The 2011 Tohoku tsunami did more than reshape Japan's coastline. It brought two closely related fish species together in newly formed ponds, where they interbred extensively, and scientists have now documented how one species' DNA was almost completely removed from the mixed population within about a decade.

In 2012, 38% of the sticklebacks sampled in tsunami-created ponds in Otsuchi Town, Iwate Prefecture, were hybrids, according to a study published Sept. 25 in Nature Ecology & Evolution. By 2020, the population was nearly pure freshwater threespine stickleback again. Because these fish produce about one generation a year, most of the foreign DNA disappeared within about 10 generations.

The findings offer a rare real-time view of how species boundaries hold up after a disaster breaks down the barriers that normally keep them apart. That question is increasingly relevant as human activity and climate change alter habitats and bring previously separated species into contact.

A Disaster That Opened New Habitat

The magnitude 9.0 to 9.1 Tohoku earthquake of March 11, 2011, triggered tsunami waves that struck Otsuchi with a height exceeding 10 meters. The waves and ground subsidence inundated what was then the town's downtown area, creating new spring-fed freshwater ponds, according to the research team.

The researchers think the incoming tsunami probably carried marine Japan Sea sticklebacks, Gasterosteus nipponicus, in from the Pacific, while the backwash brought freshwater threespine sticklebacks, Gasterosteus aculeatus, down from upstream. The two species diverged about 680,000 years ago and have strong but incomplete reproductive isolation, meaning they can still produce hybrids.

The team identified no hybrids in Otsuchi Town before the tsunami, which the authors say suggests the extensive hybridization was probably triggered by the tsunami's changes to the habitat. Over nine years, the researchers collected 2,698 sticklebacks from as many as 28 ponds in a single year, and a mark-and-recapture survey put the pond population at about 22,485 fish.

Genetic Purging Explained

When two species interbreed, their offspring carry a mix of both genomes. Over later generations, that mix can persist, or natural selection can strip out one species' genes. Biologists call the second outcome purging, and it allows species to stay distinct even after hybridizing.

In Otsuchi, the purge began with the genes that matter most for keeping the species apart. Genome regions linked to freshwater survival, migration toward the sea, mate choice, and hybrid male sterility lost most of their marine-species versions within the first few generations. The rest of the marine genome then faded across most of the fish's chromosomes, apart from a few locations.

Field experiments helped show why. In an outdoor enclosure placed in a tsunami-created pond, 53 of 60 young freshwater sticklebacks survived from October to the following March, compared with just two of 60 marine sticklebacks. In a separate test, fish carrying marine-species genes at certain locations were more likely to swim downstream toward the sea, and the researchers never observed mature migrants returning to the ponds.

"There were two major surprises in this study," study authors Takuya Hosoki and Jun Kitano said in a release distributed through EurekAlert by their research organization. They did not expect genome regions tied to major reproductive barriers to be purged so quickly, and they were surprised that most of the foreign genome kept disappearing over later generations. The research team included scientists from Japan's National Institute of Genetics and eight other institutions.

Strengths and Limits of the Nine-Year Record

The peer-reviewed study combines long-term field sampling with experiments and computer modeling. Its main strength is the time series. The researchers followed the population from shortly after hybridization through about 10 generations, something few studies of wild animals have done.

The explanation for the genome-wide purge, however, comes largely from simulations. The team found that a handful of major genes could not account for the full pattern on their own. Their models suggest that many weak genetic incompatibilities spread across the genome also helped remove marine DNA. That is a hypothesis supported by modeling, not a directly measured mechanism. Because the team analyzed a relatively small number of genetic markers, the authors say whole-genome sequencing will be needed to validate the patterns and identify the mechanisms. Sequence data from the project are deposited in public archives, and supporting files are available through the study's Dryad data repository.

The results also varied by site. At two other tsunami-affected habitats in the Tohoku region, Iwaizumi and Kuji, sampled eight years after the disaster, hybrids retained a larger share of marine-species DNA than in Otsuchi. The researchers hypothesize that differences in how many fish of each species arrived at the start may partly explain the gap.

Not every hybridization ends this way. The paper notes that a pair of threespine stickleback forms in a Canadian lake collapsed into a single hybrid population after human environmental disturbance, a process known as speciation reversal. The Japanese species pair is more genetically divergent, and its species boundary held in all three tsunami-affected habitats studied.

Lessons for a Changing Coastline

The authors write that hybridization can also result from human activities, and they cite research suggesting the severity of natural disasters, including tsunamis, may increase with climate change. They argue it is becoming more important to predict the outcome of hybridization for that reason.

The study suggests that hybridization after a disaster does not automatically erase a species' identity. In this case, where the species were relatively distinct, selection restored the boundary within about a decade. For species pairs that are less distinct, the outcome may be different, which is why the authors call for more real-time monitoring across species with varying degrees of divergence.

The researchers say their next question is whether a combination of a few strong reproductive barriers and many weak genetic incompatibilities is a general mechanism for how species boundaries survive hybridization.

What Readers Want to Know

What did the study find?

After the 2011 tsunami, 38% of sticklebacks sampled in 2012 in new ponds in Otsuchi, Japan, were hybrids between two species. By 2020, marine-species DNA had been almost completely purged, leaving a nearly pure freshwater population.

How did the tsunami cause hybridization?

Researchers think the tsunami probably carried marine sticklebacks inland while the backwash brought freshwater sticklebacks downstream into newly formed spring-fed ponds, putting the two species together.

What does genetic purging mean?

It is the process by which natural selection removes one species' genes from a hybrid population over generations, allowing the other species to keep its identity.

How fast did it happen?

Most of the marine-species genome disappeared within about 10 generations. Because these sticklebacks produce about one generation a year, that took roughly a decade.

Did the same thing happen everywhere?

Not to the same degree. At two other tsunami-affected sites, Iwaizumi and Kuji, hybrids retained more marine-species DNA, possibly because different numbers of each species arrived at the start.

Does this prove how all species handle hybridization?

No. The mechanism behind the genome-wide purge is supported by modeling, and the authors say whole-genome sequencing and studies of other species pairs are needed to test whether the pattern is general.