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Encyclopedia > Molecular evolution

Molecular evolution is the process of the genetic material in populations of organisms changing over time. It is the association of molecular biology, evolution and population genetics. The genetic material consists of DNA, long sequences of nucleotides in each individual organism. Because most heritable changes in visible traits are a result of changes in the DNA, molecular evolution must be seen as part of general evolution. The boundary between molecular and other aspects of evolution is not clearly defined. One inequivalence is that molecular evolution takes place also in DNA with no known function (so-called "junk DNA"). Therefore the DNA of a population may "evolve molecularly", while the phenotype of descendants remains constant. In biology and ecology, an organism (in Greek organon = instrument) is an assembly of organs that influence each other in such a way that they function as a more or less stable whole and have properties of life. ... Molecular biology is the study of biology at a molecular level. ... Evolutionary biology is a subfield of biology concerned with the origin and descent of species, as well as their change over time, i. ... Population genetics is the study of the distribution of and change in allele frequencies under the influence of the five evolutionary forces: natural selection, genetic drift, mutation, migration and nonrandom mating. ... Space-filling model of a section of DNA molecule Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions specifying the biological development of all cellular forms of life (and many viruses). ... The phenotype of an individual organism is either its total physical appearance and constitution, or a specific manifestation of a trait, such as size or eye color, that varies between individuals. ... Charles Darwin, father of the theory of evolution by natural selection. ... In molecular biology, junk DNA is a collective label for the portions of the DNA sequence of a chromosome or a genome for which no function has been identified. ... The phenotype of an individual organism is either its total physical appearance and constitution, or a specific manifestation of a trait, such as size or eye color, that varies between individuals. ...

Contents


Exceptions to the general description

Genomic imprinting (which is "epigenetic") constitutes hereditary information that is not coded in DNA. Whilst the genetic material in the vast majority of organisms is DNA, the genetic material in viruses may consist of DNA or RNA. Viruses with RNA genomes are known as retroviruses. Imprinting has different meanings in: Genetics: see imprinting (genetics) Psychology and ethology: see imprinting (psychology) In addition, the term imprint is used in publishing. ... Epigenetic inheritance is the transmission of information from a cell or multicellular organism to its descendants without that information being encoded in the nucleotide sequence of the gene. ... A virus is a nonliving small particle that infects cells in biological organisms. ... Genera Alpharetrovirus Betaretrovirus Gammaretrovirus Deltaretrovirus Epsilonretrovirus Lentivirus Spumavirus A retrovirus is a virus which has a genome consisting of two identical plus sense RNA molecules. ...


Principles of molecular evolution

Mutations

Main article: Mutation Mutations are permanent, sometimes transmissible (if the change is to a germ cell) changes to the genetic material (usually DNA or RNA) of a cell. ...


Mutations are permanent, transmissible changes to the genetic material (usually DNA or RNA) of a cell. Mutations can be caused by copying errors in the genetic material during cell division and by exposure to radiation, chemicals, or viruses, or can occur deliberately under cellular control during the processes such as meiosis or hypermutation. Mutations are considered the driving force of evolution, where less favorable (or deleterious) mutations are removed from the gene pool by natural selection, while more favorable (or beneficial) ones tend to accumulate. Neutral mutations do not affect the organism's chances of survival in its natural environment and can accumulate over time, which might result in what is known as punctuated equilibrium; the modern interpretation of classic evolutionary theory. ... Space-filling model of a section of DNA molecule Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions specifying the biological development of all cellular forms of life (and many viruses). ... Ribonucleic acid (RNA) is a nucleic acid consisting of a string of covalently-bound nucleotides. ... Cells in culture, stained for keratin (red) and DNA (green) The cell is the structural and functional unit of all living organisms, sometimes called the building blocks of life. ... Cell division is the process by which a cell (called the parent cell) divides into two cells (called daughter cells). ... Radiation has a variety of different meanings. ... A common alternate meaning of virus is computer virus. ... In biology, meiosis is the process that transforms one diploid cell into four haploid cells in eukaryotes. ... Hypermutation is the central aspect to making the Acquired immune system possible. ... Charles Darwin, father of the theory of evolution by natural selection. ... Natural selection is a process by which biological populations are altered over time, as a result of the propagation of heritable traits that affect the capacity of individual organisms to survive and reproduce. ... The neutral theory of molecular evolution (also, simply the neutral theory of evolution) is an influential theory that was introduced with provocative effect by Motoo Kimura in the late 1960s and early 1970s. ... Punctuated equilibrium, or punctuated equilibria, is a theory of evolution which states that changes such as speciation can occur relatively quickly, with long periods of little change—equilibria—in between. ...


