This chapter seeks to clarify the meaning of animal genetic resources, how they are formed, how they may be expected to change and the major processes which act upon them.
Within the nucleus of every mammal cell there are two complete copies of the DNA (deoxyribonucleic acid) blueprint which determines every genetically controlled feature of the animals development, physiology and much of its behaviour. DNA is a complex chemical which is very stable, can replicate with great fidelity and carries the genetic code. All living cells contain two complete copies of their DNA blueprint, or sets of chromosomes, with the exception of ova and sperm cells which carry only one copy. A new embryo is made up of a complete double set of chromosomes, with one copy inherited from each parent.
The majority of the functional DNA is identical for all animals within a species because it codes for critically important proteins, essential for the creation of a viable organism. For some genetically controlled characteristics there are, however, a number of possible ‘options’. These take the form of slightly different DNA codes which result in animals with slightly different appearance, survival or production characteristics. These may be, for example, differences in coat colour or differences in the efficiency of a particular natural hormone influencing growth rate.
If an animal inherits two different genetic ‘options’, one from each parent, it may exhibit the combined effects of both genes or the effects of only one of the genetic ‘options’. In this case the gene whose effects are observed is said to be ‘dominant’. The gene which is present, and may be inherited by the animals offspring, but whose effects are not observed in the presence of the dominant gene, is said to be ‘recessive’. In this way a gene may exist in a population for many generations without its effects being obvious.
Mutation - The Creation of New Genetic Variation
Throughout the growth of an organism and during the production of sperm and ova cells the genetic blueprint, coded in the DNA chain of every cell is repeatedly copied. The copy mechanism is extremely accurate but spontaneous changes between the original and the copy DNA codes do occur occasionally. This is known as mutation and may be due to either the mis-copying of the DNA sequence, spontaneous breaks and incorrect re-ordering of the sequence, or to damage to the DNA sequence which may be brought about by radiation or chemical interference. Mutation may result in the production of a more efficient functional gene but more often they result in non-functional or deleterious genes.
Rates of mutation have been calculated to be in the order of 1 in 100,000 per generation. An embryo inheriting a detrimental mutated section of DNA from one parent is likely to inherit a normal matching DNA segment from the other parent. In this case the normal piece of DNA will continue to function and there will be no obvious affect on the development and functioning of the animal. When this animal reaches adulthood and reproduces itself, it will pass the perfect copy of the gene to, on average, half its offspring and the miscopy to the other half. Provided its mates carry a normal copy of this particular section of DNA none of its offspring will be detrimentally affected. In this way a rare mutated gene can exist as a ‘recessive’ or hidden gene for many generations. The only time it will become apparent is when both a sperm and an ova come together, with exactly the same piece of mutant DNA. In this instance the newly formed embryo will have two copies of the mutant DNA and no original copy. Success or failure of the embryo will then depend upon the importance of that DNA segment in the development and functioning of the animal. If it codes for a critical gene the embryo will fail, resulting in the appearance of reduced fertility in the parents. If it codes for a less critical gene, a higher chance of mortality after birth or a reduced growth and development rate may result. If it codes for a non-functional section of DNA there will be no affect on development of the embryo.
The process of domestication began some ten thousand years ago, and both the process and the domesticated stock produced by it have been carried by migrating humans to all but the most remote regions of the earth. In each region and local area, domestic populations adapted and evolved in response to a great range of selection pressures. In each case the primary factors contributing to the final population were complex and included founder affects, migration, mutation, natural selection and selection by man (Clutton-Brock, 1981; Mason, 1984; Ucko, 1969; Zeuner, 1963).
