Molecular evolution
Encyclopedia
Molecular evolution is in part a process of evolution at the scale of DNA
, RNA
, and protein
s. Molecular evolution emerged as a scientific field in the 1960s as researchers from molecular biology
, evolutionary biology and population genetics
sought to understand recent discoveries on the structure and function of nucleic acids and protein. Some of the key topics that spurred development of the field have been the evolution of enzyme function, the use of nucleic acid divergence as a "molecular clock
" to study species divergence, and the origin of noncoding DNA
.
Recent advances in genomics, including whole-genome sequencing, high-throughput protein characterization, and bioinformatics
have led to a dramatic increase in studies on the topic. In the 2000s, some of the active topics have been the role of gene duplication
in the emergence of novel gene function, the extent of adaptive molecular evolution versus neutral processes of mutation and drift, and the identification of molecular changes responsible for various human characteristics especially those pertaining to infection
, disease
, and cognition
.
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.
(variant of a gene
):
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.
Molecular systematics has been made possible by the availability of techniques for DNA sequencing
, which allow the determination of the exact sequence of nucleotide
s 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 pair
s.
While recognizing the importance of random drift for silent mutations, selectionists hypotheses argue that balancing and positive selection are the driving forces of molecular evolution. Those hypotheses are often based on the broader view called panselectionism, the idea that selection is the only force strong enough to explain evolution, relaying random drift and mutations to minor roles.
Neutralists hypotheses emphasize the importance of mutation, purifying selection and random genetic drift. The introduction of the neutral theory by Kimura
, quickly followed by King and Jukes
' own findings, led to a fierce debate about the relevance of neodarwinism at the molecular level. The Neutral theory of molecular evolution
states that most mutations are deleterious and quickly removed by natural selection
, but of the remaining ones, the vast majority are neutral with respect to fitness while the amount of advantageous mutations is vanishingly small. The fate of neutral mutations are governed by genetic drift
, and contribute to both nucleotide polymorphism and fixed differences between species.
Mutationists hypotheses emphasize random drift and biases in mutation patterns. Sueoka was the first to propose a modern mutationist view. He proposed that the variation in GC content was not the result of positive selection, but a consequence of the GC mutational pressure.
. The advent of protein sequencing
allowed molecular biologists to create phylogenies based on sequence comparison, and to use the differences between homologous sequences as a molecular clock
to estimate the time since the last common ancestor. In the late 1960s, the neutral theory of molecular evolution
provided a theoretical basis for the molecular clock, though both the clock and the neutral theory were controversial, since most evolutionary biologists held strongly to panselectionism, with natural selection
as the only important cause of evolutionary change. After the 1970s, nucleic acid sequencing allowed molecular evolution to reach beyond proteins to highly conserved ribosomal RNA
sequences, the foundation of a reconceptualization of the early history of life.
The theoretical frameworks for molecular systematics were laid in the 1960s in the works of Emile Zuckerkandl
, Emanuel Margoliash
, Linus Pauling
and Walter M. Fitch
. Applications of molecular systematics were pioneered by Charles G. Sibley
(bird
s), Herbert C. Dessauer (herpetology
), and Morris Goodman
(primate
s), followed by Allan C. Wilson
, Robert K. Selander, and John C. Avise (who studied various groups). Work with protein electrophoresis
began around 1956. Although the results were not quantitative and did not initially improve on morphological classification, they provided tantalizing hints that long-held notions of the classifications of bird
s, for example, needed substantial revision. In the period of 1974–1986, DNA-DNA hybridization was the dominant technique.
through evolution
.
The study of genome evolution involves multiple fields such as structural analysis of the genome, the study of genomic parasites, gene
and ancient genome duplications, polyploidy
, and comparative genomics
. Evolutionary biologists are interested in five specific questions in regards to evolution of the genome, these are:
tic regions and noncoding regions. Genetic regions are those that encode proteins while noncoding regions refer to promoters and junk DNA. The C-value
is another term for the genome size. Within a species the C-value does not show much variation, but there is a significant difference in the C-value between species.
of organisms. This is called molecular systematics or molecular phylogenetics.
