Unravelling the evolutionary history of organisms – one of the main goals of phylogenetic research – remains a challenging prospect due to a number of theoretical and analytical aspects. Particularly, trying to reconstruct evolutionary patterns based on current genetic data (the most common way phylogenetic trees are estimated) is prone to the erroneous influence of some secondary factors. One of these is referred to as ‘incomplete lineage sorting’, which can have a major effect on how phylogenetic relationships are estimated and the statistical confidence we may have around these patterns. Today, we’re going to take a look at incomplete lineage sorting (shortened to ILS for brevity herein) using a game-based analogy – a Pachinko machine. Or, if you’d rather, the same general analogy also works for those creepy clown carnival games, but I prefer the less frightening alternative.
It shouldn’t come as a surprise to anyone with a basic understanding of evolution that it is a temporal (and also spatial concept). Time is a fundamental aspect of the process of evolution by natural selection, and without it evolution wouldn’t exist. But time is also a fickle thing, and although it remains constant (let’s not delve into that issue here) not all things experience it in the same way.
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.
This is partly where the concept of a ‘model’ comes into it: it’s much easier to pick a particular species to study as a target, and use the information from it to apply to other scenarios. Most people would be familiar with the concept based on medical research: the ‘lab rat’ (or mouse). The common house mouse (Mus musculus) and the brown rat (Rattus norvegicus) are some of the most widely used models for understanding the impact of particular biochemical compounds on physiology and are often used as the testing phase of medical developments before human trials.
One of the most obvious ways the evolution of two different species can interact is in predator and prey relationships. Naturally, prey species evolve to be able to defend themselves from predators in various ways, such as crypsis (e.g. camouflage), toxicity or behavioural changes (such as nocturnalism or group herding). Contrastingly, predators will evolve new and improved methods for detecting and hunting prey, such as enhanced senses, venom and stealth (through soft-padded feet, for example).
The pine marten is a species in the mustelid family, along with otters, weasels, stoats, and wolverines. Like many mustelids, they are carnivorous mammals which feed on a variety of different prey items like rodents, small birds and insects. One of the more abundant species that they prey upon are squirrels: both red squirrels and grey squirrels are potential food for the cute yet savage pine marten.
In a similar vein to predator and prey coevolution, pathogenic species and their unfortunate hosts also undergo a sort of ‘arms race’. Parasites must keep evolving new ways to infect and transmit to hosts as the hosts evolve new methods of resisting and avoiding the infecting species. This spiralling battle of evolutionary forces is dubbed as the ‘Red Queen hypothesis’, formulated in 1973 by Leigh Van Valen and used to describe many other forms of coevolution. The name comes from Lewis Carroll’s Through the Looking Glass, and one quote in particular:
‘Now, here, you see, it takes all the running you can do, to keep in the same place’.
Plenty of other strange and unique mechanisms of coevolution exist within nature. One of them is mimicry, the process by which one species attempts to look like another to protect itself. The most iconic group known for this is butterflies: many species, although they may be evolutionarily very different, share similar colouration patterns and body shapes as mimics. Depending on the nature of the copy, mimicry can be classified into two broad categories. In either case, the initial ‘reference’ species is toxic or unpalatable to predators and uses a type of colour signal to communicate this: think of the bright yellow colours of bees and wasps or the red of ladybirds. Where the two categories change is in the nature of the ‘mimic’ species.
Coevolution of species and the importance of species interactions
There are countless of other species interactions which could drive coevolutionary relationships in nature. These can include various forms of symbiosis, or the response of different species to ecosystem engineers: that is, species that can change and shape the environment around them (such as corals in reef systems). Understanding how a species evolves within its environment thus needs to consider how many other local species are also evolving and responding in their own ways.
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.
Evolution is a constant, endless force which seeks to push and shape species based on the context of their environment: sometimes rapidly, sometimes much more gradually. Although we often think of discrete points of evolution (when one species becomes two, when a particular trait evolves), it is nevertheless a continual force that influences changes in species. These changes are often difficult to ‘unevolve’ and have a certain ‘evolutionary inertia’ to them; because of these factors, it’s often critical to understand how a history of evolution has generated the organisms we see today.
