26/10/2024
Genetic diversity
Article
Written & Edited by Professor Dr. Kanak Baran Barua
This Article published at researchgate, Germany. This supporting link :
https://www.researchgate.net/publication/377673467_Genetic_Diversity
Genetic diversity is the biological variation that occurs within species. It makes it possible for species to adapt when the environment changes. Genetic diversity is particularly important under rapid environmental change, such as in the Baltic Sea.
Genetic diversity makes it possible for species to adapt when the environment changes. Thus, large genetic diversity – a big gene pool – positively affects ecosystem resilience and function. When we drain species of their genetic diversity we destroy their adaptive potential, and their long-term survival will be jeopardised.
Biological variation at the DNA-level forms the basis for all biodiversity. Colors represent alleles – variants of separate genes – genetic diversity.
Keep populations large and connected
The most efficient way to counteract loss of genetic diversity is to maintain large and well connected populations. Small and isolated populations will rapidly lose genetic variation resulting in lower adaptive capacity, loss of resilience and weak potential for long-term survival.
Large populations can harbour much genetic diversity (illustrated with many colors). Small populations can not do that and will rapidly loose variation.
Genetic diversity is the total number of genetic characteristics in the genetic makeup of a species, it ranges widely from the number of species to differences within species and can be attributed to the span of survival for a species.[1] It is distinguished from genetic variability, which describes the tendency of genetic characteristics to vary.
A graphical representation of the typical human karyotype.
Genetic diversity serves as a way for populations to adapt to changing environments. With more variation, it is more likely that some individuals in a population will possess variations of alleles that are suited for the environment. Those individuals are more likely to survive to produce offspring bearing that allele. The population will continue for more generations because of the success of these individuals.[2]
The academic field of population genetics includes several hypotheses and theories regarding genetic diversity. The neutral theory of evolution proposes that diversity is the result of the accumulation of neutral substitutions. Diversifying selection is the hypothesis that two subpopulations of a species live in different environments that select for different alleles at a particular locus. This may occur, for instance, if a species has a large range relative to the mobility of individuals within it. Frequency-dependent selection is the hypothesis that as alleles become more common, they become more vulnerable. This occurs in host–pathogen interactions, where a high frequency of a defensive allele among the host means that it is more likely that a pathogen will spread if it is able to overcome that allele.
Within-species diversity
Varieties of maize in the office of the Russian plant geneticist Nikolai Vavilov
A study conducted by the National Science Foundation in 2007 found that genetic diversity (within-species diversity) and biodiversity are dependent upon each other — i.e. that diversity within a species is necessary to maintain diversity among species, and vice versa. According to the lead researcher in the study, Dr. Richard Lankau, "If any one type is removed from the system, the cycle can break down, and the community becomes dominated by a single species."[3] Genotypic and phenotypic diversity have been found in all species at the protein, DNA, and organismal levels; in nature, this diversity is nonrandom, heavily structured, and correlated with environmental variation and stress.[4]
The interdependence between genetic and species diversity is delicate. Changes in species diversity lead to changes in the environment, leading to adaptation of the remaining species. Changes in genetic diversity, such as in loss of species, leads to a loss of biological diversity.[2] Loss of genetic diversity in domestic animal populations has also been studied and attributed to the extension of markets and economic globalization.[5][6]
Neutral and adaptive genetic diversity
Neutral genetic diversity consists of genes that do not increase fitness and are not responsible for adaptability.[7] Natural selection does not act on these neutral genes.[7] Adaptive genetic diversity consists of genes that increase fitness and are responsible for adaptability to changes in the environment.[7] Adaptive genes are responsible for ecological, morphological, and behavioral traits.[8] Natural selection acts on adaptive genes which allows the organisms to evolve.[7] The rate of evolution on adaptive genes is greater than on neutral genes due to the influence of selection.[8] However, it has been difficult to identify alleles for adaptive genes and thus adaptive genetic diversity is most often measured indirectly.[7] For example, heritability can be measured as
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or adaptive population differentiation can be measured as
���=��/(��+2��)[7] It may be possible to identify adaptive genes through genome-wide association studies by analyzing genomic data at the population level.[9]
Identifying adaptive genetic diversity is important for conservation because the adaptive potential of a species may dictate whether it survives or becomes extinct, especially as the climate changes.[7][10] This is magnified by a lack of understanding whether low neutral genetic diversity is correlated with high genetic drift and high mutation load.[10] In a review of current research, Teixeira and Huber (2021), discovered some species, such as those in the genus Arabidopsis, appear to have high adaptive potential despite suffering from low genetic diversity overall due to severe bottlenecks.[10] Therefore species with low neutral genetic diversity may possess high adaptive genetic diversity, but since it is difficult to identify adaptive genes, a measurement of overall genetic diversity is important for planning conservation efforts and a species that has experienced a rapid decline in genetic diversity may be highly susceptible to extinction.[10][9]
