Monterey Bay Salmon & Trout Project

By Carlos Garza (NMFS Geneticist) & Jamie Alonzo (MBSTP Board Member)

Genetics and Endangered Species Act Listed Salmonids California is Blessed with a diversity of salmonids that exceeds that of any other state in the nation. Many are anadromous, spending part of their lives in both fresh and salt water. Anadromy, along with highly variable environmental conditions, has led to widespread specialization and adaptation to local conditions.

Adaptation deals with all of the small changes that accumulate in a species over time (also called evolution). These changes help in the specialization of animals by increasing their ability to survive and reproduce in their particular environment. Genetic material called DNA acts as the instruction book for the development of all animals and during reproduction, DNA from two parents is mixed and passed down to offspring. Adaptations are 'coded for' in an animal's DNA and, thus, are also passed down through the generations. As an example, egg size in chinook (King) salmon, generally decreases as one moves north in latitude (this has to do with differences in water characteristics such as temperature, flow and productivity). Chinook salmon living in central California have relatively large eggs which better enables them to survive in this climate. This characteristic (i.e. females that produce large eggs) is passed down from generation to generation and can be considered a specialization or adaptation to local conditions.

Even though chinook salmon living on the central California coast generally have larger eggs than chinook salmon living in more northerly latitudes, there is still variation in egg size among central coast Chinook salmon. This is true with most all adaptations. It turns out that this variation in adaptations is also very important to the health of a population. These differences in adaptation between animals in the same population, even if small, can have a very large effect on the size of a population, especially over many generations and in small streams. Again, this has to do with the populations ability to survive and reproduce in its environment (discussed below). Though differences in adaptations are often difficult to measure, the fact that they are represented in an animal's DNA instruction book allows scientists to look for differences in DNA to determine if there are differences in adaptations.

As discussed previously, variation in adaptations is important to the health of an animal population. This is true for at least three reasons. First variation in adaptation keeps populations from experiencing inbreeding depression. Like adaptations, genetic diseases can also be passed down from parents to offspring through the DNA (e.g. Parkinson's Disease in humans). However, many of these diseases require that there are two copies of the disease-causing DNA in the individual before the disease is expressed: one copy from the mother and one from the father. If a population of animals has a lot of variation in adaptations, it means that they also have a lot of variation in DNA, which decreases the chance that any individual will inherit two copies of the same disease-causing DNA from its parents. Populations with low genetic variation are characterized by more genetic diseases, which make the population as a whole more unhealthy.

Second, the ability to fight off new parasites or diseases can also be genetic. If a population of animals has a lot of variation in the DNA, there is a better chance that some individuals will be able to survive when a new parasite or disease enters a population. In populations with low genetic variation, a severe epidemic could wipe out the entire population.

Third, having genetic variation is what allows fish populations to change as the environment changes. For example, we know that DNA is involved in a steelhead trout's ability to tolerate high temperatures. Fish with different kinds of DNA can tolerate very different temperatures. The presence of these different genetic types in a population could be the difference between survival or extinction if stream temperatures rise.

In the last ten years, 10 of 16 anadromous salmonid stocks in California have received protection (i.e. been "listed"), under the US and California Endangered Species Acts (ESA). One of the initial phases in the ESA listing process is the implementation of 4(d) rules that act to regulate certain activities that could result in harm to these endangered populations. These regulations are due to declines in population numbers and environmental health, and are in response to citizen petitions. The ESA 'listing' sets in motion a process that uses scientific-based criteria to direct management and regulatory decisions.

Because of the reasons described above, one of the types of scientific information used to guide such decisions is information concerning variation in adaptations and DNA. One of the activities that
Are regulated by the 4(d) rules is hatchery practices. There is a
Substantial body of evidence that hatchery practices, if not properly carried out, can cause great harm to wild stocks. Two ways that this can occur are as follows. First, salmon stocks that have become accustomed to the hatchery "way of life" can cause widespread decline by displacing and/or breeding with locally adapted stocks. Second, many times only a few parents are used for many thousands of offspring in hatcheries.Over time, these offspring generally lose some of the DNA variation found in the wild population and become inbred. If these inbred fish then replace or breed with the wild populations, the new resulting population is missing much of the variation in DNA necessary for survival.

One way to combat this problem is to look at the DNA of the parents before breeding so that the variation in DNA is maximized and inbreeding minimized. Big Creek hatchery, run by MBSTP, does this. One specific 4(d) regulation that prohibits fish from being moved between basins, is based on another genetic principle called outbreeding depression.

Though we outlined above how variation in DNA or adaptations is good, there are some cases where it can be bad. Imagine that two adult salmon are brought to the hatchery for breeding from a stream far away, where the environment is very different. These salmons' adaptations won't necessarily match the new environment around the hatchery. As a result, their offspring will experience low survival and reproduction In this new and different environment as will the offspring of the natural fish they breed with. In this way, fish in different basins can be at risk for outbreeding depression if introduced to 'foreigners'.

These are just some of the complex and difficult issues involved in The management and recovery of our salmonid fisheries. While many are skeptical that recovery can be achieved, if it does not, the science-based approach will not be to blame. A lot of human activity over a long period of time is responsible for many of the problems that we see today. The science-based approach is meant to shorten the time and activity that will be required to reverse the effects. Though regulation will likely leave all parties feeling as if they are making unnecessary sacrifices, it is the eventual hope that all of the groups involved will be able to work together to ensure the preservation of these magnificent fish.

Finally, it is worth mentioning that hatcheries are not always Considered the 'bad guys' when it comes to raising salmon. In fact, many scientists believe that, if hatchery practices are carried out properly, hatchery stocks will not be a detriment to the natural populations and that they can actually play an important role in recovery and conservation. Many of the problems observed in hatchery stocks come from the large industrial hatcheries where, historically, little thought was given to product quality or the potential consequences associated with raising 'un-natural' fish.

Smaller operations, such as the Big Creek hatchery, can and do take more care in raising a quality product. This has a lot to do with their ability to adapt their hatchery practices as the science behind raising fish improves. Unfortunately, hatcheries tend to be managed as a group with regulation based on the worst offenders.

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