Working with faculty mentor, undergrad unlocks secrets of ‘living fossils’

A few months ago, Chase Brownstein, a Yale undergraduate, and Professor Thomas Near were at odds. Together, the pair had authored a first-of-its-kind study reconstructing the evolutionary history of lampreys — an ancient group of jawless fish — using materials from the fossil record and genomic analysis. Now they disagreed on where to submit their findings.

Aiming high, Brownstein hoped to publish their work in one of the field’s most prestigious journals. Near, a distinguished ichthyologist who has published dozens of papers, was feeling less ambitious.

“I said, ‘Chase, this is great work, but I’m not sure that Nature or Current Biology are quite within our reach,” said Near, professor of ecology and evolutionary biology in Yale’s Faculty of Arts and Sciences.

Brownstein, a Yale College senior and the paper’s lead author, stood his ground. His persistence paid off: Near eventually relented and, in late December, the paper was published in Current Biology, a top-tier academic journal.

“Chase was right,” Near said, pleased to eat a little crow. “He said, ‘If you don’t play, you can’t win.’ It was the right call and a good example of the enthusiasm he brings to our work.”

It is the third peer-reviewed study that Near and Brownstein have published since November, with the undergraduate serving as lead author on all three. Each helps illuminate the evolutionary tree of a specific lineage of “living fossils,” a term Charles Darwin coined in “On the Origin of Species” to describe living organisms that closely resemble extinct species found in the fossil record or those with species-poor lineages that stretch back several hundred million years. (Horseshoe crabs are a common example.) The two other studies examine bowfin and gar, freshwater fish that, like lampreys, have ancient lineages.

Near and Brownstein’s ongoing collaboration exemplifies an invaluable opportunity available to Yale undergraduates: the chance to conduct research with seasoned scholars whose work expands the horizons of their respective fields.

It also highlights the power of Yale’s collections — in this case, those housed at the Yale Peabody Museum — to support and enable innovative research collaborations.

Exciting discoveries

The three studies offer new clarity and context to foundational aspects of vertebrate evolution, said Brownstein, 21, a resident of Yale’s Pierson College, who expects to graduate this spring.

The lamprey research illustrates this point well. The earliest vertebrates, like today’s lampreys, lacked jaws. After fish first evolved mandibles 450 million years ago, they rapidly eclipsed their jawless counterparts. Lampreys and hagfish are the only surviving jawless fish.

Prior to the study, the origins of the approximately 50 extant lamprey species and the identity of their common ancient ancestor were unclear.

Using genetic data, Brownstein and Near constructed the first complete phylogeny, or evolutionary history, of living lampreys. They tied it to a fossil, Mesomyzon mengae, which they dated to about 125 million years ago and determined is the oldest known common ancestor of today’s lampreys. The discovery allowed them to time-calibrate the phylogeny, leading to another revelation: The species diversification of lampreys is relatively recent compared to other major groups, or clades, of vertebrates.

“We found that the overwhelming majority of species diversity in living lampreys in the past 100 million years, as opposed to 300 million years,” Brownstein said. “Their tempo of speciation ramped up after the mass extinction event at the Cretaceous-Paleogene boundary — the asteroid strike that killed off most dinosaurs.

“This means the diversity we see in lampreys is more contemporaneous and similar to what we see in groups of vertebrates that are much less ancient than lampreys are,” he said.

The finding has implications for living lampreys. The jawless fish have two lifestyle types: In one, adults use rasping tongues to bore holes in the flesh of their hosts, and in the other, lampreys remain embryos for most of their lives before briefly becoming non-parasitic adults that spawn and then die.

“What we’re seeing is that the splits in the phylogeny where we have the evolution of a non-parasitic and parasitic species are all recent and shallow, indicating that they might not be separate species after all,” said Near, who is also Bingham Oceanographic Curator of Ichthyology at the Peabody Museum. “These might just be different life-history strategies that a single species is using given environmental conditions. If it’s a bad year to be a parasitic adult, they just stay an embryo. This would be a very dramatic lifestyle plasticity.”

The findings also offer insight into lampreys’ biogeography — their distribution over time and space — showing how they dispersed around the globe as the continents separated.

The second study focuses on gars, a clade of ray-finned fish distributed in eastern North America, Central America, the Caribbean, and Cuba. It also combines genomics and fossil analysis to gain a better understanding of the group’s biogeography and how it changed as the continents shifted.

“What Chase’s work is showing is that the patterns of lineage diversification through deep time to the present match very deep time paleogeographic events that affected the continents,” Near said of the study, which was published in December the journal Systematic Biology.

The third study, published in November in the Royal Society journal Biology Letters, focuses on species diversity in bowfins, a bony fish native to eastern North America and another example of a living fossil.

For that study, the Brownstein and Near used genetic data and fossil evidence to see whether there was hidden diversity in the bowfin’s branch of the evolutionary tree, which was previously thought to contain just a single living species. They found evidence that there are two species of bowfins — the newly discovered one inhabiting the eastern Gulf Coast of the United States and the other distributed throughout the U.S. Northeast, the Great Lakes region, and the Mississippi River.

“This new species breaks the bowfin’s long evolutionary branch in two,” Brownstein said.

Collaboration supported by collections

Near and Brownstein’s collaboration benefits from their proximity to the Peabody Museum, which houses extensive collections of fossils and specimens of living species.

The gar and bowfin studies involved analyzing fossil specimens from the Peabody. (The bowfin analysis involved peering into the skulls of fossilized fish using a CT scanner.) The tissue samples used in the various genomics analyses were drawn from the museum’s cryo collection, which preserves tissues under ultra-cold conditions.

“You need strong museum collections to do this work,” Brownstein said. “The hypotheses we’re using as the basis for our assumptions, need to be validated with specimens, which requires a museum. We happen to have a great one right here.”

When Brownstein first arrived on campus a few years ago, he was eager to combine his interests in paleontology and evolutionary biology. Working in Near’s lab has allowed him to do just that, while also making significant scientific discoveries in the process.

“I think drawing insights from both fossils and living species to get a better understanding of the tree of life is the path forward for this type of evolutionary biology,” he said. “I feel very lucky to be here doing this work under the guidance of advisors like Professor Near and with access to the Peabody’s extraordinary collections.”

For Near, who is also the head of Saybrook College, mentoring talented undergraduates is a highlight of working at Yale.

“I used to say that a particularly capable undergraduate was a once-in-a-career student,” Near said. “I’ve stopped saying that because I kept being proven wrong. The high intellectual curiosity of so many of our students is one of the joys of being here. Yale is a special place in that regard.”

He emphasized that the point of their collaboration isn’t to mold Brownstein into an ichthyologist, but to give him space to explore his interests. Last fall, he was a lead author of another study, published in Nature Communications, that identified the oldest-known, definitive members of an evolutionary group that includes all living lizards and their closest extinct relatives. He collaborated on the paper with Yale paleontologists Jacques Gauthier and Bhart-Anjan S. Bhullar, both curators at the Peabody Museum.

“It’s not about funneling talented students into your research program,” he said. “It’s about getting students matched up with the people who are best situated to help them develop their skills and pursue their interests. We aim to provide a supportive environment where any student at Yale can find the path that’s best for them.”

That supportive environment includes the freedom to disagree, Near said, citing their amicable dispute over where to submit the lamprey study.

The pair has more studies in the pipeline. For one, which is currently under review, they are seeking to clarify the definition of the term “living fossil” for some species, a question that still causes disagreement in the field. (Experts haven’t settled on a single, precise definition for the term.)

“There’s more to come,” Near said.