speciation continuum

The space for species: how spatial aspects influence speciation

November 1, 2018November 1, 2018thegcatblog2 Comments

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).

An identity crisis: using genomics to determine species identities

July 18, 2018thegcatblog6 Comments

This is the fourth (and final) part of the miniseries on the genetics and process of speciation. To start from Part One, click here.

In last week’s post, we looked at how we can use genetic tools to understand and study the process of speciation, and particularly the transition from populations to species along the speciation continuum. Following on from that, the question of “how many species do I have?” can be further examined using genetic data. Sometimes, it’s entirely necessary to look at this question using genetics (and genomics).

Cryptic species

A concept that I’ve mentioned briefly previously is that of ‘cryptic species’. These are species which are identifiable by their large genetic differences, but appear the same based on morphological, behavioural or ecological characteristics. Cryptic species often arise when a single species has become fragmented into several different populations which have been isolated for a long time from another. Although they may diverge genetically, this doesn’t necessarily always translate to changes in their morphology, ecology or behaviour, particularly if these are strongly selected for under similar environmental conditions. Thus, we need to use genetic methods to be able to detect and understand these species, as well as later classify and describe them.

Cryptic species heatmap example — The level of genetic differentiation between the fish in the above example. The phylogenies on the left and top of the figure demonstrate the evolutionary relationships of these four fish. The matrix shows a heatmap of the level of differences between different pairwise comparisons of all four fish: red squares indicate zero genetic differences (such as when comparing a fish to itself; the middle diagonal) whilst yellow squares indicate increasingly higher levels of genetic differentiation (with bright yellow = all differences). By comparing the different fish together, we can see that Fish 1 and 2, and Fish 3 and 4, are relatively genetically similar to one another (red-deep orange). However, other comparisons show high level of genetic differences (e.g. 1 vs 3 and 1 vs 4). Based on this information, we might suggest that Fish 1 and 2 belong to one cryptic species (A) and Fish 3 and 4 belong to a second cryptic species (B).

Genetic tools to study species: the ‘Barcode of Life’

A classically employed method that uses DNA to detect and determine species is referred to as the ‘Barcode of Life’. This uses a very specific fragment of DNA from the mitochondria of the cell: the cytochrome c oxidase I gene, CO1. This gene is made of 648 base pairs and is found pretty well universally: this and the fact that CO1 evolves very slowly make it an ideal candidate for easily testing the identity of new species. Additionally, mitochondrial DNA tends to be a bit more resilient than its nuclear counterpart; thus, small or degraded tissue samples can still be sequenced for CO1, making it amenable to wildlife forensics cases. Generally, two sequences will be considered as belonging to different species if they are certain percentage different from one another.

Annotated mitogeome — The full (annotated) mitochondrial genome of humans, with the different genes within it labelled. The CO1 gene is labelled with the red arrow (sometimes also referred to as COX1) whilst blue arrows point to other genes often used in phylogenetic or taxonomic studies, depending on the group or species in question.

Despite the apparent benefits of CO1, there are of course a few drawbacks. Most of these revolve around the mitochondrial genome itself. Because mitochondria are passed on from mother to offspring (and not at all from the father), it reflects the genetic history of only one sex of the species. Secondly, the actual cut-off for species using CO1 barcoding is highly contentious and possibly not as universal as previously suggested. Levels of sequence divergence of CO1 between species that have been previously determined to be separate (through other means) have varied from anywhere between 2% to 12%. The actual translation of CO1 sequence divergence and species identity is not all that clear.

Gene tree – species tree incongruences

One particularly confounding aspect of defining species based on a single gene, and with using phylogenetic-based methods, is that the history of that gene might not actually be reflective of the history of the species. This can be a little confusing to think about but essentially leads to what we call “gene tree – species tree incongruence”. Different evolutionary events cause different effects on the underlying genetic diversity of a species (or group of species): while these may be predictable from the genetic sequence, different parts of the genome might not be as equally affected by the same exact process.

A classic example of this is hybridisation. If we have two initial species, which then hybridise with one another, we expect our resultant hybrids to be approximately made of 50% Species A DNA and 50% Species B DNA (if this is the first generation of hybrids formed; it gets a little more complicated further down the track). This means that, within the DNA sequence of the hybrid, 50% of it will reflect the history of Species A and the other 50% will reflect the history of Species B, which could differ dramatically. If we randomly sample a single gene in the hybrid, we will have no idea if that gene belongs to the genealogy of Species A or Species B, and thus we might make incorrect inferences about the history of the hybrid species.

