Whimsical cartoon of zooplankton invaders in a black canoe, with a ship in the background.


A tiny Great Lakes invader teases future climate challenges

Perhaps Carol Eunmi Lee was always coming back to the St. Lawrence River. Her parents started taking her camping and fishing at the age of four. Her dad, on a physics post-doc in Montreal, loved to fish. They often cast into the nearby St. Lawrence River and its sprawling estuary. They explored the Adirondacks, Vermont, Quebec, New Brunswick.

They couldn’t know that Lee, now a professor in the University of Wisconsin–Madison’s Department of Integrative Biology, would return decades later as a scientific investigator. Now she tracks invaders across the salinity divide, where sea meets freshwater. What she’s learning will help us understand forces working on every species facing climate extinction. And they’ll help foretell the future of one of one of the most significant freshwater reserves on the planet, the Great Lakes.

Lee’s family left for South Korea when she was ten. There she read a lot of John Steinbeck, fell in love with California, and returned to the states via Stanford University and Monterey Bay. Thanks to Cannery Row, she was in love with Monterey even before she saw it. Then she slipped beneath the surface, learning to SCUBA dive in the legendary maritime oasis.

“If you’re diving in Monterey, in the kelp forest, it’s just stunning. It’s like a religious experience,” says Lee. “It’s like a cathedral.” She became a dive jock, and in 1991 secured the Our World Underwater dive scholarship supported by Rolex.

Forget the iconic sea otters of Monterey Bay, Lee was enthralled by the sea slugs. “I wanted to work on the invertebrates because they’re so beautiful,” says Lee. “I fell in love with the sea slugs.”

Then she experienced some amazing plankton tows. This involves running a fine mesh net, long and conical like a wind sock, through the water. Copepod zooplankton form the largest biomass of animals in the world’s oceans, so their diversity, abundance, and ecological importance all intrigued her.

She really loved the calanoid copepods. An extra joint in their tails spring loads their swimming. “I was captivated by their locomotion,” she says.

In grad school at the University of Washington Lee roamed the Pacific coast on weekends in a red Toyota pickup truck, sampling zooplankton and running population genetics. Tow the Columbia River estuary on the Washington-Oregon border and you can capture thousands upon thousands in a single tow. They’d look pink because they’re constantly eating red algae. These zooplankton are a critical food source for larval salmon — and why salmon are pink. Zooplankton are a lynchpin in marine ecosystems, supporting salmon, herring, anchovy, sardine, and many more fisheries besides. 

While assembling the jigsaw of zooplankton genetics in the PNW, her attention snapped eastward, to the Great Lakes and the St. Lawrence River, and a species complex called Eurytemora affinis. A species complex is a group of related organisms that has evolved to take advantage of a variety of niches. Evolved from a common ancestor, they might look identical.

From coastal Alaska, Eurytemora live in a wide range of salinities. But here they were also invading freshwater habitats. Strong boundaries separate saltwater and freshwater species. Of the 32 or so animal phyla, only 16 have any representatives in freshwater.

Lee was amazed by the parallel evolutionary track that led to this significant physiological shift. “They were evolving, and the evolutionary change was big,” she says. “I just wanted to figure out how they were doing it.”

Ecology at the most fundamental level looks at demography — how many animals are there? Is their population changing? What are the predator-prey dynamics?

But these animals were evolving in real time, and ecological ideas alone weren’t sufficient to answer her questions. She’d need to unravel the genetic composition of a changing population. “That’s how I became an evolutionary biologist,” says Lee.

An unknown species of Acartia demonstrates the mesmeric movement patterns of calanoid copepods. (Video courtesy of George von Dassow of the Oregon Institute of Marine Biology at the University of Oregon.)


When humans think about climate change, we tend to think in terms of decades, looking out to targets in 2030 and 2050. But the extreme warmth we’ve been experiencing over the last year, including 12 consecutive months of global ocean temperature records, also has some very simple and very immediate effects.

Ice melts, releasing freshwater. At the scale of an ice-bound behemoth like Greenland, entire regions can get less salty. Climate shifts are also implicated in dropping salinity in the Baltic Sea. Shifts across this salinity barrier, from sea water to brackish to fresh and back again, are happening all over the world. Whether it’s saltwater encroachment from rising seas or salt pollution of freshwater, it’s a feature of this anthropogenic era.

