0:00:01.4 John Sheehan: About a year ago, Gary Longo was researching Pacific sardine, as one does in California, specifically looking at their genetic structure.

0:00:10.0 Gary Longo: We observed two highly distinct groups off the West Coast of North America, and these two groups differed at levels normally observed between species.

0:00:19.6 JS: And that was weird.

0:00:21.4 GL: Because previous genetic work on Pacific sardine had suggested there was essentially no differentiation along the entire US West Coast.

0:00:30.1 JS: Normally, there had been only one species of sardine, but.

0:00:34.5 GL: We determined that the data set indeed included two phenotypically similar sardine species, that is, the Pacific sardine and Japanese sardine.

0:00:42.9 JS: Here they were, Japanese sardine off the coast of California.

0:00:47.5 GL: So this was the first time that Japanese sardine had been detected in the eastern Pacific, as their normal range is in the temperate western Pacific from Korea to Russia, thousands and thousands of kilometers away. So this was pretty shocking to say the least.

0:01:03.5 JS: This is Dive In with NOAA Fisheries. I'm John Sheehan, and today we're going to scratch at this mystery of Japanese sardine appearing in US waters. How did they get here? What does it mean for the native Pacific sardine? Are they staying?

0:01:19.0 GL: They're still here. We've analyzed samples in 2023 and 2024.

0:01:23.9 JS: This is my guest, Dr. Gary Longo, a research scientist at NOAA's Southwest Fisheries Science Center and one of the authors of a new study documenting this discovery.

0:01:33.5 GL: And then after we detected Japanese sardine in 2022, we thought we'd just look back 10 years to see if, in fact, 2022 was the first year they showed up.

0:01:42.7 JS: It was.

0:01:43.6 GL: It was the first year that they showed up.

0:01:47.6 JS: So we'll get more into what this means for sardines in a little bit. But first, let's talk a little bit more about how you made the discovery. You can't... Can you tell them apart visually where you like, that one looks strange.

0:02:02.4 GL: That's a great question. And no, you can't phenotypically. So externally, they look identical. So you can't tell them apart just by looking at them.

0:02:10.8 JS: Wow. Have you... What about taste? Can you tell them apart by taste?

0:02:15.6 GL: That's a great question. We need to set up a taste test, a blind taste test to really get at that.

0:02:21.0 JS: All right, follow up interview we'll get the taste test going.

0:02:23.4 GL: That sounds great.

0:02:24.4 JS: So you said it was pretty shocking. And for a little background on Pacific sardines off the West Coast, sardines are a big deal in California. Can you give us a little context on just how much of a staple fishery it is?

0:02:40.2 GL: Sure. Well, historically, Pacific sardine from the 1920s to the 1940s represented the largest fishery on the West Coast of the US with a peak catch of around 700,000 metric tons. But following the 1940s, there was a pretty dramatic crash, and there wasn't much of a fishery until the 1980s when numbers started to rebound. But numbers never really rebounded to the numbers we saw in the 1920s and '40s. And again, the numbers began to decline in the early 2000s, and in 2015, the fishery was closed and has been closed since then.

0:03:18.8 JS: Yeah. And it is also a forage fish. This is something that, it's a species that is observed carefully.

0:03:28.2 GL: Correct. Yeah. So ecologically, outside of, you know, obviously being part of the National Marine Fishery Service, we're interested in fishes that are federally managed. But outside of that, ecologically, sardine are incredibly important to the California current ecosystem and whatever ecosystem they occur in, they are eaten by many, many things and allow a transfer from energy from phytoplankton to higher up in the food chain.

0:03:54.1 JS: So do we know how these Japanese sardines showed up on the West Coast? I mean, it's probably hard to pin down an exact reason, but are there theories?

0:04:02.6 GL: Yeah, we have some theories. We don't... We, like you said, we don't know for sure how they managed to cross the North Pacific and get over here. But there's a couple things that are at play. One thing is that you may have heard, but there's been some recent warming trends on planet Earth. And Japanese sardine are found in the western Pacific in temperate waters. Pacific sardine are in the eastern Pacific. And so we have really, really cold water up north in the Arctic and warm water down near the equator that have really acted as kind of dispersal barriers to keep these two species separated over hundreds of thousands of years. However, as things have warmed up in the Arctic, it appears that some of those dispersal barriers, in other words, that cold water, has warmed up enough that there may have been a potential habitat corridor that opened up and allowed for Japanese sardine to expand into that warmer water, which is now in a threshold where they can survive. And another important factor is that sardine, like many coastal pelagic species, during times of abundance, their range will expand. So Japanese sardines have gone through similar cycles of crashing and growing.