Causes of change in allele frequency

Main article: Population genetics Population genetics is the study of the distribution of and change in allele frequencies under the influence of the five evolutionary forces: natural selection, genetic drift, mutation, migration and nonrandom mating. ...


There are four known processes that affect the survival of a characteristic; or, more specifically, the frequency of an allele (variant of a gene): An allele is any one of a number of viable DNA codings of the same gene (sometimes the term refers to a non-gene sequence) occupying a given locus (position) on a chromosome. ... This stylistic schematic diagram shows a gene in relation to the double helix structure of DNA and to a chromosome (right). ...

  • Mutation detailed above.
  • Genetic drift describes changes in gene frequency that cannot be ascribed to selective pressures, but are due instead to events that are unrelated to inherited traits. This is especially important in small mating populations, which simply cannot have enough offspring to maintain the same gene distribution as the parental generation.
  • Gene flow: or gene admixture is the only one of the agents that makes populations closer genetically while building larger gene pools.
  • Selection, in particular natural selection produced by differential mortality and fertility. Differential mortality is the survival rate of individuals before their reproductive age. If they survive, they are then selected further by differential fertility – that is, their total genetic contribution to the next generation. In this way, the alleles that these surviving individuals contribute to the gene pool will increase the frequency of those alleles.

The production and redistribution of variation is produced by three of the four agents of evolution: mutation, genetic drift, and gene flow. Natural selection, in turn, acts on the variation produced by these agents. Mutations are permanent, sometimes transmissible (if the change is to a germ cell) changes to the genetic material (usually DNA or RNA) of a cell. ... Genetic drift is a mechanism of evolution that acts in concert with natural selection to change the characteristics of species over time. ... Gene flow (also known as gene migration) is the transfer of genes from one population to another. ... For computer science algorithms that find the kth smallest number in a list, see selection algorithm. ... Natural selection is a process by which biological populations are altered over time, as a result of the propagation of heritable traits that affect the capacity of individual organisms to survive and reproduce. ...


Molecular study of phylogeny

Main articles: Molecular systematics, Phylogenetics Molecular systematics is a product of the traditional field of systematics and the growing field of bioinformatics. ... In biology, Phylogenetics (Greek: phylon = race and genetic = birth) is the taxonomical classification of organisms based on how closely they are related in terms of evolutionary differences. ...


Molecular systematics is a product of the traditional field of systematics and molecular genetics. It is the process of using data on the molecular constitution of biological organisms' DNA, RNA, or both, in order to resolve questions in systematics, i.e. about their correct scientific classification or taxonomy from the point of view of evolutionary biology. Systematics is the term used by John G Bennett for the study of multi-term systems. ... Molecular genetics is the field of biology which studies the structure and function of genes at a molecular level. ... Space-filling model of a section of DNA molecule Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions specifying the biological development of all cellular forms of life (and many viruses). ... Ribonucleic acid (RNA) is a nucleic acid consisting of a string of covalently-bound nucleotides. ... Scientific classification or biological classification is how biologists group and categorize extinct and living species of organisms. ... Taxonomy (from Greek ταξινομία (taxinomia) from the words taxis = order and nomos = law) may refer to either the classification of things, or the principles underlying the classification. ... Evolutionary biology is a subfield of biology concerned with the origin and descent of species, as well as their change over time, i. ...


