May 2018 – The G-cat

All the world in the palm of your hand: whole genome sequencing for evolution and conservation

May 30, 2018thegcatblog4 Comments

Building an entire genome

If bigger is better, then biggest is best. Having the genome of a particular study species fully sequenced allows us to potentially look at all of the genetic variation in the entire gene pool: but how do we sequence the entirety of the genome? And what are the benefits of having a whole genome to refer to?

Whole genome assembly — A very, very simplified overview of whole genome sequencing. Similar to other genomic technologies, we start by fragmenting the genome into much smaller, easier to sequence parts (reads). We then use a computer algorithm which pieces these reads together into a consecutive sequence based on overlapping DNA sequence (like building a chain out of Lego blocks). From this assembled genome, we can then attach annotations using information from other species’ genomes or genetic studies, which can correlate a particular sequence to a gene, a function of that gene, and the resultant protein from these gene (although not always are all of these aspects included).

Well, assembling the whole genome of an organism for the first time is a very tricky process. It involves taking DNA sequence from only a few individuals, breaking them down into smaller fragments and multiplying these fragments into the billions (moreorless the same process used in other genomics technologies: the real difference is that we need the full breadth of the genome so that we don’t miss any spaces). From these fragments, we use a complex computer algorithm which builds up a consensus sequence like a Lego tower; by finding parts of sequences which overlap, the software figures out which pieces connect to one another. Hopefully, we eventually end up with one very long continuous sequence; the genome! Sometimes, we might end with a few very large blocks (called contigs), but this is also useful for analyses (correlated with how many/big blocks there are). With this full genome, we use information from other more completed genomes (such as those from model species like humans, mice or even worms) to figure out which sections of the genome relate to specific genes. We can then annotate these sections by labelling them as clear genes, complete with start and end point, and attach a particular physical function of that gene.

The benefits of whole genomes

Having an entire genome as a reference is an extremely helpful tool in conservation and evolutionary studies. The first, and perhaps most obvious benefit, is the sheer scale of the data we can use. By having the entirety of the genome available, we can use potentially billions of base pairs of sequence in our genetic analyses (for reference, the human genome is >3 billion base pairs long). Even if we don’t sequence the full genome for all of our samples, having a reference genome as basis for assembly our reduced datasets significantly improves the quantity and quality of sequences we can use.

Another very important benefit is the ability to prescribe function in our studies. Many of our processes for obtaining data, even for genomic technologies, use random and anonymous fragments of the genome. Although this is a cost-effective way to obtain a very large amount of data, it unfortunately means that we often have no idea which part of the genome our sequences came from. This means that we don’t know which sequences relate to specific genes, and even if we did we would have no idea what those genes are or do! But with an annotated genome, we can take even our fragmented sequence and check it against the genome and find out what genes are present.

Understanding adaptation

Based on that, it seems pretty obvious about exactly how having an annotated genome can help us in studies of adaptation. Knowing the functional aspect of our genetic data allows us to more directly determine how evolution is happening in nature; instead of only being able to say that two species are evolving differently from one another, for example, we can explicitly look at how they are evolving. Is one evolving tolerance to hotter temperatures? Are they evolving different genes to handle different diets? Are they evolving in response to an external influence, like a viral outbreak or changing climate? What are the physiological consequences of these changes? These questions are critical in understanding past and future evolution, and full genome analysis allows us to delve into them much deeper.

Manhattan plot example — A (slightly edited) figure of full genome comparisons between domestic dogs and wild wolves by Axelsson *et al.* (2013), with the aim of understanding the evolutionary changes associated with domestication. For avid readers, this figure probably looks familiar. This figure compares the genetic differentiation across the entire genome between dogs and wolves, with some sections of the genome (circled) showing clear differences. As there is an annotated dog genome, the authors then delved into these genes to understand the functional differences between the two. By comparing their genetic differences to functional genes, the authors can more explicitly suggest mechanisms or changes associated with the domestication process (such as adaptation to a starch-heavy and human-influenced diet).

