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Genetic test reveals Baltic flounder migration routes and a new species

  • Look-alike flounders in the Gulf of Finland are not one but two different species, and the predominant species about thirty years ago has now almost completely disappeared from there.
  • Using flounder inner ear samples collected over the last 40 years, researchers used a genetic test to map the distribution of the two species over time.
  • The disappearance of one species in the early ‘90s coincided with environmental change in the central Baltic Sea, the spawning grounds from where larvae or juveniles are thought to migrate to more northern waters off the Finnish coast.
  • Real-time monitoring of catch data using the genetic test may help target individual conservation efforts for the two species.

The waters of the eastern Baltic Sea around Finland are home to the flounder, a flatfish with both its eyes on one side of the head that uses its camouflage to move cryptically along the sea floor.

Its renown in the region was mainly as a mainstay of Baltic fisheries for centuries. That is, until recently, when scientists discovered that the flounders off the coast of Finland are not one, but two different species that look nearly identical.

A European flounder (Platichthys flesus) near the Åland Islands, Finland. P. flesus was until recently thought to be the only flounder species in the Baltic Sea. Image © OCEANA Carlos Suárez.

Moreover, researchers report, the predominant species found in the Gulf of Finland about 30 years ago has now almost completely disappeared from there. And since the two species likely react differently to climate change and overfishing, unique conservation strategies may be required for each.

Baltic fishers began by catching flatfish, which were abundant in the waters south of the Finnish coast, at the beginning of last century. The 1970s and 1980s saw a dramatic decline in the number of flounders caught, which has been attributed to climate change, overfishing, and several other environmental factors.

In a new study, a research team led by Paolo Momigliano of the University of Helsinki, put forth a new hypothesis. They propose that the near-complete disappearance of one flounder species coincided with the drop in fishing catch and that this disappearance could be one reason for the lower overall flounder populations.

Flounder larvae catch sea currents to migrate

The European flounder (Platichthys flesus), a common fish in the Baltic Sea, was historically thought to be one species. Flounder researchers in the late 1960s and early 1970s began noticing two different spawning behaviors. Some flounders laid eggs in the Baltic’s deepwater basins, where salinity is higher. These eggs floated to the surface, and the larvae drifted along with the ocean currents, migrating far from the spawning sites. Other flounders were observed to spawn near the sea floor close to the coast. Further research showed that there were genetic differences between the flounders with different spawning behaviors.

Dorsal and ventral views of a female Baltic flounder, from the western Gulf of Finland. The species, identified as distinct from the European flounder, was just described in 2018. Image is adapted from Figure 6 of its species description by Momigliano and colleagues (2018), CC BY 4.0.

“Two years ago, we discovered that these two spawning types are actually two distinct species Momigliano told Mongabay. He and his colleagues named the species spawning near the sea bottom Platichthys solemdali, which today is the more abundant type in the Gulf of Finland (GoF), the Baltic Sea’s eastern arm.

At that same time, they found a few fish of the P. flesus type, those with eggs that float and drift, in areas where it is not possible for it to spawn, such as the GoF. “Given that flounders do not move that much,” Momigliano said, “we hypothesized that they must have reached the Gulf of Finland from southern spawning grounds transported by currents, as larvae or juveniles.”

The greater Baltic Sea with the Gulf of Finland and Aland Sea study areas marked. Scientists believe larval or juvenile European flounder (Platichthys flesus) travel north from the species’ East Gotland Basin spawning grounds to the Gulf of Finland. Image by Sue Palminteri, produced in Global Forest Watch.

The Eastern Gotland Basin in the central Baltic is the northernmost region where P. flesus can spawn and the likely origin of larvae transported by currents to the GoF. The GoF extends east from Helsinki to St. Petersburg, Russia, far from the Baltic’s connection to the inflows of seawater and oxygen from the world’s oceans.

In recent decades, the Eastern Gotland Basin has seen increased sea surface temperatures and acidification, decreased water salinity, and greater eutrophication, a process where an overabundance of nitrogen, phosphorous, and other nutrients in water bodies causes dense growth of vegetation, often suffocating other marine species. During this time, the flounder catch dropped dramatically.

Momigliano and his colleagues speculated that dispersing P. flesus larvae were the main source of the GoF flounder population that the eutrophication and other environmental changes in the Gotland Basin might be affecting both the dispersal of P. flesus larvae and, in turn, the overall flounder catch in the GoF.

A European flounder displaying impressive camouflage off the Hanko Peninsula in the Gulf of Finland (). European flounder don’t spawn in the GoF but populate it when larvae or juvenile fish ride the currents north from the central Baltic. Environmenal changes have affected spawning grounds and lowered this replenishment of the GoF, reducing GoF populations. Image © OCEANA.

