evolutionary history

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

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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).

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

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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.

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Incomplete lineage sorting through Pachinko – a visual analogy

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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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Evolutionary clocks out of sync

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Evolutionary time

It shouldn’t come as a surprise to anyone with a basic understanding of evolution that it is a temporal (and also spatial concept). Time is a fundamental aspect of the process of evolution by natural selection, and without it evolution wouldn’t exist. But time is also a fickle thing, and although it remains constant (let’s not delve into that issue here) not all things experience it in the same way.

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Genes in parallel

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Adaptation from genetic variation

One of the central themes of this blog, and indeed of evolutionary biology as a whole, is the notion that adaptation is often underpinned by genes. Genetic variation acts as the basis for natural selection to favour or disfavour traits: while this is directly through phenotypic traits (e.g. fur colour, morphology, behaviour), these traits are typically determined by a genetic component. In the early stages of adaptation, evolution can often be observed by changes in the frequency of genetic variants (alleles) within a species or population over time as natural selection acts, gradually leading to the observable (and sometimes dramatic) change in species over time.

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