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Molecular evolution is the process of change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and
population genetics Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and pop ...
to explain patterns in these changes. Major topics in molecular evolution concern the rates and impacts of single nucleotide changes,
neutral evolution The neutral theory of molecular evolution holds that most evolutionary changes occur at the molecular level, and most of the variation within and between species are due to random genetic drift of mutant alleles that are selectively neutral. The ...
vs. natural selection, origins of new genes, the genetic nature of
complex traits Complex traits, also known as quantitative traits, are traits that do not behave according to simple Mendelian inheritance laws. More specifically, their inheritance cannot be explained by the genetic segregation of a single gene. Such traits show ...
, the genetic basis of
speciation Speciation is the evolutionary process by which populations evolve to become distinct species. The biologist Orator F. Cook coined the term in 1906 for cladogenesis, the splitting of lineages, as opposed to anagenesis, phyletic evolution within ...
, evolution of development, and ways that evolutionary forces influence genomic and phenotypic changes.


History

The history of molecular evolution starts in the early 20th century with comparative
biochemistry Biochemistry or biological chemistry is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided into three fields: structural biology, enzymology and ...
, and the use of "fingerprinting" methods such as immune assays,
gel electrophoresis Gel electrophoresis is a method for separation and analysis of biomacromolecules ( DNA, RNA, proteins, etc.) and their fragments, based on their size and charge. It is used in clinical chemistry to separate proteins by charge or size (IEF ...
and paper chromatography in the 1950s to explore
homologous protein A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology). Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if no sequence similar ...
s. The field of molecular evolution came into its own in the 1960s and 1970s, following the rise of molecular biology. 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 The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotid ...
to estimate the time since the last universal common ancestor. In the late 1960s, the
neutral theory of molecular evolution The neutral theory of molecular evolution holds that most evolutionary changes occur at the molecular level, and most of the variation within and between species are due to random genetic drift of mutant alleles that are selectively neutral. The ...
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 Evolutionary thought, the recognition that species change over time and the perceived understanding of how such processes work, has roots in antiquity—in the ideas of the ancient Greeks, Romans, Chinese, Church Fathers as well as in mediev ...
, 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 Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal ...
sequences, the foundation of a reconceptualization of the early
history of life The history of life on Earth traces the processes by which living and fossil organisms evolved, from the earliest emergence of life to present day. Earth formed about 4.5 billion years ago (abbreviated as ''Ga'', for ''gigaannum'') and ev ...
.


Forces in molecular evolution

The content and structure of a genome is the product of the molecular and population genetic forces which act upon that genome. Novel genetic variants will arise through mutation and will spread and be maintained in populations due to genetic drift or natural selection.


Mutation

Mutations are permanent, transmissible changes to the genetic material ( DNA or RNA) of a
cell Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Locations * Monastic cell, a small room, hut, or cave in which a religious recluse lives, alternatively the small precursor of a monastery w ...
or virus. Mutations result from errors in DNA replication during
cell division Cell division is the process by which a parent cell divides into two daughter cells. Cell division usually occurs as part of a larger cell cycle in which the cell grows and replicates its chromosome(s) before dividing. In eukaryotes, there a ...
and by exposure to radiation, chemicals, and other environmental stressors, or viruses and transposable elements. Most mutations that occur are single nucleotide polymorphisms which modify single bases of the DNA sequence, resulting in
point mutation A point mutation is a genetic mutation where a single nucleotide base is changed, inserted or deleted from a DNA or RNA sequence of an organism's genome. Point mutations have a variety of effects on the downstream protein product—consequences ...
s. Other types of mutations modify larger segments of DNA and can cause duplications, insertions, deletions, inversions, and translocations. Most organisms display a strong bias in the types of mutations that occur with strong influence in GC-content. Transitions (A ↔ G or C ↔ T) are more common than
transversion Transversion, in molecular biology, refers to a point mutation in DNA in which a single (two ring) purine ( A or G) is changed for a (one ring) pyrimidine ( T or C), or vice versa. A transversion can be spontaneous, or it can be caused by ioni ...
s ( purine (adenine or guanine)) ↔
pyrimidine Pyrimidine (; ) is an aromatic, heterocyclic, organic compound similar to pyridine (). One of the three diazines (six-membered heterocyclics with two nitrogen atoms in the ring), it has nitrogen atoms at positions 1 and 3 in the ring. The othe ...
(cytosine or thymine, or in RNA, uracil)) and are less likely to alter
amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...
sequences of proteins. Mutations are stochastic and typically occur randomly across genes. Mutation rates for single nucleotide sites for most organisms are very low, roughly 10−9 to 10−8 per site per generation, though some viruses have higher mutation rates on the order of 10−6 per site per generation. Among these mutations, some will be neutral or beneficial and will remain in the genome unless lost via genetic drift, and others will be detrimental and will be eliminated from the genome by natural selection. Because mutations are extremely rare, they accumulate very slowly across generations. While the number of mutations which appears in any single generation may vary, over very long time periods they will appear to accumulate at a regular pace. Using the mutation rate per generation and the number of nucleotide differences between two sequences, divergence times can be estimated effectively via the
molecular clock The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotid ...
.