Molecular systematics has been made possible by the availability of techniques for gene sequencing, which allow the determination of the exact sequence of nucleotides or bases in either DNA or RNA. At present it is still a long and expensive process to sequence the entire genome of an organism, and this has been done for only a few species. However it is quite feasible to determine the sequence of a defined area of a particular chromosome. Typical molecular systematic analyses require the sequencing of around 1000 base pairs. Gene sequencing refers to the process of recording the exact sequence of nucleotides in the section of an organisms DNA corresponding to a specific gene. ... A nucleotide is a monomer or the structural unit of nucleotide chains forming nucleic acids as RNA and DNA. A nucleotide consists of a heterocyclic nucleobase, a pentose sugar (ribose or deoxiribose), and a phosphate or polyphosphate group. ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... Figure 1: Chromosome. ... In molecular biology, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair (often abbreviated bp). ...


The neutral theory

Main article: Neutral theory of molecular evolution The neutral theory of molecular evolution (also, simply the neutral theory of evolution) is an influential theory that was introduced with provocative effect by Motoo Kimura in the late 1960s and early 1970s. ...


One of the questions concerning molecular evolution is what proportion of mutations are neutral with respect to natural selection, meaning mutations that do not convey a selective advantage or disadvantage to the individual that inherits them. Neutralists believe the driving forces of molecular evolution are random genetic drift and mutations, while selectionists explain molecular evolution with advantageous mutations and balancing selection. The first explanation was thought and defended by Motoo Kimura, while John H. Gillespie is considered the main proponent of selectionism. Resolving this controversy is an aim of population genetics. Mutations are permanent, sometimes transmissible (if the change is to a germ cell) changes to the genetic material (usually DNA or RNA) of a cell. ... The neutral theory of molecular evolution (also, simply the neutral theory of evolution) is an influential theory that was introduced with provocative effect by Motoo Kimura in the late 1960s and early 1970s. ... Natural selection is a process by which biological populations are altered over time, as a result of the propagation of heritable traits that affect the capacity of individual organisms to survive and reproduce. ... For computer science algorithms that find the kth smallest number in a list, see selection algorithm. ... The neutral theory of molecular evolution (also, simply the neutral theory of evolution) is an influential theory that was introduced with provocative effect by Motoo Kimura in the late 1960s and early 1970s. ... Genetic drift is a mechanism of evolution that acts in concert with natural selection to change the characteristics of species over time. ... Mutations are permanent, sometimes transmissible (if the change is to a germ cell) changes to the genetic material (usually DNA or RNA) of a cell. ... Mutations are permanent, sometimes transmissible (if the change is to a germ cell) changes to the genetic material (usually DNA or RNA) of a cell. ... Balancing selection refers to forms of natural selection which work to maintain genetic polymorphisms (or multiple alleles) within a population. ... Motoo Kimura (木村資生, born on November 13, 1924 in Okazaki, Aichi Prefecture - November 13, 1994) was a highly influential Japanese mathematical biologist, working in the field of theoretical population genetics. ... John H. Gillespie is an evolutionary biologist interested in molecular evolution and natural selection. ... Population genetics is the study of the distribution of and change in allele frequencies under the influence of the five evolutionary forces: natural selection, genetic drift, mutation, migration and nonrandom mating. ...


