolved: most notably, by red squirrels changing to a mostly arboreal lifestyle and avoiding the ground as much as possible. Grey squirrels, however, have not had the evolutionary history to learn this lesson and are easy food for a smart pine marten. Thus, in regions where pine martens have been conserved or reintroduced, they are actively controlling the invasive grey squirrel population, which in turn boosts the native red squirrel population by reduction of competition. The coevolutionary link between red squirrels and pine martens is critical for combating the invasive species.

 

Martens and squirrels figure.jpg
The relationship between pine marten abundance and the abundance of both red (native) and grey (invasive) squirrels. On the left, without pine martens the invasive species runs rampant, outcompeting the native species. However, as pine martens increase in the ecosystem, the grey squirrels are predated on much more than the red squirrels due to their naivety, leading to the ‘natural’ balance on the right.
Martens and squirrels stats.jpg
A diagram of how the abundance of squirrels changes relative to the number of pine martens. The invasive grey squirrels are significantly depleted by pine marten presence, which in turn allows the native red squirrels to increase in population size after being freed from competition.

Host-parasite coevolution

In a similar vein to predator and prey coevolution, pathogenic species and their unfortunate hosts also undergo a sort of ‘arms race’. Parasites must keep evolving new ways to infect and transmit to hosts as the hosts evolve new methods of resisting and avoiding the infecting species. This spiralling battle of evolutionary forces is dubbed as the ‘Red Queen hypothesis’, formulated in 1973 by Leigh Van Valen and used to describe many other forms of coevolution. The name comes from Lewis Carroll’s Through the Looking Glass, and one quote in particular:

‘Now, here, you see, it takes all the running you can do, to keep in the same place’.

The quote references how species must continually adapt and respond to the evolution of other species just keep existing and prevent extinction. Species that remain static and stop evolving will inevitably go extinct as the world around them changes.

Mimicry

Plenty of other strange and unique mechanisms of coevolution exist within nature. One of them is mimicry, the process by which one species attempts to look like another to protect itself. The most iconic group known for this is butterflies: many species, although they may be evolutionarily very different, share similar colouration patterns and body shapes as mimics. Depending on the nature of the copy, mimicry can be classified into two broad categories. In either case, the initial ‘reference’ species is toxic or unpalatable to predators and uses a type of colour signal to communicate this: think of the bright yellow colours of bees and wasps or the red of ladybirds. Where the two categories change is in the nature of the ‘mimic’ species.

Müllerian mimicry

If the mimic is also toxic or unpalatable, we call this Müllerian mimicry (after Johann Friedrich Theodor Müller). By sharing the same colouration patterns and both being toxic, the two mimicking species boost the potential for the signal to be learnt by predators. If a predator eats either species, it will associate that colour pattern with toxicity and neither species are as likely to be preyed upon in the future. In this sense, it is a cooperative coevolutionary relationship between the two physically similar species.

Mullerian mimicry figure
A (somewhat familiar) example of Müllerian mimicry with two species of butterflies, the monarch and the viceroy. Although this has traditionally been thought of as a textbook case of Batesian mimicry (see below), the toxicity of both species likely makes it a scenario of Müllerian mimicry instead. Since both butterflies share the same pattern and both are toxic, it sends a strong signal to predators such as wasps to avoid them both.

Batesian mimicry

In contrast, the mimic might not actually be toxic or unpalatable, and simply copying a toxic species. This is referred to as Batesian mimicry (after Henry Walter Bates), and involves a mimic species relying on the association of colour and toxicity to have been learnt by predators through the ‘reference’ species. Although the mimic is not toxic, it is essentially piggy-backing on the hard evolutionary work that has already been done by the actually toxic species. In this case, the coevolutionary relationship is more parasitic as the mimic benefits from the ‘reference’ but the favour is not returned.

Batesian mimicry figure
An example of Batesian mimicry, with hoverflies and wasps. Hoverflies are not at all toxic, and are generally harmless; however, by mimicking the clear bright yellow warning systems of more dangerous species like wasps and bees, they avoid being eaten by predators such as birds.

Coevolution of species and the importance of species interactions

There are countless of other species interactions which could drive coevolutionary relationships in nature. These can include various forms of symbiosis, or the response of different species to ecosystem engineers: that is, species that can change and shape the environment around them (such as corals in reef systems). Understanding how a species evolves within its environment thus needs to consider how many other local species are also evolving and responding in their own ways.