Evolutionary importance of genetic diversity
Adaptation
Variation in the population's gene pool allows natural selection to act upon traits that allow the population to adapt to changing environments. Selection for or against a trait can occur with changing environment – resulting in an increase in genetic diversity (if a new mutation is selected for and maintained) or a decrease in genetic diversity (if a disadvantageous allele is selected against).[11] Hence, genetic diversity plays an important role in the survival and adaptability of a species.[12] The capability of the population to adapt to the changing environment will depend on the presence of the necessary genetic diversity[13][14] The more genetic diversity a population has, the more likelihood the population will be able to adapt and survive. Conversely, the vulnerability of a population to changes, such as climate change or novel diseases will increase with reduction in genetic diversity.[15] For example, the inability of koalas to adapt to fight Chlamydia and the koala retrovirus (KoRV) has been linked to the koala's low genetic diversity.[16] This low genetic diversity also has geneticists concerned for the koalas' ability to adapt to climate change and human-induced environmental changes in the future.[16]
Small populations
Large populations are more likely to maintain genetic material and thus generally have higher genetic diversity.[11] Small populations are more likely to experience the loss of diversity over time by random chance, which is an example of genetic drift. When an allele (variant of a gene) drifts to fixation, the other allele at the same locus is lost, resulting in a loss in genetic diversity.[17] In small population sizes, inbreeding, or mating between individuals with similar genetic makeup, is more likely to occur, thus perpetuating more common alleles to the point of fixation, thus decreasing genetic diversity.[18] Concerns about genetic diversity are therefore especially important with large mammals due to their small population size and high levels of human-caused population effects.[16]
A genetic bottleneck can occur when a population goes through a period of low number of individuals, resulting in a rapid decrease in genetic diversity. Even with an increase in population size, the genetic diversity often continues to be low if the entire species began with a small population, since beneficial mutations (see below) are rare, and the gene pool is limited by the small starting population.[19] This is an important consideration in the area of conservation genetics, when working toward a rescued population or species that is genetically healthy.
Today, the conservation and sustainable use of PGRs is a priority of the global community to solve issues surrounding food security and other problems arising from increased population growth. In the future, these resources will completely vanish if proper and stringent PGR conservation practices and policies are not implemented [11]. This challenge can be overcome by bringing all stakeholders, including farmers, ethnobotanists, indigenous knowledge-holding people, plant breeders, NGOs, seed banks, and policymakers together to share information, create PGR diversity awareness, develop new technologies, and deploy systematic and scientific conservation. Biotechnological techniques, such as cryopreservation, molecular markers, high-throughput sequencing, and genetic engineering, have improved the conservation of endangered and rare PGRs. Priority should also be given to the exploration of local germplasm and underutilized crop species and the maximum utilization of traditionally local landraces, with the involvement of local people. The Convention on Biological Diversity (CBD) and international undertaking on PGRs [12] are working in harmony for the conservation and sustainable utilization of PGRs under the umbrella of the Earth Summit of the United Nations Conference on Environment and Development (UNCED). A well-planned strategic and forward-looking vision is required for the conservation and sustainable utilization of these genetic resources.
2. Importance of Genetic Diversity in Plant Genetic Resources
Genetic diversity is the genetic base for crop improvement [13]. Diverse PGRs enable plant breeders to develop or improve crop varieties with desirable qualities. While developing new cultivars, due consideration must be given to the farmers’ preferences, such as high-yielding varieties, quality, and resistance to diseases and insect pests. In ancient times, humans selected desirable genotypes based on natural genetic variability in the population [14]. The preference for the development of new crop varieties shifts over a period with environmental changes. Plant breeders develop climate-resilient varieties possessing all the desirable traits, including resistance to various biotic and abiotic stresses. Genetic diversity in the form of mutant lines, wild species, breeding stocks, etc., is used for the improvement and development of modern crop varieties [13]. For the development of climate-resilient varieties, novel genes tolerant to biotic and abiotic stresses need to be conserved for future use in breeding programs. Additionally, the plant genotypes possessing genes for quality traits and aesthetic properties should be preserved in the available germplasm. Genetic diversity within and between plant species allows plant breeders to select superior genotypes, which can then be used for the development of genetic stock for hybridization programs or the release of a crop variety [13]. Genetic diversity enables PGRs to adapt to varied climatic conditions [14,15]. Moreover, the negative impact of inbreeding in populations can be reduced by enhancing genetic diversity. Higher levels of genetic diversity in PGRs support resilience to adverse environmental changes, integrity, community structure, and ecosystem functions [16,17]. Additionally, it helps plant breeders to utilize genetically diverse parents in a breeding program to improve the productivity of varieties of agriculture and horticulture crops [18] (Figure 1).
