Building Blueprints – How to assemble a genome

The utility of a reference genome

In the 18 years since the completion of the Human Genome Project, the practicality of assembling full genomes for a wide range of taxa beyond ourselves has only improved. While model taxa systems have achieved genomes before many others, it is now possible for whole genomes to be assembled for a range of non-model organisms as well. But how do we assemble the genome of a species for the very first time (often de novo – literally “from the new”)? What can we do with this genome? Why is it so useful? Let’s delve into the process and outcomes of genome assembly a little more.

Continue reading

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

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

Piñataversity – a biodiversity assessment of Viva Piñata

Revisiting Piñata Island

Every now and then, my gaming habits tend to take a bit of a wander down memory lane. Of late, that means cracking out one of my classic faves – the life simulation and “collectathon” Viva Piñata by Rare. Originally released in 2006, with successor (expanded version, essentially) Viva Piñata: Trouble in Paradise released in 2008, the game essentially involves creating a lavish garden to attract wild piñata-like animals. Although a little light on plot, the main goal is to entice these wild creatures (Wilds) to stay in your garden (becoming Residents), to later be sent off to parties across the globe. Trouble in Paradise boasts a roster of 88 different species of Piñatas to collect, as well as a variety of fruiting trees, plants, and flowers to grow.

Continue reading

A simplified guide to genomic vulnerability

Predicting the future for biodiversity

Conservation biology is frequently referred to as a “crisis discipline“, a status which doesn’t appear to be changing any time soon. Like any response to a crisis, biologists of all walks of life operate under a prioritisation scheme – how can our finite resources be best utilised to save as much biodiversity as possible? This approach requires some knowledge of both current vulnerability and future threat – we need to focus our efforts on those populations and species which are most at-risk of extinction in the near (often immediate) future.

Continue reading

Incomplete lineage sorting through Pachinko – a visual analogy

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