Tools and concepts developed in the study of molecular evolution are now commonly used for comparative genomics
and molecular genetics, while the influx of new data from these fields has been spurring advancement in molecular evolution.
, molecular biology
, genomics
, systematics
, or evolutionary biology. The Society for Molecular Biology and Evolution publishes the journal "Molecular Biology and Evolution" and holds an annual international meeting.
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
, RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
, and protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s. Molecular evolution emerged as a scientific field in the 1960s as researchers from molecular biology
Molecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
, evolutionary biology and population genetics
Population genetics
Population genetics is the study of allele frequency distribution and change under the influence of the four main evolutionary processes: natural selection, genetic drift, mutation and gene flow. It also takes into account the factors of recombination, population subdivision and population...
sought to understand recent discoveries on the structure and function of nucleic acids and protein. Some of the key topics that spurred development of the field have been the evolution of enzyme function, the use of nucleic acid divergence as a "molecular clock
Molecular clock
The molecular clock is a technique in molecular evolution that uses fossil constraints and rates of molecular change to deduce the time in geologic history when two species or other taxa diverged. It is used to estimate the time of occurrence of events called speciation or radiation...
" to study species divergence, and the origin of noncoding DNA
Noncoding DNA
In genetics, noncoding DNA describes components of an organism's DNA sequences that do not encode for protein sequences. In many eukaryotes, a large percentage of an organism's total genome size is noncoding DNA, although the amount of noncoding DNA, and the proportion of coding versus noncoding...
.
Recent advances in genomics, including whole-genome sequencing, high-throughput protein characterization, and bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
have led to a dramatic increase in studies on the topic. In the 2000s, some of the active topics have been the role of gene duplication
Gene duplication
Gene duplication is any duplication of a region of DNA that contains a gene; it may occur as an error in homologous recombination, a retrotransposition event, or duplication of an entire chromosome.The second copy of the gene is often free from selective pressure — that is, mutations of it have no...
in the emergence of novel gene function, the extent of adaptive molecular evolution versus neutral processes of mutation and drift, and the identification of molecular changes responsible for various human characteristics especially those pertaining to infection
Infection
An infection is the colonization of a host organism by parasite species. Infecting parasites seek to use the host's resources to reproduce, often resulting in disease...
, disease
Disease
A disease is an abnormal condition affecting the body of an organism. It is often construed to be a medical condition associated with specific symptoms and signs. It may be caused by external factors, such as infectious disease, or it may be caused by internal dysfunctions, such as autoimmune...
, and cognition
Cognition
In science, cognition refers to mental processes. These processes include attention, remembering, producing and understanding language, solving problems, and making decisions. Cognition is studied in various disciplines such as psychology, philosophy, linguistics, and computer science...
.
Mutations
Mutations are permanent, transmissible changes to the genetic material (usually DNADNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
or RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
) of a cell
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....
. Mutations can be caused by copying errors in the genetic material during cell division
Cell division
Cell division is the process by which a parent cell divides into two or more daughter cells . Cell division is usually a small segment of a larger cell cycle. This type of cell division in eukaryotes is known as mitosis, and leaves the daughter cell capable of dividing again. The corresponding sort...
and by exposure to radiation
Radiation
In physics, radiation is a process in which energetic particles or energetic waves travel through a medium or space. There are two distinct types of radiation; ionizing and non-ionizing...
, chemicals, or viruses, or can occur deliberately under cellular control during the processes such as meiosis
Meiosis
Meiosis is a special type of cell division necessary for sexual reproduction. The cells produced by meiosis are gametes or spores. The animals' gametes are called sperm and egg cells....
or hypermutation. Mutations are considered the driving force of evolution
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
, where less favorable (or deleterious) mutations are removed from the gene pool by natural selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....
