How did pygmy perch swim across the desert?

“Pygmy perch swam across the desert”

As regular readers of The G-CAT are likely aware, my first ever scientific paper was published this week. The paper is largely the results of my Honours research (with some extra analysis tacked on) on the phylogenomics (the same as phylogenetics, but with genomic data) and biogeographic history of a group of small, endemic freshwater fishes known as the pygmy perch. There are a number of different messages in the paper related to biogeography, taxonomy and conservation, and I am really quite proud of the work.

Southern_pygmy_perch 1 MHammer
A male southern pygmy perch, which usually measures 6-8 cm long.

To my honest surprise, the paper has received a decent amount of media attention following its release. Nearly all of these have focused on the biogeographic results and interpretations of the paper, which is arguably the largest component of the paper. In these media releases, the articles are often opened with “…despite the odds, new research has shown how a tiny fish managed to find its way across the arid Australian continent – more than once.” So how did they manage it? These are tiny fish, and there’s a very large desert area right in the middle of Australia, so how did they make it all the way across? And more than once?!

 The Great (southern) Southern Land

To understand the results, we first have to take a look at the context for the research question. There are seven officially named species of pygmy perches (‘named’ is an important characteristic here…but we’ll go into the details of that in another post), which are found in the temperate parts of Australia. Of these, three are found with southwest Western Australia, in Australia’s only globally recognised biodiversity hotspot, and the remaining four are found throughout eastern Australia (ranging from eastern South Australia to Tasmania and up to lower Queensland). These two regions are separated by arid desert regions, including the large expanse of the Nullarbor Plain.

Pygmyperch_distributionmap
The distributions of pygmy perch species across Australia. The dots and labels refer to different sampling sites used in the study. A: the distribution of western pygmy perches, and essentially the extent of the southwest WA biodiversity hotspot region. B: the distribution of eastern pygmy perches, excluding N. oxleyana which occurs in upper NSW/lower QLD (indicated in C). C: the distributions relative to the map of Australia. The black region in the middle indicates the Nullarbor Plain. 

 

The Nullarbor Plain is a remarkable place. It’s dead flat, has no trees, and most importantly for pygmy perches, it also has no standing water or rivers. The plain was formed from a large limestone block that was pushed up from beneath the Earth approximately 15 million years ago; with the progressive aridification of the continent, this region rapidly lost any standing water drainages that would have connected the east to the west. The remains of water systems from before (dubbed ‘paleodrainages’) can be seen below the surface.

Nullarbor Plain photo
See? Nothing here. Photo taken near Watson, South Australia. Credit: Benjamin Rimmer.

Biogeography of southern Australia

As one might expect, the formation of the Nullarbor Plain was a huge barrier for many species, especially those that depend on regular accessible water for survival. In many species of both plants and animals, we see in their phylogenetic history a clear separation of eastern and western groups around this time; once widely distributed species become fragmented by the plain and diverged from one another. We would most certainly expect this to be true of pygmy perch.

But our questions focus on what happened before the Nullarbor Plain arrived in the picture. More than 15 million years ago, southern Australia was a massively different place. The climate was much colder and wetter, even in central Australia, and we even have records of tropical rainforest habitats spreading all the way down to Victoria. Water-dependent animals would have been able to cross the southern part of the continent relatively freely.

Biogeography of the enigmatic pygmy perches

This is where the real difference between everything else and pygmy perch happens. For most species, we see only one east and west split in their phylogenetic tree, associated with the Nullarbor Plain; before that, their ancestors were likely distributed across the entire southern continent and were one continuous unit.

Not for pygmy perch, though. Our phylogenetic patterns show that there were multiple splits between eastern and western ancestral pygmy perch. We can see this visually within the phylogenetic tree; some western species of pygmy perches are more closely related, from an evolutionary perspective, to eastern species of pygmy perches than they are to other western species. This could imply a couple different things; either some species came about by migration from east to west (or vice versa), and that this happened at least twice, or that two different ancestral pygmy perches were distributed across all of southern Australia and each split east-west at some point in time. These two hypotheses are called “multiple invasion” and “geographic paralogy”, respectively.

MCC_geographylabelled
The phylogeny of pygmy perches produced by this study, containing 45 different individuals across all species of pygmy perch. Species are labelled in the tree in brackets, and their geographic location (east or west) is denoted by the colour on the right. This tree clearly shows more than one E/W separation, as not all eastern species are within the same clade. For example, despite being an eastern species, N. variegata is more closely related to Nth. balstoni or N. vittata than to the other eastern species (N. australisN. obscuraN. oxleyana and N. ‘flindersi’.