This includes allowing us to better understand how adaptation actually works in nature. As we’ve discussed before, more traditional studies often assumed that single, or very few, genes were responsible for allowing a species to adapt and change, and that these genes had very strong effects on their physiology. But what we see far more often is polygenic adaptation; small changes in a very large number of genes which, combined together, allow the species to adapt and evolve. By having the entirety of the genome available, we are much more likely to capture all of the genes that are under natural selection in a particular population or species, painting a clearer picture of their evolutionary trajectory.

Understanding demography

The much larger dataset of full genomes is also important for understanding the non-adaptive parts of evolution; the demographic history. Given that selectively neutral impacts (e.g. reductions in population size) are likely to impact all of the genes in the gene pool somewhat equally, having a full genome allows us to more accurately infer the demographic state and historical patterns of species.

For both adaptive and non-adaptive variation, it is also important to consider what we call linkage disequilibrium. Genetic sequences that are physically close to each other in the genome will often be inherited together due to the imprecision of recombination (a fairly technical process, so I won’t delve into this): what this can mean is that if a gene is under very strong selection, then sequences around this gene will also look like they’re under selection too. This can give falsely positive adaptive genes (i.e. sequences that look like genes under selection but are just linked to a gene that is) or can interfere with demographic analyses (since they often assume no selection, or linkage to selection, on the sequences used). With a whole genome, we can actually estimate how far away a base pair has to be before it’s not linked anymore; we call these linkage blocks, and they’re very useful additions to analyses.

Linkage_example — An example of linkage as a process. We start with a particular sequence (top); during recombination, this sequence may randomly break and rearrange into different parts. In this example, I’ve simulated four different ‘breaks’ (dashed coloured lines) due to recombination. Each of these breaks leads to two separate blocks of fragments; for example, the break at the blue line results in the second two sequence blocks (middle). If we focus on one target base pair in the sequence (golden A), then we can see in some fragments it remains with certain bases, but sometimes it gets separated by the break. If we compare how often the golden A is in the same block (i.e. is co-inherited) as each of the other bases, across all 4 breaks, then we see that the bases that are closest to it (the golden A is represented by the golden bar) are almost always in the same block. This makes sense: the further away a base is from our target, the more likely that there will be a break between it. This is shown in the frequency distributions at the bottom: the left figure shows the actual frequencies of co-inheritance (i.e. linkage) using the top example and those 4 breaks. The right figure shows a more realistic depiction of how linkage looks in the genome; it rapidly decays as we move away from the target (although the width and rate of this can vary).

Improving conservation management

In a similar fashion to demography, full genome datasets can improve our estimates of relatedness and pedigrees in captive breeding programs. The massive scale of whole genomes allows us to more easily trace the genealogical history of individuals, allowing us to assign parents more accurately. This also helps with our estimations of genetic relatedness, arguably the most critical aspect of genetic-based breeding programs. This is particularly helpful for species with tricky mating patterns, such as polyamory, brood spawning or difficult to track organisms.

The way forwards

While many non-model species are still lacking in the available genomic information, whole genomes are progressively being sequenced for more and more species. As this astronomical dataset grows, our ability to investigate, discover and test theories about evolution, natural selection and conservation will also improve. Many projects already exist which aim specifically to increase the number of whole genomes available for certain taxonomic groups such as birds and bats: these will no doubt prove to be invaluable resources for future studies.

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

May 23, 2018thegcatblog1 Comment

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.

Why we should always pander to diversity

May 16, 2018thegcatblog5 Comments

Diversity in the natural world

‘Diversity’ is a term that gets used a lot these days, albeit usually in reference to social changes and structures. However, diversity is not merely a human construct and reflects an extremely important aspect of the natural world at a variety of levels. From the smallest genes to the biggest ecosystems, diversity is a trait that confers a massive range of benefits to individuals, populations, species and even the entire globe. Let’s dissect this diversity down at different scales and see how beneficial it can be.

