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.

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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.

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Sweeping under the genomic rug: hard and soft sweeps

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 Bad and the Ugly of evolution: an introduction to maladaptation

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.

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Scanning for causes: an introduction to genome-wide association studies

Understanding genetic determinants

You’ve probably been exposed to one news headline or another in the recent past (let’s say the last 5 years) that reads something like “SCIENTISTS DISCOVER GENES THAT CAUSE (X).” X, of course, varies massively based on the study itself (and sometimes the bastardisation of said study by media): it can include describing medical conditions such as cancer, autism or congenital diseases; behavioural traits, such as sexual preferences; or broad physical traits, such as the classic problem of the inheritability of height. Unsurprisingly, you may think that trying to find the genes responsible for some traits should be either a) super easy, or b) super hard, depending on your own philosophical preference or the trait in question. So how do these studies come about, anyway?

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