A Chinook jumps Rainie Falls on the Rogue River. Photo: Tim Palmer

Written by Native Fish Society member Renee Fitts

Thompson et al., in their new paper,“Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations,” have addressed an important question with convincing science.


When a dam is removed from a river, thereby making new habitat available for Chinook salmon, will it be possible to restore the salmon population to include both early run (spring) and late run (fall) fish? This is an important question for all rivers facing changes in fish populations that are presumed to have happened as a result of human intervention, i.e., construction of dams that may now be removed. If an effort is made to restore fish populations to include variants that were present historically, what fish should be introduced?

Rogue River Chinook:

The Lost Creek Dam has changed at least the temperature and flow regime in the habitat of the Rogue River for salmon. Over time, the numbers of early run Chinook have dramatically decreased. It is not known whether this decrease would have occurred in the absence of the dam construction and correlated effects on the river (just called “the dam” here), if the dam accelerated the decrease, or if the dam is wholly responsible for the decrease. Whatever caused the decrease in the early run Chinook population is called selection – either in favor of the late run Chinook, or against the early run Chinook.

How early run (spring) and late run (fall) Chinook are different:

There is a genetic difference between early run (spring) and late run (fall) Chinook salmon that appears to be correlated with early vs late migration. In other words, there do not seem to be multiple reasons for a fish to be an early or late migrator, but just one.

This difference is detected by a sequence associated with the GREB1L gene. The function of this gene is not understood, nor is it clear that this actual gene is responsible for the difference in migration of spring and fall salmon. This is a “genetic marker” that detects this difference.

Most animals have chromosomes that match up as pairs, one from mom and one from dad. Thus, one copy of a gene comes from mom, and the other from dad. These are called “alleles”. Alleles can have identical DNA sequences, or can have different sequences. The differences in DNA sequence may cause differences in functionality in the gene. When the alleles are identical, the animal is called a homozygote for the gene; when they are different, the animal is called a heterozygote.

Spring and fall salmon can reproduce to generate a heterozygote that has one copy of the early run GREB1L allele and one copy of the late run GREB1L allele. These heterozygotes migrate in the summer, and are thus neither early run nor late run. If these heterozygote fish reproduce with each other, their offspring would include homozygote babies for the early run GREB1L allele, homozygote babies for the late run GREB1L allele, and more heterozygote babies. Thus, in some situations, introducing heterozygote fish could provide a “reservoir” of the early run allele, i.e., a way to generate more early run Chinook fish in a population.

Heterozygote early run/late run Chinook are “summer run” fish, in between early run and late run fish. It is not clear, though, whether these fish can reproduce normally or at all in the river.

The Klamath as an example:

The Klamath River historically had both healthy early run and late run Chinook populations. By studying archaeological fish samples, the authors of this paper correlated the genetic composition of early run Chinook and fall run Chinook in areas where they were reported to have been caught before dam construction. Dam construction and its consequences have been associated with a dramatic loss of early run Chinook over time.

The authors asked if the salmon that currently populate the “below dam” waters have the early run allele. These could be heterozyogotes with both the early run and late run alleles, or could be early run homozygotes that have somehow adapted to the environment. Conclusively, the authors showed that these “below dam” fish were almost exclusively late run homozygotes, with only one tenth of the early run/late run heterozygotes that might be expected in the population. The early run/late run heterozygotes have thus not been reproducing in a way that would generate early run homozygotes. Repopulation of the early run Chinook population is extremely unlikely to happen from these “below dam” fish if they are left to themselves.

The authors also asked if this “loss” of the early run allele is happening in other rivers, and found a similar result in the Scott River.

So what fish to use to repopulate the early run Chinook?

Because there just seems to be one difference, i.e., one mutation in the evolution of early run and late run Chinook from one common ancestor fish, it is unlikely that this mutation event and selection for this mutant can happen again in the foreseeable future. What exactly the DNA sequence is that causes this difference in migration in these fish is not known, nor the function of the gene, nor the selection in nature that favored the fish that carried the early run allele. In other words, we cannot wait “for nature to take its course” for early run Chinook to evolve from late run Chinook. If we want more early run Chinook in the rivers, we need to find another way.

Why not use early run/late run heterozygote fish to repopulate?

Heterozygote fish seem to migrate at a time that is between early run and late run fish. Because the frequency of these heterozygotes is so low in the river populations studied, it suggests that heterozygotes have little advantage over their homozygote parents. Biologically, that could be detrimental, as these fish may not have enough time to sexually mature to reproduce in the fall like their homozygote parent fish. Whatever selection is occurring against the early run Chinook may also be affecting the heterozygotes, or the heterozygotes may have problems of their own.

Will removal of dams also remove the selection against early run and heterozygote Chinook?

This is the million dollar question. It is assumed that the human influence imposed on the rivers by building dams is responsible for selecting against the early run Chinook and, possibly, the heterozygotes. If so, then introducing early run Chinook should help to restore early run Chinook populations.

But what about heterozygote Chinook? These fish may still not be able to reproduce effectively or compete in nature with their homozygous parents. Introduction of early run/late run heterozygotes would then not result in the repopulation of early run homozygous Chinook.

How can we tell what would work?

Without more information about the viability of heterozygotes in nature, about the function of the GREB1L gene or some other gene that determines early versus late migration, or about what the selection pressure actually is in the river, we can’t tell. Introduction of early run Chinook or early run/late run heterozygote Chinook into a river under restoration after dam removal is an experiment that with current tools, such as the genetic analyses used by these authors, could allow a real time evaluation of the effectiveness of repopulation, and that would have applicability over a wide range of diverse rivers.

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