Convergent evolution defeats the "Tape and Tree of Life"


A recent study investigated the evolution of composite gene families in animals. Composite gene families are formed when two or more distinct gene families fuse together to create a new gene. The study found that composite gene families are relatively rare, making up only about 5% of all animal gene families. However, their phylogenetic distribution suggests that they emerged abruptly rather than gradually during animal evolution. The study also found that composite gene families are often found at major nodes in animal phylogeny, suggesting that they may play an important role in animal evolution.

The study also found that composite gene families are frequently reused in different animal lineages. This suggests that the same evolutionary solutions to protein innovation have evolved time and again in animals. This finding challenges the traditional view of evolution as a branching tree, and suggests that evolution is more complex and non-linear than previously thought.

The study's findings have important implications for our understanding of how protein coding genes evolve in animals, the prevalence of convergent evolution, how we construct gene families, and how we annotate function between homologous genes.

Here are some of the key takeaways from the study:

  • Composite gene families are relatively rare, but they play an important role in animal evolution.

  • Composite gene families often emerge abruptly rather than gradually during animal evolution.

  • Composite gene families are frequently reused in different animal lineages.

  • The study's findings challenge the traditional view of evolution as a branching tree.

The study provides a valuable new perspective on the evolution of protein coding genes in animals.


Article snippets:

Bursts of novel composite gene families at major nodes in animal evolution

Here we show that ∼5% of all animal gene families are composite, and their phylogenetic distribution suggests an abrupt, rather than gradual, emergence during animal evolution

we show that new genes formed by fusing distinct homologous gene families together comprise a significant portion of the animal proteome.

Their pattern of emergence through time is not gradual throughout the animal phylogeny - it is intensified on nodes of major transition in animal phylogeny.

we see that evolution replays the tape frequently in these genes.

Using a large representative dataset, we provide a statistically sound framework to elucidate the rate of independent evolution of composite genes in animals

The most recognisable part of evolutionary biology is the Tree of Life with its continually diverging branches emerging from the root. This narrative has hugely influenced how we think about evolutionary history, and it influences what we expect to see when we examine genomes. 

In addition to, and perhaps influenced by, the Tree of Life perspective, there is a feeling that evolution rarely, if ever, repeats itself. This last idea was most forcefully expressed by the palaeontologist Stephen Jay Gould who asked whether the tape of life was replayable  – a question to which Gould answered: No.



Fortunately, with the sequencing of an extensive array of genomes from many taxa across the diversity of animals we can address issues relating to the non-treelike aspects of evolution on one hand, as well as whether genome evolution is contingent on genetic background.

If evolution is contingent on prior evolutionary events, then we expect that with increasingly divergent genetic backgrounds we are less likely to see repeated evolution, while on the other hand if evolution is largely deterministic, then despite differences in genetic backgrounds we expect to see the same evolutionary events occurring in different lineages.

we see that repeatability has happened and it has happened across animal evolution many, many times.

This work has important implications for our understanding of how protein coding genes evolve in animals, the prevalence of convergent evolution, how we construct gene families, and how we annotate function between homologous genes.

https://www.biorxiv.org/content/10.1101/2023.07.10.548381v1


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