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.

“Who Do You Think You Are?”: studying the evolutionary history of species

The constancy of evolution

Evolution is a constant, endless force which seeks to push and shape species based on the context of their environment: sometimes rapidly, sometimes much more gradually. Although we often think of discrete points of evolution (when one species becomes two, when a particular trait evolves), it is nevertheless a continual force that influences changes in species. These changes are often difficult to ‘unevolve’ and have a certain ‘evolutionary inertia’ to them; because of these factors, it’s often critical to understand how a history of evolution has generated the organisms we see today.

What do I mean when I say evolutionary history? Well, the term is fairly diverse and can relate to the evolution of particular traits or types of traits, or the genetic variation and changes related to these changes. The types of questions and points of interest of evolutionary history can depend at which end of the timescale we look at: recent evolutionary histories, and the genetics related to them, will tell us different information to very ancient evolutionary histories. Let’s hop into our symbolic DeLorean and take a look back in time, shall we?

Labelled_evolhistory
A timeslice of evolutionary history (a pseudo-phylogenetic tree, I guess?), going from more recent history (bottom left) to deeper history (top right). Each region denoted in the tree represents the generally area of focus for each of the following blog headings. 1: Recent evolutionary history might look at individual pedigrees, or comparing populations of a single species. 2: Slightly older comparisons might focus on how species have arisen, and the factors that drive this (part of ‘phylogeography’). 3: Deep history might focus on the origin of whole groups of organisms and a focus on the evolution of particular traits like venom or sociality.

Very recent evolutionary history: pedigrees and populations

While we might ordinarily consider ‘evolutionary history’ to refer to events that happened thousands or millions of years ago, it can still be informative to look at history just a few generations ago. This often involves looking at pedigrees, such as in breeding programs, and trying to see how very short term and rapid evolution may have occurred; this can even include investigating how a particular breeding program might accidentally be causing the species to evolve to adapt to captivity! Rarely does this get referred to as true evolutionary history, but it fits on the spectrum, so I’m going to count it. We might also look at how current populations are evolving differently to one another, to try and predict how they’ll evolve into the future (and thus determine which ones are most at risk, which ones have critically important genetic diversity, and the overall survivability of the total species). This is the basis of ‘evolutionarily significant units’ or ESUs which we previously discussed on The G-CAT.

Captivefishcomic
Maybe goldfish evolved 3 second memory to adapt to the sheer boringness of captivity? …I’m joking, of course: the memory thing is a myth and adaptation works over generations, not a lifetime.

A little further back: phylogeography and species

A little further back, we might start to look at how different populations have formed or changed in semi-recent history (usually looking at the effect of human impacts: we’re really good at screwing things up I’m sorry to say). This can include looking at how populations have (or have not) adapted to new pressures, how stable populations have been over time, or whether new populations are being ‘made’ by recent barriers. At this level of populations and some (or incipient) species, we can find the field of ‘phylogeography’, which involves the study of how historic climate and geography have shaped the evolution of species or caused new species to evolve.

Evolution of salinity
An example of trait-based phylogenetics, looking at the biogeographic patterns and evolution/migration to freshwater in perch-like fishes, by Chen et al. (2014). The phylogeny shows that a group of fishes adapted to freshwater environments (black) from a (likely) saltwater ancestor (white), with euryhaline tolerance evolving two separate times (grey).

One high profile example of phylogeographic studies is the ‘Out of Africa’ hypothesis and debate for the origination of the modern human species. Although there has been no shortage of debate about the origin of modern humans, as well as the fate of our fellow Neanderthals and Denisovans, the ‘Out of Africa’ hypothesis still appears to be the most supported scenario.

human phylogeo
A generalised diagram of the ‘Out of Africa’ hypothesis of human migration, from Oppenheimer, 2012. 

Phylogeography is also component for determining and understanding ‘biodiversity hotspots’; that is, regions which have generated high levels of species diversity and contain many endemic species and populations, such as tropical hotspots or remote temperate regions. These are naturally of very high conservation value and contribute a huge amount to Earth’s biodiversity, ecological functions and potential for us to study evolution in action.

