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Genetic principles and tools for wildlife management

8 January 2015

From Chapter 25 in Game Ranch Management, sixth edition

www.leopard.tvOver the past decade wildlife production in South Africa has grown into a significant industry with huge financial investments. Wildlife are no longer limited to wildlife reserves and national parks and are now being produced extensively in fenced enclosures and intensively in smaller enclosed areas of variable size. This poses risks for small gene pools and of ecological imbalances. At the same time, such wildlife production leads to human controlled selection. It is important that the modern wildlife producer take note of the basic principles of population genetics and the currently available DNA technology in the genetic management of any such operation. Good practice dictates that management of wildlife ranches and reserves must be based on several lines of information including genetic diversity of particular types of wildlife, the environment and natural conditions on the ranch or reserve. In this chapter some of the genetic principles are discussed that will assist in maintaining genetic diversity and preventing inbreeding, with some reference to the available DNA technology that can be applied in the genetic management of wildlife. Useful terminology and concepts relevant to the genetic management of wildlife are also given.

The topics of discussion include:


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  1. Maintaining genetic diversity

    The Asiatic lion Panthera leo persica is a good example. By 1965 the population consisted of only 12 animals in the Gir Sanctuary in India. It had a low genetic heterogeneity and a high degree of sperm morphological abnormalities. In 1965, strict conservation was started and the population size in 2013 was more than 400 animals. It still had a low genetic heterogeneity but the sperm morphological abnormalities had become normal. To further safeguard them and to improve the current low genetic heterogeneity, the Indian Supreme Court in March 2013 ordered a new population to be established in the same region within six months. The advantage of such an approach is that populations are protected from catastrophic environmental events and/or exposure to disease which might exterminate entire populations or affect gene pools negatively. Wildlife reserves and ranches should therefore be as large and diverse in habitat as possible to accommodate more populations of a given type of animal and provide for natural distribution and competition.

    The fencing of wildlife ranches invariably creates small populations of animals which have genetic management implications. As in the case of the Asiatic lion, small populations typically have lower levels of genetic diversity and may become inbred because of the smaller population sizes. Lower diversity is the result of fewer individuals that contribute to the gene pool. Even in large populations containing closely related individuals the genetic diversity may be lower than expected. Over time, new genetic or evolutionary lineages may even form as a result of genetic rather than reproductive isolation. The recognition of different genetic lineages and taxa to form evolutionary significant units as valid taxonomic entities is a relatively new concept that is already influencing the genetic management of wildlife.

    The following steps may be taken to determine the minimum effective size of a wildlife ranch for maintaining genetic integrity and ensuring effective genetic management:

    • Identify the key taxonomically recognized types of wildlife, the disappearance of which will decrease the biological diversity of the ranch. Common types of wildlife that may disappear should be given a smaller weighting in the decision-making process than the rarer ones. Adhere to the legislation in South Africa that aims to maintain biological diversity. Some examples include the National Environmental Management Act (NEMA Act Number 14 of 2009) and the National Environmental Management: Biodiversity Act (NEMBA Act Number 10 of 2004) and their various regulations.
    • Determine the minimum size of the population that is necessary to ensure the survival and genetic diversity of the wildlife. Make use of known population densities and calculate the minimum size of the habitat that is necessary to accommodate at least a minimum population of each type.
    • Consider the social behaviour of the wildlife involved so as to prevent dominant males from killing young animals, as may happen in a variety of wildlife, including the white rhinoceros and the sable antelope.
    • Prevent competition between ecologically related herbivores that prefer the same type of habitat, especially on smaller wildlife ranches. For example, avoid keeping the nyala and the bushbuck or the nyala and the waterbuck in the same area on small wildlife ranches.
    • Prevent hybridization of various taxonomic groups by maintaining genetically viable populations and eliminating closely related groups. For example, do not keep black wildebeest and blue wildebeest in small numbers on the same wildlife ranch, nor subspecies such as the blesbok and bontebok, and do not allow different subspecies to cross-breed. Note that this is also prohibited legally because it harms natural biodiversity.

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    1. Effective population size
    2. The maintenance of genetic diversity implies sufficient variation on a genetic level to avoid the loss of fertility and general fitness. In small populations that are being kept in isolation for a long time with limited introgression of new males on a regular basis there is always the danger of inbreeding. Inbreeding occurs when animals breed that are more closely related than the mean of the population from which they originate. Among other things, inbreeding leads to the loss of genetic fitness, increased mortality in young animals, reduced fertility and depressed growth. This phenomenon is known as inbreeding depression.