Recombination

Recombination is a process that results in genetic exchange between chromosomes or chromosomal regions. Recombination counteracts physical linkage between adjacent genes, thereby reducing genetic hitchhiking. The resulting independent inheritance of genes results in more efficient selection, meaning that regions with higher recombination will harbor fewer detrimental mutations, more selectively favored variants, and fewer errors in replication and repair. Recombination can also generate particular types of mutations if chromosomes are misaligned.


Gene conversion

Gene conversion is a type of recombination that is the product of DNA repair where nucleotide damage is corrected using an homologous genomic region as a template. Damaged bases are first excised, the damaged strand is then aligned with an undamaged homolog, and DNA synthesis repairs the excised region using the undamaged strand as a guide. Gene conversion is often responsible for homogenizing sequences of duplicate genes over long time periods, reducing nucleotide divergence.


Genetic drift

Genetic drift is the change of allele frequencies from one generation to the next due to stochastic effects of
random sampling In statistics, quality assurance, and survey methodology, sampling is the selection of a subset (a statistical sample) of individuals from within a statistical population to estimate characteristics of the whole population. Statisticians attemp ...
in finite populations. Some existing variants have no effect on fitness and may increase or decrease in frequency simply due to chance. "Nearly neutral" variants whose
selection coefficient In population genetics, a selection coefficient, usually denoted by the letter ''s'', is a measure of differences in relative fitness. Selection coefficients are central to the quantitative description of evolution, since fitness differences deter ...
is close to a threshold value of 1 / the
effective population size The effective population size (''N'e'') is a number that, in some simplified scenarios, corresponds to the number of breeding individuals in the population. More generally, ''N'e'' is the number of individuals that an idealised population w ...
will also be affected by chance as well as by selection and mutation. Many genomic features have been ascribed to accumulation of nearly neutral detrimental mutations as a result of small effective population sizes. With a smaller effective population size, a larger variety of mutations will behave as if they are neutral due to inefficiency of selection.


Selection

Selection occurs when organisms with greater fitness, i.e. greater ability to survive or reproduce, are favored in subsequent generations, thereby increasing the instance of underlying genetic variants in a population. Selection can be the product of natural selection, artificial selection, or sexual selection. Natural selection is any selective process that occurs due to the fitness of an organism to its environment. In contrast
sexual selection Sexual selection is a mode of natural selection in which members of one biological sex choose mates of the other sex to mate with (intersexual selection), and compete with members of the same sex for access to members of the opposite sex (int ...
is a product of mate choice and can favor the spread of genetic variants which act counter to natural selection but increase desirability to the opposite sex or increase mating success.
Artificial selection Selective breeding (also called artificial selection) is the process by which humans use animal breeding and plant breeding to selectively develop particular phenotypic traits (characteristics) by choosing which typically animal or plant ma ...
, also known as selective breeding, is imposed by an outside entity, typically humans, in order to increase the frequency of desired traits. The principles of population genetics apply similarly to all types of selection, though in fact each may produce distinct effects due to clustering of genes with different functions in different parts of the genome, or due to different properties of genes in particular functional classes. For instance, sexual selection could be more likely to affect molecular evolution of the sex chromosomes due to clustering of sex specific genes on the X, Y, Z or W.


Intragenomic conflict

Selection can operate at the gene level at the expense of organismal fitness, resulting in
intragenomic conflict Intragenomic conflict refers to the evolutionary phenomenon where genes have phenotypic effects that promote their own transmission in detriment of the transmission of other genes that reside in the same genome. The selfish gene theory postulates ...
. This is because there can be a selective advantage for selfish genetic elements in spite of a host cost. Examples of such selfish elements include transposable elements, meiotic drivers, killer X chromosomes, selfish mitochondria, and self-propagating introns.