Hierarchy of diversity — The generalised hierarchy at life, with diversity being an important component of each tier. At the smallest tier, genes underpin all life. The collection of genetic diversity is often summarised into a population (as a single cohesive genetic unit). Several populations can be pooled together into a single (usually) cohesive species. Different species are then components of a larger community (which in turn are components of a broader ecosystem).

Genetic diversity

At the smallest scale in the hierarchy of genetic differentiation, we have the genes themselves. It is a well-established concept that having a diversity of genetic variants (alleles) within a population or species is critical to their future adaptation, evolution and persistance. This is because different alleles will have different benefits (or costs) depending on the environmental pressure that influences them; natural selection might favour one allele over another at one time, but a different one as the pressure changes. Having a higher number of alleles within the population or species means that there is a greater chance at least a few individuals will possess an adaptive gene with the changing environment (which we know can be quite rapid and very, very strong). The diversity serves as a ‘buffer’ against extinction; evolution by natural selection functions best when there are many options to choose from.

Without this diversity, species run the risk of having no adaptive genes at the ready to deal with a selective pressure. Either a new adaptive gene must mutate (or come about in other ways, such as through gene flow from another population or species) or the population/species will suffer and potentially go extinct. As strong selection causes the species to dwindle, it enters what is referred to as the ‘extinction vortex’. Without genetic diversity, they can’t adapt: thus, more individuals die off, causing more genetic diversity to be lost from the population. This pattern is a vicious cycle which can inevitably destroy species (without serious intervention).

Extinction vortex — A very dramatic representation of the extinction vortex.

For this reason, captive breeding programs aim to maintain as much of the genetic diversity of the original population as possible. This reduces the probability of entering a downward extinction spiral from inbreeding depression and helps to maintain populations into the future (both the captive one and the wild population when we reintroduce individuals into the wild).

“Population” diversity

Because genetic diversity is critically important for species survival, we must also try to preserve the diversity of the entire gene pool of a species. This means conserving highly genetically differentiated populations within a species as a priority, as they may be the only ones that possess the necessary adaptive genes to save the rest of the species. This adaptive genetic variation can then be introduced into other populations in genetic rescue programs and serve as a means to semi-naturally allow the species to evolve. Evolutionarily-significant units (ESUs) are one measure of the invaluable nature of genetically unique populations.

Although many more traditional conservationists strongly believe that ESUs should be managed entirely independently of one another (to preserve their evolutionary ‘pedigree’ and prevent the risk of outbreeding depression), it has been suggested that the benefit of genetic rescue in many cases significantly outweighs this risk of outbreeding depression. For some species, this really is an act of rescue: they are at the edge of extinction, and if we do nothing we condemn them to die out.

Introducing genetic material across populations (or even species!) can generate new functional genes that allow the recipient species to adapt to selective pressures. This might sound very strange, and could be extremely rare, but examples of adaptive genetic material in one species originating from another species through hybridisation do exist in nature. For example, the black coat of wolves is a highly adaptive trait in some populations and is encoded for by the Melanocortin 1 receptor (Mc1r) gene. However, the specific mutation in Mc1r gene that generates the black coat colour actually first originated in domestic dogs; when wild wolves and domestic dogs interbred, this mutation was transferred into the wolf gene pool. Natural selection strongly favoured this new variant, and it very rapidly underwent strong positive selection. Thus, the adaptiveness of black wolves is thanks to a domestic dog mutation!

Species diversity

At a higher level of the hierarchy, the diversity of species within a particular community or ecosystem has been shown to be important for the health and stability of said community. Every species, however small or seemingly unimpressive, plays a role in the greater ecosystem balance, through interactions with other species (e.g. as predator, as prey, as competitor) and the abiotic environment. While some species are known to have very strong impacts on the immediate ecosystem (often dubbed ‘keystone species’, such as apex predators), all species have some influence on the world around them (we’re especially good at it).

