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Distinctly different Chinook salmon are part of the same population

Two groups of Chinook salmon in northern California that have distinctly different migratory patterns are often considered to be separate species. But now, a new study from UC Santa Cruz reveals that seemingly complex differences in these salmon can be traced to one simple region of DNA.

Chinook salmon within a drainage basin like the Klamath River are characterized as separate ecotypes depending on whether they migrate during spring runs or fall runs. Scientists expected that these groups had diverged from one another due to a lack of interbreeding, resulting in complex genetic differences. 

The new study shows that the salmon do not have complex genetic differences after all, and are all part of a single diverse population. The only DNA that they do not share is a small genomic region that was found to be strongly associated with run timing, but not with other traits like development.

“It’s like blue and brown eye color in humans – it just depends on what genotype you inherit from your parents,” said study co-author Professor John Carlos Garza. He noted that the outcome of the research is very good news. 

The findings provide scientists with a new way to understand salmon ecotypes and will ultimately help in the management and conservation of Chinook salmon, the largest species of salmon. 

For the investigation, the experts sequenced the complete genomes of 160 Chinook salmon from the Klamath River and Sacramento River drainages. The only consistent differences between spring-run and fall-run fish were found within a single region on chromosome 28. Here, they identified a shorter “Region of Strongest Association” (RoSA) that occurs in two versions, “E” for early migration and “L” for late migration.

Next, the researchers sampled 502 Chinook salmon harvested by the Yurok Tribe in the Klamath River Estuary. There was no overlap in the timing of migration for fish with the “homozygous” EE and LL genotypes. EE fish migrate in the spring, and LL fish migrate in the fall. Fish with the “heterozygous” EL genotype had intermediate migration times, overlapping with those of the homozygous genotypes. 

According to Professor Garza, these results show that seasonal differences in migration are completely attributable to the RoSA genetic variants. “That was an extraordinary finding. I know of no other gene region that so completely determines a complex migratory behavior in the wild in a vertebrate.”

The discovery is particularly surprising because of the differences among spring-run and fall-run salmon in their fat content and other features. But in fact, said Professor Garza, all those differences are tied to the timing of migration as determined by the RoSA genotype.

“Spring-run and fall-run fish all start maturing at the same time in the ocean, but during that period after the spring run enters freshwater, they experience different environmental conditions, leading to differences in where and when they spawn,” said Professor Garza. “Also, people notice differences in fat content and body condition because they are encountering spring-run fish earlier in the maturation process than fall-run fish.”

The analysis of carcasses from the Salmon River, a major tributary of the Klamath, revealed that the spring-run and fall-run salmon were freely interbreeding. 

“It’s hard to come up with any scenario where you could classify individuals from the same nest as belonging to different populations,” said Professor Garza. “For me, one of the underlying messages is that, in our attempt to categorize things, we’ve overlooked the fact that these are fundamentally the same animal.”

The study is published in the journal Science.

By Chrissy Sexton, Staff Writer


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