Figure 1
Different sources of genetic diversity and their potential utilization in the development of new crop varieties.
Genetic diversity in plant species depends on the heritable variation present within and between populations. It occurs due to genetic variation in the nucleotide sequence of DNA, chromosome mutations, and recombination during sexual reproduction [19]. In the sexual reproduction of plant species, the F1 and advanced generations are developed by crossing two or more diverse parents. The offspring developed from two genetically diverse parents possess genetic variations because of recombination during meiosis. Hence, genetically dissimilar offspring from parents are produced. However, this is the genetic material of individuals underlying the variability within, as well as between, species [20]. Generally, genetic diversity can be observed at three levels: diversity between species, diversity between populations within one species, and diversity between individuals within one population. It is genetic variability that provides evolutionary flexibility, resilience, and adaptability in plant species [21]. Before the identification of diverse parents in plant breeding programs, breeders and biotechnologists used a multitude of techniques for the characterization of the germplasm to know the genetic diversity [22]. For the characterization of the genetic diversity of PGRs and the identification of superior genotypes, various techniques are used, such as phenotypic or morphological traits, biochemical or allozyme techniques, and molecular techniques.
3. Factors Affecting Genetic Diversity
Genetic diversity changes over time owing to several factors. The main factors responsible for changes in genetic diversity are mutation, selection, genetic drift, and gene flow. Over time, natural and artificial selections play a substantial role in the choosing of superior genotypes, which significantly affects the gene and genotypic frequencies of the population [23]. As per Charles Darwin’s theory of evolution (1859), the desired genotypes are selected for and passed onto subsequent generations [24,25,26]. However, the domestication of desirable genotypes results from the superior genotypes being selected by farmers and breeders and neglects other undesirable genotypes. This leads to a reduction in inferior alleles over generations. During evolution, various morphological, physiological, and biochemical changes take place in plant species and can take different directions under domestication depending on the part of the plant used. Some plant species lose their sexual reproduction during selection for large size of the tuber or root, which is associated with selection for polyploid types, resulting in sterility. Some polyploid plant species, such as allohexaploid wheat and potato, show diploidization behavior during sexual reproduction. Some crops have been turned into annuals from their original form of perennials. In the domestication process, the complete genetic transformation of wild species occurs in the development of modern cultivars through natural and artificial selection [23]. After some time, some domesticated cultivars become susceptible to diseases and pests, which can be improved by incorporating genes from wild plant relatives [27]. During the process of domestication, desirable traits have been selected by breeders as per their preferences [27,28]. However, plant breeders prefer to choose crop varieties with a high yield, resistance to biotic and abiotic stresses, wide adaptation, non-shattering nature, large-sized seeds, early maturing, good quality traits, etc. [29,30]. The main factors affecting genetic diversity will be addressed in the following subsections.
3.1. Mutation
Mutations are sudden heritable changes that occur due to aberrations in the nucleotide sequence of DNA. A mutation is the source of genetic variation impacting the phenotype in crop species. Genetic diversity caused by mutations can have neutral, positive, and negative impacts on various characteristics of a plant species. Genetic variations caused by mutations in DNA are the principal cause of changes in the allele frequencies in a population besides selection and genetic drift. From the beginning, natural or spontaneous mutations have played a significant role in creating the genetic variation that has led to food security [31]. Mutations are the ultimate source of plant evolution when they frequently encounter environmental changes. Mutation rates proceed rapidly in response to environmental changes or even changes in the demographical locations related to the socio-economic conditions of the human population in a geographical area. Stress-inducible mutagenesis has been observed because of the use of different external inputs which accelerate adaptive evolution in plants. During mutagenesis, many kinds of genetic changes have been observed such as insertions, deletions, copy number variations, gross chromosomal rearrangements, and the movement of mobile elements. Earlier plant breeders utilized natural mutations as the main source of genetic variation for improving and developing crop varieties. However, modern technologies have accelerated the process by inducing mutation through mutagenesis The concept of mutation breeding was introduced to create more genetic diversity among crop species to improve traits such as disease and insect pest resistance, tolerance to abiotic stresses, and nutritional enhancement in crop varieties [32].
