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Cracking the Code: Scientists Use DNA to Examine Differences between Hatchery and Wild Chinook Salmon in Southeast Alaska

February 14, 2024

Hatchery-reared salmon show genetic differences from wild populations in only a few generations, but those differences vary among hatcheries.

Large school of fish swimming in greenish water

A new genetic study shows hatchery salmon’s adaptation to their environment can lead to potentially adaptive genetic differences between hatchery and wild salmon populations in only a few generations. The collaborative research was conducted by scientists from the Alaska Fisheries Science Center, Alaska Department of Fish and Game, and Texas Christian University. It’s some of the strongest and most fine-scale evidence to date of these differences.

Pacific salmon hatcheries are used to increase harvest opportunities and supplement declining wild populations. Many hatcheries generally aim to minimize the genetic and ecological impacts of hatchery techniques during the collection, mating, and rearing of fish. These practices aim to preserve the original genetic composition of the wild population in captivity.

However, evidence suggests that hatchery rearing can inadvertently select for traits that may be disadvantageous in the wild. This could have downstream implications for native stocks, if these fish breed with wild fish when they are released. One of the goals of this study was to identify the genetic signatures of hatchery-induced adaptation, known as domestication selection. The information could aid in the development of management approaches that reduce unwanted change in hatchery-reared fish.

Several published studies have investigated domestication selection in Pacific salmon on a genomic level. However, this is only one of two studies that paired samples of hatchery-raised fish and their stock of origin from several locations.

Domestication selection is the primary mechanism that leads to reduced fitness (the ability to survive and reproduce) for hatchery fish. Yet, scientists do not know which traits may be driving the observed fitness reductions. They also don’t know how it may affect the ability of hatchery salmon to adapt to future environmental change. 

“We don't know if domestication selection acts consistently across hatcheries, or if responses of salmon are unique to each facility. The purpose of our study was to determine if levels of domestication selection varied among hatcheries and if there were any commonalities across the populations,” said lead author and Texas Christian University student Natasha Howe. 

“For example, if we observed the same pattern across all hatchery populations at certain locations in the genome, then that would be pretty striking evidence that those regions are likely influenced by hatchery rearing. Then, we could target those regions in future studies to understand what’s driving domestication. We predicted that hatchery practices could have a large influence on the amount of domestication selection occurring. Hatchery practices that prioritize genetic diversity can potentially reduce the genetic impacts of domestication,” added Howe. 

Domestication Selection in Salmon Hatcheries

Unlike most methods of captive breeding, hatchery-reared salmon are released into the wild once they complete their freshwater juvenile life stage. Juvenile fish in hatcheries are reared in a stable environment with abundant food and no predators. As a result, compared to wild fish, hatchery fish show:

  • Increased competitive behavior and aggressiveness
  • Faster growth
  • Reduced predator avoidance

The stable environment also increases their survival rates at this early stage of development. For example, egg to smolt survival in hatcheries is commonly greater than 85 percent, compared to 1–10 percent in the wild. 

However, when hatchery fish are released into the wild, they generally have reduced reproductive success and decreased survival rates compared to their wild counterparts. This poses a risk to wild populations if hatchery-reared individuals interbreed with wild individuals. 

Whole Genome Sequencing

All organisms (bacteria, plants, animals) have a unique genetic code, or genome, that is composed of organic molecules (Adenine (A), Cytosine (C), Guanine (G) and Thymine (T)). If you know the sequence of the molecules in an organism, you have identified its unique DNA fingerprint, or pattern. Determining the composition and order of these molecules is called sequencing. Whole genome sequencing is a laboratory procedure that determines the composition and order of molecules in the genome of an organism and how the order may vary between organisms. This is helpful for scientists studying domestication selection because it allows them to view genomic differences across a population, rather than only an individual.

Scientist with lab work and scientific equipment
Scientists used whole genome sequencing to look for signals of domestication selection in three separate hatchery populations of Chinook salmon in Southeast Alaska. Credit: NOAA Fisheries

Scientists used whole genome sequencing to look for signals of domestication selection in three separate hatchery populations of Chinook salmon in Southeast Alaska. In Alaska, salmon hatcheries are primarily intended to enhance fisheries rather than to directly supplement wild populations.

Differences Among Hatchery Populations

Hatcheries locations marked with a circle and wild salmon marked with a square on a map of Alaska
Site map of Southeast Alaska and the corresponding locations for each hatchery population (circle) and corresponding wild population (square). Matching colors are indicative of hatchery-wild population pairs. Credit: Natasha Howe.

The three hatchery populations selected for this study differed substantially in their fish culture methods and goals. Whitman Lake Hatchery and Macaulay Hatchery are production-focused hatcheries. They produce larger numbers of fish (returns larger than 10,000; broodstock sizes greater than 400) to supplement commercial and recreational fisheries. The fish in Whitman Lake are descendants of fish collected from the Chickamin River. The Macaulay Hatchery brood is derived from Andrew Creek, a tributary of the lower Stikine River.

In contrast, Little Port Walter is a research facility that maintains a hatchery stock of  Chinook salmon for research purposes and to support Pacific Salmon Treaty management. The line is derived from the Unuk River, located near Ketchikan, Alaska. The hatchery produces smaller returns (one to two thousand) and broodstock sizes (100–200 fish in most years).

Scientists found that hatchery lines from all three hatcheries were subtly to moderately diverged from their wild stocks of origin. This is not surprising since these hatchery populations have been separated for approximately 30–40 years. 

Notably, the Andrew Creek and Chickamin stocks at Macaulay and Whitman lake hatcheries were more similar to their wild populations than the Unuk stock at Little Port Walter. This finding is largely due to the fact that the production-focused facilities spawn more fish each year than the smaller, research-focused facility. This is good news, as larger populations can help preserve overall genetic diversity. 

“Interestingly, changes in the genetic sequences between hatchery and wild salmon were not the same across the different hatcheries, suggesting that domestication of hatchery fish can occur through different genetic pathways. Unfortunately, we lacked phenotypic data such as length, weight, and fecundity of individual fish for two of the hatchery populations, so we still do not know which traits are most affected by hatchery rearing,” said Charlie Waters, research fish biologist at Alaska Fisheries Science Center and manager of Little Port Walter Research Station. 

Looking Ahead

Graphic showing differences in genetics between salmons from hatcheries versus wild salmon
Genetic differences or variation of base-pairs between individuals may lead to differences in an individual’s expressed traits such length or weight. In this example, a single base-pair substitution (A-T to C-G) results in a smaller individual. Credit: NOAA Fisheries

The results from this study highlight the need for hatchery monitoring programs to collect paired genotype-phenotype data. The genotype of an organism is defined as the genetic sequence at one or more genes of interest. The phenotype of an organism is the observable physical or biochemical characteristics of an organism (such as length or weight), determined by both genetic make-up and environmental influences. 

Identifying the links between the genetic code (genotype) and expressed traits (phenotype) in salmon will be key to future research efforts. It will help scientists and managers understand how the fitness of hatchery fish may be affected and how salmon may respond to changing environmental conditions. 

Scientific and technological advances have enabled the rapid generation and screening of genome-wide data to identify associations with selection and the emergence of harmful traits. Research examining the link between genetic code variations and fitness-related traits holds promise. It can offer insights valuable for hatchery management, aiming to reduce domestication selection and safeguard wild stocks.

Last updated by Alaska Fisheries Science Center on March 08, 2024