Genome architecture


Genome size

Genome size is influenced by the amount of repetitive DNA as well as number of genes in an organism. The
C-value paradox C-value is the amount, in picograms, of DNA contained within a haploid nucleus (e.g. a gamete) or one half the amount in a diploid somatic cell of a eukaryotic organism. In some cases (notably among diploid organisms), the terms C-value and geno ...
refers to the lack of correlation between organism 'complexity' and genome size. Explanations for the so-called paradox are two-fold. First, repetitive genetic elements can comprise large portions of the genome for many organisms, thereby inflating DNA content of the haploid genome. Secondly, the number of genes is not necessarily indicative of the number of developmental stages or tissue types in an organism. An organism with few developmental stages or tissue types may have large numbers of genes that influence non-developmental phenotypes, inflating gene content relative to developmental gene families. Neutral explanations for genome size suggest that when population sizes are small, many mutations become nearly neutral. Hence, in small populations repetitive content and other 'junk' DNA can accumulate without placing the organism at a competitive disadvantage. There is little evidence to suggest that genome size is under strong widespread selection in multicellular eukaryotes. Genome size, independent of gene content, correlates poorly with most physiological traits and many eukaryotes, including mammals, harbor very large amounts of repetitive DNA. However,
birds Birds are a group of warm-blooded vertebrates constituting the class Aves (), characterised by feathers, toothless beaked jaws, the laying of hard-shelled eggs, a high metabolic rate, a four-chambered heart, and a strong yet lightweight ...
likely have experienced strong selection for reduced genome size, in response to changing energetic needs for flight. Birds, unlike humans, produce nucleated red blood cells, and larger nuclei lead to lower levels of oxygen transport. Bird metabolism is far higher than that of mammals, due largely to flight, and oxygen needs are high. Hence, most birds have small, compact genomes with few repetitive elements. Indirect evidence suggests that non-avian theropod dinosaur ancestors of modern birds also had reduced genome sizes, consistent with endothermy and high energetic needs for running speed. Many bacteria have also experienced selection for small genome size, as time of replication and energy consumption are so tightly correlated with fitness.


Repetitive elements

Transposable elements are self-replicating, selfish genetic elements which are capable of proliferating within host genomes. Many transposable elements are related to viruses, and share several proteins in common....


Chromosome number and organization

The number of chromosomes in an organism's genome also does not necessarily correlate with the amount of DNA in its genome. The ant ''Myrmecia pilosula'' has only a single pair of chromosomes whereas the Adders-tongue fern ''
Ophioglossum ''Ophioglossum'', the adder's-tongue ferns, is a genus of about 50 species of ferns in the family Ophioglossaceae. The name ''Ophioglossum'' comes from the Greek meaning "snake-tongue".
reticulatum'' has up to 1260 chromosomes.
Cilliate The ciliates are a group of alveolates characterized by the presence of hair-like organelles called cilia, which are identical in structure to eukaryotic flagella, but are in general shorter and present in much larger numbers, with a different ...
genomes house each gene in individual chromosomes, resulting in a genome which is not physically linked. Reduced linkage through creation of additional chromosomes should effectively increase the efficiency of selection. Changes in chromosome number can play a key role in speciation, as differing chromosome numbers can serve as a barrier to reproduction in hybrids. Human
chromosome 2 Chromosome 2 is one of the twenty-three pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 2 is the second-largest human chromosome, spanning more than 242 million base pairs and representing almost ...
was created from a fusion of two chimpanzee chromosomes and still contains central
telomeres A telomere (; ) is a region of repetitive nucleotide sequences associated with specialized proteins at the ends of linear chromosomes. Although there are different architectures, telomeres, in a broad sense, are a widespread genetic feature mos ...
as well as a vestigial second
centromere The centromere links a pair of sister chromatids together during cell division. This constricted region of chromosome connects the sister chromatids, creating a short arm (p) and a long arm (q) on the chromatids. During mitosis, spindle fibers a ...
. Polyploidy, especially allopolyploidy, which occurs often in plants, can also result in reproductive incompatibilities with parental species. ''Agrodiatus'' blue butterflies have diverse chromosome numbers ranging from n=10 to n=134 and additionally have one of the highest rates of speciation identified to date.


