11 min read

Gene Pool Maintenance

Written by Russell McAndrews

This article is intended to be global in nature.  My impetus for writing it stems from my participation in the AAZPA’s Victorian Species Survival Program (VSSP).  Lake Victoria’s species flock are endangered by the man-introduced Nile perch (Lates niloticus).

The scientific community has neither the space nor the funds available to handle a problem of this scale.  On the other hand, the hobby, even just on a national level, has enormous resources and astounding potential in this regard.

The serious hobbyist can and should augment the scientific community.  Techniques ranging from record keeping to controlled experimentation can be helpful.  Any collection of data must be recorded if it is to be of any use.  One of the simplest means of accomplishing this is to write.  The best way to gain proficiency at any task is to practice it.  Keeping a simple note book is very valuable, these notes can even provide material for future writing.


Gene pool maintenance is a problem which exists primarily in the aquarium hobby where breeders small and large without enough awareness of population genetics, conduct evolutionary mayhem.  Generation after generation, many species are bred sibling to sibling.  The fact that they are bred at all is fabulous, and lays the foundation for all those efforts aspiring to bring a section of the aquarium hobby far enough in line with science to be scientifically useful.

The aquarist is a naturalist at heart he or she already possess valuable skills and usually has a keen desire to learn.  The three largest problems, two of which the hobbyist can help overcome, are ignorance, inconvenience and money.  The latter primarily lies in the domain of grant writers and fund raisers who are much more restricted group, but just as desperately  needed.  The first two hurdles, ignorance and inconvenience, both require coordinated efforts on two fronts.  Aquarists must not only be willing to learn, but someone, or some network, must also be willing to teach them.  Once the aquarist has some understanding of conservation biology and knows what to do, there is still no assurance that it will be done, effort is required.  What an active network can do is make it more convenient to locate and obtain required animals, not to mention the benefits or communication in the war on ignorance.

The average hobbyist is unwilling to spend the money on obtaining wild stock with its added cost of international shipping.  This tendency means that domestic stock is generally more marketable than wild stock.  Unfortunately, it can be very difficult to trace.  Domestic stock would need to be traced for generation identification (number of generations removed from the wild), or collection location.  As we’re finding out, many species can be extremely variable or “plastic”.  A different color morph is only one of the features which can vary from location to location.  What we assume today to be racial variation could turn out to be an entirely different species, we just can’t be sure.

An inventory of “species” presently in the hobby would list many popular hybrids and sports, particularly livebearers.  If we were to predict the future of the hobby by extending the situation of today, without a gene pool maintenance program, we would probably see the deterioration of most domestically raised species, the introduction of several new hybrids and the possible extinction of some presently endangered species.  The most immediate need for a program is centered around these endangered species.  Due to the fact that some wild stock has become endangered or extinct, these species have become irreplaceable.  As such they must be cherished, built upon, diversified and guarded against contamination.

From the perspective of the hobby, species could be threatened in other ways.  Much needed collection restrictions and local political turmoil represent two importation limitations.  Inbreeding and hybridization domestically and abroad are so extensive that they should instill real doubt as to the validity of entire tank-raised populations.

The word “species” is difficult to define.  There are no clear lines of demarcations between the words sport, variant, race, subspecies, and species.  There is no fixed amount of variation required to define speciation.  Instead, these words are relative because the concepts themselves are relative.  A species could be defined as a dynamic collection.  Dynamic describes the ever-shifting and fluid nature of a collection of genetic material.  In the following pages I shall outline two plans for maintaining a gene pool.  The first is a reasonably thorough controlled experiment, while the second, of limited control, is the more realistic approach.  My hope is that through implementation of either of these plans, the active hobbyist will be able to strip away false perceptions and the confusion that they cause.  Inbreeding and hybridization are the two main stumbling blocks which I’ve expounded upon in the formation of these plans.


Naturally occurring hybridization, although rare, does take place and is possibly to a lesser extent, responsible for the diverse cichlid fauna of Africa.  Inter-specific hybridization in L. Victoria is directly responsible for the extirpation of the two endemic tilapiines.  Although this is not strictly a “natural” incident, it is indicative of the process as it pertains to extinction and population dynamics.

Hybridization occurs in the hobby constantly.  Most all species will hybridize, and some people intentionally hybridize their fishes.  I’m happy to say that public taste seems to be swinging away from hybrids, although,  sometimes the commercial market’s appetite for anything new sets the hobbyist up  for a fall.  Unfortunately, there are plenty of breeders and fish farmers still harboring the ideas that fish are fish and a new fish is nothing more than an exclusive sales item.  All this aside, I believe that the majority of hybridizations that result in the contamination of specific gene pools are unintentional.