Gene tree incongruence figure — A diagram of gene tree – species tree incongruence. Each individual coloured line represents a single gene as we trace it back through time; these are mostly bound within the limits of species divergences (the black borders). For many genes (such as the **blue** ones), the genes resemble the pattern of species divergences very well, albeit with some minor differences in how long ago the splits happened (at the top of the branches). However, the **red** genes contrast with this pattern, with clear movement across species (from A and C into B): this represents genes that have been transferred by hybridisation. The **green** line represents a gene affected by what we call incomplete lineage sorting; that is, we cannot trace it back far enough to determine exactly how/when it initially diverged and so there are still two separate green lines at the very top of the figure. You can think of each line as a separate phylogenetic tree, with the overarching species tree as the **average pattern** of all of the genes.

There are a number of other processes that could similarly alter our interpretations of evolutionary history based on analysing the genetic make-up of the species. The best way to handle this is simply to sample more genes: this way, the effect of variation of evolutionary history in individual genes is likely to be overpowered by the average over the entire gene pool. We interpret this as a set of individual gene trees contained within a species tree: although one gene might vary from another, the overall picture is clearer when considering all genes together.

Species delimitation

In earlier posts on The G-CAT, I’ve discussed the biogeographical patterns unveiled by my Honours research. Another key component of that paper involved using statistical modelling to determine whether cryptic species were present within the pygmy perches. I didn’t exactly elaborate on that in that section (mostly for simplicity), but this type of analysis is referred to as ‘species delimitation’. To try and simplify complicated analyses, species delimitation methods evaluate possible numbers and combinations of species within a particular dataset and provides a statistical value for which configuration of species is most supported. One program that employs species delimitation is Bayesian Phylogenetics and Phylogeography (BPP): to do this, it uses a plethora of information from the genetics of the individuals within the dataset. These include how long ago the different populations/species separated; which populations/species are most related to one another; and a pre-set minimum number of species (BPP will try to combine these in estimations, but not split them due to computational restraints). This all sounds very complex (and to a degree it is), but this allows the program to give you a statistical value for what is a species and what isn’t based on the genetics and statistical modelling.

Vittata cryptic species — The cryptic species of pygmy perches identified within my research paper. This represents part of the main phylogenetic tree result, with the estimates of divergence times from other analyses included. The pictures indicate the physiology of the different ‘species’: Nannoperca pygmaea is morphologically different to the other species of Nannoperca vittata. Species delimitation analysis suggested all four of these were genetically independent species; at the very least, it is clear that there must be at least 2 species of Nannoperca vittata since A is more related to N. pygmaea than to other N. vittata species. Photo credits: N. vittata = Chris Lamin; N. pygmaea = David Morgan.

The end result of a BPP run is usually reported as a species tree (e.g. a phylogenetic tree describing species relationships) and statistical support for the delimitation of species (0-1 for each species). Because of the way the statistical component of BPP works, it has been found to give extremely high support for species identities. This has been criticised as BPP can, at time, provide high statistical support for genetically isolated lineages (i.e. divergent populations) which are not actually species.

Improving species identities with integrative taxonomy

Due to this particular drawback, and the often complex nature of species identity, using solely genetic information such as species delimitation to define species is extremely rare. Instead, we use a combination of different analytical techniques which can include genetic-based evaluations to more robustly assign and describe species. In my own paper example, we suggested that up to three ‘species’ of N. vittata that were determined as cryptic species by BPP could potentially exist pending on further analyses. We did not describe or name any of the species, as this would require a deeper delve into the exact nature and identity of these species.

As genetic data and analytical techniques improve into the future, it seems likely that our ability to detect and determine species boundaries will also improve. However, the additional supported provided by alternative aspects such as ecology, behaviour and morphology will undoubtedly be useful in the progress of taxonomy.

From mutation to speciation: the genetics of species formation

July 11, 2018July 11, 2018thegcatblog4 Comments

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?

July 4, 2018July 4, 2018thegcatblog9 Comments

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 cats. A) 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!).

The G-cat

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