A genetic model for puntuated equilibria

Using a combination of developmental genes and transposable elements to explain patterns in the fossil record.

The evolutionary biologist Stephen Jay Gould is one of my personal heroes. He has written wonderful essays about evolution and the history of science. And he was not afraid to challenge the scientific status-quo with radical new ideas. I think every evolutionary biologist should read “The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme” (with Richard Lewontin) and “Punctuated equilibria: an alternative to phyletic gradualism” (with Niles Eldredge).

In this blog post, I will focus on the theory of punctuated equilibria, which tries to explain the patterns we see in the fossil record. Darwin’s theory of evolution focused on gradualism, the slow change of species over time. But this gradual change was not apparent in the fossil record, instead new species seem to suddenly pop into existence (from a paleontological perspective). This mismatch between Darwin’s gradualism and the sudden appearance of new fossil species was attributed to the incompleteness of the fossil record. Gould and Eldredge challenged this explanation and argued that the pattern in the fossils reflects reality. For most of evolutionary time, species do not change much (so-called stasis), but during speciation events organisms change quickly and drastically. Hence, the stable stasis (equilibrium) is occasionally punctuated by rapid speciation events and big morphological changes.


The model of punctuated equilibria versus gradualism. From: Wikipedia


Developmental Regulatory Genes

Since the publication of this model in 1972, numerous studies have confirmed patterns of punctuated equilibria (although some fossil series are still better explained by gradualism). However, one main weakness of punctuated equilibria is the absence of a genetic mechanism. Recently, Emily Casanova and Miriam Konkel proposed a genetic model in the journal BioEssays.

Their idea – dubbed the Developmental Gene Hypothesis – focuses on conserved non-coding elements (CNEs) in the genomes of organisms. These DNA-sequences are shared between distantly related species and often play a role in gene regulation. Specifically, the CNEs that contribute to embryonic development, the developmental regulatory genes (DevReg), might be key to explaining punctuated equilibria. These genes are under strong stabilizing selection (a wrong mutation mostly leads to an unviable embryo) and they can thus account for the morphological stasis we observe in the fossil record.


Transposable Elements

What about the punctuations? Here, transposable elements (TEs) come into the picture. These genetic parasites can jump around the genome through a cut-and-paste or copy-and-paste mechanism. Mostly they wreak havoc in the genome, but occasionally they end up in the right location and invoke a significant change in the organism. If they jump into or close to a developmental regulatory gene, TEs can lead to important morphological changes by altering developmental pathways. The result is rapid evolutionary change: a punctuation.

In their paper, Casanova and Konkel give the example of live birth (vivipary). TEs have played an important role in the evolution of mammalian pregnancy. The gene syncytin – which contributes to the formation of the placenta – can be traced back to a retrovirus. Interestingly, the Mabuya lizard, which is also viviparous, has a mammal-like placenta that expresses a retrovirus-derived gene similar to syncytin. And the fossil record harbors evidence of marine reptiles (the ichthyosaurs) giving birth to live young. Could this also be mediated by TEs?


A fossil of an ichthyosaur giving birth. From: Casanova & Konkel (2019) BioEssays



What does this model have to do with hybridization (the main topic of this website). At first sight, not much. I just thought this paper was really cool and decided to cover it. However, there is a link with hybrdization (which the authors don’t mention). It has been shown that hybridization leads to genome instability and the activation of silenced TEs. Hence, hybridization is another mechanism that can lead to rapid evolutionary change. Perhaps some of the punctuated patterns in the fossil record can be explained by massive hybridization events?



Casanova, E. L., & Konkel, M. K. (2019). The Developmental Gene Hypothesis for Punctuated Equilibrium: Combined Roles of Developmental Regulatory Genes and Transposable Elements. BioEssays, 1900173.

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