Evolution: Is It Always Genetic?

Biologists have always maintained that evolution happens strictly and solely inside the genome. Find out how scientists looking at a variety of yeast have challenged the orthodox view.

I remember my biology teacher, Mr. Pollard, telling us about an experiment where researchers cut off the tails of mice. Of course, descendants of those mice came into the world sporting long, healthy tails.

He followed up the story with one of his many endearing if groan-worthy puns. This one conflated changing genes with changing jeans in some way. I forget the details of the joke now.

His point was that evolution by natural selection is genetic. Mr. Pollard taught us that human evolution comes strictly and solely from our DNA and not from other biological or environmental influences.


That’s what everyone thought back then. Over the years though, new discoveries have emerged from molecular biology.

For instance, they’ve found that other chemical compounds exist that trigger gene expression (turn genes on or off) when they interact with DNA. These compounds are called epigenetic (outside the genes). Eva Jablonka and Marion J. Lamb discuss the distinction between genetics and epigenetics in their book Evolution In Four Dimensions: Genetic, Epigenetic, Behavioral, And Symbolic Variation In The History Of Life.

The set of epigenetic compounds added to a genome are its epigenome. Epigenetic effects don’t last over the long run so traditionally they’ve never taken a place in the theory of evolution.


One type of epigenetic modification is called methylation. The methyl groups are chemical compounds formed from tiny molecules with one carbon and three hydrogen atoms.

When a methyl group attaches to a DNA segment, the gene in that segment turns off. Once it’s off, it stops producing proteins.

Turning off gene activity is usually a good thing. We don’t want to trigger the gene for hair growth in muscle cell types for instance.


On the other hand, if a methyl group changes the wrong human genome activity by mistake, it can cause a genetic disease. This can include cancers and degenerative disorders among other things.

Last month, researchers from UC San Francisco released conclusive proof that descent with modification can be epigenetic. That means evolutionary theory may be about to change.

The team looked at a kind of yeast called Cryptococcus neoformans. It causes human disease in people with weak immune systems.


In fact, it’s responsible for about 20% of HIV/AIDS-related deaths. It contains what biochemists call epigenetic marks for the methylation process we just described.

The DNA in this toxic yeast is regulated by methylation. What makes this study noteworthy is that the methylation mark for this species of yeast should have died out at the time of the dinosaurs.

Two enzymes regulated methylation in the prehistoric ancestor of this yeast species. The de novo enzyme added the methylation marks to the DNA while the maintenance enzyme made copies.


What’s puzzling is that this yeast species started to lose its de novo enzyme somewhere between 50 and 150 million years ago. Despite this, its methylation kept going and we can still see it happening today.

Professor Hiten Madhani is the senior author of the study. He described the puzzling finding this way, “We didn’t understand how methylation could still be in place since the Cretaceous period without a de novo enzyme.” 

Without the de novo enzyme, DNA methylation should have gradually died out in this species of yeast within about a century. Professor Madhani explained, “Natural selection is maintaining methylation at much higher levels than would be expected from a neutral process of random gains and losses.”


The answer to this methylation puzzle seems to have to do with jumping genes. Jumping genes are DNA segments that leap out of their assigned seat in the genome and then butt in somewhere else in the sequence.

If the jumping gene ends up in a vital spot, it can stop an essential gene function, killing the cell. It appears that methylation keeps jumping genes in their place.

That’s a huge, natural incentive for an organism to try to keep methylation going. Some sort of natural selection process seems to have rewarded those yeast cells that somehow managed to keep adding methyl groups to their DNA without the missing enzyme.


As Professor Madhani put it, “This is the epigenetic equivalent of Darwinian evolution.” 

That’s what makes this discovery noteworthy. Professor Madhani explained, “Previously, there was no evidence of this kind of selection happening over these time scales. This is an entirely novel concept,” 

Evolution through natural selection is much more than a theory. As the National Academy of Sciences puts it, “The past and continuing occurrence of evolution is a scientific fact.”


This is the new story that we can tell each other about why there are so many living things. It’s especially vital to tell this story to our kids.

As Charles Darwin put it, “There is grandeur in this view of life.” Even something as mundane as a nasty kind of yeast can show us this grandeur if we search for it with an open mind.

The National Academy of Sciences went on to say “Scientists no longer question whether biological evolution has occurred and is continuing to occur. Instead, they investigate the mechanisms of evolution, how rapidly evolution can take place, and related questions.”

“Is this happening AND IF SO, how do we find it?”

That’s what Professor Madhani’s team and biologists around the world continue to do. He concluded by saying, “Now the big question is ‘Is this happening outside of this exceptional circumstance, and if so, how do we find it?’

We always have more to learn if we dare to know.

Learn More:
UC San Francisco
Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase
Evolution In Four Dimensions: Genetic, Epigenetic, Behavioral, And Symbolic Variation In The History Of Life
Origin of Life Before Origin of Species – 4 Theories
Life Began Even Earlier Than Thought
Did Life Begin in Soda Lakes?
Meteorites Brought Space Sugar to Earth


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