3.2. Selection
Natural and artificial selections act on the phenotypic characteristics of the plant species. The phenotypic expression of the plant species depends upon the heritable and non-heritable components in which the genotype–environment interaction also plays a significant role. The selection of superior genotypes depends on the availability of genetic variation present in the plant species. Artificial selection is effective only when sufficient genetic variation is present in the population. The genetic improvement of a genotype depends on the magnitude of genetic variability present in the population, as well as the nature of the association between different components. For example, the level of association of yield traits with other characteristics of the plant species enables the selection of various traits at a time [33]. Plant breeders make effective selection depending on the presence of substantial genetic variation in the population to enhance the maximum genetic yield potential of crop varieties [34]. It also helps in selecting better parents to be used in hybridization programs. Hence, the effective selection of genotypes in a population also depends on the degree of genetic variation in the population.
3.3. Migration
Migration is the movement of alleles from one species to another or from one population to another. It occurs through the movement of pollen and seed dispersal and planting material such as rhizomes, suckers, and other vegetative propagating materials. The rate of migration is affected by reproduction cycles and the dispersion of seeds and pollens. Migration can also occur through the moving or shifting of the germplasm from one area to another, which results in the mixing of two or more alleles through pollen and seeds [35].
3.4. Genetic Drift
Genetic drift is a mechanism in which the gene and allele frequencies of a population change due to sampling errors over generations. The sampling error changes the allele frequencies by chance, which ultimately changes the genetic diversity over generations. Every pollen grain has a different combination of alleles and can be carried by insects, wind, humans, or other means for hybridization with compatible flowers, largely determined by chance. Thus, in every reproduction cycle, the genetic diversity in crop species is lost at every generation through these chance events [36].
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4. Factors That Cause Genetic Vulnerability
Over the past century, it has been observed that the genetic diversity in wild populations is declining globally [16,37]. Genetically distinct populations for most species are also declining due to the shrinkage of geographic ranges and lack of proper management and conservation practices [38,39,40]. Most genetic diversity is lost due to infrastructure development, climate change, habitat fragmentation, population reduction, overgrazing, and overharvesting [41]. Besides this, the following subsections describe the major components responsible for the genetic vulnerability of genetic resources
Mutation
Random mutations consistently generate genetic variation.[11] A mutation will increase genetic diversity in the short term, as a new gene is introduced to the gene pool. However, the persistence of this gene is dependent of drift and selection (see above). Most new mutations either have a neutral or negative effect on fitness, while some have a positive effect.[11] A beneficial mutation is more likely to persist and thus have a long-term positive effect on genetic diversity. Mutation rates differ across the genome, and larger populations have greater mutation rates.[11] In smaller populations a mutation is less likely to persist because it is more likely to be eliminated by drift.[11]
Gene flow
Gene fled often by migration, is the movement of genetic material (for example by pollen in the wind, or the migration of a bird). Gene flow can introduce novel alleles to a population. These alleles can be integrated into the population, thus increasing genetic diversity.[20]
For example, an insecticide-resistant mutation arose in Anopheles gambiae African mosquitoes. Migration of some A. gambiae mosquitoes to a population of Anopheles coluzziin mosquitoes resulted in a transfer of the beneficial resistance gene from one species to the other. The genetic diversity was increased in A. gambiae by mutation and in A. coluzziin by gene flow.[21]
In agriculture
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In crops
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When humans initially started farming, they used selective breeding to pass on desirable traits of the crops while omitting the undesirable ones. Selective breeding leads to monocultures: entire farms of nearly genetically identical plants. Little to no genetic diversity makes crops extremely susceptible to widespread disease; bacteria morph and change constantly and when a disease-causing bacterium changes to attack a specific genetic variation, it can easily wipe out vast quantities of the species. If the genetic variation that the bacterium is best at attacking happens to be that which humans have selectively bred to use for harvest, the entire crop will be wiped out.[22]
The nineteenth-century Great Famine in Ireland was caused in part by a lack of biodiversity. Since new potato plants do not come as a result of reproduction, but rather from pieces of the parent plant, no genetic diversity is developed, and the entire crop is essentially a clone of one potato, it is especially susceptible to an epidemic. In the 1840s, much of Ireland's population depended on potatoes for food. They planted namely the "lumper" variety of potato, which was susceptible to a rot-causing oomycete called Phytophthora infestans.[23] The fungus destroyed the vast majority of the potato crop, and left one million people to starve to death.