      Effective population size, which can be defined as the number of individuals that actively contribute to breeding or to the genetic make-up of the next generation, is genetically important. The number of breeding animals present in the herd or social group influences the rate of inbreeding in each generation. In an ideal population with sexually reproductive animals the effective (breeding) population (Ne) should be equal to the census population (Nc). This implies that all individuals in a population have the ability and chance to contribute actively to the genetic variation of the next generation. Ideally, random mating should be encouraged and the number of breeding animals should be kept relatively constant or be allowed to increase over time as is explained by Kliman et al. (2008) in the bibliography.

      The objectives that are set for maintaining genetically healthy populations are often short -term (typically 100 years) and long-term (typically 1000 years). In conservation biology, a minimum viable population which would ensure survival for at least 100 years typically contains 50 breeding animals (an effective population of 50) while the long-term goal would require 1000 breeding individuals. This would ensure an inbreeding coefficient, or degree of inbreeding, of below 1% per generation. The sex ratio in a population also plays an important role in the flow of genetic material, because it affects the random variation of the gene frequencies between one generation and the next. An effective population size of 50 breeding animals can be structured according to sex with the help of the following equation:

      Ne = [4 (Nm Nf)] ÷ [(Nm + Nf)]

      where:

      Ne = The effective population size

      Nm = The number of effective breeding males

      Nf = The number of effective breeding females

      The size of a breeding herd not only influences the effective population size, but also the rate of inbreeding per generation. Suppose that a wildlife rancher wants to produce the African savanna buffalo. To be able to keep the inbreeding coefficient below 1%, 50 breeding animals are required. Suppose the sex ratio under natural conditions is 1:1. When the above equation is used, 25 sexually mature cows and 25 sexually mature bulls will be necessary in the population to keep the inbreeding coefficient below 1%. However, suppose that the rancher has a surplus of six males which he wants to utilize for trophy hunting, while at the also increasing the productivity of the herd and apply genetic conservation. Then the equation can be modified as follows:

      The number of breeding bulls required:

      (3 ÷ 8) x 50 effective breeding animals = 19 = (25 – 6 bulls for hunting)

      The number of breeding cows required:

      (5 ÷ 8) x 50 effective breeding animals = 31 = (25 + 6 cows to replace the hunted bulls)

      Therefore: Ne = [4(19)(31)] ÷ [19 + 31] = 2356 ÷ 50 = 47 animals

      Here the natural parity of the sex ratio of the herd is changed to three males for every five females. This leaves 19 breeding males and 31 breeding females, which are substituted in the above equation to give an effective breeding herd size of 50 animals. The degree of inbreeding will therefore now be a little more than 1%, with an effective population size of 47 animals. Now, suppose further that effective breeding animals form 40% of the total herd. Then the minimum herd size that is necessary to apply genetic conservation will be 125 animals. The generation interval influences the rate of inbreeding in the following way: with a generation interval of five years, the rate of increase in inbreeding will be (1.5 ÷ 5) = 0.3% per year, with an inbreeding coefficient of 1.5.

      The size of a breeding herd does not only influence the effective breeding population size, but it also influences the rate of inbreeding per generation. Suppose that a wildlife rancher wants to breed with the African savanna buffalo. To be able to keep the inbreeding coefficient below 1%, 50 breeding animals are required. Suppose the sex ratio under natural conditions is equal. Therefore, when the above equation is used, 25 sexually mature cows and 25 sexually mature bulls will be necessary to keep the breeding coefficient below 1%. However, suppose that the rancher has a surplus of six males that he wants to utilize for trophy hunting, while at the same time he wants to increase the productivity of the herd and apply genetic conservation. To do so, the natural parity of the sex ratio is changed to three males for every five females. By doing so, 19 breeding males and 31 breeding females will give an effective breeding population size of 50 animals. Now, suppose further that effective breeding animals form 40% of the total herd. Then the minimum herd size that is necessary to apply genetic conservation will be 125 animals.

      To maximize genetic diversity in the next generation, one should attempt to have equal sex ratios in breeding populations where an equal number of males and females participate in breeding. Also, one should attempt to minimize the variance in the number of offspring being produced by the different females. Through this, one can ensure that genetic diversity is maximized from one generation to the next and that single individuals do not make a proportionally larger contribution to the next generation. Should one individual (either a single male mating with all or one of the females producing the bulk of individuals in the next generation) contribute significantly more to the next generation; it will effectively decrease the genetic diversity in the that generation as a genetic material of a large number of individuals are not passed on. This is one danger of the trend among some wildlife ranchers to breed with selected individuals in an attempt to produce animals with larger trophies or with specific colour or other morphological variants.