The genetic make-up of each and every breed or population is largely dependent upon the genetic make-up of its founder group. This foundation group was in turn dependent upon the selection pressures it had previously encountered and upon the genetic make-up of its own founder group. Thus, as tribes of people migrated across the globe they took samples of their own livestock with them to their new homes. In each location the people and their livestock would adapt through selection which is the survival of those individuals genetically suited, or able to adapt to the new environment. A sample of this population would then be taken with the next human migration to be the founders of a new community in a slightly different situation. Study and measurements of the physiological variation between populations have enabled quite detailed plans of the early migrations of mankind to be produced. Protein electrophoresis, DNA hybridization, restriction site polymorphism techniques and mitochondrial DNA studies can also be used to identify variations between breeds and calculate the genetic distance between populations (Sharp 1987; Nei 1987).
The migration of people and livestock has not generally been in one continuous direction although there are exceptions where geographically isolated populations have been cut off from subsequent migratory influences, as for example in Australia and Iceland. In most regions there has been fairly constant trade in livestock from one community to the next throughout human history. When animals arose through mutation or trade, that had better survival or production characteristics than those found in the local population, more of their adapted progeny would survive and the enhanced characteristics would soon become common or even fixed within the group. Thus, other than geographically isolated situations, a gradual inflow of genes has modified every population that exists today.
Rare changes in the DNA code, caused by miscopying or damage to the DNA chemical do occur and is known as mutation (see section 2.1). Mutation is normally detrimental and often results in non-viable cells, embryos or organisms. Mutated animals may, however, survive with reduced viability, or if the affected DNA sequence was not important the mutated animal may exhibit little or no physiological affects. Very rarely mutations may occur, by chance, which confer a survival advantage on the individual as compared to other animals within the population. When this happens the mutated individual will tend to leave more offspring than other animals in the group. These offspring will inherit the mutated gene from their mutated parent, and the frequency of the new gene will increase within the population. A mutated gene which produces a considerable selection advantage, may result in that mutated gene copy becoming prevalent within the population and may eventually replace the original gene completely. (Goodenough, 1978)
Natural selection is the term used to describe all the environmental pressures acting on an individual which will result in it succeeding or failing to survive and to reproduce. Only successful individuals will pass their genes onto the next generation. Natural selection results in the survival and successful reproduction of animals genetically adapted to that environment. The principal aspects of natural selection are nutrient supply, climate, parasites and predators and competition within the species.
Abundant food supply places no selection pressure on animals, but more commonly food supply is restricted for one or more periods of the year and is often seasonal. It may occur in relatively indigestible forms, or from partially toxic plants, or it may be deficient in critical trace elements. Animals may need to migrate large distances to follow food supplies, or may need to adapt to different diets at different times of the year. There may be restrictions of water supply or available minerals and salts.
Animals have adapted to extremes of cold and heat, to humidity and to drought. There are populations adapted to swim during regular floods, and others that can survive with no access to water for long periods. There are animals adapted to high altitudes, and others whose behaviour and physiology enables them to survive vicious storms. Climatic adaptation is very complex. It involves the metabolism, physical structure and behaviour of adapted animals and it is one of the most valuable aspects of local livestock breeds and adapted domesticated species.
Parasites and disease exert a constant selection pressure upon all populations of animals. Any animal which has some resistance to, or tolerance of, a parasite or disease will be less likely to be affected by the infection, or will recover faster. Such an animal will be more likely to survive and to reproduce thereby passing its genetic ability to coexist with the parasite on to the next generation. There are examples throughout the world of populations and strains which are resistant to, or tolerant of, endemic parasites and diseases which may have a dramatic affect on other non adapted strains.
Survival and reproductive success in animals is also dependent upon their ability to compete successfully with others of the same species. Natural selection favours those individuals able to locate and defend scarce resources such as food, nest sites and good shelter. Reproductive success is also influenced by the animal's ability to secure a mate or mates. This success may be affected by direct competitive conflict between males or by female preference for colour, shape or behaviour. The animal's ability to successfully reproduce and rear their offspring is also critical in the survival of their particular genes into the next generation. All of these competitive factors impose strong selective pressures particularly on the genetically inherited behaviour of animals and the genetically controlled ability to adapt behaviour and to learn.
