Relativistic electromagnetism

From Wikipedia, the free encyclopedia

This article is about a simplified presentation of electromagnetism, incorporating special relativity. For a more general article on the relationship between special relativity and electromagnetism, see Classical electromagnetism and special relativity. For a more rigorous discussion, see Covariant formulation of classical electromagnetism.

Relativistic electromagnetism is a modern teaching strategy for developing electromagnetic field theory from Coulomb's law and Lorentz transformations. Though Coulomb's law expresses action at a distance, it is an easily understood electric force principle. The more sophisticated view of electromagnetism expressed by electromagnetic fields in spacetime can be approached by applying spacetime symmetries. In certain special configurations it is possible to exhibit magnetic effects due to relative charge density in various simultaneous hyperplanes. This approach to physics education and the education and training of electrical and electronics engineers can be seen in the Encyclopædia Britannica (1956), The Feynman Lectures on Physics (1964), Edward M. Purcell (1965), Jack R. Tessman (1966), W.G.V. Rosser (1968), Anthony French (1968), and Dale R. Corson & Paul Lorrain (1970). This approach provides some preparation for understanding of magnetic forces involved in the Biot–Savart law, Ampère's law, and Maxwell's equations.

In 1912 Leigh Page expressed the aspiration of relativistic electromagnetism:^[1]

If the principle of relativity had been enunciated before the date of Oersted’s discovery, the fundamental relations of electrodynamics could have been predicted on theoretical grounds as a direct consequence of the fundamental laws of electrostatics, extended so as to apply to charges relatively in motion as well as charges relatively at rest.

Einstein's motivation

In 1953 Albert Einstein wrote to the Cleveland Physics Society on the occasion of a commemoration of the Michelson–Morley experiment. In that letter he wrote:^[2]

What led me more or less directly to the special theory of relativity was the conviction that the electromotive force acting on a body in motion in a magnetic field was nothing else but an electric field.

This statement by Einstein reveals that he investigated spacetime symmetries to determine the complementarity of electric and magnetic forces.

Introduction

Purcell argued that the question of an electric field in one inertial frame of reference, and how it looks from a different reference frame moving with respect to the first, is crucial to understand fields created by moving sources. In the special case, the sources that create the field are at rest with respect to one of the reference frames. Given the electric field in the frame where the sources are at rest, Purcell asked: what is the electric field in some other frame?
He stated that the fundamental assumption is that, knowing the electric field at some point (in space and time) in the rest frame of the sources, and knowing the relative velocity of the two frames provided all the information needed to calculate the electric field at the same point in the other frame. In other words, the electric field in the other frame does not depend on the particular distribution of the source charges, only on the local value of the electric field in the first frame at that point. He assumed that the electric field is a complete representation of the influence of the far-away charges.

Alternatively, introductory treatments of magnetism introduce the Biot–Savart law, which describes the magnetic field associated with an electric current. An observer at rest with respect to a system of static, free charges will see no magnetic field. However, a moving observer looking at the same set of charges does perceive a current, and thus a magnetic field.

Uniform electric field — simple analysis

Figure 1: Two oppositely charged plates produce uniform electric field even when moving. The electric field is shown as 'flowing' from top to bottom plate. The Gaussian pill box (at rest) can be used to find the strength of the field.

Consider the very simple situation of a charged parallel-plate capacitor, whose electric field (in its rest frame) is uniform (neglecting edge effects) between the plates and zero outside.

To calculate the electric field of this charge distribution in a reference frame where it is in motion, suppose that the motion is in a direction parallel to the plates as shown in figure 1. The plates will then be shorter by a factor of:

than they are in their rest frame, but the distance between them will be the same. Since charge is independent of the frame in which it is measured, the total charge on each plate is also the same. So the charge per unit area on the plates is therefore larger than in the rest frame by a factor of:

The field between the plates is therefore stronger by this factor.

More rigorous analysis

Figure 2a: The electric field lines are shown flowing outward from the positive plate

Figure 2b: The electric field lines flow inward toward the negative plate

Consider the electric field of a single, infinite plate of positive charge, moving parallel to itself. The field must be uniform both above and below the plate, since it is uniform in its rest frame. We also assume that knowing the field in one frame is sufficient for calculating it in the other frame.