What do I mean when I say evolutionary history? Well, the term is fairly diverse and can relate to the evolution of particular traits or types of traits, or the genetic variation and changes related to these changes. The types of questions and points of interest of evolutionary history can depend at which end of the timescale we look at: recent evolutionary histories, and the genetics related to them, will tell us different information to very ancient evolutionary histories. Let’s hop into our symbolic DeLorean and take a look back in time, shall we?
Very recent evolutionary history: pedigrees and populations
While we might ordinarily consider ‘evolutionary history’ to refer to events that happened thousands or millions of years ago, it can still be informative to look at history just a few generations ago. This often involves looking at pedigrees, such as in breeding programs, and trying to see how very short term and rapid evolution may have occurred; this can even include investigating how a particular breeding program might accidentally be causing the species to evolve to adapt to captivity! Rarely does this get referred to as true evolutionary history, but it fits on the spectrum, so I’m going to count it. We might also look at how current populations are evolving differently to one another, to try and predict how they’ll evolve into the future (and thus determine which ones are most at risk, which ones have critically important genetic diversity, and the overall survivability of the total species). This is the basis of ‘evolutionarily significant units’ or ESUs which we previously discussed on The G-CAT.
A little further back: phylogeography and species
A little further back, we might start to look at how different populations have formed or changed in semi-recent history (usually looking at the effect of human impacts: we’re really good at screwing things up I’m sorry to say). This can include looking at how populations have (or have not) adapted to new pressures, how stable populations have been over time, or whether new populations are being ‘made’ by recent barriers. At this level of populations and some (or incipient) species, we can find the field of ‘phylogeography’, which involves the study of how historic climate and geography have shaped the evolution of species or caused new species to evolve.
Phylogeography is also component for determining and understanding ‘biodiversity hotspots’; that is, regions which have generated high levels of species diversity and contain many endemic species and populations, such as tropical hotspots or remote temperate regions. These are naturally of very high conservation value and contribute a huge amount to Earth’s biodiversity, ecological functions and potential for us to study evolution in action.
Deep, deep history: phylogenetics and the origin of species (groups)
Even further back, we start to delve into the more traditional concept of evolutionary history. We start to look at how species have formed; what factors caused them to become new species, how stable the new species are, and what are the genetic components underlying the change. This subfield of evolution is called ‘phylogenetics’, and relates to understanding how species or groups of species have evolved and are related to one another.
Sometimes, this includes trying to look at how particular diagnostic traits have evolved in a certain group, like venom within snakes or eusocial groups in bees. Phylogenetic methods are even used to try and predict which species of plants might create compounds which are medically valuable (like aspirin)! Similarly, we can try and predict how invasive a pest species may be based on their phylogenetic (how closely related the species are) and physiological traits in order to safeguard against groups of organisms that are likely to run rampant in new environments. It’s important to understand how and why these traits have evolved to get a good understanding of exactly how the diversity of life on Earth came about.
Phylogenetics also allows us to determine which species are the most ‘evolutionarily unique’; all the special little creatures of plant Earth which represent their own unique types of species, such as the tuataraor the platypus. Naturally, understanding exactly how precious and unique these species are suggests we should focus our conservation attention and particularly conserve them, since there’s nothing else in the world that even comes close!
Who cares what happened in the past right? Well, I do, and you should too! Evolution forms an important component of any conservation management plan, since we obviously want to make sure our species can survive into the future (i.e. adapt to new stressors). Trying to maintain the most ‘evolvable’ groups, particularly within breeding programs, can often be difficult when we have to balance inbreeding depression (not having enough genetic diversity) with outbreeding depression (obscuring good genetic diversity by adding bad genetic diversity into the gene pool). Often, we can best avoid these by identifying which populations are evolutionarily different to one another (see ESUs) and using that as a basis, since outbreeding vs. inbreeding depression can be very difficult to measure. This all goes back to the concept of ‘adaptive potential’ that we’ve discussed a few times before.
In any case, a keen understanding of the evolutionary trajectory of a species is a crucial component for conservation management and to figure out the processes and outcomes of evolution in the real world. Thus, evolutionary history remains a key area of research for both conservation and evolution-related studies.