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    3. Minimum social herd size
    4. Apart from relatedness among the breeding animals to maintain genetic diversity, there are also requirements regarding the minimum number of individuals in the population that are required to maintain normal social behaviour. For most wildlife the minimum social group for re-establishment is three males and five females. Such a breeding herd will usually consist of six adult animals, of which one is a bull and five are cows, plus two young males. Any young males that are born to this herd will join other young males in a bachelor herd when they leave the breeding herd later due to social pressures. The mean herd size for some wild herbivores in the Kruger National Park gives an indication of the conditions that can be expected to occur in the wild (Table 25.1).

      [Insert Table 25.1]

      Table 25.1 -The mean herd sizes for some herbivores in the Kruger National Park.
      Source: Unpublished reports of the South African National Parks.

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    5. Minimum surface area
    6. Wildlife ranchers should also consider the habitat and available range for successful breeding and social interaction to ensure effective population size and genetic diversity in the long term. To do so will require an analysis of the quantity and quality of the vegetation that is available to support specific types of wildlife. The stocking rate equivalents be used in conjunction with a detailed vegetation analysis to apportion various types of wildlife to a habitat as is explained in Chapter 41. These analyses will indicate whether it is possible to keep a genetically viable population of a specific type of animal on a ranch of given size and with specific habitat qualities.


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  3. Hybridization

    Cross-breeding and its impact on wildlife ranch management were discussed briefly in Chapter 1, but warrant more attention here. For healthy population growth to occur, a genetically viable population is essential. Wild herbivores appear to be less susceptible to inbreeding than domesticated ones because they usually have a larger genetic base compared to domesticated animals. Population size should be increased as a first objective when dealing with small or vulnerable populations. As such, numerous examples exist where large populations of wild animals have been built up from small herds or a few individual animals that were established in an area. However, it remains sound policy to obtain breeding males from another genetic source from time to time, especially when all the animals available are from the same local genetic stock.

    Wildlife-proof fences prevent the free exchange of genetic material between large herbivores on bordering or neighbouring wildlife ranches. It would therefore be advantageous for the owners of neighbouring ranches to exchange healthy breeding animals from time to time to prevent inbreeding depression in their own herds. A further option is to remove the fences between adjacent ranches to form conservancies where natural genetic exchange will occur within larger and more viable populations. Wildlife ranchers are often tempted to bring in breeding animals from areas that are geographically remote and morphologically different, especially when such animals are desired as breeding males, but a word of caution in these instances is necessary. Because of natural selection, animals become adapted to local environmental conditions. Bringing in morphological variants will most likely lead to them gradually disappearing unless they are adapted to that specific environment. After several generations the temporary advantages of bringing in exotic morphological variants, often at great cost, will have become lost. Should morphologically different breeding males be imported from areas that are ecologically different and the next generation may be less adapted to local conditions. Eventually, such action may be detrimental to the population. A sound economic and genetic rule is rather to obtain breeding stock from the available local sources than to import them at great expense from distant places. Apart from the genetic implications, losses in animals that are kept in captivity for a long time or are transported over long distances can be unacceptably high.

    Individual members of genetically impoverished herds may display conspicuous physical defects, or the herd will not produce sufficient healthy young. A classic example, and one that is often applied by researchers, involve fluctuating asymmetry, or the degree to which an animal deviates from a perfect bilateral symmetry. Numerous studies, including humans, have shown that deviations from symmetry is indicative of low levels of genetic diversity, inbreeding or stress as a result of environmental variables. A good example would be where the left and right horns are not symmetrical. Fluctuating asymmetry is therefore a useful way for a wildlife rancher to gauge the level of inbreeding in an individual or a population. Inbreeding is also detrimental to the fertility of the surviving animals and the vitality of the young animals. Any deviant individuals, such as those with colour variations, thin or twisted horns or other defects, should be removed immediately from breeding herds. It is important to remember that inbreeding can be rectified within one generation through the introduction of unrelated and different individuals that are adapted to a specific environment (The Hardy Wineberg Principle of Genetics).