In order for man to impose his own selection pressure on his animals he must first control some of the principal mortality rates determined by natural selection. He is able to control population size to ensure there is sufficient food for his selected stock, and is able to conserve fodder for periods of the year when forage is not available. He is able to protect his stock from predators and to supply housing or shelter from climatic extremes and is also able to protect livestock from some parasites and diseases.
The lifting of natural selection pressures has an immediate effect on the survivability of individuals within his flocks and herds and enables him to impose his own selection criteria. The principal selection pressures imposed by man are for human food, fuel, clothing, draught work and pleasure.
Human Food and Fuel
Selection for milk production may be based on quantity as is the case with the black and white Holstein Frisian dairy cows; the relative constituents of milk for butter or cheese making as with the Jersey, Guernsey and Brown Swiss cattle breeds; or simply the animal's propensity to let down its milk which is an important selection criteria for Murrah buffalo, Sahiwal cattle and many dairy sheep projects. Selection may be for meat production, measured by maximum growth at an early age which is the current trend in Europe, or the ultimate production of a heavy carcass which was the European fashion 80 years ago. In industrialized nations, selection is predominantly for lean meat but traditionally fat meats have been valued for their cooking characteristics, high human food value and to produce fat for fuel. This was the case with, for example, the Mangalitza pigs of Hungary and the Canastra pigs of Brazil. Selection may even be for animals able to withstand regular bleeding to supply blood for human consumption which was important in the Kerry cattle of Ireland at the beginning of the 20th century and is still important in the herds of cattle belonging to the Masai tribesmen of Kenya.
Human Clothing and Shelter
Selection pressure has been imposed to produce stronger, softer, warmer, more waterproof or differently coloured fibres. Breeds have been selected for the use of their pelts or skins for soft leather, strong hide, warm or attractive fur. This has often taken the form of parallel selection under very different environmental conditions or in association with other unrelated selection pressures. Thus a breed producing one type of fleece might also be adapted to heat or to cold, to high or to low altitudes or to quite different parasites. For example the Scottish Blackface sheep adapted to the cold wet conditions of Scotland has a dense under fleece for insulation and a long hair coat growing through it, to run off the rain and snow. The Navajo-Churro sheep from the Arizona desert region of the USA, which is historically unrelated to the Scottish Blackface, has an almost identical fleece through parallel selection but the capacity to survive in a completely different habitat with hot dry summers, cold dry winters and very sparse grazing.
Draught and Other Work
The role and importance of working animals is often greatly underestimated both in terms of the history of our own development, and our future needs, in a world where renewable energy supply is becoming a major issue.
Animals have been selected to assist with every possible labouring job. Dogs, the first domesticated species, have been selected and trained to protect or manipulate flocks and herds of grazing animals, besides those breeds selected to pull sledges across the snow. Breeds of cattle, horses, donkeys, buffalo, as well as elephants, yaks, camels and llamas have been selected for their use as draught animals. These range from fast riding animals, to strong pulling breeds with great stamina. There has been selection for distance travellers, for carriers of light and heavy packs, for steady breeds to cultivate the land and for tractable and easily trained breeds for more complex work.
No-one who has every worked with livestock can doubt that given the opportunity farmers and livestock breeders will select those animals that appeal to them. Religious, cultural and fashionable fancies exist throughout the world. Selection of the prize bull to be purchased or the young male goat to be saved from the pot have always, and are still affected by the farmer's perception of an 'attractive' animal. This may not be important in economic terms but it has added, through selection, to the range and diversity of livestock varieties in existence and to the richness and quality of rural life.
The final result of these selection pressures in their myriad of combinations is the vast range of distinct populations that exist today and that have existed in the past.