Unintentional hybridization can occur in a number of ways.  Possibly the most common and most insidious being when a hobbyist acquires a mistakenly identified pair or mate to be bred with an individual already at home.  Mistaken identities, especially regarding haplochromine females, produce innumerable hybrids which get passed off ignorantly by their owners as a species which they are not.  The tragedy taking place is two-fold.  Not only does one not know what one has, but since the hybrid looks like the desired species it is dispersed to contaminate further gene pools.  It is not too difficult to conclude that this particular problem is a proverbial “vicious circle”, every successive cycle is self propagating.

Another means by which hybridization could occur is when two or more species are housed together or even near each other.  Evolution has developed a mechanism where-by, water-born pheromones precipitate cascading spawning behavior among groups.  The benefit of this behavior becomes apparent both during the parental care cycle and at its end.  There is safety in numbers.  Typically, within the confines of an aquarium, a dominant male will spawn with any receptive females.  Even more typically, a dominant male will not allow any other similar subdominant males to spawn.  Anytime one places two species in a tank where spawning activity occurs, one is faced with the risk of producing hybrids.  The hobbyists may not even realize the two species are present.  Males or females chased out of their tanks sometimes wind up next door, mind you, they sometimes wind up three tiers down.

The last mode of hybridization which I would like to mention is that of fertilization across a divider.  Males have been known to fertilize supposedly inaccessible eggs by simply discharging enough milt to saturate the aquarium.  This can be employed as a useful technique for controlling murder in particular situations where a female stands little chance of surviving otherwise.

Granted hybridization will not always occur under the above circumstances, but there are certain simple steps which could be taken to minimize its probability.

Don’t place similar fish in the same aquarium or even within jumping distance.  Arbitrarily, I would say one species per genus per aquarium.

Positively identify each species as soon as possible.  To accomplish this end, deceased individuals should be preserved.  Freezing or 70% Ethanol for samples requiring DNA analysis; and 50-70% formation for fixation.  NOTE: (formaldehyde should be used with caution.)  Formalin is extremely carcinogenic and therefore less desirable from a handling standpoint.  Following fixation for about a week, the specimens should be stored in denatured ethanol (50-70%).

Keep records.  A note book, an informal ledger or anything else is better than nothing.  Label aquaria or animals.

Research a species prior to talking it home.  Accept responsibility for those which are brought home.  Don’t assume that the dealer will take responsibility after the fish leaves his/her shop.

Be discriminating in the dealers patronized.  If one of your local dealers is more helpful, give that dealer your  business.


Throughout the hobby, inbreeding is a way of life.  Nature, itself, is rife with cases of isolation induced inbreeding.  Circumstances which lead to isolation, whether natural or man-made, cause what I will call gene concentration.  Regardless of whether the situation is a seasonal puddle of killifish, a tiny black-water stream or a rock pile in a vast expanse of sand, isolation is the word.  Even in small populations, variations will be produced.  Given a smaller gene pool, these variations will culminate that much quicker.

Inbreeding and gene concentration are processes.  These processes are, in part, responsible for the intensely diverse cichlid fauna occurring throughout Africa.  The mechanism by which this process works is on-going.  Within the hobby a percentage of genetic material is lost with each passing generation.  Estimates for this loss run as high as 15% (Allendorf).  This will result in the passive selection of those genes which are not lost.  The layman’s term “selection” is the appropriate one for the process in each individual case, however, the term concentration more aptly describes the process within a gene pool.  An example would be a gene which concentrates via selection from 2% of the population to 50%.

Within an isolated population, the production of every successive generation is akin to shuffling a deck of cards.  Occasionally, a card will be dropped.  Similarly, a percentage of genetic material will be lost.  As a pair of aces might turn up on the top of the deck, so too recessive genes might find themselves without a dominant partner.  Even though these recessive genes may be present throughout the entire species population, it is only the probabilities of on-going concentration that enable them to show themselves.  Thus varying races are formed, typically in distinct locations.  This reiterates the importance of knowing the collection location of brood stock.  Over time,  assuming they survive and continue to vary, these races will form new species and even new genera.

Since inbreeding takes place in nature, why shouldn’t we let it take place in the aquarium?  Isolation and variation are parts of the greater process of speciation, this is evolution at work.  Within the hobby, at least for some species, we are attempting to preserve what we have “as is”.  (Granted, that with many other “species” this is  not the case and in fact new sports are desired.)  However, in the cases of threatened or endangered species, gene concentration is to be avoided if at all possible.  Developing a race or changing a species is not preservation.

A popular misconception in the hobby is that inbreeding only takes place over the course of years.  In actuality, time has nothing to do with it: every sibling to sibling spawn is inbreeding.  Unfortunately, a minor amount of this would seem to be unavoidable due mainly to the limits of availability with particular fish.  Tragically, continued sibling to sibling reproduction seems to be the rule rather than the exception at each step genetic material is lost and the viability of the stock is reduced due to fixation of lethal recessives.  Even though we seek not to concentrate recessive genes, they should not be indiscriminately eliminated either.