Species interactions flowchart

The overall health and stability of an ecosystem, as well as the benefits it can provide to all living things (including humans) is largely determined by the diversity of species. For example, ‘habitat engineers’ are types of species that, by altering the physical environment around them (such as to build a home), directly provide new habitat for other species. They are a fundamental underpinning of many incredibly vibrant ecosystems; think of what a reef system would look like if there were no corals in it. There’d be no anemones growing colourfully; no fish to live in them; no sharks to feed on these non-existent fish. This is just one example of a complex ecosystem that truly relies on its inhabiting species to function.

Ecosystem jenga — Much like Jenga, taking out one block (a species) could cause the entire stack (the ecosystem) to collapse in on itself. Even if it stands up, however, the system will still be weaker without the full diversity to support it.

Protecting our diversity

Diversity is not just a social construct and is an important phenomenon in nature, at a variety of different levels. Preserving the full diversity of life, from genetic diversity within populations and species to full species diversity within ecosystems, is critical to maintaining healthy and robust natural systems. The more diversity we have at each level of this hierarchy, the greater robustness and security we will have in the future.

The history of histories: philosophy in biogeography

May 9, 2018May 9, 2018thegcatblog1 Comment

Biogeography of the globe

The distribution of organisms across the Earth, both over time and across space, is a fundamental aspect of the field of biogeography. But our understanding of the mechanisms by which organisms are distributed across the globe, and how this affects their evolution, can be at times highly enigmatic. Why are Australia and the Americas the only two places that have marsupials? How did lemurs get all the way to Madagascar, and why are they the only primate that has made the trip? How did Darwin’s famous finches get over to the Galápagos, and why are there so many species of them there now?

All of these questions can be addressed with a combination of genetic, environmental and ecological information across a variety of timescales. However, the overall field of biogeography (and phylogeography as a derivative of it) has traditionally been largely rooted on a strong yet changing theoretical basis. The earliest discussions and discoveries related to biogeography as a field of science date back to the 18^th Century, and to Carl Linnaeus (to whom we owe our binomial classification system) and Alexander von Humboldt. These scientists (and undoubtedly many others of that era) were among the first to notice how organisms in similar climates (e.g. Australia, South Africa and South America) showed similar physical characteristics despite being so distantly separated (both in their groups and geographic distance). The communities of these regions also appeared to be highly similar. So how could this be possible over such huge distances?

Arctic and fennec final — A pretty unreasonable mechanism (and example) of dispersal in foxes. And yes, all tourists wear sunglasses and Hawaiian shirts, even arctic fox ones.

Dispersal or vicariance?

Two main explanations for these patterns are possible; dispersal and vicariance. As one might expect, dispersal denotes that an ancestral species was distributed in one of these places (referred to as the ‘centre of origin’) before it migrated and inhabited the other places. Contrastingly, vicariance suggests that the ancestral species was distributed everywhere originally, covering all contemporary ranges within it. However, changes in geography, climate or the formation of other barriers caused the range of the ancestor to fragment, with each fragmented group evolving into its own distinct species (or group of species).

Dispersal vs vicariance islands — An example of dispersal vs. vicariance patterns of biogeography in an island bird (pale blue). In the top example, the sequential separation of parts of the island also cause parts of the distribution of the original bird species to become fragmented. These fragments each evolve independently of their ancestor and form new species (red, and then blue). In the bottom example, the island geography doesn’t change but in rare events a bird disperses from the main island onto a new island. The new selective pressures of that island cause the dispersed birds to evolve into new species (red and blue). In both examples, islands that were recently connected or are easy to disperse across do not generate new species (in the sandy island in the bottom right). You’ll notice that both processes result in the same biogeographic distribution of species.

In initial biogeographic science, dispersal was the most heavily favoured explanation. At the time, there was no clear mechanism by which organisms could be present all over the globe without some form of dispersal: it was generally believed that the world was a static, unmoving system. Dispersal was well supported by some biological evidence such as the diversification of Darwin’s finches across the Galápagos archipelago. Thus, this concept was supported through the proposals of a number of prominent scientists such as Charles Darwin and A.R. Wallace. For others, however, the distance required for dispersal (such as across entire oceans) seemed implausible and biologically unrealistic.

