The Developmental Gene Hypothesis: Genetics Behind Punctuated Equilibrium?

Most of you probably know that I blog primarily about autism and Ehlers-Danlos syndrome (EDS). But as the header on Science Over a Cuppa hints, I have a secret– shall we say “fetish”?– for paleontology and evolutionary biology. After all, what are autism and EDS but side branches of the larger biological questions that ground humanity in the natural world?

Well, I’ve gone and done it. Rather than remaining satisfied with my lot as an armchair hobby paleontologist, forever jealously drooling over images of dusty postdocs and PIs digging at fossils in places like the remote arid hills of Utah or South Africa, I’ve thrown my metaphorical hat into the ring and done a little digging…

… through the genome.

This month, I published an article in BioEssays with my good friend, collaborator, and resident transposon-expert, Dr. Miriam Konkel, titled “The Developmental Gene Hypothesis for Punctuated Equilibrium.”

I’m obviously very excited about this article in part because it’s allowed me to study evolutionary biology without getting dusty and probably developing neuropathy (thank you, connective tissue disorder!). But I am also genuinely excited to potentially lend support to Edgredge and Gould’s “Punctuated Equilibrium,” a theory that has been dogged by controversy although ultimately accepted.

For those who don’t know what Punctuated Equilibrium (PE) is and are too tired to click the Wikipedia link above, this theory states that physical changes across species within the fossil record often occur in spurts and sputters but are typically bookended by long periods of relative stasis or “equilibrium.” (This isn’t always the case but generally holds true.)

This is in stark contrast to what Darwin believed we would find, that there would be a gradual but constant rate of change across species. And in fact, this assumption was held throughout most of the 20th century. Truth be told, I don’t think even Eldredge and Gould expected to find what they did. Most scientists simply assumed the punctuated appearance within the fossil record was due to missing links, not to abrupt changes across species.

Eldredge and Gould first published their theory back in the early 1970s. But one of the major criticisms was that it lacked a mechanistic or genetic underpinning. Thankfully, since the ’70s, we’ve learned a lot about genetics both at the organismal and species levels, and we continue to learn more every day.

Our new article, however, offers a more comprehensive explanation of the patterns we see in the fossil record. Specifically, while theories concerning punctuated patterns of transposable element insertion and instability have been published before, our new hypothesis posits that developmental genes in particular are responsible for the long periods of stasis that we typically see.


Many developmental genes are ancient and highly conserved little buggers. They don’t like mutations and most of the time when a mutation does occur in or near a developmental gene, that’s it, the end, organism bye-bye. In other words, most of the time these mutations are not compatible with life.


… when they do occur and don’t happen to wipe out all life as we know it, they are capable of influencing physical form. Do you see where I’m going here? The changes we see in the fossil record are a reflection of the PHYSICAL manifestion of animals. A fossil can’t generally tell us what an organism’s hemoglobin or ribosomal RNA was like, but if there’s a physical change across closely related species you can bet it involved changes to some developmental genes.

The phylotypic period of development. Many of the developmental genes expressed during this period are highly conserved across distantly related species.

Compared to developmental genes, which evolve very very slowly, other genes evolve at a faster rate, in part because they interact with simpler networks of other genes and are therefore less sensitive to change. Developmental genes, on the other hand, often maintain extremely complex interaction networks and can be foundational to the construction of organ systems. This network conservation is likely the reason that animal embryos at middle stages of development (aka the “phylotypic period”) tend to look rather similar despite that they may not have shared a common ancestor for hundreds of millions of years.

So, those are the bare bones of our hypothesis. And I look forward to see what the biology community makes of it!

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