In some cases, the affects of inbreeding might be repairable genetically over one or more generations by means of “shuffling”.  By shuffling, I mean introducing a new blood line to the existing one.  A caveat regarding shuffling; through local and national organizations more hobbyists have been able to find more fish, and this is good.  However, it has efficiently aided hybrid contamination of much of the stock in the hobby.  The Pseudotropheus zebra complex presently in the hobby is almost worthless genetically.  Since the first importation of the “zebra” no less than six forms/species have been commonly imported from Lake Malawi.  These fish have all been bred and inter bred out of ignorance.  The Ps zebra complex has recently undergone a revision - too late for the hobby I’m afraid.  We now recognize these were not after all one species.  The example given above is a simplification of the overall problem which even includes inter-generic crosses.  Perhaps these crossing can be blamed on the inescapable confines of an aquarium.  Perhaps a break down of selective recognition is taking place.  Whatever the cause, in the interest of species preservation, I’ve outlined a couple of courses to guide fellow hobbyists.


All fishes involved in the preservation program need to be tracked.  This will enable any contamination, which might have gone unnoticed, to be totally removed at any point.  Wild stock should be sought and collection location recorded, as memories do fail.  Each successive generation should be labeled.  In this way the loss of genetic material can be tracked and minimized.  Eventually, siblings should be split up and swapped for mating with other confirmed populations.  As such, gene concentration can be minimized as well.

As mentioned earlier, I shall term the above technique “shuffling”.  If properly executed, shuffling can completely eliminate further concentration of genetic material.  The most logical procedure for inter-gene-pool shuffling is to rear young to a sexable size and then ship only males.  Due to the inherent dangers of shipping and relocation stress, losses should be expected so never risk an entire gene pool in one shipment.  Although males are no less genetically important, they typically out number the females in many populations.  Additionally, the females are at risk and suffer attrition as they are often murdered by their cohorts.  The potential growth rate of and population, and its rate of recoverability, is directly proportional to the number of females within the reproductive age bracket.  Males, in their less time consuming roles, are able to service several females at any given time.

Within the maintenance program, some of each and every spawn which is good must be saved, tracked, segregated by sex and generation and integrated with other confirmed gene pools of the same generation.  Ideally, each male will spawn with each female and each spawn will  be no more represented than another.  This is the future of the viable gene pool we hope to build.  Possibly some animals will possess genes that their siblings and cousins do not.  For a gene pool to be effective it must become a vast library of genetic material.  This storehouse must be large enough to be self-sustaining but not so large as to prove unmanageable.  The population size required for each and every species will surely differ as would the size of the aquariums involved.  Due to the numerical odds alone, there seems to be a direct correlation between the total number of chromosomes and the rate of variation.


Those hobbyists interested in doing something to help, but without the time, energy or resources to carry out a controlled experiment, I would recommend another  plan of attack.  This secondary plan constitutes a trade off.  Maintaining a dynamic colony represents an elevated level of inbreeding, relative to the CONTROLLED PLAN OF ATTACK.  The positive side of the arrangement lies in the enhanced opportunity for behavioral study.  A colony of fish, maintained in such a way as to recreate typical wild social interaction, is an extraordinary experience.  In most cases it will require some sacrifices and resources to produce and maintain the quarters of the size required to eventually house a dozen or more adults.  Assuming verified stock, a couple of factors directly relate to the quality of the gene pool.  They are; the size of the gene pool, and the rate of influx of new blood.  Certainly, even thirty adults would comprise a colony whose viability is thin at best from a natural perspective.

The multitude of locally raised and regularly imported species makes it extremely difficult to be specific as to technique of habitat.  Each aquarist will have to overlay the specifics of their situation and determine how best to make use of available resources.

Having determined the initial size of the colony, a decision must limit the number of individuals from each successive spawn slated for colonial reintroduction.  A random cross section should be taken by returning two to six fish from each brood to the colony.  Once a given male has been allowed to spawn with all the females in the colony, he should be removed.  By removing the primary male, a secondary male will rise to dominance and pass his genes on through a complete cycle and so on.  This technique takes advantage of the fact that nature will cycle the females and the hobbyist need simply cycle the males.  In addition to this, it is wise to bring in new stock, again, assuming verified genetic material.  The introduction of a new adult here and there will help by providing a genetic link with other gene pools and effectively create one large gene pool.  When adding new animals to an established tank, be sure to destroy any existing social or territorial structure to prevent the new-comer from being murdered outright.  Perhaps an easier means of acquiring new blood would be to exchange fry.  The degree of detail covered in this text is necessarily limited.  The multitude of locally raised and regularly imported species makes it extremely difficult to be specific as to technique or habitat.


Due to the inherent randomness of genetics and genetic material, one can never have too many genes, but could easily have too few.

Those of us whom have hybridized species, intentionally or unintentionally, have a responsibility to see that these fish are never passed on as something that they are not, preferably never being passed on at all.

Every serious hobbyist should keep a note book to record his of her experiences.  Gene pool maintenance is no light task, as such, any untraceable stock in the hobby should be considered useless for this task unless it can be positively identified.