• A representation of the genetic differences that occur within a population is termed as genetic variation.
• The genetic variation of whole the species is usually termed as genetic diversity.
• The differences in genes or DNA segments are genetic variations and each variation of a gene is termed as an allele.
• For instance, there is a high amount of genetic variation in a population of several different alleles at a single chromosome locus.
• For natural selection, genetic variation is important, because natural selection can only increase or decrease the frequency of alleles that already exist in the population.
• Since conditions are unpredictable, genetically diverse populations may be able to adapt faster than those that do not involve genetic variation to evolving circumstances.
• All examples of genetic variations that can occur in a human population are the skin tone, hair color, dimples, freckles, and type of blood of an individual.
• The modified leaves of carnivorous plants and the development of flowers that mimic insects to attract plant pollinators are examples of genetic variation in plants.
• Albinism, cheetahs with markings, snakes flying, animals that play dead, and animals that resemble leaves are examples of genetic variation in animals.
• These variations allow the animals in their habitats to better adapt to conditions.

What are the causes of genetic variation?

• The main causes of genetic variation are:
  • Mutation
  • Gene flow
  • Sexual reproduction
  • Genetic drift
• However, there are other causes of genetic variation:
  • Random mating
  • Crossing over
  • Random fertilization
  • Non-random mating
  • Environmental variance

i. Mutation:

• In general, mutation is the primary source of genetic variation, which is the raw material for evolution through natural selection.
• A change in the DNA sequence is a mutation.
• Often these differences in gene sequences may be beneficial for an organism.
• By modifying genes and alleles in a population, mutations result in genetic variation.
• They may affect an individual gene or a whole chromosome.
• Though mutations alter the genotype of an organism (genetic makeup), they do not necessarily change the phenotype of an organism.
• They may affect an individual gene or a whole chromosome.
• Though mutations alter the genotype of an organism (genetic makeup), they do not necessarily change the phenotype of an organism.
• During replication, mutations occur in the DNA molecule, such that the daughter cells vary in sequence or DNA quantity from the parent cells.
• A mutation initially appears in a single cell of the body, but it is transferred on to all cells descended from the first.
• Mainly two types of mutation are discussed they are gene mutations and chromosomal mutations.

ii. Gene mutations:

• In the case where the nucleotide sequence is modified and is passed on to the offspring, gene mutation occurs.
• The alteration might be either insertion or deletion or substitution of one or a few nucleotides.
• The addition or deletion of nucleotides within the DNA sequence in the coded protein shifts the reading frame and hence results in highly altered sequence of amino acids.
• Substitutions of nucleotides, however, may or may not severely affect the biological function of the protein.
•  Those substitution that results in terminator codon are supposed to be harmful.
• Gene mutation take place spontaneously without being purposedly induced by humans.
• Ultraviolet light, X-rays, and other high-frequency electromagnetic radiation, as well as exposure to such mutagenic substances, such as mustard gas, can also trigger them.
• The effects of gene mutations can vary from negligible to lethal.
• Mutations that modify one or even many amino acids can have a minor or undetectable impact on the ability of the organism to live and replicate if the coded protein’s basic biological role is not hampered.
• But when an amino acid substitution influences an enzyme’s active site or changes a protein’s essential function in some other way, the effect can be severe.

iii. Chromosomal mutations:

• The mutation process produces several new genetic variants for each generation. The nucleus of each cell contains chromosomes that hold the inherited material, or DNA.
• Chromosomes occur in pairs and each of them is inherited from each parent.
• In the pair, the two members are termed as homologous chromosomes.
• As a rule, every cell of an organism and all people of the same species have the same number of chromosomes.
• However, the number, size, and organization of chromosomes differs between species.
• Alterations in the number, size, or organization of chromosomes within a species are referred as chromosomal mutations, chromosomal abnormalities, or chromosomal aberrations.
• By fusion of two chromosomes into one, by fission of one chromosome into two, or by addition or subtraction of one or more whole chromosomes or sets of chromosomes, changes in number can occur.
• Polyploidy is the condition in which one or more additional sets of chromosomes are acquired by an organism.
• Changes in the arrangement of chromosomes may occur by inversion when a chromosomal segment rotates 180 degrees in the same place; by duplication when a segment is added; by deletion when a segment is lost; or by translocation when a segment changes from one place to another.
• These are the mechanisms by which chromosomes evolve.
• The amount of DNA is not changed by inversions, translocations, fusions, and fissions.
• The significance of these mutations in evolution is that they alter the linkage relationships among genes.
• Genes that are closely related to each other are isolated and vice versa; this may impact their expression because genes are mostly sequentially transcribed, two or more at a time.

iv. Gene flow:

• It is also termed as gene migration.
• New genes are introduced into a population as organisms migrate into a new environment.
• The availability of new alleles in the gene pool makes it possible for new gene combinations.
•  The emigration, i.e., moving out of organisms from a population also alters the gene frequencies.
• The emigration results in the lack of genetic diversity.
• Immigration of new organisms into a population may favor organisms to adapt in changing environmental conditions.
• Sustained gene flow between two populations can also result to a combination of the two gene pools, decreasing the genetic variation between the two groups.
• Gene flow strongly plays role against speciation.
• It does so by the recombination of the gene pools of the groups, and hence, repairment of the developing differences in genetic variation that would have resulted to full speciation and formation of daughter species.
• For instance, if a species of grass grows on both sides of a road, pollen is likely to be migrated from one side to the other and vice versa.
• If this pollen is capable of fertilizing the plant where it ends up and producing viable offspring, then the pollen alleles have effectively connected the population to the other on one side of the road.

v. Sexual reproduction:

• Sexual reproduction enhances genetic variation by producing various gene combinations.
• The process by which gametes or sex cells are formed is known as meiosis.
• As alleles in the gametes are separated and haphazardly united upon fertilization, genetic variation occurs.
• During meiosis, the crossing over or swapping of homologous chromosomes also results in the genetic recombination of genes.

vi. Genetic drift:

• Genetic drift is the alteration of a population’s allele frequencies owing to occurrences of random chance, such as natural disasters.
• The converse of natural selection is genetic drift.
• The theory of natural selection maintains that certain individuals in a population have characteristics that allow more offspring to survive and produce, whereas other people have characteristics that are harmful and can cause them to die before reproducing.
• These selection pressures will alter the gene pool and the traits within the population over successive generations.
• A huge, strong male gorilla, for instance, will mate with more females than a small, weak male, so more of his genes will be passed on to the next generation.
• His descendants will continue to control the troops and also pass on their genes.
• Over time, in the gorilla population, the selection pressure would cause the allele frequencies to change towards big powerful males.
• Unlike natural selection, genetic drift explains the impact of chance on populations in the absence of positive or negative selection pressure.
• Allele frequencies within a population may change through random sampling, or the survival or reproduction of a random sample of individuals within a population.
• Instead of a male gorilla generating more offspring since he is stronger, he may be the only male accessible when a female is ready to mate.
• His genes are transferred on to future generation because of chance, not as he was the biggest or the strongest.
• Genetic drift is the transition of alleles within a population due to chance events that cause random samples of the population to produce offspring or not.
• Small populations are more prone to the powers of genetic drift.
• On the other hand, large populations are buffered against the consequences of chance.
• If one individual in a population of 10 happens to die at a young age before leaving any offspring to the next generation, all of their genes (1/10 of the gene pool of the population) will instantly be lost.
• The individual comprises only 1 percent of the total gene pool in a population of100; thus, genetic drift has much less effect on the genetic structure of the larger population.
• The Bottleneck effect:
  • Natural disasters, such as a natural catastrophe that destroys a large portion of the population at random, may also magnify genetic drift.
  • When only a few individuals survive, the bottleneck effect arises and reduces diversity in a population’s gene pool.
  • The survivors’ genetic structure becomes the whole population’s genetic structure, which could be very different from the pre-disaster population.
• The founder effect:
  • If any part of the population leaves to start a new population in a new location or if a population gets separated by a physical barrier of some sort, another scenario arises in which populations may experience a strong impact of genetic drift.
  • In this scenario, it is not likely that those individuals are representative of the total population, which leads to the founder effect.
  • When the genetic structure changes to match that of the founding fathers and mothers of the new population, the founder effect occurs.
  • The underlying effect is believed to have been a key factor in the genetic history of Dutch settlers in South Africa’s Afrikaner population, as evidenced by mutations that are prevalent in Afrikaners, but rare in most other populations.
  • This was likely due to the fact that these mutations were carried by a higher-than-normal proportion of the founding colonists.
  • As a result, Huntington’s disease (HD) and Fanconi anemia (FA), a genetic condition known to cause blood marrow and congenital defects, including cancer, have exceptionally high incidences in the population.

