December 2018 – The G-cat

Two Worlds: contrasting Australia’s temperate regions

December 19, 2018thegcatblog2 Comments

Temperate Australia

Australia is renowned for its unique diversity of species, and likewise for the diversity of ecosystems across the island continent. Although many would typically associate Australia with the golden sandy beaches, palm trees and warm weather of the tropical east coast, other ecosystems also hold both beautiful and interesting characteristics. Even the regions that might typically seem the dullest – the temperate zones in the southern portion of the continent – themselves hold unique stories of the bizarre and wonderful environmental history of Australia.

The two temperate zones

Within Australia, the temperate zone is actually separated into two very distinct and separate regions. In the far south-western corner of the continent is the southwest Western Australia temperate zone, which spans a significant portion. In the southern eastern corner, the unnamed temperate zone spans from the region surrounding Adelaide at its westernmost point, expanding to the east and encompassing Tasmanian and Victoria before shifting northward into NSW. This temperate zones gradually develops into the sub-tropical and tropical climates of more northern latitudes in Queensland and across to Darwin.

Labelled Koppen-Geiger map — The climatic classification (Koppen-Geiger) of Australia’s ecosystems, derived from the Atlas of Living Australia. The light blue region highlights the temperate zones discussed here, with an isolated region in the SW and the broader region of the SE as it transitions into subtropical and tropical climates northward.

The divide separating these two regions might be familiar to some readers – the Nullarbor Plain. Not just a particularly good location for fossils and mineral ores, the Nullarbor Plain is an almost perfectly flat arid expanse that stretches from the western edge of South Australia to the temperate zone of the southwest. As the name suggests, the plain is totally devoid of any significant forestry, owing to the lack of available water on the surface. This plain is a relatively ancient geological structure, and finished forming somewhere between 14 and 16 million years ago when tectonic uplift pushed a large limestone block upwards to the surface of the crust, forming an effective drain for standing water with the aridification of the continent. Thus, despite being relatively similar bioclimatically, the two temperate zones of Australia have been disconnected for ages and boast very different histories and biota.

Elevation map of NP.jpg — A map of elevation across the Australian continent, also derived from the Atlas of Living Australia. The dashed black line roughly outlines the extent of the Nullarbor Plain, a massively flat arid expanse.

The hotspot of the southwest

The southwest temperate zone – commonly referred to as southwest Western Australia (SWWA) – is an island-like bioregion. Isolated from the rest of the temperate Australia, it is remarkably geologically simple, with little topographic variation (only the Darling Scarp that separates the lower coast from the higher elevation of the Darling Plateau), generally minor river systems and low levels of soil nutrients. One key factor determining complexity in the SWWA environment is the isolation of high rainfall habitats within the broader temperate region – think of islands with an island.

SSWA environment.jpg — A figure demonstrating the environmental characteristics of SWWA, using data from the Atlas of Living Australia. **Left:** An elevation map of the region, showing some mountainous variation, but only one significant steep change along the coast (blue area). **Right:** A summary of 19 different temperature and precipitation variables, showing a relatively weak gradient as the region shifts inland.

Despite the lack of geological complexity and the perceived diversity of the tropics, the temperate zone of SWWA is the only internationally recognised biodiversity hotspot within Australia. As an example, SWWA is inhabited by ~7,000 different plant species, half of which are endemic to the region. Not to discredit the impressive diversity of the rest of the continent, of course. So why does this area have even higher levels of species diversity and endemism than the rest of mainland Australia?

speciation patterns in SWWA.jpg — A demonstration of some of the different patterns which might explain the high biodiversity of SWWA, from Rix et al. (2015). These predominantly relate to different biogeographic mechanisms that might have driven diversification in the region, from survivors of the Gondwana era to the more recent fragmentation of mesic habitats.

Well, a number of factors may play significant roles in determining this. One of these is the ancient and isolated nature of the region: SWWA has been separated from the rest of Australia for at least 14 million years, with many species likely originating much earlier than this. Because of this isolation, species occurring within SWWA have been allowed to undergo adaptive divergence from their east coast relatives, forming unique evolutionary lineages. Furthermore, the southwest corner of the continent was one of the last to break away from Antarctica in the dismantling of Gondwana >30 million years ago. Within the region more generally, isolation of mesic (wetter) habitats from the broader, arid (xeric) habitats also likely drove the formation of new species as distributions became fragmented or as species adapted to the new, encroaching xeric habitat. Together, this varies mechanisms all likely contributed in some way to the overall diversity of the region.

The temperate south-east of Australia

Contrastingly, the temperate region in the south-east of the continent is much more complex. For one, the topography of the zone is much more variable: there are a number of prominent mountain chains (such as the extended Great Dividing Range), lowland basins (such as the expansive Murray-Darling Basin) and variable valley and river systems. Similarly, the climate varies significantly within this temperate region, with the more northern parts featuring more subtropical climatic conditions with wetter and hotter summers than the southern end. There is also a general trend of increasing rainfall and lower temperatures along the highlands of the southeast portion of the region, and dry, semi-arid conditions in the western lowland region.