Deep, deep history: phylogenetics and the origin of species (groups)

Even further back, we start to delve into the more traditional concept of evolutionary history. We start to look at how species have formed; what factors caused them to become new species, how stable the new species are, and what are the genetic components underlying the change. This subfield of evolution is called ‘phylogenetics’, and relates to understanding how species or groups of species have evolved and are related to one another.

Sometimes, this includes trying to look at how particular diagnostic traits have evolved in a certain group, like venom within snakes or eusocial groups in bees. Phylogenetic methods are even used to try and predict which species of plants might create compounds which are medically valuable (like aspirin)! Similarly, we can try and predict how invasive a pest species may be based on their phylogenetic (how closely related the species are) and physiological traits in order to safeguard against groups of organisms that are likely to run rampant in new environments. It’s important to understand how and why these traits have evolved to get a good understanding of exactly how the diversity of life on Earth came about.

evolution of venom
An example of looking at trait evolution with phylogenetics, focusing on the evolution of venom in snakes, from Reyes-Velasco et al. (2014). The size of the boxes demonstrates the number of species in each group, with the colours reflecting the number of venomous (red) vs. non-venomous (grey) species. The red dot shows the likely origin of venom.

Phylogenetics also allows us to determine which species are the most ‘evolutionarily unique’; all the special little creatures of plant Earth which represent their own unique types of species, such as the tuatara or the platypus. Naturally, understanding exactly how precious and unique these species are suggests we should focus our conservation attention and particularly conserve them, since there’s nothing else in the world that even comes close!

Who cares what happened in the past right? Well, I do, and you should too! Evolution forms an important component of any conservation management plan, since we obviously want to make sure our species can survive into the future (i.e. adapt to new stressors). Trying to maintain the most ‘evolvable’ groups, particularly within breeding programs, can often be difficult when we have to balance inbreeding depression (not having enough genetic diversity) with outbreeding depression (obscuring good genetic diversity by adding bad genetic diversity into the gene pool). Often, we can best avoid these by identifying which populations are evolutionarily different to one another (see ESUs) and using that as a basis, since outbreeding vs. inbreeding depression can be very difficult to measure. This all goes back to the concept of ‘adaptive potential’ that we’ve discussed a few times before.

In any case, a keen understanding of the evolutionary trajectory of a species is a crucial component for conservation management and to figure out the processes and outcomes of evolution in the real world. Thus, evolutionary history remains a key area of research for both conservation and evolution-related studies.

 

What’s the story with these little fish?

The pygmy perches

I’ve mentioned a few times in the past that my own research centres around a particular group of fish: the pygmy perches. When I tell people about them, sometimes I get the question “why do you want to study them?” And to be fair, it’s a good question: there must be something inherently interesting about them to be worth researching. And there is plenty.

Pygmy perches are a group of very small (usually 4-6cm) freshwater fish native to temperate Australia: they’re found throughout the southwest corner of WA and the southeast of Australia, stretching from the mouth of the Murray River in SA up to lower Queensland (predominantly throughout the Murray-Darling Basin) and even in northern Tasmania. There’s a massive space in the middle where they aren’t found: this is the Nullarbor Plain, and is a significant barrier for nearly all freshwater species (since it holds practically no water).

Unmack_distributions
The distributions of different pygmy perch species (excluding Bostockia porosa, which is a related but different group), taken from Unmack et al. (2011). The black region in the bottom right part indicates the Nullarbor Plain, which separates eastern and western species.

The group consists of 2 genera (Nannoperca and Nannatherina) and 7 currently described species, although there could be as many as 10 actual species (see ‘cryptic species’: I’ll elaborate on this more in future posts…). They’re very picky about their habitat, preferring to stay within low flow waterbodies with high vegetation cover, such as floodplains and lowland creeks. Most species have a lifespan of a couple years, with different breeding times depending on the species.

Why study pygmy perches?

So, they’re pretty cute little fish. But unfortunately, that’s not usually enough justification to study a particular organism. So, why does the Molecular Ecology Lab choose to use pygmy perch as one (of several) focal groups? Well, there’s a number of different reasons.