vii. Non-random mating:

• If individuals nonrandomly mate with the other individuals within a population, i.e., they select their mate, selections can drive evolution in a population.
• There are several explanations for the phenomenon of nonrandom mating.
• Simple mate choice or sexual selection is one reason; female peahens, for instance, may prefer peacocks with larger, brighter tails.
• Traits that contribute to more matches for an individual lead to more offspring and ultimately lead to a higher prevalence of that feature in the population through natural selection.
• An individual’s desire to mate with partners that are phenotypically similar to themselves is one common type of mate choice, called positive assortative mating.
• Physical location is another cause of nonrandom mating.
• This is particularly true in large populations distributed over large geographical distances where not all individuals would have equal access to each other.
• These may be miles apart across forests or over rugged terrain, while others may live nearby immediately.

viii. Environmental variance:

• Genes are not the only players involved in population variance determination.
• Other factors, such as the environment, also affect phenotypes.
• For instance, due to daily exposure to the sun, an environmental factor, a beachgoer is likely to have darker skin than a city dweller.
• For certain animals, some major features, such as gender, are determined by the environment.
• For instance, some turtles and other reptiles have temperature-dependent sex determination (TSD).
• TSD implies that individuals grow into males if their eggs are incubated over a certain temperature range, or females at a distinct temperature range.
• Geographic separation among populations can contribute to variation in the phenotypic variation between certain populations.
• In most populations, this geographical variation is seen and can be important.
• One sort of geographic variation, named a cline, could be seen as populations of a given species differ progressively across an ecological gradient.

Gene pool:

• The term gene pool in evolutionary science refers to the collection of all available genes that can be passed down in the population of a single species from parents to offspring.
• The more variation there is in the population, the greater the gene pool.
• The gene pool decides the phenotypes (visible features) are present at any given time in the population.

How do gene pools change?

• Due to the movement of individuals into or out of a population, the gene pool can shift within a geographic region.
• When people with population-specific characteristics move abroad, the gene pool in that population shrinks and the characteristics are no longer available to be passed on to the offspring.
• In the other hand, as new people with new special features immigrate into the population, they expand the gene pool.
• A new form of diversity is added into the population when these new individuals interbreed with individuals already present.
• The size of the gene pool directly impacts the population’s evolutionary trajectory.
• The theory of evolution claims that natural selection works on a population to benefit the favorable features of that environment while weeding out the undesirable characteristics at the same time.
• The gene pool changes since natural selection operates on a population.
• Within the gene pool, beneficial adaptations become more frequent, and the less desirable characteristics become less prevalent or may even vanish entirely from the gene pool.
• Populations with larger gene pools are more likely than those with smaller gene pools to survive as the local climate changes.
• This is due to the fact that a broader range of traits are available to larger populations with wider diversity, which gives them an advantage as the environment changes and demands new adaptations.
• If there are few to no individuals with the genetic diversity needed to survive changes, a smaller and more homogeneous gene pool puts the population at risk of extinction.
• The more diverse the population, the more likely they are to survive significant changes in the environment.

