thegcatblog

Incomplete lineage sorting through Pachinko – a visual analogy

March 1, 2021March 2, 2021thegcatblogLeave a comment

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.

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Dr. G-CAT

December 30, 2020thegcatblog7 Comments

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)!

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Sweeping under the genomic rug: hard and soft sweeps

September 10, 2020thegcatblog1 Comment

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 G-CAT in 2020

January 9, 2020thegcatblog1 Comment

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!