Genetic recombination is the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent. In eukaryotes, genetic recombination during meiosis can lead to a novel set of genetic information that can be passed on from the parents to the offspring. Most recombination is occurring. During meiosis in eukaryotes, genetic recombination involves the pairing of homologous chromosomes; this may be followed by information transfer between the chromosomes. The information transfer may occur without physical exchange. Recombination may occur during mitosis in eukaryotes where it ordinarily involves the two sister chromosomes formed after chromosomal replication. In this case, new combinations of alleles are not produced since the sister chromosomes are identical. In meiosis and mitosis, recombination occurs between similar molecules of DNA. In meiosis, non-sister homologous chromosomes pair with each other so that recombination characteristically occurs between non-sister homologues.
In both meiotic and mitotic cells, recombination between homologous chromosomes is a common mechanism used in DNA repair. Gene conversion - the process during which homologous sequences are made identical falls under genetic recombination. Genetic recombination and recombinational DNA repair occurs in bacteria and archaea, which use asexual reproduction. Recombination can be artificially induced in laboratory settings, producing recombinant DNA for purposes including vaccine development. VJ recombination in organisms with an adaptive immune system is a type of site-specific genetic recombination that helps immune cells diversify to recognize and adapt to new pathogens. During meiosis, synapsis ordinarily precedes genetic recombination. Genetic recombination is catalyzed by many different enzymes. Recombinases are key enzymes. RecA, the chief recombinase found in Escherichia coli, is responsible for the repair of DNA double strand breaks. In yeast and other eukaryotic organisms there are two recombinases required for repairing DSBs.
The RAD51 protein is required for mitotic and meiotic recombination, whereas the DNA repair protein, DMC1, is specific to meiotic recombination. In the archaea, the ortholog of the bacterial RecA protein is RadA. Bacterial recombination In Bacteria there are: regular bacterial recombination, as well as noneffective transfer of genetic material, expressed as unsuccessful transfer or abortive transfer, any bacterial DNA transfer of the donor cell recipients who have set the incoming DNA as part of the genetic material of the recipient. Abortive transfer was registered in conjugation. In all cases, the transmitted fragment is diluted by the culture growth. In eukaryotes, recombination during meiosis is facilitated by chromosomal crossover; the crossover process leads to offspring having different combinations of genes from those of their parents, can produce new chimeric alleles. The shuffling of genes brought about by genetic recombination produces increased genetic variation, it allows sexually reproducing organisms to avoid Muller's ratchet, in which the genomes of an asexual population accumulate genetic deletions in an irreversible manner.
Chromosomal crossover involves recombination between the paired chromosomes inherited from each of one's parents occurring during meiosis. During prophase I the four available chromatids are in tight formation with one another. While in this formation, homologous sites on two chromatids can pair with one another, may exchange genetic information; because recombination can occur with small probability at any location along chromosome, the frequency of recombination between two locations depends on the distance separating them. Therefore, for genes sufficiently distant on the same chromosome, the amount of crossover is high enough to destroy the correlation between alleles. Tracking the movement of genes resulting from crossovers has proven quite useful to geneticists; because two genes that are close together are less to become separated than genes that are farther apart, geneticists can deduce how far apart two genes are on a chromosome if they know the frequency of the crossovers. Geneticists can use this method to infer the presence of certain genes.
Genes that stay together during recombination are said to be linked. One gene in a linked pair can sometimes be used as a marker to deduce the presence of another gene; this is used in order to detect the presence of a disease-causing gene. The recombination frequency between two loci observed, it is the frequency of crossing over between two linked gene loci, depends on the mutual distance of the genetic loci observed. For any fixed set of genetic and environmental conditions, recombination in a particular region of a linkage structure tends to be constant, the same is true for the crossing-over value, used in the production of genetic maps. In gene conversion, a section of genetic material is copied from one chromosome to another, without the donating chromosome being changed. Gene conversion occurs at high frequency at the actual site of the recombination event during meiosis, it is a process by which a DNA sequence
In biology, a mutation is the permanent alteration of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal DNA or other genetic elements. Mutations result from errors during DNA replication or other types of damage to DNA, which may undergo error-prone repair, or cause an error during other forms of repair, or else may cause an error during replication. Mutations may result from insertion or deletion of segments of DNA due to mobile genetic elements. Mutations may or may not produce discernible changes in the observable characteristics of an organism. Mutations play a part in both normal and abnormal biological processes including: evolution and the development of the immune system, including junctional diversity; the genomes of RNA viruses are based on RNA rather than DNA. The RNA viral genome can be double single stranded. In some of these viruses replication occurs and there are no mechanisms to check the genome for accuracy; this error-prone process results in mutations.
