Billions of years of evolution has produced an incredible diversity of life – “endless forms most beautiful and wonderful,” as Darwin famously put it. But a fascinating thing about evolution is it has produced such a wide variety of species with a relatively small amount of tools. Many of the roughly 23,000 human genes can be found in species as different as mice and flies, and those genes control embryonic processes that are remarkably similar despite the vastly different outcomes for an insect or a man. But sometimes, finding out just how deep this homology runs requires deep exploration.
Members of Neil Shubin’s laboratory are no strangers to adventure. The search for Tiktaalik, the famous fossil of a transitional species between fish and land-dwellers, took Shubin and his collaborators to remote stretches of the Canadian Arctic. So when J. Andrew Gillis, then a graduate student in Shubin’s laboratory, wanted to study an obscure aquatic relative of sharks with famously hard to acquire eggs, the evolutionary biologist could hardly turn him down.
“I remember when Andrew said ‘I want to get some holocephalans in the lab,’ and I thought ‘yeah, right.’ Everybody’s tried this for years; there’s a long line of people who have always wanted to get holocephalans in the laboratory,” said Shubin, the Robert R. Bensley Professor of organismal biology and anatomy at the University of Chicago. “It’s not like you can buy them at a store, it’s not like you can breed them easily in a lab. They breed on the bottom of the ocean, so you have to find places where the eggs are accessible.”
Holocephalan eggs are prized by evolutionary biologists because of a small but significant anatomical difference from their cousins, the sharks. Both share skeletons made of cartilage and other structural features, but split in terms of appendages called branchial rays, structures that grow outward from the skeletons’ central gill arches. While sharks form several sets of these rays, holocephalans only grow a single set near their head, which eventually forms the support for gill covers. Finding the genetic switch that triggers this anatomical difference, as Gillis, Shubin and colleagues did in a PNAS paper published yesterday, would shed light on the origins of appendage development across the animal kingdom, from fins to wings to limbs.
But first, a scientist needs to leave the safe world of their laboratory in order to find those precious eggs. Gillis’ quest for the embryos of the holocephalan species elephant fish, named for their prominent snout, led him halfway around the world and under the water, on SCUBA expeditions in Australia and New Zealand. Based on anecdotal information collected from local fisherman and marine biologists, Gillis was able to score a precious few eggs to take back to the laboratory for his experiments – but it wasn’t easy.
“Diving for elephant fish eggs was not always a pleasure trip,” said Gillis, now a postdoctoral researcher at the University of Cambridge. “Unfortunately, elephant fish like to lay their eggs in cold, muddy, shark-infested bays, so we spent months seeking out sites like this in southeastern Australia and New Zealand. When you finally find a few eggs in the muck, it feels like winning the lottery.”
Back in the comfort of the laboratory, the mood was still tense, as Gillis had to get all of his experiments working just right so as not to waste the valuable cargo from his expeditions. Previous work by Gillis and Shubin discovered that shark embryos use a gene called sonic hedgehog (Shh) to control the development of branchial arches. The next step was to test whether elephant fish embryos also use this genetic switch to mediate the growth of their less robust appendages.
Gillis’ experiments determined that Shh was indeed present in elephant fish, and that the anatomical difference was all in the timing. Early in development, the gene is expressed at several regions in both elephant fish and dogfish (a type of shark) embryos, along structures called the hyoid arch and the gill arches. But a few weeks later, Shh expression has disappeared from all but the foremost hyoid arch in elephant fish, while remaining strongly expressed in along the gill arches of the dogfish. Therefore, subtle differences in when and where a single gene is expressed can have dramatic consequences upon the anatomy of two very different looking fish.
“The research highlights how evolution is extremely efficient, taking advantage of preexisting mechanisms, rather than inventing new ones,” Gillis said. “By simply tinkering with the timing of when or where a gene is expressed in an embryo, you can get very different anatomical outcomes in adults.”
The finding also loops the obscure holocephalans into a broader story of how species separated by hundreds of millions of years of evolution can share the same evolutionary tools. Sonic hedgehog (which yes, is named for the video game character) was originally discovered controlling body development in the fruit fly Drosophila melanogaster, and has since been found to control limb growth in everything from whales to chickens to humans.
“You have a common nail that’s used for many different pieces of furniture,” Shubin said. “This esoteric fish with this esoteric anatomical system is showing us something very fundamental about the evolutionary tree: that there’s a common process at work among disparate types of organisms.”