MDB map — A map demonstrating the climatic variability across the Murray-Darling Basin (which makes up a large section of the SE temperate zone), from Brauer *et al.* (2018). The different heat maps on the left describe different types of variables; a) and b) represent temperature variables, c) and d) represent precipitation (rainfall) variables, and e) and f) represent water flow variables. Each variable is a summary of a different set of variables, hence the differences.

A complicated history

The south-east temperate zone is not only variable now, but has undergone some drastic environmental changes over history. Massive shifts in geology, climate and sea-levels have particularly altered the nature of the area. Even volcanic events have been present at some time in the past.

One key hydrological shift that massively altered the region was the paleo-megalake Bungunnia. Not just a list of adjectives, Bungunnia was exactly as it’s described: a historically massive lake that spread across a huge area prior to its demise ~1-2 million years ago. At its largest size, Lake Bungunnia reached an area of over 50,000 km², spreading from its westernmost point near the current Murray mouth although to halfway across Victoria. Initially forming due to a tectonic uplift event along the coastal edge of the Murray-Darling Basin ~3.2 million years ago, damming the ancestral Murray River (which historically outlet into the ocean much further east than today). Over the next few million years, the size of the lake fluctuated significantly with climatic conditions, with wetter periods causing the lake to overfill and burst its bank. With every burst, the lake shrank in size, until a final break ~700,000 years ago when the ‘dam’ broke and the full lake drained.

Lake Bungunnia map 2.jpg — A map demonstrating the sheer size of paleo megalake Bungunnia at it’s largest extent, taken from McLaren et al. (2012).

Another change in the historic environment readers may be more familiar with is the land-bridge that used to connect Tasmania to the mainland. Dubbed the Bassian Isthmus, this land-bridge appeared at various points in history of reduced sea-levels (i.e. during glacial periods in Pleistocene cycle), predominantly connecting via the still-above-water Flinders and Cape Barren Islands. However, at lower sea-levels, the land bridge spread as far west as King Island: central to this block of land was a large lake dubbed the Bass Lake (creative). The Bassian Isthmus played a critical role in the migration of many of the native fauna of Tasmania (likely including the Indigenous peoples of the now-island), and its submergence and isolation leads to some distinctive differences between Tasmanian and mainland biota. Today, the historic presence of the Bassian Isthmus has left a distinctive mark on the genetic make-up of many species native to the southeast of Australia, including dolphins, frogs, freshwater fishes and invertebrates.

Bass Strait bathymetric contours.jpg — An elevation (Etopo1) map demonstrating the now-underwater land bridge between Tasmania and the mainland. Orange colours denote higher areas whilst light blue represents lower sections.

Don’t underestimate the temperates

Although tropical regions get most of the hype for being hotspots of biodiversity, the temperate zones of Australia similarly boast high diversity, unique species and document a complex environmental history. Studying how the biota and environment of the temperate regions has changed over millennia is critical to predicting the future effects of climatic change across large ecosystems.

The reality of neutrality

December 5, 2018thegcatblog4 Comments

The neutral theory

Many, many times within The G-CAT we’ve discussed the difference between neutral and selective processes, DNA markers and their applications in our studies of evolution, conservation and ecology. The idea that many parts of the genome evolve under a seemingly random pattern – largely dictated by genome-wide genetic drift rather than the specific force of natural selection – underpins many demographic and adaptive (in outlier tests) analyses.

This is based on the idea that for genes that are not related to traits under selection (either positively or negatively), new mutations should be acquired and lost under predominantly random patterns. Although this accumulation of mutations is influenced to some degree by alternate factors such as population size, the overall average of a genome should give a picture that largely discounts natural selection. But is this true? Is the genome truly neutral if averaged?

Non-neutrality

First, let’s take a look at what we mean by neutral or not. For genes that are not under selection, alleles should be maintained at approximately balanced frequencies and all non-adaptive genes across the genome should have relatively similar distribution of frequencies. While natural selection is one obvious way allele frequencies can be altered (either favourably or detrimentally), other factors can play a role.

As stated above, population sizes have a strong impact on allele frequencies. This is because smaller populations are more at risk of losing rarer alleles due to random deaths (see previous posts for a more thorough discussion of this). Additionally, genes which are physically close to other genes which are under selection may themselves appear to be under selection due to linkage disequilibrium (often shortened to ‘LD’). This is because physically close genes are more likely to be inherited together, thus selective genes can ‘pull’ neighbours with them to alter their allele frequencies.

Linkage disequilibrium figure — An example of how linkage disequilibrium can alter allele frequency of ‘neutral’ parts of the genome as well. In this example, only one part of this section of the genome is selected for: the **green gene**. Because of this positive selection, the frequency of a particular allele at this gene increases (the **blue graph**): however, nearby parts of the genome also increase in frequency due to their proximity to this selected gene, which decreases with distance. The extent of this effect determines the size of the ‘linkage block’ (see below).

