Experimental Evolution: Failure to progress

Experiments on yeast cells that are hosts to a killer virus confirm that natural selection can sometimes reduce fitness.
  1. Duncan Greig  Is a corresponding author
  2. Jasmine Ono
  1. Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, United Kingdom

It is hard to ignore the sense that life has purpose. This idea – known as teleology – is central to religious thinking. However, it is also found in many areas of human culture and scholarship that one might expect to be free from divine influence. These other areas include, somewhat surprisingly, the study of evolution. Look at the March of Progress, for example: in this infamous illustration a knuckle-dragging beast gradually evolves to become an erect intelligent human. Experts agree that this widely parodied image gives the wrong impression, but the feeling that evolution is progressive persists.

Perhaps the problem is the word itself. To evolve originally meant to unroll, implying the roll-out of a predetermined form (Bowler, 1975). Scientists used it to describe the embryonic development of an individual, back when it was thought that every human grew from a homunculus, a complete miniature person contained within sperm, just waiting to 'evolve' (Horder, 2010). By the mid-19th century 'evolution' had evolved to mean not just the developmental changes that occurred in individuals during their lifetimes, but directional changes observed in species across the geological timescales preserved within the fossil record. Early evolutionists, such as Lamarck, proposed teleologies in which living things are innately driven to progressively evolve more advanced adaptations. But Darwinian natural selection works without these vital forces or supernatural design, and it is notable that Darwin himself rarely used the word evolution in reference to his revolutionary theory.

Evolution, in the modern Darwinian sense, is essentially a random process. Mutations are random, but they are also heritable, so those that happen to improve their own transmission (that is, to increase fitness) will spread, resulting in adaptation. This is natural selection. But there is no direction to the process. Consider eyes, organs so complex that they fool some into thinking they must have been designed by a creator. Yet, having finally evolved this magnificent complexity, eyes will quite readily un-evolve again when their owners move into lightless caves, where vision is a useless and expensive liability.

But does natural selection not imply a particular form of progress, in that fitness itself must always increase? Not necessarily. Now, in eLife, Sean Buskirk, Alecia Rokes and Greg Lang report the results of experiments confirming that natural selection can sometimes result in a reduction of fitness (Buskirk et al., 2020).

The researchers, who are based at Lehigh University, allowed populations of yeast cells to evolve for 1000 generations, freezing live samples at regular intervals to create a ‘fossil record’ from which ancestors and descendants could be defrosted and compared. They found that the most evolved generations (those from the end of the experiment) would leave more offspring than intermediate generations (from the middle of the experiments) when both were mixed and allowed to compete directly: that is, their Darwinian fitness had increased. But when mixed with their original ancestors (from the start of the experiments), they were less fit; the original ancestors left more offspring. Yet, the intermediate generations were fitter than the original ancestors. So, while fitness did in fact increase at each step, it did not add up – together, somehow, two increases made a decrease.

To understand why, we need to know that the ancestor yeast cells were host to a common ‘killer’ virus (Figure 1). The virus encodes both a deadly toxin and resistance to that toxin, so yeast cells containing the virus are immune, but the yeast cells without are not. The virus cannot infect new host cells and is only transmitted through the offspring of its hosts. However, there is no benefit to making a toxin if all your competitors are resistant. So, as the virus populations evolved, the ability to make a worthless toxin was lost. And without the toxin, there was no advantage to having resistance to it so, eventually, resistance was also lost in the most evolved generations of yeast cells.

An example of evolution going round in circles.

Buskirk et al. used yeast cells (thin orange circles) that are infected with a virus producing both a killer toxin (green arrows) and resistance to the toxin (thick blue circles) at the start of the experiment (represented by the 12 o’clock position). As evolution proceeds (black arrow), cells that no longer produce the toxin but are still resistant to it, take over. Eventually, these cells are replaced by cells that have lost their resistance (since resistance now provides no benefit). But when cells from the latest generation are pitted against cells from the original generation (grey arrows), the latter emerge victorious as the toxins they produce kill the former (open orange squiggles). However, cells from the latest generation can outcompete cells from intermediate generations, and cells from intermediate generations can outcompete cells from the original generations.

Thus, when cells from these generations were introduced to cells from the original generations, they succumbed to the viral toxin. Buskirk et al. were able to show that natural selection acting on the host genomes, the viral genomes, or both, drove the entire process, eventually reducing the long-term competitive fitness of the yeast. So, evolutionary changes, including fitness, are not necessarily progressive.