Mutation can result in many different types of change in sequences. Mutations in genes can either have no effect, alter the product of a gene, or prevent the gene from functioning properly or completely. Mutations can occur in nongenic regions. One study on genetic variations between different species of Drosophila suggests that, if a mutation changes a protein produced by a gene, the result is to be harmful, with an estimated 70 percent of amino acid polymorphisms that have damaging effects, the remainder being either neutral or marginally beneficial. Due to the damaging effects that mutations can have on genes, organisms have mechanisms such as DNA repair to prevent or correct mutations by reverting the mutated sequence back to its original state. Mutations can involve the duplication of large sections of DNA through genetic recombination; these duplications are a major source of raw material for evolving new genes, with tens to hundreds of genes duplicated in animal genomes every million years.
Most genes belong to larger gene families of shared ancestry. Novel genes are produced by several methods through the duplication and mutation of an ancestral gene, or by recombining parts of different genes to form new combinations with new functions. Here, protein domains act as modules, each with a particular and independent function, that can be mixed together to produce genes encoding new proteins with novel properties. For example, the human eye uses four genes to make structures that sense light: three for cone cell or color vision and one for rod cell or night vision. Another advantage of duplicating a gene is. Other types of mutation create new genes from noncoding DNA. Changes in chromosome number may involve larger mutations, where segments of the DNA within chromosomes break and rearrange. For example, in the Homininae, two chromosomes fused to produce human chromosome 2. In evolution, the most important role of such chromosomal rearrangements may be to accelerate the divergence of a population into new species by making populations less to interbreed, thereby preserving genetic differences between these populations.
Sequences of DNA that can move about the genome, such as transposons, make up a major fraction of the genetic material of plants and animals, may have been important in the evolution of genomes. For example, more than a million copies of the Alu sequence are present in the human genome, these sequences have now been recruited to perform functions such as regulating gene expression. Another effect of these mobile DNA sequences is that when they move within a genome, they can mutate or delete existing genes and thereby produce genetic diversity. Nonlethal mutations increase the amount of genetic variation; the abundance of some genetic changes within the gene pool can be reduced by natural selection, while other "more favorable" mutations may accumulate and result in adaptive changes. For example, a butterfly may produce offspring with new mutations; the majority of these mutations will have no effect. If this color change is advantageous, the chances of this butterfly's surviving and producing its own offspring are a little better, over time the number of butterflies with this mutation may form a larger percentage of the population.
Neutral mutations are defined as mutations whose effects do not influence the fitness of an individual. These can increase in frequency over time due to genetic drift, it is believed that the overwhelming majority of mutations have no significant effect on an organism's fitness. DNA repair mechanisms are able to mend most changes before they become permanent mutations, many organisms have mechanisms for eliminating otherwise-permanently mutated somatic cells. Beneficial mutations can improve reproductive success. Mutationism is one of several alternatives to evolution by natural selection that have existed both before and after the publication of Charles Darwin's 1859 book, On the Origin of Species. In the theory, mutation was the source of novelty
In computer science and operations research, a genetic algorithm is a metaheuristic inspired by the process of natural selection that belongs to the larger class of evolutionary algorithms. Genetic algorithms are used to generate high-quality solutions to optimization and search problems by relying on bio-inspired operators such as mutation and selection. John Holland introduced genetic algorithms in 1960 based on the concept of Darwin’s theory of evolution. In a genetic algorithm, a population of candidate solutions to an optimization problem is evolved toward better solutions; each candidate solution has a set of properties which can be altered. The evolution starts from a population of randomly generated individuals, is an iterative process, with the population in each iteration called a generation. In each generation, the fitness of every individual in the population is evaluated; the more fit individuals are stochastically selected from the current population, each individual's genome is modified to form a new generation.
The new generation of candidate solutions is used in the next iteration of the algorithm. The algorithm terminates when either a maximum number of generations has been produced, or a satisfactory fitness level has been reached for the population. A typical genetic algorithm requires: a genetic representation of the solution domain, a fitness function to evaluate the solution domain. A standard representation of each candidate solution is as an array of bits. Arrays of other types and structures can be used in the same way; the main property that makes these genetic representations convenient is that their parts are aligned due to their fixed size, which facilitates simple crossover operations. Variable length representations may be used, but crossover implementation is more complex in this case. Tree-like representations are explored in genetic programming and graph-form representations are explored in evolutionary programming. Once the genetic representation and the fitness function are defined, a GA proceeds to initialize a population of solutions and to improve it through repetitive application of the mutation, crossover and selection operators.
The population size depends on the nature of the problem, but contains several hundreds or thousands of possible solutions. The initial population is generated randomly, allowing the entire range of possible solutions; the solutions may be "seeded" in areas where optimal solutions are to be found. During each successive generation, a portion of the existing population is selected to breed a new generation. Individual solutions are selected through a fitness-based process, where fitter solutions are more to be selected. Certain selection methods rate the fitness of each solution and preferentially select the best solutions. Other methods rate only a random sample of the population, as the former process may be time-consuming; the fitness function is defined over the genetic representation and measures the quality of the represented solution. The fitness function is always problem dependent. For instance, in the knapsack problem one wants to maximize the total value of objects that can be put in a knapsack of some fixed capacity.