The term most commonly used to describe livestock populations or varieties is 'breed'. A breed is defined as:
“a group of animals that has been selected by man to possess a uniform appearance that is inheritable and distinguishes it from other groups of animals within the same species. It is a product of artificial choice of characters that are not necessarily strategies for survival but are favoured by man for economic, aesthetic, or ritual reasons, or because they increase the social status of the owner of the animals.” (Clutton-Brock, 1981)
Pedigree recording has enhanced this definition by supplying detailed parentage and relationship information for many of the 'developed' breeds. The concept of a breed, however, encompasses any population which falls within definable descriptive parameters. In essence it may apply to any group of animals which are located in a geographical area, have some phenotypic characteristics in common and are recognized by the local people as a local type. As acknowledged in Ian Mason's Dictionary of Livestock Breeds, the parameters of these groups are not uniform (Mason, 1988). For the purposes of this manual the definition of a breed will be taken in this widest possible sense.
National or regional surveys of livestock populations may report a large number of different breed names all referring to one basic population. Conversely several distinct strains may share a single breed name. In order to identify distinct populations it is therefore necessary to describe 'breeds' in detail.
Breed descriptions should include size, weight, body shape and characteristics, growth rates and milk yield and, where appropriate, fibre production and quality, and draught ability. These characteristics must also be recorded alongside the description of habitat, food supply, climatic conditions, seasonal extremes, and management practices as well as the historical origins of the breed if these are known (FAO, 1986b; FAO, 1986c). Differences between populations at this level may be significant. However, if the production characteristics and environmental conditions are very similar, and the differences between groups are only slight, for example coat colour, a more detailed examination may be required to determine the closeness of two breeds. There are electrophoretic differences between milk and blood proteins that may be detected and a range of immunological differences that may be used to determine the historical links, common origins and genetic distance of populations. More complex techniques involving the comparison of non-functional or silent sections of chromosomes or DNA fragments are also useful tools for the comparison of related breeds (Sharp, 1987).
Livestock populations frequently cross political boundaries. This issue, however, will be largely addressed by the EAAP/FAO international databank. Once breeds common to more than one country can be identified and the relevant population and production data logged in the bank, international co-operation can be initiated to ensure that optimal use is made of genetically related groups.
Extinction is an irreversible process in which identifiable populations or genetically controlled characteristics disappear. Extinction may be at the species level, for example the woolly mammoth (Mammuthus Primigenius); at the sub-species level, for example the passenger pigeon (Ectopistes Migratorius); at the breed or variety level, for example the Lincolnshire Curly Coat pig; and finally at the level of individual characteristics or genes.
Extinction is part of the natural process of evolution. The one and a half million species, which are now conservatively estimated to exist, represent less than one percent of the total number of species ever present on this planet (Nei, 1975). Extinction is only perceived as a problem when the rate of extinction exceeds that of speciation for a prolonged period, resulting in the reduction of the total variety of life forms. Such a period of mass species extinction has been occurring since the evolution of mankind, and the rate has been accelerating during the past 100 years.
Species extinction occurs naturally when there are changes in the balance of an ecosystem or habitat. These may be changes in the climatic conditions; temperature, precipitation, and wind; changes in the behaviour or effectiveness of predators, prey species, parasites and diseases; competition from individuals of other species for food supplies, nest or roost sites or other limited resources. Species are able to adapt to changes in their environment because individuals within the species are not genetically identical. Thus, some individuals will have a genetic makeup which makes them more likely to survive and reproduce than others of the same species. These genetically 'superior individuals' are better adapted to the environmental and competitive influences prevalent at the time. They will pass their genes on to the next generation. Provided the same selection pressures continue to apply, the genetically controlled characteristics of the species will begin to change, or evolve, towards a better genetic 'fit' of the species to the new environmental conditions.
When environmental changes are very large, or when the genetic variation within a population is very small, there may be too few individuals whose genetic makeup is such that they are able to survive in the new situation. In this instance insufficient individuals will survive and reproduce and the species will disappear.