Examples of gene pool in evolution:

• Individuals who are antibiotic-resistant are more likely to withstand any form of medical intervention in bacteria populations and live long enough to reproduce.
• The gene pool evolves over time (rather quickly in the case of rapidly reproducing organisms such as bacteria) to comprise only bacteria resistant to antibiotics.
• In this way, new strains of virulent bacteria are produced.
• A large number of plants that farmers classify as weeds are so tenacious because they have a diverse gene pool that helps them to adapt to a variety of environmental conditions.
• On the other hand, advanced hybrids also need very precise, even ideal conditions, because they have been bred to have a very small gene pool that prefers certain features, such as beautiful flowers or large fruits.
• It can be said that dandelions are superior to hybrid roses, on basis of size of gene pools.

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• Induced mutations are induced by known factor- such as-physical (ionizing irradiation, ultraviolet light), chemical and biological mutagens (bacteria and viruses).

Mechanism of induced mutation:

• Induced mutations occurs by at least three different mechanisms. They are-
  • By replacing nitrogenous base with base analogs
  • By base alteration-altering a base so that it specifically mispair with another base
  • By distortion of DNA molecule- damaging a base so that it no longer pair with another base

I. Incorporation of base analogs:

• Some chemical compounds are sufficiently similar to the normal nitrogenous bases of DNA known as base analogs and they can incorporated into DNA in place of normal bases.
• These analogs can base pair with other nitrogenous bases but they induce insertion of incorrect nucleotide during replication causing mutation.
• Uracil is halogenated in the carbon-5 position to give 5-bromouracil, 5-chlorouracil, and 5-iodouracil which can be incorporated into DNA in the place of thymine.
• 5-bromouracil (5-BU) bromine is formed by bromination at the carbon-5 position of uracil. The resulting structure of 5-bromouracil is similar to thymine  but thymine has CH3 group at C5 .
• 5-Bromouracil is most effective analog to thymine because size of bromine has same van der Waals radius as the methyl group in thymine.
• 5-bromouracil is highly mutagenic and it pairs with Adenine in normal condition. In 5-BU, the bromine atom is not in a position in which it can hydrogen-bond during base pairing, so the keto form of 5-BU pairs with adenine.
• However the frequency of tautomeric shift of 5-bromouracil is much higher than Thymine. It changes from keto form to either enol form or an ionized from amino form to keto form when protonated. Now, 5-bromouracil form hydrogen bond with Guanine instead of complementary base Adenine which result in base pair transition from T=A to C=G in subsequent replication cycle.
• Another commonly used base is 2-Aminopurine which is analog to adenine and pairs with thymine by two hydrogen bond. After a tautomeric shift due to protonation, it can form pair with cytosine.
• Therefore, 2-aminopurine can induce base pair transition from A=T to G=C in subsequent replication cycle.

II. Base alteration: alkylation, depurination, deamination and hydroxylation

• In this case, the mutagens do not incorporate with the DNA, however they can causes base alteration in a specific way.
• Some of the base alteration are- alkylation, depurination, deamination, hydroxylation etc.

Alkylation:

• Alkylating agents are most widely used mutagens which carry one, two or more alkyl groups in reactive form.
• Alkylating agents transfer their alkyl group (methyl or ethyl) group to nitrogenous bases of DNA and to phosphate group (alkylation).
• The most commonly used alkylating agents are- ethyl-methane sulfonate (EMS), Dimethyl sulphonate (DMS), Diethyl sulphonate (DES) etc , nitrosoguanidine (NG)
• Mechanism of alkylating agents:
  • Transfer alkyl group to phosphate group of DNA and produces unstable phosphate trimester which hydrolyses to give alkyl group. But some alkyl group may remain attached to phosphate which interfere with DNA replication cycle as well as cause breakage of sugar phosphate back bone.
  • Transfer alkyl group to 6-oxygen and 7-nitrogen of DNA bases. Among these alkylation of nitrogenous base, 7-ethylguanine is most common derivative. 7-ethylguanine is base analog to cytosine and can form base pair with thymine which ultimately cause base transition from G=C to AT.
  • Some difunctional or polyfunctional alkylating agents can crosslink with DNA strand and interfere DNA replication leading to chromosome breakage.