, while more favorable (or beneficial) ones tend to accumulate. Neutral mutations
Neutral theory of molecular evolution
The neutral theory of molecular evolution states that the vast majority of evolutionary changes at the molecular level are caused by random drift of selectively neutral mutants . The theory was introduced by Motoo Kimura in the late 1960s and early 1970s...
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
Punctuated equilibrium
Punctuated equilibrium is a theory in evolutionary biology which proposes that most species will exhibit little net evolutionary change for most of their geological history, remaining in an extended state called stasis...
; the modern interpretation of classic evolutionary theory.
Causes of change in allele frequency
There are four known processes that affect the survival of a characteristic; or, more specifically, the frequency of an alleleAllele
An allele is one of two or more forms of a gene or a genetic locus . "Allel" is an abbreviation of allelomorph. Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation...
(variant of a gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
):
- Genetic driftGenetic driftGenetic drift or allelic drift is the change in the frequency of a gene variant in a population due to random sampling.The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces...
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 flowGene flowIn population genetics, gene flow is the transfer of alleles of genes from one population to another.Migration into or out of a population may be responsible for a marked change in allele frequencies...
or Migration: or gene admixture is the only one of the agents that makes populations closer genetically while building larger gene pools. - SelectionSelectionIn the context of evolution, certain traits or alleles of genes segregating within a population may be subject to selection. Under selection, individuals with advantageous or "adaptive" traits tend to be more successful than their peers reproductively—meaning they contribute more offspring to the...
, in particular natural selectionNatural selectionNatural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....
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. Sexual selectionSexual selectionSexual selection, a concept introduced by Charles Darwin in his 1859 book On the Origin of Species, is a significant element of his theory of natural selection...
, the attraction between mates that results from two genes, one for a feature and the other determining a preference for that feature, is also very important. - Recurrent mutation can increase the frequency of a mutant allele.
Molecular study of phylogeny
Molecular systematics is a product of the traditional field of systematicsSystematics
Biological systematics is the study of the diversification of terrestrial life, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees...
and molecular genetics
Molecular genetics
Molecular genetics is the field of biology and genetics that studies the structure and function of genes at a molecular level. The field studies how the genes are transferred from generation to generation. Molecular genetics employs the methods of genetics and molecular biology...
. It is the process of using data on the molecular constitution of biological organisms' DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
, RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
, or both, in order to resolve questions in systematics, i.e. about their correct scientific classification or taxonomy
Taxonomy
Taxonomy is the science of identifying and naming species, and arranging them into a classification. The field of taxonomy, sometimes referred to as "biological taxonomy", revolves around the description and use of taxonomic units, known as taxa...
from the point of view of evolutionary biology.
Molecular systematics has been made possible by the availability of techniques for DNA sequencing
DNA sequencing
DNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA....
, which allow the determination of the exact sequence of nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
s or bases in either DNA or RNA. At present it is still a long and expensive process to sequence the entire genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
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
Chromosome
A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...
. Typical molecular systematic analyses require the sequencing of around 1000 base pair
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
s.
The driving forces of evolution
Depending on the relative importance assigned to the various forces of evolution, three perspectives provide evolutionary explanations for molecular evolution.While recognizing the importance of random drift for silent mutations, selectionists hypotheses argue that balancing and positive selection are the driving forces of molecular evolution. Those hypotheses are often based on the broader view called panselectionism, the idea that selection is the only force strong enough to explain evolution, relaying random drift and mutations to minor roles.
Neutralists hypotheses emphasize the importance of mutation, purifying selection and random genetic drift. The introduction of the neutral theory by Kimura
Motoo Kimura
was a Japanese biologist best known for introducing the neutral theory of molecular evolution in 1968. He became one of the most influential theoretical population geneticists. He is remembered in genetics for his innovative use of diffusion equations to calculate the probability of fixation of...