Within the past 100 years most common species extinction has been related, directly or indirectly to human activity. It has been the result of one or more of a number of influences including: habitat destruction by deforestation, flooding, drainage; poisoning by pollution; changes in climatic conditions which have been influenced locally if not globally by our actions; competition, predation, parasitism and disease caused by introduced species; direct hunting and harvesting by mankind. Most wildlife conservation programmes address these man-made issues (Myers, 1979; Wilson, 1988).
In general, genetically uniform populations are less able to respond to strong selection pressures, resulting from changes in environmental circumstances, than genetically diverse ones. Specialist species which have adapted over time to 'fit' a very stable and specific biological niche have less intrinsic genetic variation. They are therefore less able to change, through the genetic evolution, or respond to dramatic or sudden changes in their environment. The specialists are also often 'Kselected' which means they direct more energy into producing and caring for a small number of offspring. This further handicaps their possible response to sudden changes in their environment. This is the case for example with the mountain gorilla (Gorilla Beringei). On the other hand, the generalist species are those able to survive and reproduce in a wider range of situations, and which tend to have more intrinsic genetic variation enabling them to respond more quickly to shifts in their environmental conditions, for example the common rat (Ratus Ratus). Specialists are therefore less able to adapt than generalists. In the long term it is the generalists, those species or populations which are genetically diverse, and can respond to new selection pressures, that will inherit the earth (Beardmore, 1983; Myers, 1979; Soule, 1983).
The factors affecting the extinction and disappearance of domestic varieties are closely related to those described for wild species. During the history of domestic livestock breeding there have already been a very large number of breeds which have become extinct. As with wild species, provided the rate of creation of variants parallels the rate of extinction there is no cause for concern. However, for the past 100 years this has not been the case. There has been a high increase in the rate of extinction of breeds and varieties. This represents a dramatic loss of genetic variation within the global pool of domestic stocks.
In Europe alone, 60 breeds of livestock have become extinct this century and a further 200 are considered to be endangered (Maijala et al, 1984). In many other countries undergoing rapid agricultural development and change there has been a tendency to centre livestock breeding programmes on relatively few breeds without fully identifying, evaluating and taking steps to conserve the wide range of local stocks available (Hodges, 1990c).
In agriculture we are constantly selecting for specialization. By definition this limits the genetic variation within the selected population and creates breeds with a better biological fit between the animals and the environment in which they live, both natural and man-made. There is, however, an evolutionary pay off between diversity and efficiency which parallels that described for endangered species. If the environment, natural or man-made, changes rapidly, then the less specialized breed is better able to adapt than the highly selected specialist. For example, two British sheep breeds, the Southdown and Oxford Down are the extremes of selected meat breeds which have suffered for their specialization. The first was developed to sire small early-finishing lambs, while the second is a very large meat breed used to sire large finished carcasses. Both breeds are perfectly adapted to their own markets, but both have been close to extinction in recent years due to rapid changes in market tastes to which they cannot adapt. They now face competition from more generalist meat breeds whose lambs can be finished at a range of weights to fit the market and the fodder available each year.
Genetic variation within a population stems from the existence of different alleles, or genetic options, occurring at the same locus, or address on the chromosome, in different individual animals. The frequency of these alleles remains fairly constant in a large population in a stable environment and is characteristic of that particular population.
The pressures of selection result in some individuals producing more viable offspring than others, but conflicting selection pressures put a limit on the genetically controlled changes that are possible. For example, a larger male may be better able to fight his rivals and secure more mates. However, if this larger animal cannot find or consume enough food to sustain his large body he will not survive and will not successfully reproduce. This example shows simple conflicting selection pressures for both larger and smaller size. In real populations there are many selection pressures acting on individuals and the result is that the frequency of genetic options within populations are in a constant state of flux around a norm. Shifts in the selection pressure will result in a shift in the norm frequency of some alleles. Extreme selection pressure acting against one possible allele in favour of another may even result in the complete disappearance or extinction of the less favoured gene.