The main factors that contribute to their research interest are their other characteristics: because they’re so small and habitat specialists, they often form small, isolated populations that are naturally separated by higher flow rivers and environmental barriers. They also appear to have naturally very low genetic diversity: ordinarily, we’d expect that they wouldn’t be great at adapting and surviving over a long time. Yet, they’ve been here for a long time: so how do they do it? That’s the origin of many of the research questions for pygmy perches.

Adaptive evolution despite low genetic variation

One of the fundamental aspects of the genetic basis of evolution is the connection between genetic diversity and ‘adaptability’: we expect that populations or species with more genetic diversity are much more likely to be able to evolve and adapt to new selective pressures than those without it. Pygmy perches clearly contradict this at least a little bit, and so much of the research in the lab is about understanding exactly what factors and mechanisms contribute to the ability of pygmy perches to apparently adapt and survive what is traditionally not consider a very tolerant place to live. Recent research suggests the different expression of genes may be an important mechanism of adaptation for pygmy perch.

Recommended readings: Brauer et al. (2016); Brauer et al. (2017).

The influence of the historic environment on evolution

From an evolutionary standpoint, pygmy perches are unique in more ways than just their genetic diversity. They’re relatively ancient, with the origin of the group estimated at around 40 million years ago. Since then, they’ve diversified into a number of different species and have spread all over the southern half of the Australian continent, demonstrating multiple movements across Australia in that time. This pattern is unusual for freshwater organisms, and this combined with their ancient nature makes them ideal candidates for studying the influence of historic environment, climate and geology on the evolution and speciation of freshwater animals in Australia. And that’s the focus of my PhD (although not exclusively; plenty of other projects have explored questions in this area).

Bass Strait timelapse
The changing sea levels across the Bass Strait from A) 25 thousand years ago, B) 17.5 thousand years ago, and C) 14 thousand years ago (similar to today), from Lambeck and Chappel (2001). This is an example of one kind of environmental change that would likely have influenced the evolutionary patterns of pygmy perch, separating the populations from northern Tasmania and Victoria.

Recommended readings: Unmack et al. (2013); Unmack et al. (2011).

Conservation management and ecological role

Of course, it’s all well and good to study the natural, evolutionary history of an organism as if it hasn’t had any other influences. But we all know how dramatic the impact humans have on the environment are and unfortunately for many pygmy perch species this means that they are threatened or endangered and at risk of extinction. Their biggest threats are introduced predators (such as the redfin perch and European carp), alteration of waterways (predominantly for agriculture) and of course, climate change. For some populations, local extinction has already happened: some populations of the Yarra pygmy perch (N. obscura) are now completely gone from the wild. Many of these declines occurred during the Millennium Drought, where the aforementioned factors were exacerbated by extremely low water availability and consistently high temperatures. So naturally, a significant proportion of the work on pygmy perches is focused on their conservation, and trying to boost and recover declining populations.

This includes the formation of genetics-based breeding programs for two species, the southern pygmy perch and Yarra pygmy perch. A number of different organisations are involved in this ongoing process, including a couple of schools! These programs are informed by our other studies of pygmy perch evolution and adaptive potential and hopefully combined we can save these species from becoming totally extinct.

Yarra-breeders-vid.gif
Some of the Yarra pygmy perch from the extinct Murray-Darling Basin population, ready to make breeding groups!
Fin clipping Yarras.jpg
Me, fin clipping the Yarra pygmy perch in the breeding groups for later genetic analyses. Yes, I know, I needed a haircut.

Recommended readings: Brauer et al. (2013); Attard et al. (2016); Hammer et al. (2013).

Hopefully, some of this convinces you that pygmy perch are actually rather interesting creatures (I certainly think so!). Pygmy perch research can offer a unique insight into evolutionary history, historical biogeography, and conservation management. Also, they’re kinda cute….so that’s gotta count for something, right? If you wanted to find out more about pygmy perch research, and get updates on our findings, be sure to check out the Molecular Ecology Lab Facebook page or our website!