, quickly followed by King and Jukes
Thomas H. Jukes
Thomas Hughes Jukes was a British-American biologist known for his work in nutrition, molecular evolution, and for his public engagement with controversial scientific issues, including DDT, vitamin C and creationism...
' own findings, led to a fierce debate about the relevance of neodarwinism at the molecular level. The Neutral theory of molecular evolution
Neutral theory of molecular evolution
The neutral theory of molecular evolution states that the vast majority of evolutionary changes at the molecular level are caused by random drift of selectively neutral mutants . The theory was introduced by Motoo Kimura in the late 1960s and early 1970s...
states that most mutations are deleterious and quickly removed by natural selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....
, but of the remaining ones, the vast majority are neutral with respect to fitness while the amount of advantageous mutations is vanishingly small. The fate of neutral mutations are governed by genetic drift
Genetic drift
Genetic drift or allelic drift is the change in the frequency of a gene variant in a population due to random sampling.The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces...
, and contribute to both nucleotide polymorphism and fixed differences between species.
Mutationists hypotheses emphasize random drift and biases in mutation patterns. Sueoka was the first to propose a modern mutationist view. He proposed that the variation in GC content was not the result of positive selection, but a consequence of the GC mutational pressure.
History of the science
The history of molecular evolution starts in the early 20th century with "comparative biochemistry", but the field of molecular evolution came into its own in the 1960s and 1970s, following the rise of molecular biologyMolecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
. The advent of protein sequencing
Protein sequencing
Protein sequencing is a technique to determine the amino acid sequence of a protein, as well as which conformation the protein adopts and the extent to which it is complexed with any non-peptide molecules...
allowed molecular biologists to create phylogenies based on sequence comparison, and to use the differences between homologous sequences as a molecular clock
Molecular clock
The molecular clock is a technique in molecular evolution that uses fossil constraints and rates of molecular change to deduce the time in geologic history when two species or other taxa diverged. It is used to estimate the time of occurrence of events called speciation or radiation...
to estimate the time since the last common ancestor. In the late 1960s, the neutral theory of molecular evolution
Neutral theory of molecular evolution
The neutral theory of molecular evolution states that the vast majority of evolutionary changes at the molecular level are caused by random drift of selectively neutral mutants . The theory was introduced by Motoo Kimura in the late 1960s and early 1970s...
provided a theoretical basis for the molecular clock, though both the clock and the neutral theory were controversial, since most evolutionary biologists held strongly to panselectionism, with natural selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....
as the only important cause of evolutionary change. After the 1970s, nucleic acid sequencing allowed molecular evolution to reach beyond proteins to highly conserved ribosomal RNA
Ribosomal RNA
Ribosomal ribonucleic acid is the RNA component of the ribosome, the enzyme that is the site of protein synthesis in all living cells. Ribosomal RNA provides a mechanism for decoding mRNA into amino acids and interacts with tRNAs during translation by providing peptidyl transferase activity...
sequences, the foundation of a reconceptualization of the early history of life.
The theoretical frameworks for molecular systematics were laid in the 1960s in the works of Emile Zuckerkandl
Emile Zuckerkandl
Emile Zuckerkandl is an Austrian-American biologist considered one of the founders of the field of molecular evolution. He is best known for introducing, with Linus Pauling, the concept of the molecular clock, which set the stage for the neutral theory of molecular evolution.- Life and work...
, Emanuel Margoliash
Emanuel Margoliash
Emanuel Margoliash was a biochemist who spent much of his career studying the protein cytochrome c. He is best known for his work on molecular evolution; with Walter Fitch, he devised Fitch-Margoliash method for constructing evolutionary trees based on protein sequences.He was a member of the...
, Linus Pauling
Linus Pauling
Linus Carl Pauling was an American chemist, biochemist, peace activist, author, and educator. He was one of the most influential chemists in history and ranks among the most important scientists of the 20th century...
and Walter M. Fitch
Walter M. Fitch
Walter M. Fitch . Until his death he was professor of molecular evolution at the University of California, Irvine. He was also a member of the National Academy of Sciences, the American Philosophical Society, and the American Association for the Advancement of Science, and was a Foreign Member of...
