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Study Reviews Conservation Hatchery Practices, Recommends Strategies For Genetic Diversity
Posted on Friday, July 17, 2015 (PST)

If conservation hatcheries are to operate to maximize genetic diversity and population size while minimizing inbreeding when introducing hatchery-bred salmon to wild stocks, some hatcheries may need to alter their genetic management practices.


A recent review of conservation hatcheries provides a summary of current and potential fish hatchery genetic management practices and recommends strategies to guide management of conservation hatcheries in the future.


According to the study, published last month in the North American Journal of Aquaculture, the overarching goal of a conservation hatchery is to “prevent the extinction of threatened or endangered stocks by enhancing natural production” and rebuilding the depleted stocks of fish, while “minimizing the genetic impacts of releasing hatchery fish on wild populations.”


The study surveyed 36 hatchery programs. Some 28 of the hatcheries were conservation hatcheries with stocks as far ranging as cutthroat trout, chinook, coho, Atlantic and sockeye salmon, and steelhead.


Important goals for the conservation hatcheries, according to survey results, are preserving the stock’s genetic diversity, managing for effective population size, minimizing inbreeding and providing fish for introduction into streams.


The survey found that one of the biggest differences between non-conservation and conservation hatcheries is that non-conservation hatcheries use random mating to both select and pair fish. Conservation hatcheries, on the other hand, can use a variety of genetic methods.


“For small conservation hatcheries, we recommend genetic management techniques that maintain genetic diversity, minimize inbreeding and maintain effective population size, such as equalization of family sizes and pedigree-based mean kinship selection,” said Kathleen Fisch, computational biologist with the Center for Computational Biology and Bioinformatics at the University of California, San Diego.


Not all conservation hatcheries are meeting all these standards. Some 62 percent of conservation hatcheries use a random mating scheme and single pair mating, but few track the pedigrees of the fish. Single pair mating involves mating a single male with a single female.


“There have been several studies that demonstrate mate selection in wild populations is non-random (although mating systems may differ by species), so random mating in a hatchery likely does not mimic wild reproduction, as you are eliminating mate choice and possibly mating related individuals,” Fisch said.


Ideally, the report says, “full-sibling families should be kept separate until individuals can be uniquely marked physically or genetic marking can be implemented.”


Once that is done, a pedigree can be established, something that even fewer of the hatcheries actually do (just five of the 36 hatcheries reported have established pedigrees). Without the pedigrees, single pair mating can result in the “reproductive potential of mates being linked to one another,” the report says.


“Factorial mating” is recommended by a number of other studies. It involves “crosses between all possible parents or matings of single females to overlapping pairs of males,” the study says. Over half the conservation hatcheries use this scheme. In one study cited, “partial and full factorial mating were the most efficient mating schemes to preserve long-term genetic variability and single-pair schemes were the least efficient.”


In fact, another study concluded that the scheme could result in a 33 percent increase in the effective number of breeders over single pair mating. However, full factorial mating is generally feasible only in small populations, the survey concludes.


“Molecular relatedness” estimates can help hatchery managers avoid mating siblings and can reduce the risk of inbreeding. Conservation hatcheries that use molecular relatedness to develop breeding matrices, the report says, includes Snake River Sockeye, listed as endangered under the federal Endangered Species Act.


“In small populations, which by definition  include almost all of those in conservation hatcheries, avoiding full-sibling matings resulted in higher genetic diversity in the hatchery only so long as the practice continued,” the study says. This effect disappeared once the fish were introduced into the wild, however.


An important management scheme is equalization of family size (EFS), in which each family contributes the same number of offspring to the next generation. Methods for doing this include “culling the number of offspring from each spawning pair, mating the same number of offspring to produce the next generation, and releasing the same number of offspring from each spawning pair into the wild to reduce the reproductive variance,” the study says.


This is difficult, time-consuming and expensive, but some conservation hatcheries are beginning to use EFS to “increase effective population size in captivity,” the study says.


The report concludes that if a “manager aims to maximize genetic diversity and effective population size and minimize adaptation to captivity, this could be accomplished by starting with a large number of founders, minimizing the number of generations in captivity, using locally adapted stocks, employing factorial mating designs, and implementing procedures to equalize family size.”


The study, “Fish Hatchery Genetic Management Techniques: Integrating Theory with Implementation,” was published online June 19, 2015, in the North American Journal of Aquaculture,


In addition to Fisch, study authors include, Christine Kozfkay, Idaho Department of Fish and Game; James Ivy, Collections Department, San Diego Zoo Global; Oliver Ryder, Institution of Conservation Research, San Diego Zoo Global; Robin Waples, NOAA Fisheries NW Fisheries Science Center, Seattle.



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