The basic principle works for simple Mendelian genes controlling single characteristics, and for quantitative genes which control most of the productive traits. Alleles may therefore become fixed at a frequency of 1 (or 100%), when they are the only remaining option, or 0 when they are extinct.
The principle cause of extinction or disappearance of genes in large populations is selection. In smaller populations alleles may become fixed due to random changes in the gene frequency caused by the chance transfer of genes from one generation to the next. This drift of gene frequencies is enhanced by smaller population sizes and by inbreeding which is the mating of closely related animals. Both result in an increase in homozygotes, or the fixing of alleles at the frequency of 1 or 0 by chance (See section 3.3.2).
Genetic engineering and advanced DNA technology cannot replace the genetic material lost through extinction.
There is work being carried out with DNA fragments recovered from the remains of the extinct woolly mammoths (Mammuthus Primigenius) found frozen in the glaciers of Russia, and with DNA fragments gathered from dried muscle tissue scraped from the preserved skin of a 140 year old South African Quagga pelt. The Quagga (Equus Quagga) is an extinct species of Zebra. It is hoped that it may be possible to incorporate these salvaged DNA segments into the embryonic cells of a closely related species, via genetic engineering techniques. The resulting animals produced in this way would then carry genes from the extinct species. If the inserted DNA segments coded for phenotypic characteristics, the transgenic animals would exhibit those genetic characteristics from the extinct species. These projects are scientifically interesting and may be successful, but are unlikely to recreate viable individuals of the extinct species, let alone a viable population of these animals.
Breeds are identifiable varieties within a species. Once they have been allowed to become extinct they cannot generally be recovered. However, there are instances where the original ancestral populations, or descendant populations still exist, and where the environmental conditions and breed description is well known. In this case it is possible to recreate, through selection, a population which has many of the same phenotypic characteristics and may even carry much of the same genetic makeup. Such a project was begun during the 1920's by the Heck brothers in the Munich and Berlin zoos where they attempted to recreate the extinct cattle ancestor, the Auroch (Bos Primigenius). This projects and others like it are interesting, but serve to demonstrate that recreated populations will never have exactly the same genotype as the lost breed. In most cases suitable related or ancestral breeds are not available, and good breed evaluation data for the extinct population does not exist. Reconstruction projects are only able to recreate a few phenotypic characteristics and never the exact genotype of the extinct breed.
Lost genes can theoretically be replaced in one of three ways. Firstly, the same gene may exist in another breed or species and could be re-introduced by cross breeding or by genetic engineering. The problem is our ability to identify and locate such a parallel gene, and then to transfer it with the correct and appropriate control genes needed for its predictable expression.
Secondly, DNA sequences can be artificially manufactured. The problem here is that we must know the DNA sequence of the gene before we can manufacture it.
Finally, a gene may spontaneously appear by mutation. Mutation is the miscopying of the DNA of the chromosomes and happens at a fairly predictable and very slow rate. It also occurs at random. Thus the chances of a DNA segment mutating to produce a lost gene in an animal with a genetic makeup suitable for the recognizable expression of that gene is extremely low.
At the present time it is considerably more practical and simpler to maintain functional genes in a genetic environment in which their expression can be predicted than to allow their extinction, and then be forced to attempt their reconstruction.
For all practical purposes extinction is forever, and conservation is a relatively simple insurance policy against genetic loss.
Natural selection pressure imposed by environmental conditions, climate, parasites and predators, combined with the effects of human selection, domestication, migration and trade have created a vast array of distinct and genetically unique livestock populations. These populations may loosely be described as ‘breeds’ or groups of animals with identifiable characteristics whose offspring resemble them.
Extinction, which is part of the natural process of evolution, is now occurring at a much higher rate than speciation or the appearance of new varieties and forms. Once a species, breed or gene has become extinct it is very unlikely that it can be re-created in the future.
3. Caruncho pigs selected to produce fat meat in Brazil.
4. North Ronaldsay sheep survive on a diet of seaweed and are conserved by the Rare Breeds Survival Trust in the UK.