Phylogenetics

Species diversity on PNF-404: a biodiversity assessment of the Pikmin series

thegcatblogLeave a comment

The Pikmin series

Like many “Nerds by Profession” (scientists), much of my love for evolutionary biology as a young kid was fostered by an amazing diversity of creatures, both real and fictional. A formative influence in the latter category for me was through gaming – while I hold love for many great gaming franchises, the Nintendo series Pikmin holds a special place in my heart. The series of puzzle-cross-strategy games primarily following the misadventures of diminutive space explorer Captain Olimar, who crash lands on what is heavily implied (and later confirmed) to be a post-human Earth (or PNF-404, as it’s known). There, he is greeted by a strange plant-like species called Pikmin, who assist him in repairing his ship or collecting treasure (depending on the game). The Pikmin games require a certain degree of strategy, planning and time-efficiency in order to complete the necessary tasks within the limited timeframe of the game (or individual day).

Continue reading →

A tale of two fishes: how standing genetic diversity influences species responses to environmental change

thegcatblogLeave a comment

How can species respond to environmental change?

If you’re a somewhat avid (or even cursory) reader of The G-CAT, you may remember my wrap-up post at the conclusion of my PhD in 2020 which described the various chapters of my thesis. Well, I’m pleased to announce that data chapter 2 of that thesis – on the comparative phylogeography of two threatened Australian freshwater fishes – has just been published in the journal BMC Ecology and Evolution. It’s a pretty complex paper which tackles genetic diversity, phylogenetics, demographic history, species distribution models and how these interact together to understand the evolutionary history of these species in a comparative framework. Feel free to check it out (it’s open access and free to read!) here.

Continue reading →

Shifting lakes, coastlines and mountains: how millions of years of environmental changes shaped the evolution of a little fish

thegcatblog1 Comment

The roles of aridification and sea level changes in the diversification and persistence of freshwater fish lineages

The process of publishing science is a lengthy one – there are many rounds of revisions, assessments, and review required before a paper can be published. With that, I’m very proud to announce that the first paper from my PhD has recently been published in the journal Molecular Ecology. This paper is a collection of a lot of complex analyses, and addressing some relatively complicated biogeographical questions, so I’ve decided to provide a simplified summary here.

Continue reading →

Incomplete lineage sorting through Pachinko – a visual analogy

thegcatblogLeave 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.

Continue reading →

Dr. G-CAT

thegcatblog7 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)!

Continue reading →