Natural selection is purifying the human genome

Researchers have developed a new method for studying evolution in humans. It reveals that natural selection has been purifying our genome


It’s easy to think that evolution doesn’t really influence humans anymore. After all, natural selection is all about “survival of the fittest”. The biggest threat to my survival these days is forgetting to look up from my phone as I cross the street. We appear to have insulated ourselves from the natural world quite well.

But appearances can be deceiving. Evolutionary ones, doubly so. Scientists have repeatedly found the telltale signs of natural selection in our genome and family tree. Our skin, nose, hands, and more all seem to have been evolving recently. However, all of this talk about ongoing evolution is missing out a key component. Yes, natural selection can shape new traits. But it also plays a key role in preserving them too.

“Purifying selection” refers to when evolution removes harmful mutations, keeping our genome running along nicely.  This purification is arguably just as important as any other part of evolution. And – like those other parts – it still seems to be influencing us.

Spotting natural selection

The first step in figuring out how humans are still evolving is to find whereabouts in our genome natural selection has had influence. Spotting this is easy enough given the fairly obvious fact that not all humans are the same.

Much of this variation stems from alleles, which is the fancy scientific way of saying “gene variants”. Most genes come in a few different flavours, producing the variation we know and love in our species. You may well have studied some of these and how they interact (i.e. with some alleles being dominant) at school; although they often oversimplify it a bit. Eye colour, for example, is influenced by more than one gene (and its resulting alleles). Your teachers lied to you!

How eye colour inheritance actually works

When natural selection acts on an allele it changes its frequency in a population. The result of this is that the number of alleles overall will decrease, as one rises to prominence (because it is a beneficial mutation) or be stricken from the genome (because it is a deleterious mutation). Thus, studying natural selection is a simple case of figuring out which parts of our genome are “missing” variation.

Of course, those of you who are smart might have spotted a problem (and you’re all smart because you had the intelligence to decide to read this blog). Many different types of selection have the same effect: decrease variation. So how to tell them apart?

A shiny new method

That’s what makes a new study special. The researchers figured out a new way to disentangle the different kinds of evolution. The gist is surprisingly simple: if evolution is ongoing variation changes over generations. That’s entire synopsis of evolution. Natural selection leads to different allele frequencies over time. So younger people should have a different level of variation than their older counterparts for evolving genes.

How variation of alleles should change in different ages under different forms of selection.

The researchers could use this combined with the survival rate of these individuals to figure out the type of evolution happening. If you see variation decreasing in a gene correlated with a high mortality rate, that would be a likely indicator of some purifying evolution. The high mortality variant is being gradually purged from the genome until only less harmful ones remain.

The beauty of this approach is that it can be applied to any dataset that features people with different ages. Evolution takes a long time in humans since we have a long generation time. In the past scientists have gotten around this problem by looking for long datasets. For instance, some church records go back centuries, allowing variation over time to be studied.

But thanks to this method that sort of data isn’t needed. Just a big pool of people whose age varied. And the people who developed this method had such a pool in the form of the UK BioBank. Thanks to this they could examine variation in more than 8 million alleles across almost 60,000 people.

What’s being purified?

As I gave away in the opening, the results of this study revealed that there was a fairly high amount of purifying selection in modern humans.

Specifically, genes linked to high cholesterol levels, risk of coronary artery disease, body mass index, and asthma seemed to be showing signs of purifying selection. Extrapolating this onwards would suggest that over time these risk factors will be going down in humans. However, there were some major differences between the sexes. CHRNA 3 is linked to smoking risk and Alzheimers, but seems to only be a mortality risk in males. The fact that this would thus only be under natural selection half the time might slow the down the rate at which its purged.

Of course, these differences might not be innately tied to the sexes but rather a result of the different environments they’re exposed to. In the population used in this study, for example, smoking was just more common in males. This might explain why its more of a big deal, evolutionary speaking, in males.

Or maybe not. But that’s the beauty of this study. It pioneers a new method that can be used to investigate more datasets, shedding light on these sorts of mysteries. Plus, it’s also uncovering some new ones, so it will keep the researchers in a job at least.

References

Courtiol, A., Pettay, J., Jokela, M., Rotkirch, A., & Lummaa, V. (2012). Natural and sexual selection in a monogamous historical human population Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1118174109

Mostafavi, H., Berisa, T., Day, F., Perry, J., Przeworski, M. and Pickrell, J.K., 2017. Identifying genetic variants that affect viability in large cohorts. bioRxiv, p.085969.

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