“Perhaps,” Momigliano said, “changes in abundance of [the] immigrant P. flesus, rather than of the local population of P. solemdali, may explain the decline observed in the Gulf of Finland.”

Flounder genetics

To test their hypothesis, the researchers used genetic testing to create a time map of the distribution of the two species over the last few decades. They used DNA from preserved inner ear samples, or otoliths, collected annually as part of a sampling project from 1975-2011. From a collection of about 29,000 flounder samples, the researchers performed genetic testing on DNA from about 480 individuals. These included samples spanning across the decades and from fish caught in either the GoF, where currents would drive P. flesus larvae, or the Aland Sea, off the Swedish coast, which would be less likely to receive the larval replenishments.

The two species of flounders diverged only very recently, about 8,000 years ago, so most of their genome is very similar. Hence, standard DNA testing methods cannot be used to identify the species. However, there is a marked difference in the regions of the genome associated with adaptations to low salinity. The coastal spawning P. solemdali has adapted to spawn in low salinity waters, whereas the P. flesus requires a minimum level of salinity.

The Baltic Sea coast off Kołobrzeg, Poland. Image by Macb3t, CC 0.

Previously, Momigliano and team had developed a genetic test to differentiate the two species. The researchers identified several locations in the flounder genome where the two species differed by one nucleotide, the building blocks of DNA. Using standard techniques, they identified these positions and sequenced the portions.

In the new study, the team refined the procedure to enable this test to be performed on even very short DNA fragments. This was important, as the DNA obtained from the archived samples were highly degraded, making it difficult to obtain long DNA sequences from these samples.

The improved test screened for five different genetic locations (loci) in one reaction using very short DNA fragment, which enabled the researchers to attribute each sample to one or the other species. “The test is so sensitive that we can screen these diagnostic variants from very small amounts of highly degraded DNA, i.e. what we can reliably recover from decades-old otoliths preserved at room temperature,” Momigliano said. And they could screen hundreds of samples at the same time.

The genetic test identified the prevalence of the two species in the Gulf of Finland between 1970 and 2011. P. flesus was the dominant species in the GoF in 1983, comprising almost 87 percent of the total founder population; it nearly disappeared in 1993; and it recovered slightly to about 10 percent by 2011. These percentages correlate almost perfectly with flounder catches. The catch was the highest in the early 1980s, dropped sharply in 1993, and recovered slightly in 2003.

The results revealed that flounder populations in the GoF were not a single stock of one species, but rather consisted of two different species, with the predominance of each changing over time.

Although P. flesus dominated the waters of the Finnish coast several decades ago, they can’t reproduce in these low-salinity waters. Hence, the flounders must have spawned in the more favorable southern part of the Baltic, and larvae, juveniles, or adults must have migrated along the currents to reach the GoF.

The European and Baltic flounders are cryptic. This European flounder is hiding under sand in the southern Baltic Sea off the coast of Poland. Image © OCEANA Carlos Suárez.

During the period when the P. flesus population was declining in the GoF, its closest spawning ground, the Eastern Gotland Basin, was impacted significantly by climate change and eutrophication. The authors say it’s likely that declining environmental conditions in these nursery grounds decreased the supply of larvae or juveniles to the north, reducing their northern populations.

In the GoF, write the authors in their paper, “P. flesus has almost completely disappeared before scientists and managers even noticed their presence.” The observed population fluctuation suggests the current distribution of the flounders is only a small part of a larger and dynamic picture, and conservation efforts need to take into account environmental and population changes over time rather than solely what is seen today.

The genetic test developed to differentiate the two flounder species could be used for real-time monitoring of future catches, says Momigliano. Determining up-to-date proportions of each species can help fishery managers keep an eye on whether any species is being overfished, enabling quick corrective action, such as setting fishing quotas that reflect migration from the southern spawning grounds.

European flounders are also cryptic when they swim. Image by Vääna-Jõesuu in Estonia. CC-3.0.

Although the test cannot yet be used in the field, as it takes about a day in the lab to complete, the team is working on reducing this time to a few hours. In addition, the team plans to screen an additional 4,800 samples, almost 10 times as many as in the current study. This may provide more insights into how climate change, eutrophication, and fishing pressure will affect the flounders in the next few decades.


Momigliano P, Jokinen H, Calboli F, Aro E, Merilä J. (2019). Cryptic temporal changes in stock composition explain the decline of a flounder (Platichthys spp.) assemblage. Evol Appl., 12, 549–559.

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