Aquaculture Magazine

Octuber-Novembrer 2016

Genes Change...or, Concerns Over Genetic Sustainability

By C. Greg Lutz

Genes change. This, of course, is the basis of evolution.  And it often allows populations and species to persist when their environments change either abruptly or over time.  Individual genes can change from one generation to the next through mutation.  Relative frequencies of genes within a population can change due to any number of factors, from natural selection to population isolation to domestication pressures in an artificial setting.  These genetic changes are often a cause for concern, especially when interactions between captive and wild populations of aquatic species are considered.

By Greg Lutz*

However, the word “gene” often has too many meanings in casual conversation to explore these concepts. We use “gene” to describe not only a specific point in a chromosome that influences an observable trait such as blood type, body coloration, or disease resistance, but also to describe each of the various possible sequences of genetic instructions that one might encounter in a population. To avoid some of this confusion, it would probably be a good idea to introduce two terms that will clarify this discussion: locus (plural: loci) and allele. 
In the simplest terms, loci and alleles describe the chemical make-up of segments of DNA. Specific sequences of base pairs on chromosomes provide instructions for the production of amino acids within the cell. These combinations of amino acids in turn lead to proteins and the maintenance of cell (and organism) viability and function.  Along distinct linear portions of a specific chromosome, base pairs code for unique gene products. This physical location of instructions on a chromosome is referred to as a “locus.” The gene product(s) encoded for at any particular locus may pertain to one or many chemical processes within the cells in which they are expressed, or elsewhere within the organism. A number of distinct forms of instructions may occur at any given locus, and these distinct forms of instructions are known as alleles. When two distinct alleles are present at a given locus (one sequence on one chromosome and another on its paired homologue), one or both may be expressed.
This leads to the concept of allelic dominance.  If  two distinct alleles are present at the locus in question, the individual is referred to as “heterozygous” for that particular locus.  If both alleles are the same, the individual is “homozygous.”  In some situations heterozygous individuals are indistinguishable (phenotypically – in appearance) from certain homozygous ones.  In this situation, the allele for which homozygosity is indistinguishable from heterozygosity is referred to as dominant, and the other allele found within the heterozygote is referred to as recessive.  In contrast, if the heterozygotes are clearly distinguishable from either homozygote, the relationship between alleles is referred to as incomplete dominance.Occasionally, several to many possible alleles may occur at a single locus, resulting in complex patterns of not only dominance, but phenotypic expression as well. To further complicate things, all degrees of dominance can be found in nature, and frequently the alleles at two or more distinct loci interact in unexpected ways to influence the phenotypes we observe.
Often, many distinct loci ultimately affect traits such as growth, disease resistance, body conformation, digestive efficiency, fecundity, egg size, etc. etc. etc. These types of traits are often impacted negatively when inbreeding accumulates within a population.  Inbreeding, by its very nature, is of greater concern in small populations, where random “sampling” in the formation of genotypes from an available pool of gametes can result in the eventual exclusion of certain alleles and the fixation of others.  Clearly, not a sustainable situation.  This random loss of genetic variation is referred to as “drift.”  
A practical way to look at inbreeding is by determining the probability that both alleles at a given locus are identical by descent from a common ancestor. There is a 50 % chance of two offspring from the same individual inheriting the same allele at a given locus, and a 50 % chance for every generation thereafter that that particular allele will be passed on from parent to offspring. The tendency for smaller populations to be more prone to inbreeding is exacerbated when unequal numbers of male and female broodstock are utilized, as is often the case in aquaculture facilities. 
In traits correlated with fitness, inbreeding depression typically results from ‘directional dominance’ at the majority of loci affecting the trait, in the direction of increasing (improving) the value. The evolutionary mechanisms responsible for this tendency have historically been poorly-defined.  Nonetheless, breeding between more closely-related individuals tends to increase homozygosity of all alleles. So, as small populations  reproduce over a number of generations all alleles tend toward becoming fixed. As a consequence inbreeding results in a reduction of the mean values of traits associated with fitness (specifically in the direction of the more recessive alleles) when the effects of all loci are summed.  
The concept of conserving wild populations as genetic reservoirs to offset the consequences of inbreeding and drift in aquaculture stocks has been widely proposed in the past.  Using both models and common sense, researchers have demonstrated that when a wild population is purposely enhanced by hatchery releases, the most genetically sustainable approach to maximize diversity over time is to use only wild spawned individuals as hatchery broodstock, year after year.  This, of course, requires some means of marking hatchery fish so they can be recognized once they reach adulthood and not returned to the hatchery.  Short of this, the most sustainable strategy would be to use wild male broodstock with hatchery reared females, but this also requires some way to know which fish are which. 
How we manage our stocks can impact how much (or little) genetic variation is lost over time.  Researchers used five polymorphic loci (loci with several to many alleles) to evaluate factors leading to reductions in genetic variation among stocks of Oreochromis shiranus in Malawi. They examined 14 populations and noted that the mean number of alleles per locus was higher in wild populations than domesticated ones, reflecting reduced genetic variation.  Other measures of genetic diversity were also lower in domesticated stocks, generally reflecting the time elapsed since each stock was established.  Genetic differences among farms were strongly influenced by exchanges of breeding stocks between farms.  In this situation, socio-economic patterns and farmer behavior better explained and predicted the process of genetic change in domesticated stocks than standard population genetic time-and/or distance modeling.   
Over the past two decades studies have shown that cultured populations of Gilthead seabream from the Mediterranean and Atlantic coasts of southern Europe were highly divergent, apparently as a result of genetic drift caused by different factors pertaining to their distinct histories. In spite of these differences among production stocks, cultured populations showed only a slight decrease in overall genetic variability when compared with their wild counterparts.  This decrease was not considered sufficient to indicate inbreeding depression. Additionally, there is limited evidence for gene flow from cultured to wild populations, since high levels of differentiation have been reported between production stocks and immediately adjacent wild fish populations throughout the region. 
Some years ago, scientists documented effects of a founder event (the result of ‘sampling’ a population to establish a captive line or make an introduction elsewhere) and supplementary introductions of additional breeding stock on a captive population of the endangered Spanish killifish (Aphanius baeticus). They used 12 polymorphic loci to assess genetic change over time. While results suggested the initial founder effect was negligible, after three generations genetic differences between the captive population and its wild source were high. The incorporation of a number of wild individuals at that point decreased these differences after two generations. These efforts served to avoid rapid inbreeding and domestication selection, while providing some guidelines for maintaining long-term evolutionary potential in small, isolated populations. 
A number of interesting studies are available on this topic, and it will undoubtedly take on more importance over the next several decades.  With proper planning, habitat protection, and an understanding of species’ biology, genetic sustainability can often be maximized both for wild and captive populations of aquatic organisms. 

C. Greg Lutz, has a PhD in Wildlife and Fisheries Science from the Louisiana State University. His interests include recirculating system technology and population dynamics, quantitative genetics and multivariate analyses and the use of web based technology for result-demonstration methods.

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