FRUIT FLIES are smart. For a start—the clue is in the name—they can fly. They can also flirt; fight; form complex, long-term memories of their surroundings; and even warn one another about the presence of unseen dangers, such as parasitic wasps.
They do each of these things on the basis of sophisticated processing of sound, smell, touch and vision, organised and run by a brain composed of about 140,000 neurons—more than the 300 or so found in a nematode worm, but far fewer than the 86bn of a human brain, or even the 70m in a mouse. This tractable but non-trivial level of complexity has made fruit flies an attractive target for those who would like to build a “connectome” of an animal brain—a three-dimensional map of all its neurons and the connections between them. That attraction is enhanced by fruit flies already being among the most studied and best understood animals on Earth.
For many years the race to assemble an adult fly connectome seemed likely to be won by the FlyEM project at the Howard Hughes Medical Institute’s Janelia Research Campus, in Virginia. In 2020 FlyEM’s researchers, led by Gerry Rubin, a veteran fly biologist, published a connectome of an adult fruit-fly “hemibrain”, a set of 27,000 neurons in the middle of the organ. This was followed in 2023 by a connectome of the 3,016 neurons of a first-instar fly larva—the tiny grub that emerges from an egg. But Janelia has been pipped at the post to create a connectome of a complete brain by a group called FlyWire, based at Princeton University. Ironically, Flywire has used data collected by Janelia but abandoned in 2018 for being too difficult to analyse with the artificial-intelligence (AI) software available at the time.
Mala Murthy and Sebastian Seung, FlyWire’s creators, however, had different AI software. They started the project in 2018 with the backing of the BRAIN Initiative (an attempt by America’s government to do for neuroscience what the Human Genome Project did for genetics) to analyse Janelia’s now-abandoned data. The outcome, published this week in Nature, is a model which paints a detailed picture of a female fly’s brain with 139,255 neurons, and locates some 54.5m synaptic connections between them.
Creating a connectome means taking things apart and putting them back together. The taking apart uses an electron microscope to record the brain as a series of slices. The putting back together uses AI software to trace the neurons’ multiple projections across slices, recognising and recording connections as it does so.
Janelia’s researchers had developed two ways of doing these things. The FlyEM team used a beam of gallium atoms to blast away nanometres of tissue from a brain sample and then record an image of each newly exposed surface with a scanning electron microscope (which fires a beam of electrons at a surface and detects any radiation subsequently emitted). Their own fruit-fly connectome, of a male, should be ready within a year.
Janelia’s second method involved shaving layers from a sample with a diamond knife and recording them using a transmission electron microscope (which sends its beam through the target rather than scanning its surface). This is the data used by FlyWire. With Janelia’s library of 21m images made in this way, Dr Murthy and Dr Seung, ably assisted by 622 researchers from 146 laboratories around the world (as well as 15 enthusiastic “citizen scientist” video-gamers, who helped proofread and annotate the results), bet their software-writing credibility on being able to stitch the images together into a connectome. Which they did.
Besides the numbers of neurons and synapses in the fly brain, FlyWire’s researchers have also counted the number of types of neurons (8,577) and calculated the combined length (149.2 metres) of the message-carrying axons that connect cells. More important still, they have enabled the elucidation not only of a neuron’s links with its nearest neighbours, but also the links those neurons have with those farther afield. Neural circuitry can thus be studied in its entirety. The project’s researchers have more than doubled the number of known cell types in the fly’s all-important optic lobes, and shown how the new cell types connect in circuits that deal with different elements of vision, including motion, objects and colours.
This sort of thing is scientifically interesting. But to justify the dollars spent on them, projects such as FlyEM and FlyWire should also serve two practical goals. One is to improve the technology of connectome construction, so that it can be used on larger and larger targets—eventually, perhaps, including the brains of Homo sapiens. The other is to discover to what extent non-human brains can act as models for human ones (in particular, models that can be experimented on in ways that will be approved by ethics committees).
Here, evolutionary biology gets involved. Fruit flies and humans are on opposite sides of a 670m-year-old division splitting bilaterally symmetrical animals into two groups: protostomes and deuterostomes. This separation almost certainly predates the evolution of brains, meaning the brains of insects (which are protostomes) and those of vertebrates (deuterostomes) have separate origins. Drawing conclusions about the one from the other is thus a risky business.
This should not matter for long. Several groups are currently working on mouse connectomes, bits of which have already been put together. Though Janelia has no plans to go in this direction, Dr Rubin (who is, along with several other researchers from Janelia, a co-author of part of the package of nine Nature papers) reckons a complete mouse connectome could be created in a decade if someone were willing to stump up $1bn to pay for it. By analogy with the Human Genome Project, where the technology became steadily cheaper as things scaled up, this would also bring down the cost to a point where smaller connectomes, like those of flies, could be mass-produced.
The deuterostome-protostome division, together with more recent evolutionary shifts, also offers the possibility of a new science of comparative connectomology. In some cases it is already clear that giving natural selection multiple bites at the cherry has resulted in more than one solution to the same problem. The overarching organisation of the neurons in fly brains and vertebrate brains, for example, is completely different. In other instances, though, both brains seem to work in the same way, suggesting that might be the optimal way of doing things.
These natural experiments, the circuit-diagrams of which connectomes will make available, might even help human computer scientists. Brains are, after all, pretty successful information processors, so reproducing them in silicon could be a good idea. As it is AI models which have made connectomics possible, it would be poetic if connectomics could, in turn, help develop better AI models.