    Within herbivores in general, hybridization between species and even genera is possible, and such hybrids are often fertile. For example, members of the zebra group can interbreed and produce fertile hybrids. Similarly, hybrids between species of the genera Kobus (which includes the lechwe, waterbuck, kob and puku) or Tragelaphus (which includes the bongo, greater kudu, bushbuck, lesser kudu, mountain nyala, nyala and sitatunga) are known to be fertile or infertile depending on the type of wildlife that are involved. Genetically, all three forms of the springbok are also of the same species, but there are three distinct ecotypes which some authors regard as subspecies. The springbok from Angola are generally small and light in weight. The springbok from the Karoo, the Free State and the south-western North West provinces are slightly larger and heavier than those from Angola, with a shoulder height of approximately 0.76 m. The springbok from Limpopo, the Northern Cape, Botswana and Namibia are much larger and heavier than the rest, with a shoulder height of up to 0.87 m. Those from the Swakopmund area have the longest horns. These ecotypes should preferably not be mixed in the same population on a wildlife ranch. Black springbok and white springbok are two colour variants that may occur naturally in any population, and they are not different subspecies.

    Wild animals will also hybridize on a wildlife ranch when the area is too small and minimum herd sizes are not being maintained. Some examples of known or possible hybrids between wild animals include:

      Fertile hybrids:
    • African wild cat and domesticated cat
    • Blue wildebeest and black wildebeest
    • Bontebok and blesbok
    • Roan and sable antelope

      Infertile hybrids:
    • Tsessebe and blesbok
    • Red hartebeest and blesbok
    • Eland and greater kudu
    • Black rhinoceros and white rhinoceros
    • Hartmann’s mountain zebra and donkey

      Possible hybrids:
    • Burchell’s zebra and Cape mountain zebra
    • African savanna buffalo and Indian water buffalo
    • Nyala and greater kudu

    It is now known, based on scientific evidence, that closely related animal species, subspecies and ecotypes that are separated geographically develop unique genetic, physiological and anatomical adaptations over time. For example, genetic studies have confirmed that the blesbok and bontebok are genetically distinct with unique alleles being found in both. This genetic division is supported by morphological differences and is a natural process. Consequently, they should not be allowed to cross-breed to ensure that these unique characteristics may be maintained. Other examples of animals that have to remain isolated from each other are the black-faced impala and the common impala, , the West African roan antelope and the east /central /southern roan antelope, the northern white rhinoceros and the southern white rhinoceros, subspecies of the sable antelope and the ostriches from northern, southern and eastern Africa. Irresponsible cross-breeding can cause economic and ecological losses, especially for trophy hunting as most trophy hunters do not wish to hunt animals with a doubtful genetic origin. The Environmental Management: Biodiversity Act (Act 10 of 2004) also legally prohibits the introduction of animals to areas where they did not occur historically to prevent the hybridization of closely related, but ecologically distinct, types of wildlife.

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    1. Hybridization of ecotypes
    2. An ecotype is a group of organisms within a species that is adapted to particular environmental conditions and therefore exhibits behavioural, structural, or physiological differences from other members of the species. Compared to southern African, the West African roan antelope and the West African buffalo are prime examples. Ecotypes usually produce fertile offspring, and a number of wildlife ranchers can form a breeding group to keep certain ecotypes pure. This can be done in the same way as the study groups that are functioning in agriculture.

      In the springbok, the Kalahari springbok rams are at times used to breed with the smaller springbok ewes from central South Africa to improve meat production. These are purely functional reasons as the animals are usually harvested for their meat. It is strongly recommended that wildlife ranchers form breeding clubs or study groups to conserve and improve pure, local genetic lines. This can be achieved by selecting animals on the basis of closely related individuals following genetically tested results. However, wildlife producers must be aware that this practice can lead to inbreeding and the loss of genetic fitness if new genetic material is not introduced from time to time. Such breeding clubs should be part of extensive wildlife production while the functional breeding of wildlife for meat production or tick resistance should be part of intensive wildlife production.

      Breeding clubs can also function to breed animals with phenotypical features that represent animals that have already become extinct. An example is the breeding of quagga Equus quagga quagga look-alikes from Burchell’s zebras that only have a few stripes on their hindquarters. It is important to recognize that the environment plays a significant role in determining the phenotype of animals. In some animals the environment alone produces certain ecotypes based on the structure and nutritional quality of the habitat. This is one reason why the East African buffalo has long and slender horns.

      In most types of wildlife, the phenotype (appearance) of an individual is the result of its environment and genetic composition. In fact, an entire quantitative field of genetic study is based on this principle. An example would be to compare animals that occur in the drier western parts of South Africa to the wetter eastern parts. Animals to the west are typically lighter in colour in spite of little or no genetic differences. In the past, subspecies and even species were described based on phenotypic differences. Today, following numerous molecular studies, we know that phenotypic differences are not always supported by underlying genetic differences as in the case of some buffaloes.