0:05:14.2 GL: And in the 1990s, they crashed pretty hard, but starting in 2010, they started to rebound. And when that happens, they can expand into new habitat. And so we think the combination, or a possibility, I should say, is that with warming climate and recent marine heat waves, the Arctic has warmed up. The North Pacific has warmed up enough for winter temperatures to be just at the thermal minima which sardine can survive at. And with expanding Japanese sardine numbers, these fish may have utilized that habitat and overwintered there and then potentially continued east during the spring and summer into the California current ecosystem.

0:05:57.9 JS: It is a little mind blowing. Right? That's a long way to go.

0:06:02.9 GL: It's a really long way to go. Yeah. It's, you know, the largest body of water.

0:06:06.6 JS: And they're such a little fish.

0:06:07.5 GL: They're such little fish. But as they get bigger, they're great swimmers. They track changing environments really well or the leading edge of changing water temperatures, for instance, because they're habitat generalists, so they can kind of utilize a wide range of habitat. They're really mobile, so they can move pretty far, both as adults and as larvae. And they have short generation time. So it's, of all the species we kind of expect to follow these changing environments, sardines are one of the ones we would expect to follow it pretty quickly.

0:06:39.0 JS: Oh, cool. So not to mix metaphors, but they're a little bit like the canary.

0:06:43.8 GL: Very good metaphor.

0:06:44.8 JS: Yeah. Canary in the Pacific.

0:06:45.9 GL: They're kind of like the canary in the coal mine.

0:06:48.9 JS: And let's talk a little bit about this genetic technique that you used to, you know, that made, that proved this out in the first place. You had to sequence its genome?

0:07:02.4 GL: Correct. Yes. This is a new technique that I had never used before. It's kind of a two-step process. So the technique is called low coverage whole genome sequencing. You basically, in each individual, aim to sequence the genome at low coverage, meaning in a given individual, parts of the genome may not be sequenced. But using a probabilistic framework, we can infer those genotypes based on sequence data from other individuals that we sequenced that did get that region sequenced. And an important component to this whole thing is that you have to have really a high quality reference genome and then you can align the low coverage assemblies of each individual to that reference genome. So it's kind of a complex process, but taken all together, you get data from across the genome and it's very, very powerful.

0:07:49.9 JS: Wow. And you kind of touched on this earlier, but when you combine that with the high quality samples that you have going back years, that's really what allowed you to have the confidence to say, oh, this is the first time.

0:08:04.4 GL: Yeah, that was kind of shocking. Honestly, we only looked at initially samples in '21 and '22. And the first year the Japanese sardine showed up was 2022. And we thought, oh, most likely they've showed up earlier than that. And we looked back through over now 4,000 samples going back to 2013, and indeed the first year we really detect them is in 2022. And they showed up in pretty high numbers. Now, this doesn't necessarily represent what the actual biomass is, but around 40% of the samples we genotyped in '22 and '23 were Japanese sardine, which was shocking.

0:08:43.0 JS: Yeah, yeah. That's huge. And so, you performed this low coverage sequencing of the genome and that was what let you determine these were Japanese sardines?

0:08:56.4 GL: Yes. So a cool windfall of targeting the nuclear genome at low coverage is that you get very high coverage of the mitochondrial genome, which allows for assembly of each individual's full mitochondrial genome. This is actually how we figured out that we had detected Japanese sardines. We had seen evidence from the low coverage whole genome sequencing data from the nuclear genome that these individuals were very different from each other. But we weren't sure exactly why that was the case. It wasn't until we assembled the full mitochondrial genomes of all these individuals and then compared those to online sequences available through sequence repositories that we really figured out, aha. Okay. The reason why these look so different is because these are in fact Japanese sardine.

0:09:50.8 JS: Crazy. I mean, that's such a, it's a microscopic clue that this huge thing happened across the ocean. That's incredible.

0:09:58.5 GL: Yep. It was very fun to work on and to kind of act like a CSI investigator to figure this out. And yeah, it was a very fun project and I feel fortunate to be a part of it.

0:10:10.3 JS: And not to be alarmist, but what does that mean? Are they here to stay? Are they fighting with the Pacific? I mean, are they interbreeding? What comes next?

0:10:24.4 GL: All really good questions, some of which we don't know the answer to. So are they here to stay? Is this... We do see in other systems, dispersal events that are ephemeral and the species shows up and only stays for a couple years and then they're kind of gone. We don't see them anymore. Or then we also see cases where the dispersal event happens and that species sticks around and is here to stay. Japanese and Pacific sardine, they look identical. They really use very similar habitats, so they may stick around or there could be a temporary dispersal event. We're not sure. It's important for us to keep monitoring. Another big question that you hit on is whether or not they can hybridize. Can they reproduce and with viable offspring, meaning the offspring of the two species, can they reproduce themselves? That's something we're actively working on trying to detect. So we're currently developing another genetic assay that will allow us to detect hybrids. But as of now, we have not detected any hybridization. And there's some evidence we see in the genomes of the two species that suggest they may not be able to hybridize, but it's not for certain. We need to conduct some more analyses to be able to determine if they can hybridize.

