For anyone who has had to study geography at some point in their education, you’d likely be familiar with the idea of river courses drawn on a map. They’re so important, in fact, that they are often the delimiting factor in the edges of countries, states or other political units. Water is a fundamental requirement of all forms of life and the riverways that scatter the globe underpin the maintenance, structure and accumulation of a large swathe of biodiversity.
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.
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.
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.
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.
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.
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.
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 first major component that is needed for SDM is the occurrence data. Some methods will work with presence-only data: that is, a map of GPS coordinates which describes where that species has been found. Others work with presence-absence data, which may require including sites of known non-occurrence. This is an important aspect as the non-occurring sites defines the environment beyond the tolerance threshold of the species: however, it’s very likely that we haven’t sampled every location where they occur, and there will be some GPS co-ordinates that appear to be absent of our species where they actually occur. There are some different analytical techniques which can account for uneven sampling across the real distribution of the species, but they can get very technical.
Our SDM analysis of choice (e.g. MaxEnt) will then use various algorithms to build a model which best correlates where the species occurs with the environmental variables at those sites. The model tries to create a set of environmental conditions that best encapsulate the occurrence sites whilst excluding the non-occurrence sites from the prediction. From the final model, we can evaluate how strong the effect of each of our variables is on the distribution of the species, and also how well our overall model predicts the locality data.
Species distribution modelling continues to be a useful tool for conservation and evolution studies, and improvements in analytical algorithms, available environmental data and increased sampling of species will similarly improve SDM. Particularly, improvements in environmental projections from both the distant past and future will improve our ability to understand and predict how species will change, and have changed, with climatic changes
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.
To my honest surprise, the paper has received a decentamount 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.
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.
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.
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.
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.
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.
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 18th 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?
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, vicariancesuggests 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).
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.
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.
As I’ve mentioned a few times before, evolution is a constant force that changes and flows over time. While sometimes it’s more convenient to think of evolution as a series of rather discrete events (a species pops up here, a population separates here, etc.), it’s really a more continual process. The context and strength of evolutionary forces, such as natural selection, changes as species and the environment they inhabit also changes. This is important to remember in evolutionary studies because although we might think of more recent and immediate causes of the evolutionary changes we see, they might actually reflect much more historic patterns. For example, extremely low contemporary levels of genetic diversity in cheetah is likely largely due to a severe reduction in their numbers during the last ice age, ~12 thousand years ago (that’s not to say that modern human issues haven’t also been seriously detrimental to them). Similarly, we can see how the low genetic diversity of a small population colonise a new area can have long term effects on their genetic variation: this is called ‘founder effect’. Because of this, we often have to consider the temporal aspect of a species’ evolution.
Evolution travelling across space
If the environmental context of species and populations are also important for determining the evolutionary pathways of organisms, then we must also consider the spatial context. Because of this, we also need to look at where evolution is happening in the world; what kinds of geographic, climatic, hydrological or geological patterns are shaping and influencing the evolution of species? These patterns can influence both neutral or adaptive processes by shaping exactly how populations or species exist in nature; how connected they are, how many populations they can sustain, how large those populations can sustainably become, and what kinds of selective pressures those populations are under.
Evolution along the space-time continuum
Given that the environment also changes over time (and can be very rapid, and we’ve seen recently), the interaction of the spatial and temporal aspects of evolution are critical in understanding the true evolutionary history of species. As we know, the selective environment is what determines what is, and isn’t, adaptive (or maladaptive), so we can easily imagine how a change in the environment could push changes in species. Even from a neutral perspective, geography is important to consider since it can directly determine which populations are or aren’t connected, how many populations there are in total or how big populations can sustainably get. It’s always important to consider how evolution travels along the space-time continuum.
For phylogeography, the genetic history of populations or species gives the more accurate overview of their history; it allows us to test when populations or species became separated, which were most closely related, and whether patterns are similar or different across other taxonomic groups. Predominantly, phylogeography is based on neutral genetic variation, as using adaptive variation can confound the patterns we are testing. Additionally, since neutral variation changes over time in a generally predictable, mathematical format (see this post to see what I mean), we can make testable models of various phylogeographic patterns and see how well our genetic data makes sense under each model. For example, we could make a couple different models of how many historic populations there were and see which one makes the most sense for our data (with a statistical basis, of course). This wouldn’t work with genes under selection since they (by their nature) wouldn’t fit a standard ‘neutral’ model.
That said, there are plenty of interesting scientific questions within phylogeography that look at exploring the adaptive variation of historic populations or species and how this has influenced their evolution. Although this can’t inherently be built into the same models as the neutral patterns, looking at candidate genes that we think are important for evolution and seeing how their distributions and patterns relate to the overall phylogeographic history of the species is one way of investigating historic adaptive evolution. For example, we might track changes in adaptive genes by seeing which populations have which variants of the gene and referring to our phylogeographic history to see how and when these variants arose. This can help us understand how phylogeographic patterns have influenced the adaptive evolution of different populations or species, or inversely, how adaptive traits might have influenced the geographic distribution of species or populations.
Where did you come from and where will you go?
Phylogeographic studies can tell us a lot about the history of a species, and particularly how that relates to the history of the Earth. All organisms share an intimate relationship with their environment, both over time and space, and keeping this in mind is key for understanding the true evolutionary history of life on Earth.