A representation of a solution might be an array of bits, where each bit represents a different object, the value of the bit represents whether or not the object is in the knapsack. Not every such representation is valid, as the size of objects may exceed the capacity of the knapsack; the fitness of the solution is the sum of values of all objects in the knapsack if the representation is valid, or 0 otherwise. In some problems, it is hard or impossible to define the fitness expression; the next step is to generate a second generation population of solutions from those selected through a combination of genetic operators: crossover, mutation. For each new solution to be produced, a pair of "parent" solutions is selected for breeding from the pool selected previously. By producing a "child" solution using the above methods of crossover and mutation, a new solution is created which shares many of the characteristics of its "parents". New parents are selected for each new child, the process continues until a new population of solutions of appropriate size is generated.
Although reproduction methods that are based on the use of two parents are more "biology inspired", some research suggests that more than two "parents" generate higher quality chromosomes. These processes result in the next generation population of chromosomes, different from the initial generation; the average fitness will have increased by this procedure for the population, since only the best organisms from the first generation are selected for breeding, along with a small proportion of less fit solutions. These less fit solutions ensure genetic diversity within the genetic po
In biology, a gene is a sequence of nucleotides in DNA or RNA that codes for a molecule that has a function. During gene expression, the DNA is first copied into RNA; the RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic trait; these genes make up different DNA sequences called genotypes. Genotypes along with developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes as well as gene–environment interactions; some genetic traits are visible, such as eye color or number of limbs, some are not, such as blood type, risk for specific diseases, or the thousands of basic biochemical processes that constitute life. Genes can acquire mutations in their sequence, leading to different variants, known as alleles, in the population; these alleles encode different versions of a protein, which cause different phenotypical traits.
Usage of the term "having a gene" refers to containing a different allele of the same, shared gene. Genes evolve due to natural selection / survival of the fittest and genetic drift of the alleles; the concept of a gene continues to be refined. For example, regulatory regions of a gene can be far removed from its coding regions, coding regions can be split into several exons; some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. Therefore, a broad, modern working definition of a gene is any discrete locus of heritable, genomic sequence which affect an organism's traits by being expressed as a functional product or by regulation of gene expression; the term gene was introduced by Danish botanist, plant physiologist and geneticist Wilhelm Johannsen in 1909. It is inspired by the ancient Greek: γόνος, that means offspring and procreation; the existence of discrete inheritable units was first suggested by Gregor Mendel. From 1857 to 1864, in Brno, he studied inheritance patterns in 8000 common edible pea plants, tracking distinct traits from parent to offspring.
He described these mathematically as 2n combinations where n is the number of differing characteristics in the original peas. Although he did not use the term gene, he explained his results in terms of discrete inherited units that give rise to observable physical characteristics; this description prefigured Wilhelm Johannsen's distinction between phenotype. Mendel was the first to demonstrate independent assortment, the distinction between dominant and recessive traits, the distinction between a heterozygote and homozygote, the phenomenon of discontinuous inheritance. Prior to Mendel's work, the dominant theory of heredity was one of blending inheritance, which suggested that each parent contributed fluids to the fertilisation process and that the traits of the parents blended and mixed to produce the offspring. Charles Darwin developed a theory of inheritance he termed pangenesis, from Greek pan and genesis / genos. Darwin used the term gemmule to describe hypothetical particles. Mendel's work went unnoticed after its first publication in 1866, but was rediscovered in the late 19th century by Hugo de Vries, Carl Correns, Erich von Tschermak, who reached similar conclusions in their own research.
In 1889, Hugo de Vries published his book Intracellular Pangenesis, in which he postulated that different characters have individual hereditary carriers and that inheritance of specific traits in organisms comes in particles. De Vries called these units "pangenes", after Darwin's 1868 pangenesis theory. Sixteen years in 1905, Wilhelm Johannsen introduced the term'gene' and William Bateson that of'genetics' while Eduard Strasburger, amongst others, still used the term'pangene' for the fundamental physical and functional unit of heredity. Advances in understanding genes and inheritance continued throughout the 20th century. Deoxyribonucleic acid was shown to be the molecular repository of genetic information by experiments in the 1940s to 1950s; the structure of DNA was studied by Rosalind Franklin and Maurice Wilkins using X-ray crystallography, which led James D. Watson and Francis Crick to publish a model of the double-stranded DNA molecule whose paired nucleotide bases indicated a compelling hypothesis for the mechanism of genetic replication.
