Genetic diversity

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A graphical representation of the typical human karyotype. Human karyotype.svg
A graphical representation of the typical human karyotype.

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.

Contents

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 Maize diversity in Vavilovs office (3421259242).jpg
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 or adaptive population differentiation can be measured as . [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 populations 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.

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 flow, 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

In crops

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

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

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

A Tanzanian cheetah. Cheetah genetic diversity.jpg
A Tanzanian cheetah.

Natural

Photomontage of planktonic organisms. Plankton collage.jpg
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 sperm 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

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

Genetic diversity of a population can be assessed by some simple measures.

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]

See also

Related Research Articles

<span class="mw-page-title-main">Evolution</span> Change in the heritable characteristics of biological populations

Evolution is the change in the heritable characteristics of biological populations over successive generations. Evolution occurs when evolutionary processes such as natural selection and genetic drift act on genetic variation, resulting in certain characteristics becoming more or less common within a population over successive generations. The process of evolution has given rise to biodiversity at every level of biological organisation.

Microevolution is the change in allele frequencies that occurs over time within a population. This change is due to four different processes: mutation, selection, gene flow and genetic drift. This change happens over a relatively short amount of time compared to the changes termed macroevolution.

<span class="mw-page-title-main">Mutation</span> Alteration in the nucleotide sequence of a genome

In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, mitosis, or meiosis or other types of damage to DNA, which then may undergo error-prone repair, cause an error during other forms of repair, or cause an error during replication. Mutations may also result from insertion or deletion of segments of DNA due to mobile genetic elements.

<span class="mw-page-title-main">Inbreeding</span> Reproduction by closely related organisms

Inbreeding is the production of offspring from the mating or breeding of individuals or organisms that are closely related genetically. By analogy, the term is used in human reproduction, but more commonly refers to the genetic disorders and other consequences that may arise from expression of deleterious recessive traits resulting from incestuous sexual relationships and consanguinity. Animals avoid incest only rarely.

Genetic drift, also known as random genetic drift, allelic drift or the Wright effect, is the change in the frequency of an existing gene variant (allele) in a population due to random chance.

Small populations can behave differently from larger populations. They are often the result of population bottlenecks from larger populations, leading to loss of heterozygosity and reduced genetic diversity and loss or fixation of alleles and shifts in allele frequencies. A small population is then more susceptible to demographic and genetic stochastic events, which can impact the long-term survival of the population. Therefore, small populations are often considered at risk of endangerment or extinction, and are often of conservation concern.

Molecular evolution is the process of change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes. Major topics in molecular evolution concern the rates and impacts of single nucleotide changes, neutral evolution vs. natural selection, origins of new genes, the genetic nature of complex traits, the genetic basis of speciation, the evolution of development, and ways that evolutionary forces influence genomic and phenotypic changes.

<span class="mw-page-title-main">Neutral theory of molecular evolution</span> Theory of evolution by changes at the molecular level

The neutral theory of molecular evolution holds that most evolutionary changes occur at the molecular level, and most of the variation within and between species are due to random genetic drift of mutant alleles that are selectively neutral. The theory applies only for evolution at the molecular level, and is compatible with phenotypic evolution being shaped by natural selection as postulated by Charles Darwin.

<span class="mw-page-title-main">Population bottleneck</span> Effects of a sharp reduction in numbers on the diversity and robustness of a population

A population bottleneck or genetic bottleneck is a sharp reduction in the size of a population due to environmental events such as famines, earthquakes, floods, fires, disease, and droughts; or human activities such as genocide, specicide, widespread violence or intentional culling. Such events can reduce the variation in the gene pool of a population; thereafter, a smaller population, with a smaller genetic diversity, remains to pass on genes to future generations of offspring. Genetic diversity remains lower, increasing only when gene flow from another population occurs or very slowly increasing with time as random mutations occur. This results in a reduction in the robustness of the population and in its ability to adapt to and survive selecting environmental changes, such as climate change or a shift in available resources. Alternatively, if survivors of the bottleneck are the individuals with the greatest genetic fitness, the frequency of the fitter genes within the gene pool is increased, while the pool itself is reduced.

Population genetics is a subfield of genetics that deals with genetic differences within and among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and population structure.

<span class="mw-page-title-main">Gene flow</span> Transfer of genetic variation from one population to another

In population genetics, gene flow is the transfer of genetic material from one population to another. If the rate of gene flow is high enough, then two populations will have equivalent allele frequencies and therefore can be considered a single effective population. It has been shown that it takes only "one migrant per generation" to prevent populations from diverging due to drift. Populations can diverge due to selection even when they are exchanging alleles, if the selection pressure is strong enough. Gene flow is an important mechanism for transferring genetic diversity among populations. Migrants change the distribution of genetic diversity among populations, by modifying allele frequencies. High rates of gene flow can reduce the genetic differentiation between the two groups, increasing homogeneity. For this reason, gene flow has been thought to constrain speciation and prevent range expansion by combining the gene pools of the groups, thus preventing the development of differences in genetic variation that would have led to differentiation and adaptation. In some cases dispersal resulting in gene flow may also result in the addition of novel genetic variants under positive selection to the gene pool of a species or population

<span class="mw-page-title-main">Genetic variation</span> Difference in DNA among individuals or populations

Genetic variation is the difference in DNA among individuals or the differences between populations among the same species. The multiple sources of genetic variation include mutation and genetic recombination. Mutations are the ultimate sources of genetic variation, but other mechanisms, such as genetic drift, contribute to it, as well.