0:11:42.9 JS: Wow. Kind of going back to this idea of the sardine being kind of this canary species. Sorry if I'm making that a thing now.

0:11:53.0 GL: No, I like it.

0:11:54.3 JS: Could that, could this influence how you think about other species in the future, if there's a possibility for these kinds of migrations to happen in the future?

0:12:02.5 GL: Absolutely. That was kind of one of the conclusions we talked about in our paper was that, like you said, sardines are kind of the canary in the coal mine. They're early on expected to be some of the first species that would take advantage of such an opening in a habitat corridor. Other species may follow. What species that may be is just kind of speculation on our part. But I would guess that species with similar life histories that are again, highly mobile, they have short generation times and tend to be habitat generalists often make great dispersers. So potentially other species that have those characteristics could also take advantage of this potential habitat corridor, and we may see future dispersal events moving forward.

0:12:49.4 JS: This seems like a situation where there's a really big shift. This important species has now seen this influx from a different species. At the same time, there's not huge differences between them. Is there the potential for negative consequences or is this, is it also as possible that it's fine, everything's okay? This is something that happens in nature.

0:13:15.2 GL: That's a great question. And it's something we will continue to monitor and look at. It can really go either way. It may be like you said, they use the same habitat, they look the same, they kind of provide the same nutrients to other organisms that eat them. It may be that the presence of Japanese sardine may not change much in terms of how the ecosystem functions. That would be particularly true if they could indeed hybridize and produce viable offspring. So if Japanese and Pacific sardine can spawn with each other and their numbers aren't necessarily negatively influenced by each other, then yeah, you probably wouldn't expect to see too much change and you wouldn't necessarily need to be too worried. On the other hand, if they cannot hybridize and not produce viable offspring, there's a potential that they're competing for the same limited resources and they may be trying to spawn with each other and then wasting those eggs or sperm on other eggs and sperm that are not compatible. And so that could potentially have negative downsides. But that, again, we need to do more work and understand whether or not they can hybridize. And it may be that Japanese sardine are just here for four or five years or shorter.

0:14:38.3 GL: But again, this is just speculation on my part. We need to continue to monitor and determine whether or not this is a long term dispersal event or short term. And I think again, you hit on this earlier, but which one tastes better is probably pretty important as well.

0:14:52.6 JS: I mean, that's the most important thing to me.

0:14:54.2 GL: Yes, as a Sicilian American, yeah, I would agree that sardine taste is pretty important.

0:15:01.5 JS: This might be kind of a wild card. But did the increase in abundance of the Japanese sardines here, did that cause a crash in Asia?

0:15:13.9 GL: Oh, that's a great question. I don't think so. From the numbers I've recently looked at, the catch in Asia and Russia has been steadily increasing since 2010. So it doesn't appear that this dispersal event negatively influenced numbers in the western Pacific for Japanese sardine in their native range.

0:15:33.4 JS: And so I think one of the other big takeaways from this situation is that while it seems like there are a lot of unknowns, the big hero in this event has been time series surveys that have given you data going back many, many, many years that you're able to sort of make this declaration.

0:15:55.7 GL: Absolutely. This, in my opinion, one of the biggest takeaways from this whole study. This is very cool and it's amazing to see. And we're witnessing huge rain shifts and dispersal events. We're only able to witness this based on having these long-term data sets that monitor ecosystem level change. Without these, it would have been very unlikely that we'd be able to detect Japanese sardine and definitely very unlikely to go back and actually try and pinpoint when they showed up and what conditions may have changed that allowed for this dispersal event to happen. And so, as you said, long-term data sets provide baselines for us to be able to understand what's normal and what's not and how things change and how effects on ecosystem level and species level play out. It's really hard to do without long-term data sets.

0:16:50.4 JS: Dr. Gary Longo, thanks so much for talking with me.

0:16:53.3 GL: Thank you so much, John, for having me on.

0:16:55.8 JS: Dr. Gary Longo is a research scientist at NOAA's Southwest Fisheries Science Center and one of the authors of a new paper titled Crossing the Pacific: Genomics Reveals the Presence of Japanese Sardine in the California Current Large Marine Ecosystem. It was published in the journal Molecular Ecology. You can find links to the paper or learn all about sardine at our website fisheries.noaa.gov. I'm John Sheehan and this has been Dive In with NOAA Fisheries.