In the early 1950s the prevailing view was that the genes in a chromosome acted like discrete entities, indivisible by recombination and arranged like beads on a string. The experiments of Benzer using mutants defective in the rII region of bacteriophage T4 showed that individual genes have a simple linear structure and are to be equivalent to a linear section of DNA. Collectively, this body of research established the central dogma of molecular biology, which states that proteins are translated from RNA, transcribed from DNA; this dogma has since been shown to have exceptions, such as reverse transcription in retroviruses. The modern study of genetics at the level of DNA is known as molecular genetics. In 1972, Walter Fiers and his team were the first to determine the sequence of a gene: that of Bacteriophage MS2 coat protein; the subsequent development of chain-termination DNA sequencing in 1977 by Frederick Sanger improved the efficiency of sequencing and turned it into a routine laboratory tool.
An automated version of the Sanger method was used in early phases of the
Heredity is the passing on of traits from parents to their offspring, either through asexual reproduction or sexual reproduction, the offspring cells or organisms acquire the genetic information of their parents. Through heredity, variations between individuals can accumulate and cause species to evolve by natural selection; the study of heredity in biology is genetics. In humans, eye color is an example of an inherited characteristic: an individual might inherit the "brown-eye trait" from one of the parents. Inherited traits are controlled by genes and the complete set of genes within an organism's genome is called its genotype; the complete set of observable traits of the structure and behavior of an organism is called its phenotype. These traits arise from the interaction of its genotype with the environment; as a result, many aspects of an organism's phenotype are not inherited. For example, suntanned skin comes from the interaction between a person's sunlight. However, some people tan more than others, due to differences in their genotype: a striking example is people with the inherited trait of albinism, who do not tan at all and are sensitive to sunburn.
Heritable traits are known to be passed from one generation to the next via DNA, a molecule that encodes genetic information. DNA is a long polymer; the sequence of bases along a particular DNA molecule specifies the genetic information: this is comparable to a sequence of letters spelling out a passage of text. Before a cell divides through mitosis, the DNA is copied, so that each of the resulting two cells will inherit the DNA sequence. A portion of a DNA molecule that specifies a single functional unit is called a gene. Within cells, the long strands of DNA form condensed structures called chromosomes. Organisms inherit genetic material from their parents in the form of homologous chromosomes, containing a unique combination of DNA sequences that code for genes; the specific location of a DNA sequence within a chromosome is known as a locus. If the DNA sequence at a particular locus varies between individuals, the different forms of this sequence are called alleles. DNA sequences can change through mutations.
If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the organism. However, while this simple correspondence between an allele and a trait works in some cases, most traits are more complex and are controlled by multiple interacting genes within and among organisms. Developmental biologists suggest that complex interactions in genetic networks and communication among cells can lead to heritable variations that may underlie some of the mechanics in developmental plasticity and canalization. Recent findings have confirmed important examples of heritable changes that cannot be explained by direct agency of the DNA molecule; these phenomena are classed as epigenetic inheritance systems that are causally or independently evolving over genes. Research into modes and mechanisms of epigenetic inheritance is still in its scientific infancy, this area of research has attracted much recent activity as it broadens the scope of heritability and evolutionary biology in general.
DNA methylation marking chromatin, self-sustaining metabolic loops, gene silencing by RNA interference, the three dimensional conformation of proteins are areas where epigenetic inheritance systems have been discovered at the organismic level. Heritability may occur at larger scales. For example, ecological inheritance through the process of niche construction is defined by the regular and repeated activities of organisms in their environment; this generates a legacy of effect that modifies and feeds back into the selection regime of subsequent generations. Descendants inherit genes plus environmental characteristics generated by the ecological actions of ancestors. Other examples of heritability in evolution that are not under the direct control of genes include the inheritance of cultural traits, group heritability, symbiogenesis; these examples of heritability that operate above the gene are covered broadly under the title of multilevel or hierarchical selection, a subject of intense debate in the history of evolutionary science.
When Charles Darwin proposed his theory of evolution in 1859, one of its major problems was the lack of an underlying mechanism for heredity. Darwin believed in the inheritance of acquired traits. Blending inheritance would lead to uniformity across populations in only a few generations and would remove variation from a population on which natural selection could act; this led to Darwin adopting some Lamarckian ideas in editions of On the Origin of Species and his biological works. Darwin's primary approach to heredity was to outline how it appeared to work rather than suggesting mechanisms. Darwin's initial model of heredity was adopted by, heavily modified by, his cousin Francis Galton, who laid the framework for the biometric school of heredity. Galton found no evidence to support the aspects of Darwin's pangenesis model, which relied on acquired traits; the inheritance of acquired traits was shown to have little basis in the 1880s when August Weismann cut the tails off many generations of mice and found that their offspring continued to develop tails.
Scientists in Antiquity had a variety of ideas about heredity: Theophrastus proposed that male flowers caused f