Is this due to having two genomes – viral and nuclear – with intertwined fates? Probably not. Take the game rock-paper-scissors as an illustration. An imaginary population of reproductive rocks might evolve into mutant pieces of paper, which would have higher fitness. But once paper has taken over, it would be replaced by descendants that evolved into scissors. Are scissors fitter than their distant ancestors, the rocks? No.

Such circular interactions – where everyone can beat someone, but everyone can also be beaten by someone else – are common in nature, both between and within species (Soliveres et al., 2018; Sinervo and Lively, 1996). But Buskirk et al. show for the first time that the different players can also replace each other within a single evolutionary lineage. We sometimes feel we are making great progress – in art, architecture, fashion, or even in the unfolding of historical events – only to recognize something from the past coming round again. Evolution seems much the same.

References

    1. Horder T
    (2010)
    Encyclopedia of Life Sciences
    History of developmental biology, Encyclopedia of Life Sciences, Chichester, John Wiley & Sons, Ltd, 10.1002/9780470015902.a0003080.pub2.

Article and author information

Author details

  1. Duncan Greig

    Duncan Greig is in the Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom

    For correspondence
    d.greig@ucl.ac.uk
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8907-0253
  2. Jasmine Ono

    Jasmine Ono is in the Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom

    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3301-0507

Publication history

  1. Version of Record published: February 16, 2021 (version 1)

Copyright

© 2021, Greig and Ono

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,360
    views
  • 97
    downloads
  • 0
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Duncan Greig
  2. Jasmine Ono
(2021)
Experimental Evolution: Failure to progress
eLife 10:e66254.
https://doi.org/10.7554/eLife.66254
  1. Further reading

Further reading

    1. Computational and Systems Biology
    2. Evolutionary Biology
    Kenya Hitomi, Yoichiro Ishii, Bei-Wen Ying
    Research Article

    As the genome encodes the information crucial for cell growth, a sizeable genomic deficiency often causes a significant decrease in growth fitness. Whether and how the decreased growth fitness caused by genome reduction could be compensated by evolution was investigated here. Experimental evolution with an Escherichia coli strain carrying a reduced genome was conducted in multiple lineages for approximately 1000 generations. The growth rate, which largely declined due to genome reduction, was considerably recovered, associated with the improved carrying capacity. Genome mutations accumulated during evolution were significantly varied across the evolutionary lineages and were randomly localized on the reduced genome. Transcriptome reorganization showed a common evolutionary direction and conserved the chromosomal periodicity, regardless of highly diversified gene categories, regulons, and pathways enriched in the differentially expressed genes. Genome mutations and transcriptome reorganization caused by evolution, which were found to be dissimilar to those caused by genome reduction, must have followed divergent mechanisms in individual evolutionary lineages. Gene network reconstruction successfully identified three gene modules functionally differentiated, which were responsible for the evolutionary changes of the reduced genome in growth fitness, genome mutation, and gene expression, respectively. The diversity in evolutionary approaches improved the growth fitness associated with the homeostatic transcriptome architecture as if the evolutionary compensation for genome reduction was like all roads leading to Rome.

    1. Evolutionary Biology
    Case Vincent Miller, Jen A Bright ... Michael Pittman
    Research Article

    Enantiornithines were the dominant birds of the Mesozoic, but understanding of their diet is still tenuous. We introduce new data on the enantiornithine family Bohaiornithidae, famous for their large size and powerfully built teeth and claws. In tandem with previously published data, we comment on the breadth of enantiornithine ecology and potential patterns in which it evolved. Body mass, jaw mechanical advantage, finite element analysis of the jaw, and traditional morphometrics of the claws and skull are compared between bohaiornithids and living birds. We find bohaiornithids to be more ecologically diverse than any other enantiornithine family: Bohaiornis and Parabohaiornis are similar to living plant-eating birds; Longusunguis resembles raptorial carnivores; Zhouornis is similar to both fruit-eating birds and generalist feeders; and Shenqiornis and Sulcavis plausibly ate fish, plants, or a mix of both. We predict the ancestral enantiornithine bird to have been a generalist which ate a wide variety of foods. However, more quantitative data from across the enantiornithine tree is needed to refine this prediction. By the Early Cretaceous, enantiornithine birds had diversified into a variety of ecological niches like crown birds after the K-Pg extinction, adding to the evidence that traits unique to crown birds cannot completely explain their ecological success.