      Conservation efforts based on erroneous or incomplete information is at best inefficient, and may even be to the detriment of the species or subspecies. Several such examples exist in the literature. In the sable antelope, four subspecies were described by Ansell in 1971. They were: Hippotragus niger niger south of the Zambezi River, Hippotragus niger kirkii in Zambia, Hippotragus niger roosevelti along the east coast of Africa and Hippotragus niger variani in Angola. Based on genetic studies since 2002, the validity of these four subspecies was confirmed. However, the geographic ranges where these subspecies occur was quite different from what was previously believed based on phenotype alone. For the roan antelope, six subspecies were described by Ansell in 1971. A genetic study by Alpers et al. in 2004 indicated the presence of only two Evolutionary Significant Units comprising of animals from West Africa and the remainder of Africa (East, Central and Southern Africa. Management and conservation efforts based on phenotype alone would therefore undermine the evolutionary potential of species and subspecies. Other genetic studies have shown phenotypic variations in the African buffalo, Burchell’s zebra, red hartebeest and bushbuck.

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    3. Genetic management of ecotypes
    4. Wildlife ranchers should only keep those wild animals that are ecologically adapted to their region and are known to have occurred historically there. This will ensure that competition between ecologically equivalent animals is eliminated, for example between the sable antelope and the gemsbok. The aim should also be to keep healthy breeding herds to satisfy all the social requirements of the animals. Genetic impoverishment is difficult to determine in wild animals because of the strong tendency towards natural selection. It is recommended that when wild animals are utilized commercially and there are fewer than 50 breeding animals on a wildlife ranch, the percentage of males that is removed annually or biannually should be replaced by the same number of local males, but from unrelated herds.

      Wildlife ranchers should also preferably re-establish complete breeding herds instead of fragmented ones or parcels of unrelated individuals because it can take some time for new social groupings to form. Forcing wildlife producers to buy breeding herds of roan antelope contributed largely to the increase in their numbers. Therefore, wildlife producers should avoid buying odd parcels of wildlife at live wildlife auctions. For example, rather than buying two sable antelope each from five different sources for re-establishment, a group of ten sable antelope from the same herd should be purchased. A single individual of any type of animal that occurs on a wildlife ranch should be removed. For example, one tsessebe bull on a ranch with 100 blesbok is a clear recipe for hybridization, especially when the single animal is a bull of an anatomically stronger type. The absence of adult breeding giant sable antelope bulls during a translocation operation in Angola has also led to roan antelope bulls mating with female giant sable antelope in the new area. As a result, only one pure giant sable antelope herd remains in the wild and there is now a concerted effort in Angola to remove hybrid animals from the contaminated second herd.

      In rarer animals, such as the sable antelope, which are hunted for their trophy value, the trophies should only be taken from the bachelor or male herds, but not from herd bulls that are temporarily recuperating there. Whenever possible, the population growth of all the wild animals should be calculated during annual counts. If the rate of growth, or population increase, is inadequate, a few males should be culled from the breeding herds. For example, a growth rate of at least 5% is required for Burchell’s zebra where infertile stallions can decrease the overall population growth rate by appropriating the fertile mares without producing offspring.


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  5. Qualitative and quantitative breeding principles

    The phenotypic and genetic variation of wildlife are based on qualitative of quantitative breeding principles. Qualitative and quantitative inheritance are influenced by non-additive and additive modes of inheritance respectively.

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    1. Qualitative inheritance
    2. Qualitative inheritance includes the well known laws of Mendel and often refers to a single gene inheritance where a single pair of genes will interact and its expression can be observed in the phenotype or appearance of an individual. Examples include some coat colour variants in wildlife, eye colour in humans and animals, and comb shapes in birds. The mode of inheritance is mostly non-additive and interaction includes dominance, over dominance, no dominance and epitasis. Epitasis occurs when the effect of a gene depends on the presence of modifier genes.

      In domesticated animals colour inheritance has been studied well and apart from the wild type of agouti colour, inheritance patterns become quite complex with the presence of dilution genes, greying or depigmentation.

      The primary gene that is involved in the regulation of coat colour is melanocortin receptor 1 (MC1R) that will regulate the expression of eumelanin that is responsible for the darker pigments (black or brown) or pheomelanin which is responsible for the red and yellow tones. These two basic pigments are produced in the melanosomes, the organelles that contain the enzymes for production of the pigment. Besides the melanocortin receptor 1 gene, the TYRP1 (tyrosinase related protein 1) and SILV (silver) gene that is important in mammalian pigmentation has been studied in cattle that forms part of the extension locus that causes a dilution of the base colour.