Depurination:

• Alkylation of purine base (Adenine and Guanine) give rise to unstable quaternary nitrogenous base which interfere with glycosidic bond between nitrogenous base and deoxyribose sugar.
• The loss of purine bases from DNA is termed as Depurination.
• Once the base is depurinated, it cannot specify complimentary base to the original purine during replication which result in incorporation of wrong base.
• Therefore, this causes base pair substitution.

Deamination:

• Some mutagens react with nitrogenous base containing amino group and remove it with another functional group.
• Nitrous acid (HNO2) a chemical which reacts with amino group containing nitrogenous bases (Adenine, cytosine and guanine) and replace it.
• Deamination of adenine by nitrous acid yields hypoxanthine (H) which can base pair with cytosine. This deamination at the position of adenine result in base transition from A:T to G:C in successive replication.
• Similarly, deamination of cytosine by HNO2 results in uracil. Now uracil can base pair with adenine. Therefore, change of base from cytosine to uracil results in base transition from G:C to A:U and then A:T in successive replication cycle.
• Other example of deamination: conversion of 5-methylcytosine to thymine.

Hydroxylation:

• The mutagen hydroxylamine (NH2OH) reacts with amino group of cytosine causing hydroxylation to yield hydroxylcytosine.
• Now the hydroxylcytosine can form base pair with adenine instead of guanine. This results in base pair transition.

III. Distortion of DNA molecule:

• Some of the mutagens directly reacts with DNA molecules causing distortion and modify the structure.

i. Intercalating agents:

• Certain florescent acridine dyes such as acridine orange, proflavin causes DNA mutation by insertion or deletion of nitrogenous bases.
• Acridine dyes are planar (flat) molecule that mimic nitrogenous bases and at low concentration it can inserts or intercalates between subsequent nitrogenous bases in DNA molecule.
• Insertion of the agent stretches the distance between adjacent base pair by 0.68nm which is twice the normal distance. This distortion result in single nucleotide deletion or insertion at this position during recombination.
• Intercalating agents result in insertion of bases:
  • Intercalation of acridine dye between two nitrogenous bases in template strand result in stretch of DNA molecule.
  • During DNA replication, a new base can be inserted in the newly synthesized strand opposite of acridine molecule.
  • Now during replication of newly synthesized strand, a complimentary base in added opposite to newly added base.
• Intercalating agents result in deletion of bases:
  • Insertion of acridine molecule in DNA strand may block the base in the template strand and does not allow to base pair.
  • During replication, one base is deficient in newly synthesized strand.

ii. DNA damage: by radiation

• Various kinds of radiations can induce mutation. Mutagenic radiations are two types- non-ionizing radiation (UV rays) and ionizing radiation (X-rays, gamma rays):

