A Blog by Carl Zimmer

Fifty-seven Years of Darkness

In caves around the world, animals and other creatures have adapted to endless night. Cavefish, for example, have lost their eyes and pigment, evolving a greater power in other senses.

In 1954, Syuichi Mori, a biologist at Kyoto University, put flies into a cave of their own. He took eggs from ordinary flies of the species Drosophila melanogaster put them in milk bottles, which he placed in pots and covered in dark cloth. There they lived in utter darkness. He tended to the flies, generation after generation, dividing them into three separate lines. Meanwhile, he reared three lines of flies in normal light for comparison.

Raising flies is not an easy business. They can pick up infections and die in droves. Over the years, all the normal lines of flies died out, as did two of the dark-bred flies. But Mori managed to keep the last line of flies alive in the dark, and after his death, other Kyoto researchers kept the flies going. And today, they are still living in the dark, 57 years since their ancestors last saw light. That’s 1400 generations–which would be some 30,000 years if it were humans living in dark.

Keeping organisms in such weird conditions is one of the most interesting ways to learn about evolution. Scientists create a set of conditions and then allow organisms to grow, breed, and mutate. Mutations that let some individuals survive better and have more offspring become more common in the population due to natural selection. Other mutations can spread thanks to the luck of the genetic dice.

Mori wondered what sort of changes would occur in his dark flies. Would they lose their internal clock, controlling the daily cycles of their bodies? Would they stop responding to light? Would they evolve in other, unexpected ways?

In some respects, the flies haven’t changed much. They still have normal eyes, for example, complete with pigments. Last year, Michio Imafuku and Takashi Haramura reported that the dark flies still had their body clock. If they exposed the flies to three and a half hours of light, the insects became active and sluggish in a 24-hour cycle.

But the Japanese scientists have also found some differences. The bristles on the dark flies became unusually long, for example.
That change might simply be a fluke of rearing flies from a few related insects. To find out if the flies had experienced natural selection, Naoyuki Fuse and colleagues applied modern technology to this venerable invertebrate dynasty.

As they report in PLOS One, there are some tantalizing clues that the flies have indeed adapted to life in the dark.

For starters, the researchers observed how well the flies reproduced. After all, that’s what natural selection is all about. They counted up the eggs that the flies laid, either in the dark or the light, and compared their success to their ordinary relatives. The researchers found a major difference: when kept in the dark, dark-bred flies laid 373 eggs, plus or minus 20. Ordinary flies laid 293 eggs, plus or minus 73. Somehow, in other words, the dark-bred flies had become better at breeding in the dark.

To start hunting for the cause of this change, the Kyoto researchers sequenced the genome of the dark-bred flies and compared it to a genome from normal relatives. They found 220,000 spots in the genome where the DNA had mutated (a single nucleotide polymorphism). In addition, there were 4700 places where a stretch of DNA had been inserted or deleted.

A lot of those mutations may not have had any effect on the flies. So the researchers began to sift through the changes for ones that had good evolutionary potential. They found some promising candidates. For example, a gene for a light receptor had acquired a particularly devastating change called a nonsense mutation, which prevents the fly from making a functioning protein. A gene involved in metabolism disappeared. Once the flies were cast into darkness, flies without these proteins may have done better than the ones that held onto them.

The scientists also looked for stretches of DNA that showed signs of having experienced natural selection. Each fly carries two copies of each chromosome, and each chromosome is sprinkled with its own set of mutations. Here and there, however, the DNA on the chromosomes is identical. This close matching is sometimes the result of genes spreading quickly through a population thanks to natural selection. The scientists found 241 new mutations in these identical stretches–potentially giving the flies an advantage in the dark. One of those genes is involved in breaking down toxins. The scientists speculate that flies ordinarily use light to help break down toxins. The dark flies may have evolved a way to do so without the light.

Perhaps Mori envisioned his flies becoming like cavefish, pale and blind in their bottles. That didn’t happen. But now scientists can probe his flies far more deeply, reading their entire genome. And while they may not show obvious signs of evolution, subtler ones may be present by the hundreds.

Image: Wikipedia

24 thoughts on “Fifty-seven Years of Darkness

  1. Presuming the major work of natural selection is not to make us better, but to keep us from getting worse, he would have easily observed his dark acclimated flies do more poorly in the light. Too bad his control group died out, so this comparison would now need be made to wild flies.

  2. Interesting thing to look for would be whether the eyes evolve into a some sixth sense such as magnetic field. The sensors for magentic fields are the retinal lights sensitive cells themselves in animals that sense magnetic fields. Flies that can sense magnetic fields will have an advantage.

