MU – The G-cat

Rescuing the damselfish in distress: rescue or depression?

September 6, 2018September 6, 2018thegcatblog6 Comments

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.

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

January 17, 2018January 17, 2018thegcatblog17 Comments

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 *ecotype*. **Right:** 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).

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.