 

 

From mutation to speciation: the genetics of species formation

The genetics of speciation

Given the strong influence of genetic identity on the process and outcomes of the speciation process, it seems a natural connection to use genetic information to study speciation and species identities. There is a plethora of genetics-based tools we can use to investigate how speciation occurs (both the evolutionary processes and the external influences that drive it). One clear way to test whether two populations of a particular species are actually two different species is to investigate genes related to reproductive isolation: if the genetic differences demonstrate reproductive incompatibilities across the two populations, then there is strong evidence that they are separate species (at least under the Biological Species Concept; see Part One for why!). But this type of analysis requires several tools: 1) knowledge of the specific genes related to reproduction (e.g. formation of sperm and eggs, genital morphology, etc.), 2) the complete and annotated genome of the species (to be able to find and analyse the right genes properly) and 3) a good amount of data for the populations in question. As you can imagine, for people working on non-model species (i.e. ones that haven’t had the same history and detail of research as, say, humans and mice), this can be problematic. So, instead, we can use other genetic information to investigate and suggest patterns and processes related to the formation of new species.

Is reproductive isolation naturally selected for or just a consequence?

A fundamental aspect of studies of speciation is a “chicken or the egg”-type paradigm: does natural selection directly select for rapid reproductive isolation, preventing interbreeding; or as a secondary consequence of general adaptive differences, over a long history of evolution? This might be a confusing distinction, so we’ll dive into it a little more.

Of the two proposed models of speciation, the by-product of natural selection (the second model) has been the more favoured. Simply put, this expands on Darwin’s theory of evolution that describes two populations of a single species evolving independently of one another. As these become more and more different, both in physical (‘phenotype’) and genetic (‘genotype’) characteristics, there comes a turning point where they are so different that an individual from one population could not reasonably breed with an individual from the other to form a fertile offspring. This could be due to genetic incompatibilities (such as different chromosome numbers), physiological differences (such as changes in genital morphology), or behavioural conflicts (such as solitary vs. group living).

Certainly, this process makes sense, although it is debatable how fast reproductive isolation would occur in a given species (or whether it is predictable just based on the level of differentiation between two populations). Another model suggests that reproductive isolation actually might arise very quickly if natural selection favours maintaining particular combinations of traits together. This can happen if hybrids between two populations are not particularly well adapted (fit), causing natural selection to favour populations to breed within each group rather than across groups (leading to reproductive isolation). Typically, this is referred to as ‘reinforcement’ and predominantly involves isolating mechanisms that prevent individuals across populations from breeding in the first place (since this would be wasted energy and resources producing unfit offspring). The main difference between these two models is the sequence of events: do populations ecologically diverge, and because of that then become reproductively isolated, or do populations selectively breed (enforcing reproductive isolation) and thus then evolve independently?

Reinforcement figure.jpg
An example of reinforcement leading to speciation. A) We start with two populations of a single species (a red fish population and a green fish population), which can interbreed (the arrows). B) Because these two groups can breed, hybrids of the two populations can be formed. However, due to the poor combination of red and green fish genes within a hybrid, they are not overly fit (the red cross). C) Since natural selection doesn’t favour forming hybrids, populations then adapt to selectively breed only with similar fish, reducing the amount of interbreeding that occurs. D) With the two populations effectively isolated from one another, different adaptations specific to each population (spines in red fish, purple stripes in green fish) can evolve, causing them to further differentiate. E) At some point in the differentiation process, hybrids move from being just selectively unfit (as in B)) to entirely impossible, thus making the two populations formal species. In this example, evolution has directly selected against hybrids first, thus then allowing ecological differences to occur (as opposed to the other way around).

Reproductive isolation through DMIs

The reproductive incompatibility of two populations (thus making them species) is often intrinsically linked to the genetic make-up of those two species. Some conflicts in the genetics of Population 1 and Population 2 may mean that a hybrid having half Population 1 genes and half Population 2 genes will have serious fitness problems (such as sterility or developmental problems). Dramatic genetic differences, particularly a difference in the number of chromosomes between the two sources, is a significant component of reproductive isolation and is usually to blame for sterile hybrids such as ligers, zorse and mules.