a. Mutation caused by UV rays: Pyrimidine dimer formation

• UV rays have a wavelength of 10-390nm.
• When UV rays falls on the genetic materials, it is absorbed and due to increase in energy level electrons are excited.
• The most effective wavelength of UV rays for inducing mutation is 260nm.
• UV rays are non-ionizing radiation and have a penetration power lower than X-rays.
• Exposure of DNA to UV rays causes nitrogenous bases to become highly reactively unstable free radicals.
• One of the consequences of UV rays exposure is photochemical fusion of two pyrimidine that are adjacent to each other on a same polynucleotide chain.
• Pyrimidine dimer formation is the primary effect of UV rays on DNA molecule.
• In case of two thymine, the fusion is called thymine dimer. UV rays causes adjacent thymine on the same DNA strand to bond together by covalent linkage between carbon 5 and 6 of adjacent thymine molecule forming cyclobutane ring.
• In case of thymine adjacent to a cytosine, the resulting fusion is a thymine-cytosine dimer in which the thymine is linked via its carbon atom 6 to the carbon atom 4 of cytosine.
• This dimer structure cannot fit into DNA helix and cause distortion of DNA molecule which result in failure of DNA replication and sometime leads to lethal effect.
• Pyrimidine dimer can also formed by cross linking of pyrimidine bases of adjacent DNA strand.
• There are three types of thymine dimers
• Thymine-thymine dimer= 50%
• Thymine-cytosine dimer= 40%
• Cytosine-cytosine dimer=10%

b. Mutation caused by Ionizing radiation (IR):

• The effects of different ionizing radiation are qualitatively the same.
• In direct effect, IR breaks the phosphate ester bond in DNA. The breakage may take place at one or more points. As a result of breakage, segment of DNA either get lost or rearranged during repair. Sometimes the effect is fatal.
• In indirect effect, the ionizing radiation ionize water producing free radicals which is extremely reactive.
• The free radicals react with DNA molecule to alter its structure.

Mechanism of induced mutation: base analogs, base alteration, intercalation, pyrimidine dimer formation

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Mutation

• Mutation is the change in sequence of nucleotide of DNA.
• Change in sequence of nucleotide brings sudden change in morphological characteristics of an organism. If such change are heritable, then it is called as mutation.
• So, mutation is defined as any heritable change in the sequence of nucleotide of DNA.

Organism with mutation is called mutant while the organism without mutation is wild type.

Types of Mutation

Based on change in genotype and phenotype, mutation are of two types

1. Point mutation
2. Frameshift mutation

1. Point mutation

• It occurs as a result of replacement of one nucleotide by other in specific nucleotide sequence of gene. Point mutation brings little phenotypic change as compared to frameshift mutation.

Point mutation are two types based on the base pair substitution

i) Transition:

• It is the point mutation occur by substitution of one purine by another purine or one pyrimidine by another pyrimidine.

ii) Transversion:

• It is the point mutation occur by substitution of purine by pyrimidine and vice versa.

Based on transcriptional property point mutation are of three types.

i) Silent mutation

ii) Missense mutation

iii) Non-sense mutation

Figure: types of point mutation

i) Silent mutation:

• It is also known as neutral mutation.
• It is the mutation in which mutated codon codes same amino acids as the original codon. Since the aminoacid is same as original one, it does not effects the structure and composition of protein.
• Silent mutation causes phenotype of bacteria remain similar to that of wild type.

ii) Missense mutation:

• In this mutation mutated codon codes different amino acid (other than original). Since new aminoacid coded by mutated codon is altered, the protein formed from it is also altered. Such protein can be less active or completely inactive.
• If altered aminoacids lie on active site of protein then such protein become completely non-functional.
• The missense mutation causes phenotypic change in organism.

iii) Non sense mutation:

• Mutation in which altered codon is stop codon or chain terminating codon, such mutation is called non-sense mutation.
• Non sense mutation causes incomplete synthesis. Such incomplete protein is always non-functional.
• Non-sense mutation bring greatest change in phenotype of an organism.

2. Frameshift mutation

• It occurs as a result of addition or deletion of nucleotide in the sequence of DNA. Addition or deletion of nucleotide causes shift of the reading frame of mRNA.
• In a mRNA each codon is represented by three bases without punctuation and insertion or deletion of a nucleotide changes the entire frame. So frame shift mutation bring greater phenotypic change than point mutation.
• Insertion or deletion of one or two base pair of nucleotide causes shift in frame. However, insertion or deletion of three base pair adds or remove a whole codon, this results in addition of removal of single amino acid from polypeptide chain.

Mutation and types of mutation

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