“How do you conserve genes?”: clarifying conservation genetics

Sometimes when I talk about the concept of conservation genetics to friends and family outside of the field, there can be some confusion about what this actually means. Usually, it’s assumed that means the conservation of genetics: that is, instead of trying to conserve individual animals or plants, we try to conserve specific genes. While in some cases this is partially true (there might be genes of particular interest that we want to maintain in a wild population), often what we actually mean is using genetic information to inform conservation management and to give us the best chance of long-term rescue for endangered species.

DNA Zoo comic
Don’t worry, it’s an open range zoo: the genes have plenty of room to roam.

See, the DNA of individuals contains much more information than just the genes that make up an organism. By looking at the number, frequency or distribution of changes and differences in DNA across individuals, populations or species, we can see a variety of different patterns. Typically, genetics-based conservation analysis is based on a single unifying concept: that different forces create different patterns in the genetic make-up of species and populations, and that these can be statistically evaluated using genetic data. The exact type or scale of effect depends on how the data is collected and what analysis we use to evaluate that data, although we could do multiple types of analysis using the same dataset.

Oftentimes, we want to know about the current or historical state of a species or population to best understand how to move forward: by understanding where a species has come from, what it has been affected by, and how it has responded to different pressures, we can start to suggest and best manage these species into the future.

However, there are lots of possible avenues for exploration: here are just a few…

Evolutionary significant units (ESUs) and management units (MUs)

One commonly used application of genetic information for conservation is the designation of what we call ‘Evolutionary Significant Units’ (ESUs). Using genetics, we can determine the boundaries of particular populations which correspond to their own unique evolutionary groups. These are often the results of historical processes which have separated and driven the independent evolution of each ESU, usually with low or no gene flow across these units. Generally, managing and conserving each of these can lead to overall more robust management of the species as a whole by making sure certain groups that have unique and potentially critical adaptations are maintained in the wild. Although ESUs can sometimes be arguable (particularly when there is some, but not much, gene flow across units), it forms an important aspect of conservation designations.

In cases of shorter term separations across these populations, where there are noticeable differences in the genetics of the populations but not necessarily massively different evolutionary histories, conservationists will sometimes refer to ‘Management Units’ (MUs). These have much weaker evolutionary pressure behind them but might be indicative of very recent impacts, such as human-driven fragmentation of habitat or contemporary climate change. MUs often reflect very sudden and recent changes in populations and might have profound implications for the future of these groups: thus, they are an important way of assessing the current state of the species. The next couple of figures demonstrate this from one of my colleagues’ research papers.

YPP_map
The geographic distributions of Yarra pygmy perch populations, generously taken from Brauer et al. (2013). Each dot and number on the map represents a single population of pygmy perch used in the analysis. The colour of the population represents which MU it belongs to, whilst the shape of the marker represents the ESU. To make this easier to visualise, the solid lines indicate the boundaries of ESUs while the dashed lines represent MU boundaries. You’ll notice that MUs are subsets of ESUs, and that Population 6 actually fits into two different ESUs: see below.
YPP_Structure
An example of the output of an analysis (STRUCTURE) that determines population boundaries for Yarra pygmy perch using genetic data, generously taken from Brauer et al. (2013). Structure is an ‘assignment test’; using the input genetic information, it tries to make groups of individuals which are more similar to one another than other groups. In the graphs, each small column represents a single individual, with the colour bars representing how well it fits that (colour) population. The smaller numbers at the bottom and the labels above the graphs represent geographic populations (see the figure above). A) Shows the 4 major ESUs of Yarra pygmy perch, with some clear mixing between the Eastern ESU and the Merri/Curdies ESU in population 6. The rest of the populations fit pretty well entirely into one ESU. B) The MUs of Yarra pygmy perch, which shows the genetic structure within ESUs that can’t be seen well in A). Notice that some ESUs are made of many MUs (E.g. Central) while others are only one MU (e.g. MDB).