So, which is it? We delved deeper into this using a type of analysis called ‘ancestral clade reconstruction’. This tries to guess the likely distributions of species ancestors using different models and statistical analysis. Our results found that the earliest east-west split was due to the fragmentation of a widespread ancestor ~20 million years ago, and a migration event facilitated by changing waterways from the Nullarbor Plain pushing some eastern pygmy perches to the west to form the second group of western species. We argue for more than one migration across Australia since the initial ancestor of pygmy perches must have expanded from some point (either east or west) to encompass the entirety of southern Australia.

BGB_figure
The ancestral area reconstruction of pygmy perches, estimated using the R package BioGeoBEARS. The different pie charts denote the relative probability of the possible distributions for the species or ancestor at that particular time; colours denote exactly where the distribution is (following the legend). As you can see, the oldest E/W split at 21 million years ago likely resulted from a single widespread ancestor, with it’s range split into an east and west group. The second E/W event, at 15 million years ago, most likely reflects a migration from east to west, resulting in the formation of the N. vittata species group. This coincides with the Nullarbor Plain, so it’s likely that changes in waterway patterns allowed some eastern pygmy perch to move westward as the area became more arid.

So why do we see this for pygmy perch and no other species? Well, that’s the real mystery; out of all of the aquatic species found in southeast and southwest Australia, pygmy perch are one of the worst at migrating. They’re very picky about habitat, small, and don’t often migrate far unless pushed (by, say, a flood). It is possible that unrecorded extinct species of pygmy perch might help to clarify this a little, but the chances of finding a preserved fish fossil (let alone for a fish less than 8cm in size!) is extremely unlikely. We can really only theorise about how they managed to migrate.

Pygmy perch biogeo history
A diagram of the distribution of pygmy perch species over time, as suggested by the ancestral area reconstruction. A: the initial ancestor of pygmy perches was likely found throughout southern Australia. B: an unknown event splits the ancestor into an eastern and western group; the sole extant species of the W group is Nth. balstoniC: the ancestor of the eastern pygmy perches spreads towards the west, entering part of the pre-Nullarbor region. D: due to changes in the hydrology of the area, some eastern pygmy perches (the maroon colour in C) are pushed towards the west; these form N. vittata species and N. pygmaea. The Nullarbor Plain forms and effectively cuts off the two groups from one another, isolating them.

What does this mean for pygmy perches?

Nearly all species of pygmy perch are threatened or worse in the conservation legislation; there have been many conservation efforts to try and save the worst-off species from extinction. Pygmy perches provide a unique insight to the history of the Australian climate and may be a key in unlocking some of the mysteries of what our land was like so long ago. Every species is important for conservation and even those small, hard-to-notice creatures that we might forget about play a role in our environmental history.

The direction of evolution: divergence vs. convergence

Direction of evolution

We’ve talked previously on The G-CAT about how the genetic underpinning of certain evolutionary traits can change in different directions depending on the selective pressure it is under. Particularly, we can see how the frequency of different alleles might change in one direction or another, or stabilise somewhere in the middle, depending on its encoded trait. But thinking bigger picture than just the genetics of one trait, we can actually see that evolution as an entire process works rather similarly.

Divergent evolution

The classic view of the direction of evolution is based on divergent evolution. This is simply the idea that a particular species possess some ancestral trait. The species (or population) then splits into two (for one reason or another), and each one of these resultant species and populations evolves in a different way to the other. Over time, this means that their traits are changing in different directions, but ultimately originate from the same ancestral source.

Evidence for divergent evolution is rife throughout nature, and is a fundamental component of all of our understanding of evolution. Divergent evolution means that, by comparing similar traits in two species (called homologous traits), we can trace back species histories to common ancestors. Some impressive examples of this exist in nature, such as the number of bones in most mammalian species. Humans have the same number of neck bones as giraffes; thus, we can suggest that the ancestor of both species (and all mammals) probably had a similar number of neck bones. It’s just that the giraffe lineage evolved longer bones whereas other lineages did not.

Homology figure
A diagrammatic example of homologous structures in ‘hand’ bones. The coloured bones demonstrate how the same original bone structures have diverged into different forms. Source: BiologyWise.