A paradigm shift in biogeography

Two particular developments in theory are credited with a paradigm shift in the field; cladistics and plate tectonics. Cladistics simply involved using shared biological characteristics to reconstruct the evolutionary relationships of species (think like phylogenetics, but using physical traits instead of genetic sequence). Just as importantly, however, was plate tectonic theory, which provided a clear way for organisms to spread across the planet. By understanding that, deep in the past, all continents had been directly connected to one another provides a convenient explanation for how species groups spread. Instead of requiring for species to travel across entire oceans, continental drift meant that one widespread and ancient ancestor on the historic supercontinent (Pangaea; or subsequently Gondwana and Laurasia) could become fragmented. It only required that groups were very old, but not necessarily very dispersive.

Lemur dispersal — Surf’s up, dudes! Although continental drift was no doubt an important factor in the distribution and dispersal of many organisms on Earth, it actually probably wasn’t the reason lemurs got to Madagascar. Sorry for the mislead.

From these advances in theory, cladistic vicariance biogeography was born. The field rapidly overtook dispersal as the most likely explanation for biogeographic patterns across the globe by not only providing a clear mechanism to explain these but also an analytical framework to test questions relating to these patterns. Further developments into the analytical backbone of cladistic vicariance allowed for more nuanced questions of biogeography to be asked, although still fundamentally ignored the role of potential dispersals in explaining species’ distributions.

Modern philosophy of biogeography

So, what is the current state of the field? Well, the more we research biogeographic patterns with better data (such as with genomics) the more we realise just how complicated the history of life on Earth can be. Complex modelling (such as Bayesian methods) allow us to more explicitly test the impact of Earth history events on our study species, and can provide more detailed overview of the evolutionary history of the species (such as by directly estimating times of divergence, amount of dispersal, extent of range shifts).

From a theoretical perspective, the consistency of patterns of groups is always in question and exactly what determines what species occurs where is still somewhat debatable. However, the greater number of types of data we can now include (such as geological, paleontological, climatic, hydrological, genetic…the list goes on!) allows us to paint a better picture of life on Earth. By combining information about what we know happened on Earth, with what we know has happened to species, we can start to make links between Earth history and species history to better understand how (or if) these events have shaped evolution.

Surviving the Real-World Apocalypse

May 2, 2018May 2, 2018thegcatblog2 Comments

The changing world

Climate change seems to be the centrefold of a large amount of scientific research and media attention, and rightly so: it has the capacity to affect every living organism on the planet. It’s our duty as curators and residents of Earth to be responsible for our influences on the global environmental stage. While a significant part of this involves determining causes and solutions to our contributions to climate change, we also need to know how extensive the effects will be: for example, how can we predict how well species will do in the future?

Predicting the effect of climate change on all of the world’s biodiversity is an immense task. Climate change itself is a complicated system, and causes diverse, interconnected and complex alterations to both global and local climate. Adding on top of this, though, is that climate affects different species in different ways; where some species might be sensitive to some climatic variables (such as rainfall, available sunlight, seasonality), others may be more tolerant to the same factors. But all living things share some requirements, so surely there must be some consistency in their responses to climate change, right?

Apocalypse 2 — Lucky for Mr Fish here, he’s responding to a (very dramatic) climate change much, **much** better than his bird counterpart.

How predictable are species responses to climate change?

Well, evidence would surprisingly suggest not. Many species, even closely related ones, can show very different responses to the exact same climatic pressures or biogeographical events. There are a number of different traits that might affect a species’ ability to adapt, particularly their adaptive genetic diversity (which underpins ‘adaptive potential’). Thus, we need good information of a variety of genetic, physiological and life history traits to be able to make predictions about how likely a species is to adapt and respond to future (and current) climate changes.