That’s two huge variables, temperature and salinity, changing very quickly. For most organisms, this is the texture at which climate change takes place: Intensely local, with imminent consequences.

As environments shift in response to climate, living things have but three “options”: move, adapt, or die. Life on earth is abundant proof that populations evolve in response to challenges. But what does that look like, especially for small but ecologically mighty animals like zooplankton?

In the face of significant heat or salinity challenges, a lot of organisms will die. In the best case scenario some survive. “That is evolution. It starts in the first generation,” says Lee. “Natural selection is going to weed out the ones that can’t evolve.” Populations must evolve, or go extinct.

How organisms handle this evolutionary fork in the road is partly dictated by genetics. We can be forgiven for calling it adaptation in casual conversation — as in “the animals adapted to the heat.” But geneticists don’t use the word ‘adaptation’ casually. Adaptation has a very specific meaning: evolution due to natural selection, which happens over multiple generations.

Our genomes often get compared to libraries, books, chapters — the genes are instructions; some are complex while others are simple. Many of these genes are in use, while others may sit unused until activated by environmental circumstances. Still others sit quiet until passed along through reproduction, where chance may activate them or keep them quiet.

How one individual zooplankton handles the heat in its short life often comes down to whether or not the genetic code that they possess has the physiological tools necessary to handle the challenge. Heat tolerance would likely come via adaptation as a result of natural selection in the past. But whether any one individual survives this stressor during its life is phenotypic plasticity.

Every individual in a population has a collection — call it a bookshelf — of genes. Acclimation results from phenotypic plasticity of an individual using the genes in their bookshelf. Collectively, a population in the wild has a larger collection of genes than any individual’s bookshelf. That’s the library. Changes in this library shows adaptation.

What if there are 100 zooplankton, and only 10 with the genetic code to tolerate high heat? Around 90% of the population gets wiped out. And the next generation will have proportionally more high heat genes. That is adaptation; natural selection begins in the first generation.

How do geneticists figure this out? They sequences a lot of genome, relying on the same advances in genetics and computing power that lead to DNA breaks in cold cases. But they also recreate evolution in the lab, tinkering with salinity, temperature, and other factors to distinguish between acclimation and adaptation.

“With 20 generations, you can see a dramatic change.” she says. “Plankton are evolving very quickly in response to these changes. And that’s going to affect all the trophic levels above.”

But adaptation comes with no guarantees. Can the beneficial genetic variants rise fast enough, can they stage an evolutionary rescue?

On a computer screen, Carol Eunmi Lee looks at satellite imagery of a region rich in surface water near Juneau, Alaska where the Eurytemora affinis species complex evolved.
Carol Eunmi Lee looks at satellite imagery of a region near Juneau, Alaska where the Eurytemora affinis species complex evolved.


If you’re studying the great branch points in human evolution, you probably go to Africa. For the copepod species complex Eurytemora affinis, you go to Alaska. Eurytemora emerged more than 5 million years ago somewhere near Juneau. Now there are 21 native species of named Eurytemora — with probably a couple dozen more waiting to be discovered. Only about five of the species have migrated out of Alaska.

A map of the region reveals a labyrinth of countless lakes and tide pools. They’re connected, but unpredictably. Sea level changes, storm events, precipitation patterns, and even tidal waves keep shuffling the deck. As a result, salt levels in the water are very dynamic, changing a lot.

Over time, populations of Eurytemora get cut off from each other. Then the salt concentration changes. Different lake shapes and sizes and depths further mold the environment. Time rolls on, and species that look identical evolve to fit both subtle and substantial differences in local conditions. Over 5 million years, the pattern gets interesting.

Eurytemora handles this unique environmental challenge with advanced chemistry.

The difference between salt water and fresh water is mineral ions. Essential ions are precious in fresh water, but every single cell in your body needs ions like potassium and sodium. Cells build ion transporters to pass them through the cell membrane.

Humans have two genes coded to build one sodium transporter, named NHA. Drosophila, one of our favorite study animals, also has two. But the Eurytemora affinis species complex has 8 of these genes, all a little bit different. 

Not only does Eurytemora often have multiple copies of these genes, they’re concentrated in the mouth and legs — both places that experience a lot of water flow. Eurytemora’s evolution in Alaska seems to have concentrated many critical ion transporter genes into “supergenes.” That versatility, that chemical fluency, facilitates its ability to adapt to fresh water, creating a “super invader.”