. Applications of molecular systematics were pioneered by Charles G. Sibley
Charles Sibley
Charles Gald Sibley was an American ornithologist and molecular biologist. He had an immense influence on the scientific classification of birds, and the work that Sibley initiated has substantially altered our understanding of the evolutionary history of modern birds.Sibley's taxonomy has been a...
(bird
Bird
Birds are feathered, winged, bipedal, endothermic , egg-laying, vertebrate animals. Around 10,000 living species and 188 families makes them the most speciose class of tetrapod vertebrates. They inhabit ecosystems across the globe, from the Arctic to the Antarctic. Extant birds range in size from...
s), Herbert C. Dessauer (herpetology
Herpetology
Herpetology is the branch of zoology concerned with the study of amphibians and reptiles...
), and Morris Goodman
Morris Goodman
Morris Goodman was an American scientist known for his work in molecular evolution and molecular systematics...
(primate
Primate
A primate is a mammal of the order Primates , which contains prosimians and simians. Primates arose from ancestors that lived in the trees of tropical forests; many primate characteristics represent adaptations to life in this challenging three-dimensional environment...
s), followed by Allan C. Wilson
Allan Wilson
Allan Charles Wilson was a pioneer in the use of molecular approaches to understand evolutionary change and reconstruct phylogenies, and a contributor to the study of human evolution. He was one of the most controversial figures in post-war biology; his work attracted a great deal of attention...
, Robert K. Selander, and John C. Avise (who studied various groups). Work with protein electrophoresis
Protein electrophoresis
Protein electrophoresis is a method for analysing the proteins in a fluid or an extract. The electrophoresis may be performed with a small volume of sample in a number of alternative ways with or without a supporting medium: SDS polyacrylamide gel electrophoresis Protein electrophoresis is a method...
began around 1956. Although the results were not quantitative and did not initially improve on morphological classification, they provided tantalizing hints that long-held notions of the classifications of bird
Bird
Birds are feathered, winged, bipedal, endothermic , egg-laying, vertebrate animals. Around 10,000 living species and 188 families makes them the most speciose class of tetrapod vertebrates. They inhabit ecosystems across the globe, from the Arctic to the Antarctic. Extant birds range in size from...
s, for example, needed substantial revision. In the period of 1974–1986, DNA-DNA hybridization was the dominant technique.
Genome evolution
Genomic evolution is a set of phenomena involved in the changing of the structure of a genomeGenome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
through evolution
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
.
The study of genome evolution involves multiple fields such as structural analysis of the genome, the study of genomic parasites, gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
and ancient genome duplications, polyploidy
Polyploidy
Polyploid is a term used to describe cells and organisms containing more than two paired sets of chromosomes. Most eukaryotic species are diploid, meaning they have two sets of chromosomes — one set inherited from each parent. However polyploidy is found in some organisms and is especially common...
, and comparative genomics
Comparative genomics
Comparative genomics is the study of the relationship of genome structure and function across different biological species or strains. Comparative genomics is an attempt to take advantage of the information provided by the signatures of selection to understand the function and evolutionary...
. Evolutionary biologists are interested in five specific questions in regards to evolution of the genome, these are:
- How did the genome evolve into its current size?
- What is the content within the genome, is it mostly junk or not?
- What is the distribution of genes within a genome?
- What is the composition of the nucleotides within the genome?
- How does translation of the genetic code evolve?
Genome size
Genome size is all the DNA that makes the genome. A genome can consist of geneGene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
tic regions and noncoding regions. Genetic regions are those that encode proteins while noncoding regions refer to promoters and junk DNA. The C-value
C-value
The term C-value refers to the amount of DNA contained within a haploid nucleus or one half the amount in a diploid somatic cell of a eukaryotic organism, expressed in picograms...
is another term for the genome size. Within a species the C-value does not show much variation, but there is a significant difference in the C-value between species.
