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.
We’ve discussed standing genetic variation before on The G-CAT, but often in a different light (and phrasing). For example, when we’ve talked about founder effect: that is, when a population is formed from only a few different individuals which causes it to be very genetically depauperate. In populations under strong founder effect, there is very little standing genetic variation for natural selection to act upon. This has long been an enigma for many pest species: how have they managed to proliferate so widely when they often originate from so few individuals and lack genetic diversity?
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.
Meaning: Octorokus from [octorok] in Hylian; infletus from [inflate] in Latin.
Translation: inflating octorok; all varieties use an inflatable air sac derived from the swim bladder to float and scan the horizon.
Octorokus infletus hydros [aquatic morphotype]
Octorokus infletus petram [mountain morphotype]
Octorokus infletus silva [forest morphotype]
Octorokus infletus arctus [snow morphotype]
Octorokus infletus imitor [deceptive morphotype]
Kingdom Animalia; Phylum Mollusca; Class Cephalapoda; Order Octopoda; Family Octopididae; GenusOctorokus; Speciesinfletus
The species is found throughout all major habitat regions of Hyrule, with localised morphotypes found within specific habitats. The only major region where the variable octorok is not found is within the Gerudo Desert, suggesting some remnant dependency of standing water.
Habitat choice depends on the physiology of the morphotype; so long as the environment allows the octorok to blend in, it is highly likely there are many around (i.e. unseen).
Behaviour and ecology
The variable octorok is arguably one of the most diverse species within modern Hyrule, exhibiting a large number of different morphotypic forms and occurring in almost all major habitat zones. Historical data suggests that the water octorok (Octorokus infletus hydros) is the most ancestral morphotype, with ancient literature frequently referring to them as sea-bearing or river-traversing organisms. Estimates from the literature suggests that their adaptation to land-based living is a recent evolutionary step which facilitated rapid morphological radiation of the lineage.
Several physiological characteristics unite the variable morphological forms of the octorok into a single identifiable species. Other than the typical body structure of an octopod (eight legs, largely soft body with an elongated mantle region), the primary diagnostic trait of the octorok is the presence of a large ‘balloon’ with the top of the mantle. This appears to be derived from the swim bladder of the ancestral octorok, which has shifted to the cranial region. The octorok can inflate this balloon using air pumped through the gills, filling it and lifting the octorok into the air. All morphotypes use this to scan the surrounding region to identify prey items, including attacking people if aggravated.
Diets of the octorok vary depending on the morphotype and based on the ecological habitat; adaptations to different ecological niches is facilitated by a diverse and generalist diet.
Although limited information is available on the amount of gene flow and population connectivity between different morphotypes, by sheer numbers alone it would appear the variable octorok is highly abundant. Some records of interactions between morphotypes (such as at the water’s edge within forested areas) implies that the different types are not reproductively isolated and can form hybrids: how this impacts resultant hybrid morphotypes and development is unknown. However, given the propensity of morphotypes to be largely limited to their adaptive habitats, it would seem reasonable to assume that some level of population structure is present across types.
The variable octorok appears remarkably diverse in physiology, although the recent nature of their divergence and the observed interactions between morphological types suggests that they are not reproductively isolated. Whether these are the result of phenotypic plasticity, and environmental pressures are responsible for associated physiological changes to different environments, or genetically coded at early stages of development is unknown due to the cryptic nature of octorok spawning.
All octoroks employ strong behavioural and physiological traits for camouflage and ambush predation. Vegetation is usually placed on the top of the cranium of all morphotypes, with the exact species of plant used dependent on the environment (e.g. forest morphotypes will use grasses or ferns, whilst mountain morphotypes will use rocky boulders). The octorok will then dig beneath the surface until just the vegetation is showing, effectively blending in with the environment and only occasionally choosing to surface by using the balloon. Whether this behaviour is passed down genetically or taught from parents is unclear.
Few management actions are recommended for this highly abundant species. However, further research is needed to better understand the highly variable nature and the process of evolution underpinning their diverse morphology. Whether morphotypes are genetically hardwired by inheritance of determinant genes, or whether alterations in gene expression caused by the environmental context of octoroks (i.e. phenotypic plasticity) provides an intriguing avenue of insight into the evolution of Hylian fauna.
Nevertheless, the transition from the marine environment onto the terrestrial landscape appears to be a significant stepping stone in the radiation of morphological structures within the species. How this has been facilitated by the genetic architecture of the octorok is a mystery.
Given the strong influence of genetic identity on the process and outcomes of the speciation process, it seems a natural connection to use genetic information to study speciation and species identities. There is a plethora of genetics-based tools we can use to investigate how speciation occurs (both the evolutionary processes and the external influences that drive it). One clear way to test whether two populations of a particular species are actually two different species is to investigate genes related to reproductive isolation: if the genetic differences demonstrate reproductive incompatibilities across the two populations, then there is strong evidence that they are separate species (at least under the Biological Species Concept; see Part One for why!). But this type of analysis requires several tools: 1) knowledge of the specific genes related to reproduction (e.g. formation of sperm and eggs, genital morphology, etc.), 2) the complete and annotated genome of the species (to be able to find and analyse the right genes properly) and 3) a good amount of data for the populations in question. As you can imagine, for people working on non-model species (i.e. ones that haven’t had the same history and detail of research as, say, humans and mice), this can be problematic. So, instead, we can use other genetic information to investigate and suggest patterns and processes related to the formation of new species.
Is reproductive isolation naturally selected for or just a consequence?
A fundamental aspect of studies of speciation is a “chicken or the egg”-type paradigm: does natural selection directly select for rapid reproductive isolation, preventing interbreeding; or as a secondary consequence of general adaptive differences, over a long history of evolution? This might be a confusing distinction, so we’ll dive into it a little more.
The reproductive incompatibility of two populations (thus making them species) is often intrinsically linked to the genetic make-up of those two species. Some conflicts in the genetics of Population 1 and Population 2 may mean that a hybrid having half Population 1 genes and half Population 2 genes will have serious fitness problems (such as sterility or developmental problems). Dramatic genetic differences, particularly a difference in the number of chromosomes between the two sources, is a significant component of reproductive isolation and is usually to blame for sterile hybrids such as ligers, zorse and mules.
We can study the process of speciation in the natural world without focussing on the ‘reproductive isolation’ element of species identity as well. For many species, we are unlikely to have the detail (such as an annotated genome and known functions of genes related to reproduction) required to study speciation at this level in any case. Instead, we might choose to focus on the different factors that are currently influencing the process of speciation, such as how the environmental, demographic or adaptive contexts of populations plays a role in the formation of new species. Many of these questions fall within the domain of phylogeography; particularly, how the historical environment has shaped the diversity of populations and species today.
Although these can help answer some questions related to speciation, new tools are constantly needed to provide a clearer picture of the process. Understanding how and why new species are formed is a critical aspect of understanding the world’s biodiversity. How can we predict if a population will speciate at some point? What environmental factors are most important for driving the formation of new species? How stable are species identities, really? These questions (and many more) remain elusive for a wide variety of life on Earth.