      Evolutionary, wildlife have developed in such a way that different skin colour, coat colour and coat patterns are primarily used as a defence mechanism against predators. These different colours, such as white, golden or black, were always present in the environment. However, it is easier for a lion to see a white variant than one with a normal coat colour when it moves. A single white greater kudu in a small herd will also draw the attention of the predator as the odd one out. Other environmental factors such as sunlight will cause cancers around the eye and lead to blindness. A blind animal is more easily caught by a predator than one with sight. Some wildlife ranchers are collecting or producing wildlife with different coat colours to offer a wider range of wildlife to hunters. These coat colour mutants are being bred artificially by keeping them together in the absence of predators under intensive production conditions in small camps to eliminate the competition of males of the normal coat colour. This management technique has made it possible to increase the number of animals with different coat colours. Colour variant breeding is a fashion that is being driven by short-term financial gain and these ranchers will return to normal breeding once the supply and demand has been satisfied by the breeders. Moreover, some trophy hunters are not interested in hunting so-called farm-produced wildlife as it is called by CIC which represents the European hunters.

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    3. Quantitative inheritance
    4. Quantitative inheritance refers to additive gene action where a number of genes contribute to the final expression of the phenotypic trait. These traits follow a continual distribution or cline in factors such as weight, length or height, and much variation may be seen within a population. These traits follow a normal distribution and are often referred to as polygenic traits. Most of the traits that are of economic importance are influenced by additive gene action which has been well studied in domesticated animals due to the ability to measure and weigh the animals objectively. This has resulted in large and extensive data bases for the genetic evaluation of domesticated animals with the development of genetic tools for genetic selection and improvement.

      Although it is not practical to measure and weigh wildlife in extensive operations, it is possible to gain from the vast amount of information on traits that are applicable to all animals, such as heritability and growth. It has been shown that the heritability for fitness traits (including fertility and survival) are low, while growth traits are moderately to highly heritable. The heritability refers to the variation that is observed in the phenotype due to the additive genetic component and is the portion that is passed on from parent to progeny for a specific trait in a population. It is useful to take note of the heritability for traits especially when animals are being selected or purchased with a specific breeding goal in mind.

      In wildlife, selection will be based primarily on functional phenotypic traits that are observed in the animals due to lack of pedigree and recording information. Besides selection of a functional specimen with regard to reproductive organs, conformation and characteristics, wildlife ranchers may consider the following and more recent genetic tools to assist in selection and breeding:


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  7. Biotechnology as a genetic management tool in wildlife

    Biotechnology in general refers to all the techniques that are associated with the improvement or altering of biological organisms.

    1. Reproductive biotechnology
    2. Reproductive biotechnology includes artificial insemination, embryo transfer and reproductive cloning, as well as genomics where information derived from DNA is used in breeding and selection. Cloning is not a viable option for extensive wildlife production systems, may lead to a serious decrease in genetic diversity and has high costs with a limited success rate.

      A technique such as artificial insemination is routinely used in domesticated animals, but it has certain limitations in its application to wildlife. In wildlife management, biotechnology that is associated with the manipulation of reproduction may find a practical application, as may molecular techniques for studying genetic variation, species or subspecies identification, scatology and searching for genes that are associated with genetic defects or other traits which may be of economic importance to the wildlife industry.

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    3. DNA-based biotechnology
    4. The rapid development of molecular techniques and studies of the genomes of a vast number of organisms have created new means for studying the genetic composition and origin of an individual animal or a taxon (a taxonomic group of animals). To date, the genomes of many domesticated animals have been mapped or fully sequenced. For a several types of wildlife, DNA-markers, including mitochondrial and/or nuclear markers, are available and have been applied in wildlife management for the identification of hybrids, the estimation of genetic diversity for conservation purposes and the genetic management of populations. Nuclear DNA is contained within the nucleus of a cell, encodes all the genes of an organism and passes it on to all its offspring and can be of a paternal or maternal origin. Mitochondrial DNA is found in the mitochondria which are located in the cytoplasm of the cell. The mitochondria of a male are located in the tail of the sperm which is lost when an ovum has been fertilized and consequently is not transmitted from father to offspring. Therefore, mitochondrial DNA shows the maternal lineages. DNA can be extracted from a variety of biological materials including bone, blood, tissue, hair follicles and even faecal material. The latter provides a valuable source of DNA when studying nocturnal or elusive wildlife, especially for obtaining census data and genetic variation within a species or subspecies in fenced areas, because there is no need to capture any animal.