However, subtler genetic differences can also have a strong effect: for example, the unique combination of Population 1 and Population 2 genes within a hybrid might interact with one another negatively and cause serious detrimental effects. These are referred to as “Dobzhansky-Müller Incompatibilities” (DMIs) and are expected to accumulate as the two populations become more genetically differentiated from one another. This can be a little complicated to imagine (and is based upon mathematical models), but the basis of the concept is that some combinations of gene variants have never, over evolutionary history, been tested together as the two populations diverge. Hybridisation of these two populations suddenly makes brand new combinations of genes, some of which may be have profound physiological impacts (including on reproduction).

DMI figure
An example of how Dobzhansky-Müller Incompatibilities arise, adapted from Coyne & Orr (2004). We start with an initial population (center top), which splits into two separate populations. In this example, we’ll look at how 5 genes (each letter = one gene) change over time in the separate populations, with the original allele of the gene (lowercase) occasionally mutating into a new allele (upper case). These mutations happen at random times and in random genes in each population (the red letters), such that the two become very different over time. After a while, these two populations might form hybrids; however, given the number of changes in each population, this hybrid might have some combinations of alleles that are ‘untested’ in their evolutionary history (see below). These untested combinations may cause the hybrid to be infertile or unviable, making the two populations isolated species.

DMI table
The list of ‘untested’ genetic combinations from the above example. This table shows the different combinations of each gene that could be made in a hybrid if these two populations interbred. The red cells indicate combinations that have never been ‘tested’ together; that is, at no point in the evolutionary history of these two populations were those two particular alleles together in the same individual. Green cells indicate ones that were together at some point, and thus are expected to be viable combinations (since the resultant populations are obviously alive and breeding).

How can we look at speciation in action?

We can study the process of speciation in the natural world without focussing on the ‘reproductive isolation’ element of species identity as well. For many species, we are unlikely to have the detail (such as an annotated genome and known functions of genes related to reproduction) required to study speciation at this level in any case. Instead, we might choose to focus on the different factors that are currently influencing the process of speciation, such as how the environmental, demographic or adaptive contexts of populations plays a role in the formation of new species. Many of these questions fall within the domain of phylogeography; particularly, how the historical environment has shaped the diversity of populations and species today.

Phylogeo of speciation
An example of the interplay between speciation and phylogeography, taken from Reyes-Velasco et al. (2018). They investigated the phylogeographic history of several different groups of species within the frog genus Ptychadena; in this figure, we can see how the different species (indicated by the colours and tree on the left) relate to the geography of their habitat (right).

A variety of different analytical techniques can be used to build a picture of the speciation process for closely related or incipient species. A good starting point for any speciation study is to look at how the different study populations are adapting; is there evidence that natural selection is pushing these populations towards different genotypes or ecological niches? If so, then this might be a precursor for speciation, and we can build on this inference with other complementary analyses.

For example, estimating divergence times between populations can help us suggest whether there has been sufficient time for speciation to occur (although this isn’t always clear cut). Additionally, we could estimate the levels of genetic hybridisation (‘introgression’) between two populations to suggest whether they are reasonably isolated and divergent enough to be considered functional species.

The future of speciation genomics

Although these can help answer some questions related to speciation, new tools are constantly needed to provide a clearer picture of the process. Understanding how and why new species are formed is a critical aspect of understanding the world’s biodiversity. How can we predict if a population will speciate at some point? What environmental factors are most important for driving the formation of new species? How stable are species identities, really? These questions (and many more) remain elusive for a wide variety of life on Earth.

 

Of birds and bees: where do species come from?

This is Part 2 of a four part miniseries on the process of speciation: how we get new species, how we can see this in action, and the end results of the process. This week we’re taking a look at how new species are formed from natural selection. For Part 1, on the identity and concept of the species, click here.

The Origin of Species

Despite Darwin’s scientifically ground-breaking revelations over 150 years ago, the truth of the origin of species has remained a puzzling and complex question in biology. While the fundamental concepts of Darwin’s theory remain heavily supported – that groups which become separated from one another and undergo differing evolutionary pathways through natural selection may over time form new species – the mechanisms leading to this are mysterious. Even though the heritable component of evolution (DNA) was not uncovered for a hundred years after publishing ‘On the Origin of Species’, Darwin’s theory can largely explain many patterns of the formation of species on Earth.

