Epigenetics and evolution

| October 16, 2023

I’m assuming that because you are reading this you are interested in evolution and that you most likely have a well-informed view of what evolution is about.

Nevertheless, I think it important that I tell you my account of evolution, just in case we have different things in our heads and get off to a bad start.

All living things appear to have a common ancestor that emerged from the primeval slime about 3.8 billion years ago.

There are lots of different ways to think about evolution—it’s a vast subject with strong specialisations whose practitioners don’t talk to each other that much. This means that while almost every biologist sees the living world through the lens of evolution, they can have different perspectives about it.

A palaeontologist who unearths fossils of Cambrian trilobites for a living has a very different job from a behavioural ecologist who spends their days trying to understand the conflicts and alliances in an extended mongoose family.

Both would correctly claim to be evolutionary biologists, but they have different skill sets and ways of writing and thinking.

It’s therefore entirely possible that my concept of evolution is a bit different to yours.

All evolutionary biologists recognise that all living things have a common ancestor that lived about 3.8 billion years ago. Living things are not immutable.

Species change over time. Some species go extinct. Some come into existence; evolution drives both diversity and stasis.

The key insight of a single origin of life on this planet has enormous explanatory and predictive power.

For instance, a medical researcher can do experiments on rats, say, safe in the knowledge that the outcomes will have some relevance for human beings because our two species are genetically close (the last common ancestor was about 80 million years ago).

A major factor in determining whether a gene will be transcribed is whether transcription factors – proteins that facilitate the binding of RNA polymerase near a gene – can access the DNA strands within the chromosome.

If a closer model to humans is needed, it might be better to use macaques (last common ancestor 25 million years ago).

But for a basic understanding of human gene expression, yeast (separated from us by a billion years of evolution) provides a great model that is easy to grow and manipulate and is unlikely to bring us into contact with an ethics committee.

Many processes that contribute to evolutionary change result from some kind of genomic upheaval, rather than being the immediate result of natural selection on existing variation.

The duplication of a developmental or sex-determining gene, or a successful hybridisation event between species, are examples of what I mean by a genomic upheaval. Such an event can potentially initiate a period of rapid change and biological innovation.

Further, it is increasingly clear that there are mechanisms that generate genomic upheaval.

These mechanisms go far beyond the regular rearrangement and exchange of genetic material between parents that follow from sex and fertilisation. They include cellular processes that actively move bits of the genome around and generate new genes.

The mechanisms are not ’designed’ to cause evolutionary change, even though they can do so. Rather, they are a consequence of the fact that genomes are typically infested with transposable elements.

During chromosome replication the histone protein is replicated along with DNA in a synchronous process. This is one way that epigenetic information can be transferred between cell divisions.

These ancient genomic sequences are actively suppressed in cells, but when they are accidentally released they cause havoc, inserting themselves in existing genes rendering them silent, moving bits of DNA around, or duplicating whole chromosomal regions

Epigenetics is the study of changes in phenotype (physical form) arising from changes in gene expression rather than changes in DNA sequence.

Epigenetic processes are central to the development of complex organisms because they cause particular genes to be turned on and off in particular tissues. These processes are inherited across cell divisions and are difficult to reverse.

So, for example, liver cells give rise to new liver cells and not to neurones.

There are three major epigenetic mechanisms: the methylation of DNA, the acetylation and methylation of histone proteins (the proteins that DNA is wrapped around) and the transfer of small regulatory RNAs across cell divisions and across cells. All three mechanisms regulate gene expression.

Mostly, epigenetic information is stripped out during early embryogenesis (the formation and development of an embryo) and is re-established as the embryo develops.

This makes sense because the cells of the early embryo need to have complete totipotency so that they can develop into any cell type.

But we are now learning that all three known epigenetic mechanisms can be transferred between generations. When they do, they can transfer heritable information from parent to offspring that is not dependent on DNA sequence.

New ways of thinking about epigenetics are changing our understanding of evolution – the subject of this book.

This article was published by Pursuit and is an edited extract of Emeritus Professor Benjamin Oldroyd’s new book, Beyond DNA: How Epigenetics is Transforming our Understanding of Evolution.