The plate however could have a non zero component of electric field in the direction of motion as in Fig 2a. Even in this case, the field of the infinite plane of negative charge must be equal and opposite to that of the positive plate (as in Fig 2b), since the combination of plates is neutral and cannot therefore produce any net fields. When the plates are separated, the horizontal components still cancel, and the resultant is a uniform vertical field as shown in Fig 1.

If Gauss's law is applied to pillbox as shown in Fig 1, it can be shown that the magnitude of the electric field between the plates is given by:

where the prime (') indicates the value measured in the frame in which the plates are moving. represents the surface charge density of the positive plate. Since the plates are contracted in length by the factor

then the surface charge density in the primed frame is related to the value in the rest frame of the plates by:

But the electric field in the rest frame has value σ / ε₀ and the field points in the same direction on both of the frames, so

The E field in the primed frame is therefore stronger than in the unprimed frame. If the direction of motion is perpendicular to the plates, length contraction of the plates does not occur, but the distance between them is reduced. This closer spacing however does not affect the strength of the electric field. So for motion parallel to the electric field E,

In the general case where motion is in a diagonal direction relative to the field the field is merely a superposition of the perpendicular and parallel fields., each generated by a set of plates at right angles to each other as shown in Fig 3. Since both sets of plates are length contracted, the two components of the E field are

and

where the y subscript denotes perpendicular, and the x subscript, parallel.
These transformation equations only apply if the source of the field is at rest in the unprimed frame.

The field of a moving point charge[edit]

Figure 3: A point charge at rest, surrounded by an imaginary sphere.

Figure 4: A view of the electric field of a point charge moving at constant velocity.

A very important application of the electric field transformation equations is to the field of a single point charge moving with constant velocity. In its rest frame, the electric field of a positive point charge has the same strength in all directions and points directly away from the charge. In some other reference frame the field will appear differently.

In applying the transformation equations to a nonuniform electric field, it is important to record not only the value of the field, but also at what point in space it has this value.

In the rest frame of the particle, the point charge can be imagined to be surrounded by a spherical shell which is also at rest. In our reference frame, however, both the particle and its sphere are moving. Length contraction therefore states that the sphere is deformed into an oblate spheroid, as shown in cross section in Fig 4.

Consider the value of the electric field at any point on the surface of the sphere. Let x and y be the components of the displacement (in the rest frame of the charge), from the charge to a point on the sphere, measured parallel and perpendicular to the direction of motion as shown in the figure. Because the field in the rest frame of the charge points directly away from the charge, its components are in the same ratio as the components of the displacement:

In our reference frame, where the charge is moving, the displacement x' in the direction of motion is length-contracted:

The electric field at any point on the sphere points directly away from the charge. (b) In a reference frame where the charge and the sphere are moving to the right, the sphere is length-contracted but the vertical component of the field is stronger. These two effects combine to make the field again point directly away from the current location of the charge. (While the y component of the displacement is the same in both frames).

However, according to the above results, the y component of the field is enhanced by a similar factor:

whilst the x component of the field is the same in both frames. The ratio of the field components is therefore

So, the field in the primed frame points directly away from the charge, just as in the unprimed frame. A view of the electric field of a point charge moving at constant velocity is shown in figure 4. The faster the charge is moving, the more noticeable the enhancement of the perpendicular component of the field becomes. If the speed of the charge is much less than the speed of light, this enhancement is often negligible. But under certain circumstances, it is crucially important even at low velocities.

The origin of magnetic forces

Figure 5, lab frame: A horizontal wire carrying a current, represented by evenly spaced positive charges moving to the right whilst an equal number of negative charges remain at rest, with a positively charged particle outside the wire and traveling in a direction parallel to the current.

In the simple model of events in a wire stretched out horizontally, a current can be represented by the evenly spaced positive charges, moving to the right, whilst an equal number of negative charges remain at rest. If the wire is electrostatically neutral, the distance between adjacent positive charges must be the same as the distance between adjacent negative charges.

Assume that in our 'lab frame' (Figure 5), we have a positive test charge, Q, outside the wire, traveling parallel to the current, at the speed, v, which is equal to the speed of the moving charges in the wire. It should experience a magnetic force, which can be easily confirmed by experiment.

Figure 6, test charge frame: The same situation as in fig. 5, but viewed from the reference frame in which positive charges are at rest. The negative charges flow to the left. The distance between the negative charges is length-contracted relative to the lab frame, while the distance between the positive charges is expanded, so the wire carries a net negative charge.