Rare spontaneous errors in DNA replication cause the mutations that drive molecular evolution. The molecular clock technique, which researchers use to date when two species diverged by comparing their DNA, deduces elapsed time from the number of differences. The technique was inspired by the once common assumption that the DNA error rate is constant--not just over time, but across all species and every part of a genome that you might want to compare. Because the enzymes that replicate DNA differ only very slightly between species, the assumption seemed reasonable a priori. But as molecular evidence has accumulated, the constant-rate assumption has proven false--or at least overly general. Molecular clock users are developing workaround solutions. DNA replication. ... The molecular clock (based on the molecular clock hypothesis (MCH)) is a technique in genetics, which researchers use to date when two species diverged. ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... Ribbon diagram of the catalytically perfect enzyme TIM. Factor D enzyme crystal prevents the immune system from inappropriately running out of control. ...


Infinite alleles model

The Japanese geneticist Motoo Kimura and American geneticist James Crow (1964) introduced the infinite alleles model, an attempt to determine for a finite population what proportion of loci would be homozygous. This was, in part, motivated by assertions by other geneticists that more than 50 percent of Drosophila loci were heterozygous, a claim they initially doubted. In order to answer this question they assumed first, that there were a large enough number of alleles so that any mutation would lead to a different allele (that is the probability of back mutation to the original allele would be low enough to be negligible); and second, that the mutations would result in a number of different outcomes from neutral to deleterious. Motoo Kimura (木村資生, born on November 13, 1924 in Okazaki, Aichi Prefecture - November 13, 1994) was a highly influential Japanese mathematical biologist, working in the field of theoretical population genetics. ... An allele is any one of a number of viable DNA codings of the same gene (sometimes the term refers to a non-gene sequence) occupying a given locus (position) on a chromosome. ... Homozygote cells are diploid or polyploid and have the same alleles at a locus (position) on homologous chromosomes. ... Binomial name Drosophila melanogaster Meigen, 1830 dorsal view Drosophila melanogaster (Black-bellied Dew-lover) a dipteran (two-winged) insect, is the species of fruit fly that is commonly used in genetic experiments; it is among the most important model organisms. ... Heterozygote cells are diploid or polyploid and have different alleles at a locus (position) on homologous chromosomes. ... Mutations are permanent, sometimes transmissible (if the change is to a germ cell) changes to the genetic material (usually DNA or RNA) of a cell. ...


They determined that in the neutral case, the probability that an individual would be homozygous, F, was:

where u is the mutation rate, and Ne is the effective population size. From this it is possible to determine an upper limit to the number of possible alleles in a population, n as the inverse of the homozygosity: The effective population size (Ne) is defined as the number of breeding individuals in an idealized population that would show the same amount of dispersion of allele frequencies under random genetic drift or the same amount of inbreeding as the population under consideration (Sewall Wright). ...

If the effective population is large, then a large number of alleles can be maintained. However, this result only holds for the neutral case, and is not necessarily true for the case when some alleles are more or less fit than others, for example when the fittest genotype is a heterozygote (a situation often referred to as overdominance or heterosis). Fitness (often denoted in population genetics models) is a central concept in evolutionary theory. ... Overdominance describes a genetic relationship between two alleles when the phenotype of the heterozygote is greater than that of either homozygote. ... Heterosis is increased strength of different characteristics in hybrids; the possibility to obtain a better individual by combining the virtues of its parents. ...


In the case of overdominance, because Mendel's second law (the law of segregation) necessarily results in the production of homozygotes (which are by definition in this case, less fit), this means that population will always harbor a number of less fit individuals, which leads to a decrease in the average fitness of the population. This is sometimes referred to as genetic load, in this case it is a special kind of load known as segregational load. Crow and Kimura showed that at equilibrium conditions, for a given strength of selection (s), that there would be an upper limit to the number of fitter alleles (polymorphisms) that a population could harbor for a particular locus. Beyond this number of alleles, the selective advantage of presence of those alleles in heterozygous genotypes would be cancelled out by continual generation of less fit homozygous genotypes. Mendelian inheritance (or Mendelian genetics or Mendelism) is a set of primary tenets that underlie much of genetics developed by Gregor Mendel in the latter part of the 19th century. ... In population genetics, genetic load or genetic burden is a measure of the cost of lost alleles due to selection (selectional load) or mutation (mutational load). ...