Prokaryotic genome
Prokaryotes are unicellular organisms that do not have membrane-bound organelles and lack a structurally distinct nucleus. Research on prokaryotic genomes shows that there is a significant positive correlation between the C-value of prokaryotes and the amount of genes that compose the genome. This indicates that gene size is the main factor influencing the size of the genome.Eukaryotic genome
In eukaryotic organisms, there is a paradox observed, namely that the number of genes that make up the genome does not correlate with genome size. In other words, the genome size is much larger than would be expected given the total number of protein coding genes.Related fields
An important area within the study of molecular evolution is the use of molecular data to determine the correct biological classificationBiological classification
Biological classification, or scientific classification in biology, is a method to group and categorize organisms by biological type, such as genus or species. Biological classification is part of scientific taxonomy....
of organisms. This is called molecular systematics or molecular phylogenetics.
Tools and concepts developed in the study of molecular evolution are now commonly used for comparative genomics
Genomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
and molecular genetics, while the influx of new data from these fields has been spurring advancement in molecular evolution.
Key researchers in molecular evolution
Some researchers who have made key contributions to the development of the field:- Motoo KimuraMotoo Kimurawas a Japanese biologist best known for introducing the neutral theory of molecular evolution in 1968. He became one of the most influential theoretical population geneticists. He is remembered in genetics for his innovative use of diffusion equations to calculate the probability of fixation of...
— Neutral theory - Masatoshi NeiMasatoshi Neiis Evan Pugh Professor of Biology at Pennsylvania State University and Director of the since 1990. He was born in 1931 in Miyazaki Prefecture, on Kyūshū Island, Japan...
— Adaptive evolution - Walter M. FitchWalter M. FitchWalter M. Fitch . Until his death he was professor of molecular evolution at the University of California, Irvine. He was also a member of the National Academy of Sciences, the American Philosophical Society, and the American Association for the Advancement of Science, and was a Foreign Member of...
— Phylogenetic reconstruction - Walter GilbertWalter GilbertWalter Gilbert is an American physicist, biochemist, molecular biology pioneer, and Nobel laureate.-Biography:Gilbert was born in Boston, Massachusetts, on March 21, 1932...
— RNA world - Joe FelsensteinJoe FelsensteinJoseph "Joe" Felsenstein is Professor in the Departments of Genome Sciences and Biology and Adjunct Professor in the Departments of Computer Science and Statistics at the University of Washington in Seattle...
— Phylogenetic methods - Susumu OhnoSusumu Ohnowas an Asian American geneticist and evolutionary biologist, and seminal researcher in the field of molecular evolution.- Biography :Susumu Ohno was born of Japanese parents in Seoul, Korea, on February 1, 1928. The second of five children, he was the son of the minister of education of the...
— Gene duplication - John H. GillespieJohn H. GillespieJohn H. Gillespie is an evolutionary biologist interested in theoretical population genetics and molecular evolution. In molecular evolution, he emphasized the importance of advantageous mutations and balancing selection. For that reason, Gillespie is well known for his selectionist stance in the...
— Mathematics of adaptation - Dan GraurDan GraurDan Graur is an American scientist working in the fields of molecular evolution. He is currently the John and Rebecca Moores Professor at the University of Houston. He is coauthor along with Wen-Hsiung Li of Fundamentals of Molecular Evolution.-Biography:...
- Neutral models of molecular evolution - Wen-Hsiung LiWen-Hsiung LiWen-Hsiung Li is a Taiwanese American scientist working in the fields of molecular evolution, population genetics, and genomics...
- Neutral models of molecular evolution
Journals and societies
Journals dedicated to molecular evolution include Molecular Biology and Evolution, Journal of Molecular Evolution, and Molecular Phylogenetics and Evolution. Research in molecular evolution is also published in journals of geneticsGenetics
Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....