Gene content and distribution

Different organisms house different numbers of genes within their genomes as well as different patterns in the distribution of genes throughout the genome. Some organisms, such as most bacteria, ''Drosophila'', and ''Arabidopsis'' have particularly compact genomes with little repetitive content or non-coding DNA. Other organisms, like mammals or maize, have large amounts of repetitive DNA, long introns, and substantial spacing between different genes. The content and distribution of genes within the genome can influence the rate at which certain types of mutations occur and can influence the subsequent evolution of different species. Genes with longer
introns An intron is any nucleotide sequence within a gene that is not expressed or operative in the final RNA product. The word ''intron'' is derived from the term ''intragenic region'', i.e. a region inside a gene."The notion of the cistron .e., gene. ...
are more likely to recombine due to increased physical distance over the coding sequence. As such, long introns may facilitate
ectopic recombination Ectopic recombination is an atypical form of recombination in which crossing over occurs at non-homologous, rather than along homologous, loci. //This needs to be edited, as it is 1)incorrect and 2)contradicts what's written below, namely the ne ...
, and result in higher rates of new gene formation.


Organelles

In addition to the nuclear genome, endosymbiont organelles contain their own genetic material typically as circular plasmids. Mitochondrial and chloroplast DNA varies across taxa, but membrane-bound proteins, especially electron transport chain constituents are most often encoded in the organelle. Chloroplasts and mitochondria are maternally inherited in most species, as the organelles must pass through the egg. In a rare departure, some species of mussels are known to inherit mitochondria from father to son.


Origins of new genes

New genes arise from several different genetic mechanisms including gene duplication, de novo origination, retrotransposition, chimeric gene formation, recruitment of non-coding sequence, and gene truncation.
Gene duplication Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. ...
initially leads to redundancy. However, duplicated gene sequences can mutate to develop new functions or specialize so that the new gene performs a subset of the original ancestral functions. In addition to duplicating whole genes, sometimes only a domain or part of a protein is duplicated so that the resulting gene is an elongated version of the parental gene. Retrotransposition creates new genes by copying mRNA to DNA and inserting it into the genome. Retrogenes often insert into new genomic locations, and often develop new expression patterns and functions.
Chimeric gene Chimeric genes (literally, made of parts from different sources) form through the combination of portions of two or more coding sequences to produce new genes. These mutations are distinct from fusion genes which merge whole gene sequences into ...
s form when duplication, deletion, or incomplete retrotransposition combine portions of two different coding sequences to produce a novel gene sequence. Chimeras often cause regulatory changes and can shuffle protein domains to produce novel adaptive functions. ''De novo'' gene birth can also give rise to new genes from previously non-coding DNA. For instance, Levine and colleagues reported the origin of five new genes in the ''D. melanogaster'' genome from noncoding DNA. Similar de novo origin of genes has been also shown in other organisms such as yeast, rice and humans. De novo genes may evolve from transcripts that are already expressed at low levels. Mutation of a
stop codon In molecular biology (specifically protein biosynthesis), a stop codon (or termination codon) is a codon (nucleotide triplet within messenger RNA) that signals the termination of the translation process of the current protein. Most codons in m ...
to a regular codon or a
frameshift Ribosomal frameshifting, also known as translational frameshifting or translational recoding, is a biological phenomenon that occurs during translation that results in the production of multiple, unique proteins from a single mRNA. The process can ...
may cause an extended protein that includes a previously non-coding sequence. The formation of novel genes from scratch typically can not occur within genomic regions of high gene density. The essential events for de novo formation of genes is recombination/mutation which includes insertions, deletions, and inversions. These events are tolerated if the consequence of these genetic events does not interfere in cellular activities. Most genomes comprise prophages wherein genetic modifications do not, in general, affect the host genome propagation. Hence, there is higher probability of genetic modifications, in regions such as prophages, which is proportional to the probability of de novo formation of genes. ''De novo'' evolution of genes can also be simulated in the laboratory. For example, semi-random gene sequences can be selected for specific functions. More specifically, they selected sequences from a library that could complement a
gene deletion In genetics, a deletion (also called gene deletion, deficiency, or deletion mutation) (sign: Δ) is a mutation (a genetic aberration) in which a part of a chromosome or a sequence of DNA is left out during DNA replication. Any number of nucleot ...
in '' E. coli''. The deleted gene encodes ferric enterobactin esterase (Fes), which releases iron from an iron
chelator Chelation is a type of bonding of ions and molecules to metal ions. It involves the formation or presence of two or more separate coordinate bonds between a polydentate (multiple bonded) ligand and a single central metal atom. These ligands ar ...
,
enterobactin Enterobactin (also known as enterochelin) is a high affinity siderophore that acquires iron for microbial systems. It is primarily found in Gram-negative bacteria, such as ''Escherichia coli'' and ''Salmonella typhimurium''. Enterobactin is the ...
. While Fes is a 400
amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...
protein, the newly selected gene was only 100 amino acids in length and unrelated in sequence to Fes.