The population-speciation continuum

The understanding that groups that are separated progress into species through differential adaptation leads to a phenomenon as the ‘speciation continuum’: all populations exist at some point on the continuum, with those that are most differentiated (i.e. most progressed) are distinct species, whereas those least differentiated are closely related or the same population. Whether or not populations progress along this continuum, and how fast this progression happens, depends on the difference in selective pressure and speed of evolution in the populations. Even if two populations are physically separated, they might not necessarily form new species if the separation is too short-term or if they do not evolve in different ways. Even if they do differentially evolve, whether or not they develop reproductive isolation is not always consistent.

Speciation continuum figure
A vague diagram of the population-speciation continuum. In this figure, we have two different organisms (Taxa 1 and Taxa 2) and we’re comparing their genetic similarity/differences (the grey arrow). At the bottom left of the chart, there are very few genetic differences between the two, likely indicated that they are from the same population (or closely related e.g. siblings). As we progress towards the upper left, the two start to diverge from one another, first to different populations of the same species, different subspecies of the same overarching species, and eventually becoming so different that they must be new species (i.e. are genetically incompatible and thus reproductively isolated). Exactly where this cut-off is a bit of a grey area (the species boundary) and is unlikely to be consistent across species.

Furthermore, how these populations are changing may affect the rate or success of speciation: if the traits that evolve differently across the population also cause them to be unable to breed, then they may quickly become reproductively isolated and thus new species. For example, Momigliano et al. (2017) demonstrated the fastest known rate of speciation (within 3000 generations) in a marine vertebrate in a species of flounders. Flounders that adapted to a higher salinity environment became reproductively isolated from their sister population as their sperm could not tolerate the high salinity conditions (directly preventing breeding and causing reproductive isolation).  This strong and rapid selection to an environment, and its subsequent selection on reproductive ability, was cutely described as a “magic trait”.

Modes of speciation

Darwin’s model of speciation describes what is called “allopatric speciation”, whereby physical separation of populations by some form of barrier (often attributed to changes such as climatic shifts, mountain range formations or island separation) isolates populations which then independently evolve until they reach a point of differentiation where they can no longer interbreed. Thus, they are now separate species (based on the Biological Species Concept, anyway). Allopatric speciation has traditionally believed to be the most common process of speciation, and is consistently used as the model for teaching and understanding speciation.

While this physical separation is the strongest and most immediately obvious method of speciation, other forms without geographic barriers have been documented. “Sympatric speciation” involves speciation events where there are no apparent geographical barriers that separate populations: instead, other factors may be driving their divergence from one another. This can relate to different microenvironments within the same area, where one population migrates and adapts to an environment which excludes the other population. This is referred to as “ecological speciation” and has been particularly noted within lake fish radiating into different habitats. There are a number of other mechanisms by which sympatric speciation could also occur, however, including temporal isolation (e.g. different flowering times in plants), sexual selection (e.g. a mutation leads to a new physiology that is more attractive to others with that physiology) or polyploidy (e.g. a ‘mutation’ causes an organism to have multiple copies of its genome, making it effectively reproductively isolated from its neighbours due to incompatible sex cells).

Allopatric vs sympatric speciation
Representations of allopatric and sympatric speciation using our friends the fruit-eating catsA) An example of allopatric speciation. Similar to how we’ve seen it before, a geographic barrier (the dashed green line) separates the ancestral species in two; each of these groups then evolve in different directions based on the different environmental pressures of each zone. After enough divergence, these two groups become reproductively isolated from one another and thus are different species. B) An example of sympatric speciation. We start with a single species of red apple eating cats, which form one contiguous group. A mutation within the group produces a new type of fruit-eating cat; one that feeds on green apples (grey cats). Because these feed on a different food source, they move into a different part of the environment, associating with other green apple-eating cats and less with red apple-eating cats. Over time, and with strong enough selection for apple preferences, these two types may become different species.

Sympatric speciation has received a great deal of controversy, due to the fact that some levels of gene flow could occur across the two populations with relative ease (compared to allopatric populations). This gene flow should cause the two populations to reconnect and prevent each population from evolving differently from one another (as changes in one population’s gene pool will be introduced into the other). Speciation with gene flow has been shown for some species, based on the idea that the pressure of natural selection (i.e. being adapted to the right habitat) is much stronger than the level of gene flow (i.e. the introduction of non-adapted genes from the other population), so the two populations still diverge genetically.