These results became important in the formation of the neutral theory, because neutral (or nearly neutral) alleles create no such segregational load, and allow for the accumulation of a great deal of polymorphism. When Richard Lewontin and J. Hubby published their groundbreaking results in 1966 which showed high levels of genetic variation in Drosophila via protein electrophoresis, the theoretical results from the infinite alleles model were used by Kimura and others to support the idea that this variation would have to be neutral (or result in excess segregational load). Richard Charles Lewontin (born March 29, 1929) is an evolutionary biologist, geneticist, and social commentator at Harvard University. ... Electrophoresis is the movement of an electrically charged body under the influence of an electric field. ...


Related fields

An important area within the study of molecular evolution is the use of molecular data to determine the correct scientific classification of organisms. This is called molecular systematics. Scientific classification or biological classification is how biologists group and categorize extinct and living species of organisms. ... Molecular systematics is a product of the traditional field of systematics and the growing field of bioinformatics. ...


See also

The neutral theory of molecular evolution (also, simply the neutral theory of evolution) is an influential theory that was introduced with provocative effect by Motoo Kimura in the late 1960s and early 1970s. ... Genetic drift is a mechanism of evolution that acts in concert with natural selection to change the characteristics of species over time. ... Parsimony, in the general sense, means taking extreme care at arriving at a course of action; or unusual or excessive frugality, extreme economy or stinginess. ... For computer science algorithms that find the kth smallest number in a list, see selection algorithm. ... The molecular clock (based on the molecular clock hypothesis (MCH)) is a technique in genetics, which researchers use to date when two species diverged. ...

References

  • Li, W.H. (1997) Molecular Evolution, Sinauer. ISBN 0-87893-463-4
  • Kimura, M. and Crow, J (1964). The Number of Alleles that Can Be Maintained in a Finite Population. Genetics 49: 725-738.
  • Page, R.D.M. and Holmes, E.C. (1998) Molecular Evolution: A Phylogenetic Approach, Blackwell Science. ISBN 0-86542-889-1

Motoo Kimura (木村資生, born on November 13, 1924 in Okazaki, Aichi Prefecture - November 13, 1994) was a highly influential Japanese mathematical biologist, working in the field of theoretical population genetics. ... Genetics is a monthly scientific journal publishing investigations bearing on heredity and variation. ...

External links

  • MIT History of Science
Basic topics in evolutionary biology
Processes of evolution: evidence - macroevolution - microevolution - speciation
Mechanisms: selection - genetic drift - gene flow - mutation
Modes: anagenesis - catagenesis - cladogenesis
History: History of evolutionary thought - Charles Darwin - The Origin of Species - modern evolutionary synthesis
Subfields: population genetics - ecological genetics - human evolution - molecular evolution - phylogenetics - systematics - evo-devo
List of evolutionary biology topics | Timeline of evolution

  Results from FactBites:
 
NodeWorks - Encyclopedia: Molecular evolution (1180 words)
Molecular evolution is the process of the genetic material in populations of organisms changing over time.
One of the questions concerning molecular evolution is what proportion of mutations are neutral with respect to natural selection, meaning mutations that do not convey a selective advantage or disadvantage to the individual that inherits them.
An important area within the study of molecular evolution is the use of molecular data to determine the correct scientific classification of organisms.
Evolution: Library: Molecular Evolution: Neutral Drift (554 words)
One hypothesis suggests that most molecular evolution is driven by random changes in genes, or "neutral drift." The other proposes that natural selection favoring beneficial variations in an organism's genes is the primary mechanism.
That is, changes affect the "letters" (four different types of chemical units) in the genetic blueprints -- the genes -- that are carried in their cells.
The changes and variations in genetic code that occur over time are referred to as "molecular evolution." The molecular evolution of an organism can be very different from its morphological (body features) evolution.
  More results at FactBites »

 
 

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