Why might ‘neutral’ models not be neutral?

The assumption that the vast majority of the genome evolves under neutral patterns has long underpinned many concepts of population and evolutionary genetics. But it’s never been all that clear exactly how much of the genome is actually evolving neutrally or adaptively. How far natural selection reaches beyond a single gene under selection depends on a few different factors: let’s take a look at a few of them.

Linked selection

As described above, physically close genes (i.e. located near one another on a chromosome) often share some impacts of selection due to reduced recombination that occurs at that part of the genome. In this case, even alleles that are not adaptive (or maladaptive) may have altered frequencies simply due to their proximity to a gene that is under selection (either positive or negative).

Recombination blocks and linkage figure — A (perhaps familiar) example of the interaction between recombination (the breaking and mixing of different genes across chromosomes) and linkage disequilibrium. In this example, we have 5 different copies of a part of the genome (**different coloured sequences**), which we randomly ‘break’ into separate fragments (**breaks indicated by the dashed lines**). If we focus on a particular base in the sequence (the **yellow A**) and count the number of times a particular base pair is on the same fragment, we can see how physically close bases are more likely to be coinherited than further ones (**bottom column graph**). This makes mathematical sense: if two bases are further apart, you’re more likely to have a break that separates them. This is the very basic underpinning of linkage and recombination, and the size of the region where bases are likely to be coinherited is called the ‘linkage block’.

Under these circumstances, for a region of a certain distance (dubbed the ‘linkage block’) around a gene under selection, the genome will not truly evolve neutrally. Although this is simplest to visualise as physically linked sections of the genome (i.e. adjacent), linked genes do not necessarily have to be next to one another, just linked somehow. For example, they may be different parts of a single protein pathway.

The extent of this linkage effect depends on a number of other factors such as ploidy (the number of copies of a chromosome a species has), the size of the population and the strength of selection around the central locus. The presence of linkage and its impact on the distribution of genetic diversity (LD) has been well documented within evolutionary and ecological genetic literature. The more pressing question is one of extent: how much of the genome has been impacted by linkage? Is any of the genome unaffected by the process?

Background selection

One example of linked selection commonly used to explain the proliferation of non-neutral evolution within the genome is ‘background selection’. Put simply, background selection is the purging of alleles due to negative selection on a linked gene. Sometimes, background selection is expanded to include any forms of linked selection.

Under the first etymology of background selection, the process can be divided into two categories based on the impact of the linkage. As above, one scenario is the purging of neutral alleles (and therefore reduction in genetic diversity) as it is associated with a deleterious maladaptive gene nearby. Contrastingly, some neutral alleles may be preserved by association with a positively selected adaptive gene: this is often referred to as ‘genetic hitchhiking’ (which I’ve always thought was kind of an amusing phrase…).

Genetic hitchhiking picture.jpg — Definitely not how genetic hitchhiking works.

The presence of background selection – particularly under the ‘maladaptive’ scenario – is often used as a counter-argument to the ‘paradox in variation’. This paradox was determined by evolutionary biologist Richard Lewontin, who noted that despite massive differences in population sizes across the many different species on Earth, the total amount of ‘neutral’ genetic variation does not change significantly. In fact, he observed no clear relationship (directly) between population size and neutral variation. Many years after this observation, the influence of background selection and genetic hitchhiking on the distribution of genomic diversity helps to explain how the amount of neutral genomic variation is ‘managed’, and why it doesn’t vary excessively across biota.

What does it mean if neutrality is dead?

This findings have significant implications for our understanding of the process of evolution, and how we can detect adaptation within the genome. In light of this research, there has been heated discussion about whether or not neutral theory is ‘dead’, or a useful concept.

Genome wide allele frequency figure.jpg — A vague summary of how a large portion of the genome might not actually be neutral. In this section of the genome, we have neutral (**blue**), maladaptive (**red**) and adaptive (**green**) elements. Natural selection either favours, disfavours, or is ambivalent about each of this sections alone. However, there is significant ‘spill-over’ around regions of positively or negatively selected sections, which causes the allele frequency of even the neutral sections to fluctuate widely. The **blue dotted line** represents this: when the line is above the genome, allele frequency is increased; when it is below it is decreased. As we travel along this section of the genome, you may notice it is rarely ever in the middle (the so-called ‘neutral‘ allele frequency, in line with the genome).

Although I avoid having a strong stance here (if you’re an evolutionary geneticist yourself, I will allow you to draw your own conclusions), it is my belief that the model of neutral theory – and the methods that rely upon it – are still fundamental to our understanding of evolution. Although it may present itself as a more conservative way to identify adaptation within the genome, and cannot account for the effect of the above processes, neutral theory undoubtedly presents itself as a direct and well-implemented strategy to understand adaptation and demography.