Reconstructing evolutionary history
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.
Overview of 2020
As you may have gathered, The G-CAT has been significantly less active in this our most Cursed year. There are a number of reasons for that – not just the overall disaster that has been world events – including the fact that this was the last year of my PhD. I’m delighted to announce that now, after ~3.5 years of hard work, I am officially Dr. Buckley (not Dr. G-CAT, as I may have led you to believe)!
Of alleles and selection
If you’ve read this blog more than once before, you’re probably sick of hearing about how genetic variation underlies adaptation. It’s probably the most central theme of this blog, and similarly one of the biggest components of contemporary biology. We’ve talked about different types of selection; different types of genes; different ways genes and selection can interact. And believe it or not, there’s still heaps to talk about! Continue reading
The new year and decade
It’s been a few minutes (okay, several weeks) since the last post here on The G-CAT. Naturally, over that time I’ve spent holidays with both my own family and my partner’s family. Hopefully, you’ve enjoyed your own Christmas/New Year/Other-Non-Denominational-Celebrations break (and for us Aussies, that you’ve managed to avoid much of the devastation of the recent bushfire epidemic).
Because of this period of time (and a few other more pressing deadlines I had for the start of the new year), I haven’t prepared a new post in some time. However, I’d like to take this time to address how the nature of this blog might change of the next year or so (and into the future).
A new schedule
For those of you who keep more up-to-date with my academic progress, you’ll be aware that this year is the final year of my PhD. As it stands, I’m due to submit my thesis in August of this year (which feels much, much sooner than it really is). Similarly, for anyone who has ever interacted with a PhD student in the final year of their studies, you’ll also be aware that this can be a time of high stress, stacking deadlines and the overall impending doom of D-Day (thesis submission).
In light of all of this, I have decided to move away from the more predictable fortnightly post routine in favour of a more organic timetable. This will likely mean a fairly significant reduction in the frequency of blog posts, whereby I will post as a topic comes into my mind or when it appears relevant to other parts of my studies (e.g. in reading for writing manuscripts, etc.). This decision has also been playing on my mind for some time to also balance the quality of the posts I write: in some circumstances, I feel like the consistent deadline of once per fortnight causes some posts to suffer a little as I rush to produce something at least in the vicinity of every second Wednesday.
The future of The G-CAT
It is not my intention to completely abandon this project: The G-CAT is something that I have invested a fair time and inspiration into and provides a solid avenue for science communication. As always, my inbox (on whichever platform you choose) is wide open for suggestions on topics of discussion. I’m looking forward to a more organic schedule that will allow me to properly explore and expand on the topics of interest whilst maintaining a healthy balance of PhD progression and down-time.
Here’s to 2020!
The nature of phylogeography
Studying the interaction of environmental changes and species evolution is a critical component for predicting how species might – or might not – respond to new environmental stressors induced by climate change. We can study this at a variety of different levels and using many different data types, ranging from ‘traditional’ ecological studies which correlate phenotypic changes and environment to more narrower studies of ecological genetics and how allelic frequencies change in association with environmental gradients.
In the previous post on The G-CAT, we talked about the role of maladaptation in the evolution of populations and species, and how this might impact their future. To summarise, maladaptation is the process (or trait responsible for) which causes a reduction in the fitness. As we discussed, this can come about a number of ways – such as from a shift in the selective environment or from fitness trade-offs in traits over time – and predominantly impacts on species by reducing their capacity to adapt. Particularly, this is important for small populations or those lacking in genetic diversity, which are already at risk of entering an extinction vortex and lack the capability to respond well to extreme selective changes (such as contemporary climate change).
Adaptation and natural selection
Adaptation via natural selection is one of the most fundamental components of understanding evolution. It describes how species can continually evolve new, innovative traits and produce the wondrous diversity of the natural world. This process is inevitably underpinned by particular heritable traits often linked to particular genetic variants (alleles). Remember that the underlying genetic trait (the allele) is referred to as the genotype; the physical outcomes of that allele (i.e. how it changes the physiological, behaviour or ecology of the organism) is the phenotype; and the scale of the benefit of possessing that trait is referred to as its fitness. Under the normal process of natural selection, phenotypes which increase fitness are selected for, which results in a shift in genotypes underpinning it.
The fundamentals of population genetics
Many times in the past, we’ve discussed the importance of genetic diversity within populations as a foundation for adaptation and evolution. It includes both adaptive variation (which encompasses genetic variation directly under natural selection), as well as neutral variation (which is predominantly generated and maintained by non-selective forces such as demographic history and genetic drift). This pool of genetic variation acts as the underlying architecture for evolution by natural selection, and is a critically important component for future and ongoing evolution.
This all sounds important from an academic perspective: that population genetics can reveal a significant amount of information about the processes and outcomes of evolution and provide novel insights into concepts that have been around for ages. But how can this information be applied to real scenarios? With the ever-growing availability of massive genetic datasets for an increasing number of species, the sheer volume of information in existence that can be used is monumental.
Beyond mutations in the genome
Although genetic variation is, in itself, often considered to be one of the fundamental underpinnings of adaptation by natural selection, it can appear through a number of different forms. Typically, we think of genetic variation in terms of individual mutations at a single site (referred to as ‘single nucleotide polymorphisms’, or SNPs), which may vary in frequency across a population or species in response to selective pressures. However, we’ve also discussed some other types of genetic-related variation within The G-CAT before, such as differential gene expression or epigenetic markers.
The Australian aquascape
To anyone who has lived within Australia for a given period time, and likely many from across the globe, it is clear that water is a precious resource. Rainfall across much of the continent is patchy and variable, and the availability of water is a critical aspect in the distribution, survival and evolution of many Australian species. Expectedly, these aspects play an even bigger role for those taxonomic groups that heavily rely on the presence of water; freshwater-dependent taxa such as fish, amphibians or aquatic invertebrates show a keen evolutionary relationship with water across the landscape.