Although this can be hard to study in species of high extinction risk (getting a good number of samples is always an issue…), traditional phylogeographic methods might help us to make some comparisons. See, although the modern Earth is rapidly changing (undoubtedly influenced by human society), the climate of the globe has always varied to some degree. There has always been some tumultuousness in the climate and specific Earth history events like volcano eruptions, sea-level changes, or glaciation periods (‘ice ages’) have had diverse effects on organisms globally.

Using comparative phylogeography to predict species responses

One tool for looking at how different species have, in the past, responded to the same biogeographical force is the domain of ‘comparative phylogeography’. Phylogeography itself is something we have discussed before: the ‘comparative’ aspect simply means comparing (with complex statistical methods) these patterns across different and often unrelated species to see how universal (‘congruent’) or unique (‘incongruent’) these patterns are among species. The more broadly we look at the species community in the region, the more we can observe widespread effects of any given environmental or geographical event: if we only look at fish, for example, we might not to be able to infer what response mammals, birds or invertebrates have had to our given event. Sometimes this still meets the scale we wish to focus; other times, we want to see how all the species of an area have been affected.

Actual island diagram — An (very busy) example of different species responses to a single environmental event. In this example, we have three species (a fish, a lizard, and a bird) all living on the same island. In the middle of the island, there is a small mountain range (A). At this point in time, all three species are connected across the whole island; fish can travel via lakes and wetlands (green arrows), lizards can travel across the land (blue arrow) and birds can fly anywhere. However, as the mountain range grows with tectonic movements, the waterways are altered and the north and south are disconnected (B). The fish species is now split into two evolutionarily separate groups (green and gold), while lizards and birds are not. As the range expands further, however, the dispersal route for lizards is cut off, causing them to eventually also become separated into blue and black groups (C). Birds, however, have no problems flying over the mountain range and remain one unified and connected orange group over time (D). Thus, each species has a different response to the formation of the mountain range.

Evol history of island diagram — The phylogenetic history of the three different species in the above example. As you can see, each lineage has a slightly different pattern; birds show no divergences at all, whereas the timing of the lizard and fish N/S splits are different (i.e. temporally incongruent).

Typically, comparative phylogeographic studies have looked at the neutral components of species’ evolution (as is the realm of traditional phylogeography). This includes studying the size of populations over time, how well connected they are and were, what their spatial patterns are and how these relate to the environment. Comparing all of these patterns across species can allow us to start painting a fuller picture of the history of biota in a region. In this way, we can start to see exactly which species have shown what responses and start to relate these to the characteristics that allowed them to respond in that certain way (and including adaptation in our studies). So, what kinds of traits are important?

What traits matter? Who wins?

Often, we find that life history traits of an organism better dictates how they will respond to a certain pressure than other factors such as phylogeny (e.g. one group does not always do better than another). Instead, individual species with certain physical characteristics might handle the pressure better than others. For example, a fish, bird and snake that are all able to tolerate higher temperatures than other fish, birds or snakes in that region are more likely to survive a drought. In this case, none of the groups (fish, birds or snakes) inherently do better than the other two groups. Thus, it can be hard to predict how a large swathe of species will respond to any given environmental change, unless we understand the physical characteristics of every species.

Climate change risk flowchart — A generalised framework of various factors, and their interactions, on the vulnerability of species under current and future climate changes by Williams et al. 2018. The schematic includes genetic, ecological, physical and environmental factors and how these can interact with one another to alleviate or exacerbate the risk of extinction.

We can also see that other physiological or ecological traits, such as climatic preferences and tolerance thresholds, can be critical for adapting to climatic pressures. Naturally, the genetic diversity of species is also an important component underlying their ability to adapt to these new selective pressures and to survive into the future. Trying to incorporate all of these factors into a projected model can be difficult, but with more data of higher quality we can start to make more refined predictions. But by understanding how particular traits influence how well a species may adapt to a changing climate, as well as knowing the what traits different species have, might just be the key to predicting who wins and who dies in the real-world Game of Thrones.

The G-cat

Dive head-first into the science of conservation, ecology, evolution and genetics

Month: May 2018