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    5. Bio-banking of biological material
    6. For wildlife producers to make maximal use of the DNA technology that is currently available, it is recommended that biological samples such as hair, blood and/or tissue of animals be collected routinely during the hunting season, or at any other opportunity, such as when animals have to be handled. Samples can also be obtained by using special biopsy darting. These biological samples can be stored on wildlife ranches where every wildlife producer can essentially build an own tissue bank. Blood samples have to be refrigerated, but tissue samples can be stored on a shelf at room temperature in a saturated salt solution that is supplemented with 15% dimethyl sulfoxide (DMSO). Hair samples should include a follicle that is intact to allow the extraction of sufficient DNA for analysis, and should be stored in a paper and not in a plastic container.

      As an alternative, samples can be stored at a central facility where a DNA biological bank for the species or subspecies can be maintained and analyzed as required. The Wildlife Biological Research Centre and its partners in BioBank SA have created a biological resource bank that is dedicated to the acquisition, processing, banking, using and provision of biomaterials to the scientific and conservation communities. This bank is viable, diverse and representative of southern Africa wildlife populations. Banked biomaterials include tissue from muscles, kidneys, fat, liver, embryos, fibroblast cultures, blood, sperm, hair, eggshells, fluids, cells and more. Biomaterials are made available for research, biodiversity conservation and biotechnology development, and are used in many disciplines, including genetics, reproduction, nutrition, taxonomy and disease studies. Biomaterials from selected wildlife are also useful for the detection and monitoring of persistent organic pollutants and other potentially harmful substances that are found in the environment.

      The biomaterials are made available to third parties with prior consent from the biomaterials’ ‘owner’, but only after the signing of a customised material transfer agreement or a cooperative research and development agreement. The training of staff from the national parks and provincial wildlife reserves, zoological gardens, animal breeders and laboratories to collect these biological samples is being done on a regular basis, with the aim of securing good-quality biomaterials. Sampling kits are made available to persons who are tasked with the collection of wildlife biomaterials. The Biobank SA consortium acts as an integrated resource centre that links all the partner collections. The consortium’s operational arm, the Wildlife Biological Research Centre, is active in the development of relevant policies, regulations and legislation pertaining to biomaterials, including access and benefit-sharing systems. The main sponsor of the project is the Department of Science and Technology of the national government of South Africa

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    7. Wildlife production and conservation
    8. Knowledge of the genetic biodiversity of the wildlife that occur on wildlife ranches and the genotypic information of endangered species and subspecies are of major importance for the future of wildlife production. It will soon become an essential component of any wildlife producer’s management programme as it has real economic and conservation implications. Researchers and wildlife ranchers should collaborate and apply DNA technology to ensure effective genetic management of the wildlife resource that is present on wildlife ranches and smaller nature conservation areas. Ideally, all wildlife auctions should provide detailed genetic information on the animals on offer, with translocation being limited to specific regions only, if necessary, in accordance with the National Environmental Management: Biodiversity Act (Act 10 of 2004) and its various regulations.

      Some service providers for genetic analyses in South Africa include: BioBank SA; CSSR; TRACE Network; TRAFFIC; FSSI Trace; Agricultural Research Council (Irene); SA Police Services (Forensics); the National Zoological Gardens; and the Universities of Cape Town, Free State, Johannesburg, KwaZulu-Natal (Allerton Laboratory), Pretoria (Veterinary Genetics Laboratory and Department of Animal and Wildlife Sciences), and Stellenbosch.

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    9. Genetics as a forensic tool in wildlife management
    10. Genetics are a useful broad forensic tool in wildlife management as the following example concerning the white rhinoceros will illustrate. A DNA profiling method has been validated and optimized for rhinoceros horn. The number of loci that was used in the original test has almost doubled and the horn DNA extraction method has been re-assessed and uses the latest technology that is available for human forensic DNA extraction. This method is now being used routinely in the Veterinary Genetics Laboratory at Onderstepoort to identify rhinoceros horn from stockpiles individually, for security purposes and to link recovered horns to individual poaching cases. In doing so, a horn trafficker can be linked to a poaching incident or a poacher who was caught with horns in his possession can be linked with the carcass of an individual rhinoceros. Each rhinoceros poaching incident that is being investigated has the collection of samples for DNA testing as part of its standard operating procedure. The method also indicates how closely various animals are related. It is now known that the current rhinoceros populations in South Africa came from a small genetic pool a century ago. Therefore, breeding with the most unrelated rhinoceroses possible is a valuable tool for the experienced wildlife rancher. More information on rhinoceros poaching control appears in Chapter 19.


