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Evolution can seem deceptively simple. Survival of the fittest is an easy to remember, but misses mountains of nuance. Add a pandemic to the mix, and we’re sure to get things wrong.
Let’s see why understanding evolving pathogens can be tricky: https://infectiousmatter.com/evolution/
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Let’s see why understanding evolving pathogens can be tricky: https://infectiousmatter.com/evolution/
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In this simulation, we focus on Neutral mutations. That is, random changes in the genome of a pathogen that don’t affect fitness.
Every time a pathogen mutates, we’ll change its color a random amount. That’s it. Nothing else about the pathogen will be different.
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![In this simulation, we focus on Neutral mutations. That is, random changes in the genome of a pathogen that don’t affect fitness. Every time a pathogen mutates, we’ll change its color a random amount. That’s it. Nothing else about the pathogen will be different. [2/n]](https://pbs.twimg.com/media/EZBsc9hXkAY3dk4.png "In this simulation, we focus on Neutral mutations. That is, random changes in the genome of a pathogen that don’t affect fitness. Every time a pathogen mutates, we’ll change its color a random amount. That’s it. Nothing else about the pathogen will be different. [2/n]")
Every time a pathogen mutates, we’ll change its color a random amount. That’s it. Nothing else about the pathogen will be different.
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You can watch as a pathogen mutates and spreads across the (small) world! Like last time, you can experiment with different amounts of local/global movement.
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It would be nice to see the relationships between pathogen genotypes as they spread. To visualize these, we'll add a phylogenetic network to the simulation.
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A Phylogenetic Network depicts each pathogen genotype as a node, and the edges indicate the genetic relationship between pathogens. As new mutations spread, differently colored pathogen hubs form.
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![A Phylogenetic Network depicts each pathogen genotype as a node, and the edges indicate the genetic relationship between pathogens. As new mutations spread, differently colored pathogen hubs form.[5/n]](https://pbs.twimg.com/media/EZBtN-GXsAAB13z.jpg "A Phylogenetic Network depicts each pathogen genotype as a node, and the edges indicate the genetic relationship between pathogens. As new mutations spread, differently colored pathogen hubs form.[5/n]")
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Here's one, because they're fun to watch!
Sometimes you might see a pretty dramatic shift in color, like the pink in this video.
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Sometimes you might see a pretty dramatic shift in color, like the pink in this video.
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Now imagine if you were analyzing this phylogenetic network without knowing that every mutation was neutral. You'd probably think the pink-colored pathogen was spreading because it is more fit!
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We have the luxury of already knowing they're neutral. But if we didn't, we could use evolutionary models (like this one) to help us calibrate our expectations!
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See this great article by @jeremydraghi and @big_data_kane for more about why models are important for understanding evolution!
https://undark.org/2020/05/14/covid-19-evolution-mutation/
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https://undark.org/2020/05/14/covid-19-evolution-mutation/
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You might have seen the article about a new and more contagious strain of SARS-CoV-2 that was spreading. Hopefully you also heard that it probably isn't true.
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The science wasn't poorly done or intentionally misleading. But, it was reported on before being properly vetted (e.g., peer review).
Being wrong is a normal part of the scientific process, especially when the situation is constantly changing.
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Being wrong is a normal part of the scientific process, especially when the situation is constantly changing.
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But science and science reporting looks a bit different these days... This article by @edyong209 captures the story more elegantly than I could.
https://www.theatlantic.com/health/archive/2020/05/coronavirus-strains-transmissible/611239/
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https://www.theatlantic.com/health/archive/2020/05/coronavirus-strains-transmissible/611239/
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Neutral mutations spreading during a pandemic can look a lot like a more fit strain is spreading.
Evolution can be tricky like that.
Hopefully you got to see that first hand in your browser!
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Evolution can be tricky like that.
Hopefully you got to see that first hand in your browser!
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Shout out to @BrianRWasik for being a great colleague willing to shout at the media, and @trvrb for doing amazing work tracking pathogen evolution in real time for all of us to see!