''In vitro'' molecular evolution experiments

Principles of molecular evolution can be discovered and tested using laboratory experimentation. This usually involves the cloning and ''in vitro'' modification of genes and proteins outside cells. Since the pioneering work of Sol Spiegelmann in 1967 ef involving RNA that replicates itself with the aid of an enzyme extracted from the Qß virus ef several groups (such as Kramers efand Biebricher/Luce/Eigen ef studied mini and micro variants of this RNA in the 1970s and 1980s that replicate on the timescale of seconds to a minute, allowing hundreds of generations with large population sizes (e.g. 10^14 sequences) to be followed in a single day of experimentation. The chemical kinetic elucidation of the detailed mechanism of replication ef, refmeant that this type of system was the first molecular evolution system that could be fully characterised on the basis of physical chemical kinetics, later allowing the first models of the genotype to phenotype map based on sequence dependent RNA folding and refolding to be produced ef, ref Subject to maintaining the function of the multicomponent Qß enzyme, chemical conditions could be varied significantly, in order to study the influence of changing environments and selection pressures ef Experiments with ''in vitro'' RNA quasi species included the characterisation of the error threshold for information in molecular evolution ef the discovery of ''de novo'' evolution efleading to diverse replicating RNA species and the discovery of spatial travelling waves as ideal molecular evolution reactors ef, ref Later experiments employed novel combinations of enzymes to elucidate novel aspects of interacting molecular evolution involving population dependent fitness, including work with artificially designed molecular predator prey and cooperative systems of multiple RNA and DNA ef, ref Special evolution reactors were designed for these studies, starting with serial transfer machines, flow reactors such as cell-stat machines, capillary reactors, and microreactors including line flow reactors and gel slice reactors. These studies were accompanied by theoretical developments and simulations involving RNA folding and replication kinetics that elucidated the importance of the correlation structure between distance in sequence space and fitness changes ef including the role of neutral networks and structural ensembles in evolutionary optimisation.


in vitro protein function evolution

Mutagenic hot spots in enzymes can be identified using NMR spectroscopy. In a proof-of-concept study, Bhattacharya and colleagues converted myoglobin, a non-enzymatic oxygen storage protein, into a highly efficient Kemp eliminase using only three mutations. This demonstrates that only few mutations are needed to radically change the function of a protein.