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  9. Useful genetic terminology

    A few useful genetic concepts are next defined briefly. Most of them are basic animal breeding and genetic concepts that are being used in these disciplines and were adapted from Bourdon (2000) and Adendorf et al. (2010).

    • An allele is the alternative form of a gene. For a specific gene there may be several different alleles within the population, therefore the reference to allelic variation such as A, B, C or more. The bontebok and blesbok differ in at least 13 alleles.
    • Artificial selection: This procedure is being practised by stud breeders of livestock where specific individuals are selected for breeding based on their performance traits in producing offspring of a superior quality. In the case of wildlife, specific breeding males are, for example, selected for larger horns or other unique physical features such as exotic colour variations.
    • Breeding goal: The overall aim of what a breeder wants to achieve, such as the improvement of the production of the unit. To achieve the breeding goal, the breeder will set specific criteria or traits; such as horn development and size, colour, or body size in wildlife. All of these must be included in the selection of the founder animals.
    • Breeding value: The value of an animal as a parent in its ability to transmit certain genetic traits to its offspring. In domesticated livestock, a breeding value can be estimated for the animals based on objective phenotypic measurements that are collected over a period of time.
    • Coefficient of inbreeding: A measure of the level of inbreeding in a population, expressed as the expected proportion of homozygous loci in an individual of which both the alleles can be traced to the same ancestor. This coefficient therefore measures the probability that an individual has received both alleles of a pair at a given locus from an identical ancestral source.
    • Correlation: An association between two traits that vary together. A phenotypic correlation is observed on the animal, while genetic correlation is due to one gene affecting both traits and is inherited over generations.
    • Inbreeding: A mating system between animals that are more closely related than the mean of the population from which they originate.
    • Inbreeding depression: Decreased vigour in individuals as a result of inbreeding, or low genetic variation, with fitness traits such as fertility and survival being mostly affected.
    • Line breeding: A lesser form of inbreeding that attempts to maintain a high frequency of individuals with superior or specific genetic qualities in a population. The animals involved tend to have high genetic relatedness with one or more ancestors.
    • Locus: The position of an allele or gene on the chromosome.
    • Outcrossing: The mating of two individuals of the same species, subspecies, breed or type that are not closely related.
    • Ecotype: A group of organisms within a species or subspecies that is adapted to particular environmental conditions and therefore exhibits behavioural, morphological or physiological differences from other members of the same species or subspecies.
    • Genotype: The genetic composition of an animal which includes all the genes that are responsible for its the survival and production.
    • Phenotype: The appearance of the animal. This can include all the observable traits such as coat colour, horn formation and size, body conformation, and all the measurable traits such as the weight and height of an animal.
    • Phenotypic: Selection of animals that is based on their superior performance for a specific trait. Performance information is usually based on pedigree information and production records which are based on performance traits which can be measured objectively.
    • Genetic selection: Selection that is based on the genotypic information of the animal and which can only be obtained by performing DNA analyses.
    • Genetic diversity: The genetic variation that is based on the allelic diversity for a specific trait in a population, species or subspecies.
    • Genome: The total genetic information of an animal as it is carried on all the chromosomes. Each individual has a specific diploid set of chromosomes (chromosomes in pairs) which is carried in each body cell, except for the sex cells which only have a haploid set (a single set of unpaired chromosomes).
    • Genome map: A map that contains a large number of different DNA markers. Different genome maps are available, depending on the type and number of markers, such as a genetic map/linkage map or a physical map.
    • Genome sequence: The order of the DNA nucleotides on all the chromosomes of a specific taxon or individual.
    • Heritability: The variation that is due to the additive portion of the total phenotypic variation that is inherited by the next generation. Heritability is a population parameter and refers to the traits within the population and not the individual.
    • Natural selection: Under certain conditions specific individuals are favoured as a result of being better adapted to a specific environment. These individuals will make a proportionally larger contribution to the next generation. Under strong selection, individuals that are selected against may die and will therefore not contribute to the next generation.
    • Selection criteria: Traits that can be measured or quantified; such as weight, height and length; and which are included in the selection programme to reach a breeding goal.
    • Polymorphism: The allelic variation that is observed at a locus. A high degree of polymorphism will imply the presence of a large number of different alleles. Polymorphism is in contrast to homomorphism which implies the presence of only one allele. Polymorphism at many loci is important to ensure genetic variation.

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Reference:

Du Toit, J G, E van Marle-Köster, J du P Bothma & B Jansen van Vuuren. In Print. In J du P Bothma & J G du Toit (reds), Game Ranch Management, sixth edition. Pretoria: Van Schaik.

article by Prof J du P Bothma

  

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