Gene flow across populations (through hybridisation) will balance out the different allele frequencies of the two gene pools, preventing adaptive alleles from moving towards fixation as per the standard natural selection process. While the effect of gene flow might slow the process, taking longer for the populations to diverge to the species level, speciation can still be achieved. Thus, the balance of gene flow and adaptive divergence is critical in determining whether ecological speciation is possible.

Sympatric speciation figure
A slightly more convoluted example of sympatric speciation. A) We start with a single species of small orange cats (top row), which can share readily share genes with one another. A mutation within the species creates a new type of cat; one that is much larger and has tufted ears. Although there are somewhat morphologically distinct from one another, they’re still genetically similar enough to continue to breed and share genes across the two types. However, with the big size comes a new ecological niche and these big cats differentially evolve to be grey (to hide better from their new bigger prey, perhaps) whilst the non-mutated group stays the same size and colour. Because large grey cats will preferentially breed with other large grey cats and not with small orange cats, this group genetically diverges from the ancestor to form a new species. B) A representation of the genetic changes between the two groups over time. The figure shows the genome (the grey bar) of the cat; the y-axis is the level of genetic differentiation between the two (measured as Fst). The different coloured sections represent specific genes within the genome, whilst the dashed line represents the average Fst across the whole genome. At initial divergence (top), there is little difference between the two. However, as the new big cats form and evolve, we can see the average Fst increase, with strong peaks around particular genes (blue and green; those related to the changes in physiology). As the two groups continue to diverge, this average raises even higher until genetic changes cause the reproduction-related genes (red and yellow) to become too different to allow for hybridisation, making the two species reproductively isolated (the red X in A)).

The reality of species

While the distinction between divergent populations and species might be a complex one, development in genomic technologies and greater understanding of evolutionary patterns is helping us uncover the real origin of species. And while species might not be as concrete a concept as one might expect, understanding the processes that generate new species and diversity is critical for understanding the diversity within nature that we see today, and also the potential diversity for the future (and why protecting said diversity is important!).

What is a species, anyway?

This is Part 1 of a four part miniseries on the process of speciation; how we get new species, how we can see this in action, and the end results of the process. This week, we’ll start with a seemingly obvious question: what is a species?

The definition of a ‘species’

‘Species’ are a human definition of the diversity of life. When we talk about the diversity of life, and the myriad of creatures and plants on Earth, we often talk about species diversity. This might seem glaringly obvious, but there’s one key issue: what is a species, anyway? While we might like to think of them as discrete and obvious groups (a dog is definitely not the same species as a cat, for example), the concept of a singular “species” is actually the result of human categorisation.

In reality, the diversity of life is spread across a huge spectrum of differentiation: from things which are closely related but still different to us (like chimps), to more different again (other mammals), to hardly relatable at all (bacteria and plants). So, what is the cut-off for calling something a species, and not a different genus, family, or kingdom? Or alternatively, at what point do we call a specific sub-group of a species as a sub-species, or another species entirely?

This might seem like a simple question: we look at two things, and they look different, so they must be different species, right? Well, of course, nature is never simple, and the line between “different” and “not different” is very blurry. Here’s an example: consider that you knew nothing about the history, behaviour or genetics of dogs. If you simply looked at all the different breeds of dogs on Earth, you might suggest that there are hundreds of species of domestic dogs. That seems a little excessive though, right? In fact, the domestic dog, Eurasian wolf, and the Australian dingo are all the same species (but different subspecies, along with about 38 others…but that’s another issue altogether).

Dogs
Morphology can be misleading for identifying species. In this example, we have A) a dog, B) also a dog, C) still a dog, D) yet another dog, and E) not a dog. For the record, A-D are all Canis lupus of some variety; and are domestic dogs (Canis lupus familiaris), C is a dingo (Canis lupus dingo) and is a grey wolf (Canis lupus lupus). E, however, is the Ethiopian wolf, Canis simensis.

How do we describe species?

This method of describing species based on how they look (their morphology) is the very traditional approach to taxonomy. And for a long time, it seemed to work…until we get to more complex scenarios like the domestic dog. Or scenarios where two species look fairly similar, but in reality have evolved entirely differently for a very, very long time. Or groups which look close to more than one other species. So how do we describe them instead?