Molecular phylogenetics

Molecular systematics is the product of the traditional fields of systematics and
molecular genetics Molecular genetics is a sub-field of biology that addresses how differences in the structures or expression of DNA molecules manifests as variation among organisms. Molecular genetics often applies an "investigative approach" to determine the ...
. It uses DNA, RNA, or protein sequences to resolve questions in systematics, i.e. about their correct
scientific classification Taxonomy is the practice and science of categorization or classification. A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are organized into groups or types. A ...
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 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 pair A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA ...
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. Selectionist hypotheses argue that selection is the driving force of molecular evolution. While acknowledging that many mutations are neutral, selectionists attribute changes in the frequencies of neutral alleles to linkage disequilibrium with other loci that are under selection, rather than to random genetic drift. Biases in codon usage are usually explained with reference to the ability of even weak selection to shape molecular evolution. Neutralist hypotheses emphasize the importance of mutation, purifying selection, and random genetic drift. The introduction of the neutral theory by
Kimura Kimura (written: lit. "tree village") is the 17th most common Japanese surname. Notable people with the surname include: *, Japanese novelist *, Japanese footballer *, Japanese botanist *, Japanese idol and singer *, Japanese footballer *, Japanes ...
, quickly followed by King and Jukes' own findings, led to a fierce debate about the relevance of
neodarwinism Neo-Darwinism is generally used to describe any integration of Charles Darwin's theory of evolution by natural selection with Gregor Mendel's theory of genetics. It mostly refers to evolutionary theory from either 1895 (for the combinations of Dar ...
at the molecular level. The
Neutral theory of molecular evolution The neutral theory of molecular evolution holds that most evolutionary changes occur at the molecular level, and most of the variation within and between species are due to random genetic drift of mutant alleles that are selectively neutral. The ...
proposes that most mutations in DNA are at locations not important to function or fitness. These neutral changes drift towards fixation within a population. Positive changes will be very rare, and so will not greatly contribute to DNA polymorphisms. Deleterious mutations do not contribute much to DNA diversity because they negatively affect fitness and so are removed from the gene pool before long. This theory provides a framework for the molecular clock. The fate of neutral mutations are governed by genetic drift, and contribute to both nucleotide polymorphism and fixed differences between species.The nearly neutral theory expanded the neutralist perspective, suggesting that several mutations are nearly neutral, which means both random drift and natural selection is relevant to their dynamics. In the strictest sense, the neutral theory is not accurate. Subtle changes in DNA very often have effects, but sometimes these effects are too small for natural selection to act on. Even synonymous mutations are not necessarily neutral because there is not a uniform amount of each codon. The nearly neutral theory expanded the neutralist perspective, suggesting that several mutations are nearly neutral, which means both random drift and natural selection is relevant to their dynamics. The main difference between the neutral theory and nearly neutral theory is that the latter focuses on weak selection, not strictly neutral. Another concept is
constructive neutral evolution Constructive neutral evolution (CNE) is a theory that seeks to explain how complex systems can evolve through neutral transitions and spread through a population by chance fixation (genetic drift). Constructive neutral evolution is a competitor for ...
(CNE), which explains that complex systems can emerge and spread into a population through neutral transitions with the principles of excess capacity, presuppression, and ratcheting, and it has been applied in areas ranging from the origins of the spliceosome to the complex interdependence of microbial communities. 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 In molecular biology and genetics, GC-content (or guanine-cytosine content) is the percentage of nitrogenous bases in a DNA or RNA molecule that are either guanine (G) or cytosine (C). This measure indicates the proportion of G and C bases out o ...
was not the result of positive selection, but a consequence of the GC mutational pressure.


Protein evolution

While genomes store information and accumulate mutations, proteins are the active products of genes. Hence the evolution of protein function is critical to understand molecular evolution. Evolution of proteins is studied by comparing the sequences and structures of proteins from many organisms. Similar sequences/structures indicating that the proteins diverged from a common origin; these proteins are '' homologous''.
Phylogenetic In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups o ...
analysis of proteins has revealed how proteins evolve and change their structure and function over time. Evolutionary rate. Using the amino acid sequences of hemoglobin and
cytochrome c The cytochrome complex, or cyt ''c'', is a small hemeprotein found loosely associated with the inner membrane of the mitochondrion. It belongs to the cytochrome c family of proteins and plays a major role in cell apoptosis. Cytochrome c is high ...
from multiple species, scientists were able to derive estimations of protein evolution rates. Each protein has its own rate, and that rate is relatively constant across phylogenies (i.e., hemoglobin does not evolve at the same rate as cytochrome c, but hemoglobins from humans, mice, etc. do have comparable rates of evolution). Not all regions within a protein mutate at the same rate; functionally important areas mutate more slowly and amino acid substitutions involving similar amino acids occurs more often than dissimilar substitutions. Overall, the level of polymorphisms in proteins seems to be fairly constant. Several species (including humans, fruit flies, and mice) have similar levels of protein polymorphism. Functional evolution. Numerous enzymes and other proteins have been shown to change their function over the course of evolution. For example,
ribonucleotide reductase Ribonucleotide reductase (RNR), also known as ribonucleoside diphosphate reductase (rNDP), is an enzyme that catalyzes the formation of deoxyribonucleotides from ribonucleotides. It catalyzes this formation by removing the 2'-hydroxyl group of th ...
(RNR) is known from thousands of organisms and has evolved a multitude of structural and functional variants. Class I RNRs use a
ferritin Ferritin is a universal intracellular protein that stores iron and releases it in a controlled fashion. The protein is produced by almost all living organisms, including archaea, bacteria, algae, higher plants, and animals. It is the primary ...
subunit and differ by the metal they use as cofactors. In class II RNRs, the thiyl radical is generated using an
adenosylcobalamin Adenosylcobalamin (AdoCbl), also known as coenzyme B12, cobamamide, and dibencozide, is, along with methylcobalamin (MeCbl), one of the biologically active forms of vitamin B12. Adenosylcobalamin participates as a cofactor in radical-mediated 1,2 ...
cofactor and these enzymes do not require additional subunits (as opposed to class I which do). In class III RNRs, the thiyl radical is generated using
S-adenosylmethionine ''S''-Adenosyl methionine (SAM), also known under the commercial names of SAMe, SAM-e, or AdoMet, is a common cosubstrate involved in methyl group transfers, transsulfuration, and aminopropylation. Although these anabolic reactions occur throug ...
bound to a
4Fe-4S Iron–sulfur proteins (or iron–sulphur proteins in British spelling) are proteins characterized by the presence of iron–sulfur clusters containing sulfide-linked di-, tri-, and tetrairon centers in variable oxidation states. Iron–sulfur ...
] cluster. That is, within a single family of proteins numerous structural and functional mechanisms can evolve.