, molecular biology
Molecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
, genomics
Genomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
, systematics
Systematics
Biological systematics is the study of the diversification of terrestrial life, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees...
, or evolutionary biology. The Society for Molecular Biology and Evolution publishes the journal "Molecular Biology and Evolution" and holds an annual international meeting.
See also
- History of molecular evolutionHistory of molecular evolutionThe history of molecular evolution starts in the early 20th century with "comparative biochemistry", but the field of molecular evolution came into its own in the 1960s and 1970s, following the rise of molecular biology...
- AbiogenesisAbiogenesisAbiogenesis or biopoesis is the study of how biological life arises from inorganic matter through natural processes, and the method by which life on Earth arose...
- EvolutionEvolutionEvolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
- Genetic driftGenetic driftGenetic drift or allelic drift is the change in the frequency of a gene variant in a population due to random sampling.The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces...
- E. coli long-term evolution experimentE. coli long-term evolution experimentThe E. coli long-term evolution experiment is an ongoing study in experimental evolution led by Richard Lenski that has been tracking genetic changes in 12 initially identical populations of asexual Escherichia coli bacteria since 24 February 1988...
- Evolutionary physiologyEvolutionary physiologyEvolutionary physiology is the study of physiological evolution, which is to say, the manner in which the functional characteristics of individuals in a population of organisms have responded to selection across multiple generations during the history of the population.It is a subdiscipline of both...
- Genomic organizationGenomic organizationright|thumb|300px|Genome sizes and corresponding composition of six major model organisms as pie charts. The increase in [[genome]] size correlates with the vast expansion of noncoding and repeat [[DNA]] sequences in more complex...
- HeterotachyHeterotachyHeterotachy refers to shifts in site-specific evolutionary rates over time. In the field of molecular evolution, the principle of heterotachy states that the substitution rate of sites in a gene can change through time. It has been proposed that the positions that show switches in substitution rate...
- Horizontal gene transferHorizontal gene transferHorizontal gene transfer , also lateral gene transfer , is any process in which an organism incorporates genetic material from another organism without being the offspring of that organism...
- Human evolutionHuman evolutionHuman evolution refers to the evolutionary history of the genus Homo, including the emergence of Homo sapiens as a distinct species and as a unique category of hominids and mammals...
- Evolution of dietary antioxidants
- Molecular clockMolecular clockThe molecular clock is a technique in molecular evolution that uses fossil constraints and rates of molecular change to deduce the time in geologic history when two species or other taxa diverged. It is used to estimate the time of occurrence of events called speciation or radiation...
- Comparative phylogenetics
- Neutral theory of molecular evolutionNeutral theory of molecular evolutionThe neutral theory of molecular evolution states that the vast majority of evolutionary changes at the molecular level are caused by random drift of selectively neutral mutants . The theory was introduced by Motoo Kimura in the late 1960s and early 1970s...
- Nucleotide diversityNucleotide diversityNucleotide diversity is a concept in molecular genetics which is used to measure the degree of polymorphism within a population.One commonly used measure of nucleotide diversity was first introduced by Nei and Li in 1979...
- Parsimony
- Population geneticsPopulation geneticsPopulation genetics is the study of allele frequency distribution and change under the influence of the four main evolutionary processes: natural selection, genetic drift, mutation and gene flow. It also takes into account the factors of recombination, population subdivision and population...
- SelectionSelectionIn the context of evolution, certain traits or alleles of genes segregating within a population may be subject to selection. Under selection, individuals with advantageous or "adaptive" traits tend to be more successful than their peers reproductively—meaning they contribute more offspring to the...
Further reading
- A. Meyer (Editor), Y. van de Peer, "Genome Evolution: Gene and Genome Duplications and the Origin of Novel Gene Functions", 2003, ISBN 978-1402010217
- T. Ryan Gregory, "The Evolution of the Genome", 2004, YSBN 978-0123014634