Cats and foxes
A), a fox. B), a cat. C), a foxy cat? A catty fox? A cat-fox hybrid? Something unrelated to cat or a fox?

 

Believe it or not, there are dozens of ways of deciding what is a species and what isn’t. In Speciation (2004), Coyne & Orr count at least 25 different reported Species Concepts that had been suggested within science, based on different requirements such as evolutionary history, genetic identity, or ecological traits. These different concepts can often contradict one another about where to draw the line between species…so what do we use?

The Biological Species Concept (BSC)

The most commonly used species concept is called the Biological Species Concept (BSC), which denotes that “species are groups of interbreeding natural populations that are reproductively isolated from other such groups” (Mayr, 1942). In short, a population is considered a different species to another population if an individual from one cannot reliably breed to form fertile, viable offspring with an individual from the other. We often refer to this as “reproductive isolation.” It’s important to note that reproductive isolation doesn’t mean they can’t breed at all: just that the hybrid offspring will not live a healthy life and produce its own healthy offspring.

For example, a horse and zebra can breed to produce a zorse, however zorse are fundamentally infertile (due to the different number of chromosomes between a horse and a zebra) and thus a horse is a different species to a zebra. However, a German Shepherd and a chihuahua can breed and make a hybrid mutt, so they are the same species.

zorse
A zorse, which shows its hybrid nature through zebra stripes and horse colouring. These two are still separate species since zorses are infertile, and thus are not a singular stable entity.

You might naturally ask why reproductive isolation is apparently so important for deciding species. Most directly, this means that groups don’t share gene pools at all (since genetic information is introduced and maintained over time through breeding events), which causes them to be genetically independent of one another. Thus, changes in the genetic make-up of one species shouldn’t (theoretically) transfer into the gene pool of another species through hybrids. This is an important concept as the gene pool of a species is the basis upon which natural selection and evolution act: thus, reproductively isolated species may evolve in very different manners over time.

RI example
An example of how reproductive isolation maintains genetic and evolutionary independence of species. In A), our cat groups are robust species, reproductively isolated from one another (as shown by the black box). When each species undergoes natural selection and their genetic variation changes (colour changes on the cats and DNA), these changes are kept within each lineage. This contrasts to B), where genetic changes can be transferred between species. Without reproductive isolation, evolution in the orange lineage and the blue lineage can combine within hybrids, sharing the evolutionary pathways of both ancestral species.

Pitfalls of the BSC

Just because the BSC is the most used concept doesn’t make it infallible, however. Many species on Earth don’t easily demonstrate reproductive isolation from one another, nor does the concept even make sense for asexually reproducing species. If an individual reproduced solely asexually (like many bacteria, or even some lizards), then by the BSC definition every individual is an entirely different species…which seems a little excessive. Even in sexually reproducing organisms, it can be hard to establish reproductive isolation, possibly because the species never come into contact physically.

This raises the debate of whether two species could, let alone will, hybridise in nature, which can be difficult to determine. And if two species do produce hybrid offspring, assessing their fertility or viability can be difficult to detect without many generations of breeding and measurements of fitness (hybrids may not be sustainable in nature if they are not well adapted to their environment and thus the two species are maintained as separate identities).

Hybrid birds
An example of unfit hybrids causing effective reproductive isolation. In this example, we have two different bird species adapted to very different habitats; a smaller, long-tailed bird (left) adapted to moving through dense forest, and a large, longer-legged bird (right) adapted to traversing arid deserts. When (or if) these two species hybridised, the resultant offspring would be middle of the road, possessing too few traits to be adaptive in either the forest or the desert and no fitting intermediate environment available. Measuring exactly how unfit this hybrid would be is a difficult task in establishing species boundaries.

 

Integrative taxonomy

To try and account for the issues with the BSC, taxonomists try to push for the usage of “integrative taxonomy”. This means that species should be defined by multiple different agreeing concepts, such as reproductive isolation, genetic differentiation, behavioural differences, and/or ecological traits. The more traits that can separate the two, the greater support there is for the species to be separated: if they disagree, then more information is needed to determine exactly whether or not that should be called different species. Debates about taxonomy are ongoing and are likely going to be relevant for years to come, but form critical components of understanding biodiversity, patterns of evolution, and creating effective conservation legislation to protect endangered or threatened species (for whichever groups we decide are species).