Convergent evolution

But of course, evolution never works as simply as you want it to, and sometimes we can get the direct opposite pattern. This is called convergent evolution, and occurs when two completely different species independently evolve very similar (sometimes practically identical) traits. This is often caused by a limitation of the environment; some extreme demand of the environment requires a particular physiological solution, and thus all species must develop that trait in order to survive. An example of this would be the physiology of carnivorous marsupials like Tasmanian devils or thylacines: despite being in another Class, their body shapes closely resemble something more canid. Likely, the carnivorous diet places some constraints on physiology, particularly jaw structure and strength.

Convergent evol intelligence
A surprising example of convergent evolution is cognitive ability in apes and some bird groups (e.g. corvids). There’s plenty of other animal groups more related to each of these that don’t demonstrate the same level of cognitive reasoning (based on the traits listed in the centre): thus, we can conclude that cognition has evolved twice in very, very different lineages. Source: Emery & Clayton, 2004.

A more dramatic (and potentially obvious) example of convergent evolution would be wings and the power of flight. Despite the fact that butterflies, bees, birds and bats all have wings and can fly, most of them are pretty unrelated to one another. It seems much more likely that flight evolved independently multiple times, rather than the other 99% of species that shared the same ancestor lost the capacity of flight.

Parallel evolution

Sometimes convergent evolution can work between two species that are pretty closely related, but still evolved independently of one another. This is distinguished from other categories of evolution as parallel evolution: the main difference is that while both species may have shared the same start and end point, evolution has acted on each one independent of the other. This can make it very difficult to diagnose from convergent evolution, and is usually determined by the exact history of the trait in question.

Parallel evolution is an interesting field of research for a few reasons. Firstly, it provides a scenario in which we can more rigorously test expectations and outcomes of evolution in a particular environment. For example, if we find traits that are parallel in a whole bunch of fish species in a particular region, we can start to look at how that particular environment drives evolution across all fish species, as opposed to one species case studies.

Marsupial handedness.jpg
Here’s another weird example; different populations of marsupials (particularly kangaroos and wallabies) show preferential handedness depending on where the population is. That is, different populations of different species of marsupials shows parallel evolution of handedness, since they’re related to one another but have evolved it independently of the other species. Source: Giljov et al. (2015).

Following from that logic, it is then important to question the mechanisms of parallelism. From a genetic point of view, do these various species use the same genes (and genetic variants) to produce the same identical trait? Or are there many solutions to the selective question in nature? While these questions are rather complicated, and there has been plenty of evidence both for and against parallel genetic underpinning of parallel traits, it seems surprisingly often that many different genetic combinations can be used to get the same result. This gives interesting insight into how complex genetic coding of traits can be, and how creative and diverse evolution can be in the real world.

Where is evolution going?

Cat phylogeny
An example of all three types of evolutionary trajectory in a single phylogeny of cats (you know how we do it here at The G-CAT). This phylogeny consists of two distinct genera; one with one species (P. aliquam) and another of three species (the red box indicates their distance). Our species have three main physical traits: coat colour, ear tufts and tail shape. At the ancestral nodes of the tree, we can see what the ancestor of these species looked like for these three traits. Each of these traits has undergone a different type of evolution. The tufts on the ears are the result of divergent evolution, since F. tuftus evolved the trait differently to its nearest relative, F. griseo. Contrastingly, the orange coat colour of F. tuftus and P. aliquam are the result of convergent evolution: neither of these species are very closely related (remembering the red box) and evolved orange coats independently of one another (since their ancestors are grey). And finally, the fluffy tails of F. hispida and F. griseo can be considered parallel evolution, since they’re similar evolutionarily (same genus) but still each evolved tail fluff independently (not in the ancestor). This example is a little convoluted, but if you trace the history of each trait in the phylogeny you can more easily see these different patterns.

So, where is evolution going for nature? Well, the answer is probably all over the place, but steered by the current environmental circumstances. Predicting the evolutionary impacts of particular environmental change (e.g. climate change) is exceedingly difficult but a critical component of understanding the process of evolution and the future of species. Evolution continually surprises us with creative solution to complex problems and I have no doubt new mysteries will continue to be thrown at us as we delve deeper.

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

The endemics of Australia

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

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

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

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

Early arrivals and naturalisation to the Australian ecosystem 

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

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

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

Invaders of the Australian continent

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

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

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

But is native always better?

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

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

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

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

“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.