Relation to nucleic acid evolution

Protein evolution is inescapably tied to changes and selection of DNA polymorphisms and mutations because protein sequences change in response to alterations in the DNA sequence. Amino acid sequences and nucleic acid sequences do not mutate at the same rate. Due to the degenerate nature of DNA, bases can change without affecting the amino acid sequence. For example, there are six codons that code for leucine. Thus, despite the difference in mutation rates, it is essential to incorporate nucleic acid evolution into the discussion of protein evolution. At the end of the 1960s, two groups of scientists—Kimura (1968) and King and Jukes (1969)—independently proposed that a majority of the evolutionary changes observed in proteins were neutral. Since then, the neutral theory has been expanded upon and debated.


Discordance with morphological evolution

There are sometimes discordances between molecular and morphological evolution, which are reflected in molecular and morphological systematic studies, especially of bacteria, archaea and eukaryotic microbes. These discordances can be categorized as two types: (i) one morphology, multiple lineages (e.g.
morphological convergence Convergent evolution is the independent evolution of similar features in species of different periods or epochs in time. Convergent evolution creates analogous structures that have similar form or function but were not present in the last com ...
, cryptic species) and (ii) one lineage, multiple morphologies (e.g. phenotypic plasticity, multiple life-cycle stages).
Neutral evolution The neutral theory of molecular evolution holds that most evolutionary changes occur at the molecular level, and most of the variation within and between species are due to random genetic drift of mutant alleles that are selectively neutral. The ...
possibly could explain the incongruences in some cases.


Journals and societies

The Society for Molecular Biology and Evolution publishes the journals "Molecular Biology and Evolution" and "Genome Biology and Evolution" and holds an annual international meeting. Other journals dedicated to molecular evolution include ''Journal of Molecular Evolution'' and ''Molecular Phylogenetics and Evolution''. Research in molecular evolution is also published in journals of genetics, molecular biology,
genomics Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dim ...
, systematics, and evolutionary biology.


See also

*
Abiogenesis In biology, abiogenesis (from a- 'not' + Greek bios 'life' + genesis 'origin') or the origin of life is the natural process by which life has arisen from non-living matter, such as simple organic compounds. The prevailing scientific hypothes ...
* Adaptor protein evolution * Comparative phylogenetics * Evolution * ''E. coli'' long-term evolution experiment * Evolutionary physiology * Evolution of dietary antioxidants *
Genomic organization 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 (i.e., intronic, intergenic, and interspersed repeat sequences) and repeat DN ...
* Genetic drift *
Genome evolution Genome evolution is the process by which a genome changes in structure (sequence) or size over time. The study of genome evolution involves multiple fields such as structural analysis of the genome, the study of genomic parasites, gene and ancient ...
* Heterotachy * History of molecular evolution * Horizontal gene transfer *
Human evolution Human evolution is the evolutionary process within the history of primates that led to the emergence of ''Homo sapiens'' as a distinct species of the hominid family, which includes the great apes. This process involved the gradual development of ...
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Molecular clock The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotid ...
* Molecular paleontology *
Neutral theory of molecular evolution The neutral theory of molecular evolution holds that most evolutionary changes occur at the molecular level, and most of the variation within and between species are due to random genetic drift of mutant alleles that are selectively neutral. The ...
* Nucleotide diversity *
Parsimony Parsimony refers to the quality of economy or frugality in the use of resources. Parsimony may also refer to * The Law of Parsimony, or Occam's razor, a problem-solving principle ** Maximum parsimony (phylogenetics), an optimality criterion in p ...
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Population genetics Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and pop ...
* Selection


References


Further reading

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