  3. I am not an evolutionary biologist, but it does seem like the simple version of evolution has significant holes as a theory. For example, over time, some species change in ways that have absolutely nothing to do with reproductive success.

    There also seems (for reasons I can not understand) to be a strong and universal bias towards explaining (no matter how contorted and unlikely) any feature or characteristic of a species in terms of how that feature helps that creature survive longer and/or reproduce more. This is done without any supporting data, and sometimes it is even done in direct contradiction to the data that is available.

    These are some of the things that make my suspect that there is much more going on, and that there is much more complexity, than any evolutionary theory I am aware of.

  4. You need to read more: founder effect, genetic drift, neutral theory.

    That’s why the experimenters, after observing changes, began a battery of tests to find out, if they could if the changes were adaptive or random.

  5. Wil,

    Regarding your first point, there are many changes that are likely to be the result of genetic drift. A variation does have some probability of surviving to the next generation even if it confers no advantage (as long as it doesn’t confer too much disadvantage).

    The degree to which this explains natural variation is a classic question in evolutionary biology, called the Neutralist-Selectionist Debate. See:


    Regarding your second paragraph, there is an unfortunate tendency toward “just so” stories of evolution, especially in pop science writing. Just because an evolutionary explanation exists does not mean it is the truth; alternate hypotheses should be tested against each other.

    Regarding your third paragraph, evolutionary theory is a model; so is Newtonian physics. Reality is always more complex. The complexity of reality doesn’t invalidate the model, it enriches it.

  6. Just trying to set my gauge here….

    How many genomic changes would we expect to see from one fly to its direct offspring?

    [CZ: The scientists note that the mutation rate in Drosophila is between 1/10 to the 9th to 1/10 8th per nucleotide per generation. For more on the number of expected mutations, you can go straight to the paper, which has a length discussion under the “Genome history of the dark-fly” and is open access.]

  7. There is another similar experiment going on with bacteria and the evolution of different strains emerged from a common clone. That was mentioned in one of the latest books of Dawkins (probably the “greatest show on earth”).
    Scientist could show that some bacteria change their metabolic system according to the amount of AA available on the grow jar. Bacteria multiply faster than flies and the process of replication is simpler , that may have helped the arise and analyses of different strains as well.

  8. Very temping to think that the longer bristles were favored in the absence of light. Hopefully further work will answer that question.

  9. The changes after 1400 generations seem fairly small, and I’m curious if that may be due to the fact that there isn’t a lot of competitive pressure on these flies.

  10. It’s interesting that this sort of thing can be traced and detected… imagine if we were to eventually do this with larger animals?

  11. I think it would be interesting to find out what those 241 mutations are and how exactly do they give the flies in the dark the advantage.

  12. So this is science? This has been going on scince the dawn of government. Treat us like mushrooms, keep us in the dark and feed us bullshit. Sounds very familiar. People have been the flies for quite a long time.

  13. This article was very interesting and I learned many things about fly generations that i did not know before, for example A lot of those mutations may not have had any effect on the flies. So the researchers began to sift through the changes for ones that had good evolutionary potential. They found some promising candidates.

  14. I found this fascinating that they could and would blind themselves because of their environment, but i wonder do they stay in the cave all the time.

  15. This is not the first time in history that this experiement has been done. Fernandus Payne’s classic 1910 paper in the Biological Bulletin entitled “Forty-nine Generations in the Dark” performed essentially the same experiment in order to test Lamarkian evolution. I find it very odd that the current work does not cite this classic paper especially given that Payne’s project is widely known to be instrumental in T.H. Morgan’s choice to focus on Drosophila melanogaster as a model organism for research in genetics.

    See the original paper here: http://www.biolbull.org/content/18/4/188.full.pdf+html

    See also a discussion of the role of the original “Dark Fly” experiment on the history of Genetics here: http://www.jstor.org/stable/228840

  16. “The researchers found a major difference: when kept in the dark, dark-bred flies laid 373 eggs, plus or minus 20. Ordinary flies laid 293 eggs, plus or minus 73. Somehow, in other words, the dark-bred flies had become better at breeding in the dark.”
    Perhaps the lack of light, caused a lack of visual stimuli, leading to less fly lounging as they see no interest to fly too. So the flies just end up running into each other while flying, and thus as the only available stimuli… they smash

    “The scientists speculate that flies ordinarily use light to help break down toxins. The dark flies may have evolved a way to do so without the light.”
    Or perhaps they have different pathways that are used when needed, such as the pathway for glucose metabolism, gluconeogenesis, or fatty acid oxidation.

    Its like once we see a differentiating statistics, we automatically can’t wait to wine and dine Darwin and bring him home to momma

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