Genetic diversity in agriculture does not only relate to disease, but also herbivores. Similarly, to the above example, monoculture agriculture selects for traits that are uniform throughout the plot. If this genotype is susceptible to certain herbivores, this could result in the loss of a large portion of the crop.[24][25] One way farmers get around this is through inter-cropping. By planting rows of unrelated, or genetically distinct crops as barriers between herbivores and their preferred host plant, the farmer effectively reduces the ability of the herbivore to spread throughout the entire plot.[26][27][28]
In livestock
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The genetic diversity of livestock species permits animal husbandry in a range of environments and with a range of different objectives. It provides the raw material for selective breeding programmes and allows livestock populations to adapt as environmental conditions change.[29]
Livestock biodiversity can be lost as a result of breed extinctions and other forms of genetic erosion. As of June 2014, among the 8,774 breeds recorded in the Domestic Animal Diversity Information System (DAD-IS), operated by the Food and Agriculture Organization of the United Nations (FAO), 17 percent were classified as being at risk of extinction and 7 percent already extinct.[29] There is now a Global Plan of Action for Animal Genetic Resources that was developed under the auspices of the Commission on Genetic Resources for Food and Agriculture in 2007, that provides a framework and guidelines for the management of animal genetic resources.
Awareness of the importance of maintaining animal genetic resources has increased over time. FAO has published two reports on the state of the world's animal genetic resources for food and agriculture, which cover detailed analyses of our global livestock diversity and ability to manage and conserve them.
Viral implications
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High genetic diversity in viruses must be considered when designing vaccinations. High genetic diversity results in difficulty in designing targeted vaccines, and allows for viruses to quickly evolve to resist vaccination lethality. For example, malaria vaccinations are impacted by high levels of genetic diversity in the protein antigens.[30] In addition, HIV-1 genetic diversity limits the use of currently available viral load and resistance tests.[31]
Coronavirus populations have considerable evolutionary diversity due to mutation and homologous recombination.[32] For example, the sequencing of 86 SARS-CoV-2 coronavirus samples obtained from infected patients revealed 93 mutations indicating the presence of considerable genetic diversity.[33] Replication of the coronavirus RNA genome is catalyzed by an RNA-dependent RNA polymerase. During replication this polymerase may undergo template switching, a form of homologous recombination.[34] This process which also generates genetic diversity appears to be an adaptation for coping with RNA genome damage.[35]
Coping with low genetic diversity
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A Tanzanian cheetah.
Natural
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Photomontage of planktonic organisms.
The natural world has several ways of preserving or increasing genetic diversity. Among oceanic plankton, viruses aid in the genetic shifting process. Ocean viruses, which infect the plankton, carry genes of other organisms in addition to their own. When a virus containing the genes of one cell infects another, the genetic makeup of the latter changes. This constant shift of genetic makeup helps to maintain a healthy population of plankton despite complex and unpredictable environmental changes.[36]
Cheetahs are a threatened species. Low genetic diversity and resulting poor s***m quality has made breeding and survivorship difficult for cheetahs. Moreover, only about 5% of cheetahs survive to adulthood[37] However, it has been recently discovered that female cheetahs can mate with more than one male per litter of cubs. They undergo induced ovulation, which means that a new egg is produced every time a female mates. By mating with multiple males, the mother increases the genetic diversity within a single litter of cubs.[38]
Human intervention
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Attempts to increase the viability of a species by increasing genetic diversity is called genetic rescue. For example, eight panthers from Texas were introduced to the Florida panther population, which was declining and suffering from inbreeding depression. Genetic variation was thus increased and resulted in a significant increase in population growth of the Florida Panther.[39] Creating or maintaining high genetic diversity is an important consideration in species rescue efforts, in order to ensure the longevity of a population.
Measures
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Genetic diversity of a population can be assessed by some simple measures.
Gene diversity is the proportion of polymorphic loci across the genome.
Heterozygosity is the fraction of individuals in a population that are heterozygous for a particular locus.
Alleles per locus is also used to demonstrate variability.
Nucleotide diversity is the extent of nucleotide polymorphisms within a population, and is commonly measured through molecular markers such as micro- and minisatellite sequences, mitochondrial DNA,[40] and single-nucleotide polymorphisms (SNPs).
Furthermore, stochastic simulation software is commonly used to predict the future of a population given measures such as allele frequency and population size.[41]
Genetic diversity can also be measured.The various recorded ways of measuring genetic diversity include:[42]
Species richness is a measure of the number of species
Species abundance a relative measure of the abundance of species
Species density an evaluation of the total number of species per unit area
See also
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Evolutionary biology portal
Biodiversity
Genetic variance
Center of diversity
Genetic variation
Genetic resources
Human genetic variation
Human Variome Project
International HapMap Project
Conservation biology
QST (genetics)
References
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