<span class="mw-page-title-main">Founder effect</span> Effect in population genetics

In population genetics, the founder effect is the loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population. It was first fully outlined by Ernst Mayr in 1942, using existing theoretical work by those such as Sewall Wright. As a result of the loss of genetic variation, the new population may be distinctively different, both genotypically and phenotypically, from the parent population from which it is derived. In extreme cases, the founder effect is thought to lead to the speciation and subsequent evolution of new species.

<span class="mw-page-title-main">Mutation rate</span> Rate at which mutations occur during some unit of time

In genetics, the mutation rate is the frequency of new mutations in a single gene, nucleotide sequence, or organism over time. Mutation rates are not constant and are not limited to a single type of mutation; there are many different types of mutations. Mutation rates are given for specific classes of mutations. Point mutations are a class of mutations which are changes to a single base. Missense and Nonsense mutations are two subtypes of point mutations. The rate of these types of substitutions can be further subdivided into a mutation spectrum which describes the influence of the genetic context on the mutation rate.

In population genetics and population ecology, population size is a countable quantity representing the number of individual organisms in a population. Population size is directly associated with amount of genetic drift, and is the underlying cause of effects like population bottlenecks and the founder effect. Genetic drift is the major source of decrease of genetic diversity within populations which drives fixation and can potentially lead to speciation events.

<span class="mw-page-title-main">Conservation genetics</span> Interdisciplinary study of extinction avoidance

Conservation genetics is an interdisciplinary subfield of population genetics that aims to understand the dynamics of genes in a population for the purpose of natural resource management, conservation of genetic diversity, and the prevention of species extinction. Scientists involved in conservation genetics come from a variety of fields including population genetics, research in natural resource management, molecular ecology, molecular biology, evolutionary biology, and systematics. The genetic diversity within species is one of the three fundamental components of biodiversity, so it is an important consideration in the wider field of conservation biology.

Genetic hitchhiking, also called genetic draft or the hitchhiking effect, is when an allele changes frequency not because it itself is under natural selection, but because it is near another gene that is undergoing a selective sweep and that is on the same DNA chain. When one gene goes through a selective sweep, any other nearby polymorphisms that are in linkage disequilibrium will tend to change their allele frequencies too. Selective sweeps happen when newly appeared mutations are advantageous and increase in frequency. Neutral or even slightly deleterious alleles that happen to be close by on the chromosome 'hitchhike' along with the sweep. In contrast, effects on a neutral locus due to linkage disequilibrium with newly appeared deleterious mutations are called background selection. Both genetic hitchhiking and background selection are stochastic (random) evolutionary forces, like genetic drift.

In genetics, a selective sweep is the process through which a new beneficial mutation that increases its frequency and becomes fixed in the population leads to the reduction or elimination of genetic variation among nucleotide sequences that are near the mutation. In selective sweep, positive selection causes the new mutation to reach fixation so quickly that linked alleles can "hitchhike" and also become fixed.

Host–parasite coevolution is a special case of coevolution, where a host and a parasite continually adapt to each other. This can create an evolutionary arms race between them. A more benign possibility is of an evolutionary trade-off between transmission and virulence in the parasite, as if it kills its host too quickly, the parasite will not be able to reproduce either. Another theory, the Red Queen hypothesis, proposes that since both host and parasite have to keep on evolving to keep up with each other, and since sexual reproduction continually creates new combinations of genes, parasitism favours sexual reproduction in the host.

In genetics, when multiple copies of a beneficial mutation become established and fix together it is called soft sweep. Depending on the origin of these copies, linked variants might then be retained and emerge as haplotype structures in the population. There are two major forms of soft sweeps:

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  40. ↑ Kawabe, K.; Worawut, R.; Taura, S.; Shimogiri, T.; Nishida, T.; Okamoto, S. (2014-01-01). "Genetic Diversity of mtDNA D-loop Polymorphisms in Laotian Native Fowl Populations". Asian-Australasian Journal of Animal Sciences. 27 (1): 19–23. doi:10.5713/ajas.2013.13443. PMC   4093284 . PMID   25049921.
  41. ↑ Hoban, Sean (2014-04-30). "An overview of the utility of population simulation software in molecular ecology". Molecular Ecology. 23 (10): 2383–2401. doi: 10.1111/mec.12741 . PMID   24689878.
  42. ↑ diversity, measuring. "measuring species diversity" (PDF).
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