The two can be thought of as part of the same hierarchy, with ESUs reflecting more historic, evolutionary groups and MUs reflecting more recent (but not necessarily evolutionary) groups. For conservation management, this has traditionally meant that individuals from one ESU were managed independent of one another (to preserve their ‘pure’ evolutionary history) whilst translocations of individuals across MUs were common and often recommended. This is based on the idea that mixing very genetically different populations could cause adaptive genes in each population to become ‘diluted’, negatively affecting the ability of the populations to evolve: this is referred to as ‘outbreeding depression’ (OD).

Coffee comic
Sometimes, adding something can make what you had even worse than before. The most depressing analogy of outbreeding depression; a ruined coffee.

However, more recent research has suggested that the concerns with OD from mixing across ESUs are less problematic than previously thought. Analysis of the effect of OD versus not supplementing populations with more genetic diversity has shown that OD is not the more dangerous option, and there is a current paradigm push to acknowledge the importance of mixing ESUs where needed.

Adaptive potential and future evolution

Understanding the genetic basis of evolution also forms an important research area for conservation management. This is particularly relevant for ‘adaptive potential’: that is, the ability for a particular species or population to be able to adapt to a variety of future stressors based on their current state. It is generally understood that having lots of different variants (alleles) of genes in the total population or species is a critical part of evolution: the more variants there are, the more choices there are for natural selection to act upon.

We can estimate this from the amount of genetic diversity within the population, as well as by trying to understand their previous experiences with adaptation and evolution. For example, it is predicted that species which occur in much more climatically variable habitats (such as in desert regions) are more likely to be able to handle and tolerate future climate change scenarios since they’ve demonstrated the ability to adapt to new, more extreme environments before. Examples of this include the Australian rainbowfishes, which are found in pretty well every climatic region across the continent (and therefore must be very good at adapting to new, varying habitats!).

Rainbowfish both.jpg
Left: The distribution of rainbowfish across Australia, with each colour representing a particular ecotypeRight: A photo of a (very big) tropical rainbowfish taken from a recent MELFU field trip. Source: MELFU Facebook page. He really got around after that one stint in that children’s story.

Genetics-based breeding programs and pedigrees

A much more direct use of genetic information for conservation is in designing breeding programs. We know that breeding related individuals can have very bad results for offspring (this is referred to as ‘inbreeding depression’): so obviously, we would avoid breeding siblings together. However, in complex breeding systems (such as polygamous animals), or in wild populations, it can be very difficult to evaluate relationships and overall relatedness.

That’s where genetics comes in: by looking at how similar or different the DNA of two individuals are, we can not only check what relationship they are (e.g. siblings, cousins, or very distantly related) but also get an exact value of their genetic relatedness. Since we know that having a diverse gene pool is critical for future adaptation and survival of a species, genetics-based breeding programs can maximise the amount of genetic diversity in following generations. We can even use a computer algorithm to make the very best of breeding groups, using a quirky program called SWINGER.

Cats DNA dating
If You Are the One, conservation genetics edition.

Taxonomy for conservation legislation

Another (slightly more complicated) application of genetics is the designation of species status. Large amounts of genetic information can often clarify complex issues of species descriptions (later issues of The G-CAT will discuss exactly how this works and why it’s not so straightforward…).

Why should we care what we call a species or not? Well, much of the protective legislation at the government level is designed at the species-level: legislative protections are often designated for a particular species, but doesn’t often distinguish particular populations. Thus, misidentified species can sometimes but lost if they were never detected as a unique species (and assumed to be just a population of another species). Alternatively, managing two species as one based on misidentification could mess with the evolutionary pathways of both by creating unfit hybrid species which do not naturally come into contact together (say, breeding individuals from one species with another because we thought they were the same species).

Cryptic cats comic
Awkward.

Additionally, if we assume that multiple different species are actually only one species, this can provide an overestimate of how well that species is doing. Although in total it might look like there are plenty of individuals of the species around, if this was actually made of 4 separate species then each one would be doing ¼ as well as we thought. This can feed back into endangered status classification and thus conservation management.

 

These are just some of the most common examples of applied genetics in conservation management. No doubt going into the future more innovative and creative methods of applying genetic information to maintaining threatened species and populations will become apparent. It’s an exciting time to be in the field and inspires hope that we may be able to save species before they disappear from the planet permanently.