Before 1959 Eurytemora had occupied many saline habitats in the St. Lawrence drainage, including salt marshes and estuaries. Huge and complex, and fed by a wealth of tributaries, it stretches 655 kilometers (407 miles) between the Great Lakes and the Atlantic. It’s one of the largest such systems in the world. Eurytemora lives throughout the system, and probably has for tens of thousands of years, allowing genetic diversity to develop locally. 

The opening of the St. Lawrence Seaway in 1959 set the stage Eurytemora’s invasion of the Great Lakes. Like so many other invaders they arrived in ballast water — this class of zooplankton represent the largest biomass of ship ballast water. With some 12 billion tons of ballast water transported every year, large quantities of water from outside the Great Lakes gets dumped into inland fresh waters, with their passengers. More than 180 non-native species have managed to establish in the Great Lakes basin, and a third of these are considered invasive. The threats are numerous and well documented and have irrevocably altered ecosystems in the Great Lakes and beyond.

Lee’s genetic analysis of the Eurytemora invasion suggest that this has happened multiple times, dispersing genetically distinct populations to different regions of the Great Lakes. This genetic diversity is probably good for Eurytemora. We don’t know if it’s good for Great Lakes ecosystems. 

Right now Eurytemora lives in the margins, carving out their own niche near sewage pipes, ports, and breakwaters: “Somehow my copepod can make it there,” says Lee.

By occupying an untended niche, Eurytemora in the Great Lakes doesn’t yet present an ecological hazard. But evolution is hard to predict. “Once they evolve to become a completely freshwater beast, they can venture out and start displacing the native copepods,” says Lee. Fish often suffer when native copepods are displaced.

Eurytemora affinis.


With climate change right now, some things are changing super fast. That makes zooplankton a kind of canary, but what kind of canary?

What economists and government ministers want to know is what’s going to happen to the fish as temperature and salinity changes. But fish evolve more slowly; many of the species that people care about reproduce once a year. Eurytemora, meanwhile, reproduce every 20 days — and more quickly in warmer conditions.

That’s 6 generations per year in an icy system like the Great Lakes where cold plunges the zooplankton into a reproductive state called diapause. We can learn even more in the lab — some of Lee’s experiments have run 60 generations.

Fish don’t evolve as quickly as zooplankton. We may be able to learn more about their prospects by looking at what’s happening to the zooplankton. Flashback to the trophic cascade, that flow of ecological energy through food webs: If you really want to holistically understand an ecosystem, you need to look at the grazers and not just the fish.

“I think all the trophic levels need to be examined if you want to understand how the system works, and understand how it’s going to respond,” says Lee. And with climate change, ecology and evolution are intertwined. “If you just modeled ecological interactions, you’re not accounting for the rapid evolutionary changes that are occurring.”

How that plays out is hard to guess. But we do know this much: It’s hard to evolve in response to both variables at once. For example, salinity and temperature changes may be linked in the physical world — higher temperatures leading to reduced salinity in wet, icy places, or increased salinity in warmer, dryer places.

But there is no guarantee that the genes for a challenge like heat are linked to the genes for salinity. Gaining one trait might actually lose you another depending on how the generational mixing falls out. An evolutionary response to simultaneous temperature and salinity change is difficult to mount. 

And some populations cannot evolve because they simply don’t have a better gene for the job. “If it’s getting hotter, and you don’t have any high temperature adapted alleles, you can’t evolve,” says Lee.

Invaders in the Great Lakes may foretell one part of a broader future. Many originate from fluctuating, dynamic habitats like those where Eurytemora gave rise. Like Eurytemora, they had evolutionary answers.

“If the habitat changes, can the population evolve? Does it have the genetic variation upon which natural selection can act so that it escapes extinction? That’s how evolutionary biologists think about resilience,” says Lee. “A lot of what’s going to take over the planet are these resilient species that come from habitats with dynamic change.”

An image of global oceans shaded to show salinity changes. Primary text reads: Climate change is drastically altering habitat salinity across the globe. Increases in ice melt and precipitation patterns.
Salinity changes in the ocean may seem hard to comprehend, but they are widespread. (From a slide provided by Carol Eunmi Lee.)


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