Inside 'test charge frame'(Fig. 6), the only possible force is the electrostatic force F_e = Q * E because, although the magnetic field is the same, the test charge is at rest and, therefore, cannot feel it. In this frame, the negative charge density has Lorentz-contracted with respect to what we had in lab frame because of the increased speed. This means that spacing between charges has reduced by the Lorentz factor with respect to the lab frame spacing, l:

Thus, positive charges have Lorentz-expanded (because their speed has dropped):

Both of these effects combine to give the wire a net negative charge in the test charge frame. Since the negatively charged wire exerts an attractive force on a positively charged particle, the test charge will therefore be attracted and will move toward the wire.

For , we can concretely compute both,^[3] the magnetic force sensed in the lab frame

and electrostatic force, sensed in the test charge frame, where we first compute the charge density with respect to the lab frame length, l:

and, keeping in mind that current , resulting electrostatic force

which comes out exactly equal to the magnetic force sensed in the lab frame, .

The lesson is that observers in different frames of reference see the same phenomena but disagree on their reasons.
If the currents are in opposite directions, consider the charge moving to the left. No charges are now at rest in the reference frame of the test charge. The negative charges are moving with speed v in the test charge frame so their spacing is again:

The distance between positive charges is more difficult to calculate. The relative velocity should be less than 2v due to special relativity. For simplicity, assume it is 2v. The positive charge spacing contraction is then:

relative to its value in their rest frame. Now its value in their rest frame was found to be

So the final spacing of positive charges is:

To determine whether l₍₊₎ or l_(-) is larger we assume that v << c and use the binomial approximation that

After some algebraic calculation it is found that l₍₊₎ < l_(-), and so the wire is positively charged in the frame of the test charge.^[4]

One may think that the picture, presented here, is artificial because electrons, which accelerated in fact, must condense in the lab frame, making the wire charged. Naturally, however, all electrons feel the same accelerating force and, therefore, identically to the Bell's spaceships, the distance between them does not change in the lab frame (i.e. expands in their proper moving frame). Rigid bodies, like trains, don't expand however in their proper frame, and, therefore, really contract, when observed from the stationary frame.

Calculating the magnetic field

The Lorentz force law

A moving test charge near a wire carrying current will experience a magnetic force dependent on the velocity of the moving charges in the wire. If the current is flowing to the right, and a positive test charge is moving below the wire, then there is a force in a direction 90° counterclockwise from the direction of motion.

The magnetic field of a wire

Calculation of the magnitude of the force exerted by a current-carrying wire on a moving charge is equivalent to calculating the magnetic field produced by the wire. Consider again the situation shown in figures. The latter figure, showing the situation in the reference frame of the test charge, is reproduced in the figure. The positive charges in the wire, each with charge q, are at rest in this frame, while the negative charges, each with charge −q, are moving to the left with speed v. The average distance between the negative charges in this frame is length-contracted to:

where is the distance between them in the lab frame. Similarly, the distance between the positive charges is not length-contracted:

Both of these effects give the wire a net negative charge in the test charge frame, so that it exerts an attractive force on the test charge.

Classical electromagnetism and special relativity

From Wikipedia, the free encyclopedia

The theory of special relativity plays an important role in the modern theory of classical electromagnetism. First of all, it gives formulas for how electromagnetic objects, in particular the electric and magnetic fields, are altered under a Lorentz transformation from one inertial frame of reference to another. Secondly, it sheds light on the relationship between electricity and magnetism, showing that frame of reference determines if an observation follows electrostatic or magnetic laws. Third, it motivates a compact and convenient notation for the laws of electromagnetism, namely the "manifestly covariant" tensor form.

Maxwell's equations, when they were first stated in their complete form in 1865, would turn out to be compatible with special relativity.^[1] Moreover, the apparent coincidences in which the same effect was observed due to different physical phenomena by two different observers would be shown to be not coincidental in the least by special relativity. In fact, half of Einstein's 1905 first paper on special relativity, "On the Electrodynamics of Moving Bodies," explains how to transform Maxwell's equations.

Transformation of the fields between inertial frames

The E and B fields

This equation, also called the Joules-Bernoulli equation, considers two inertial frames. As notation, the field variables in one frame are unprimed, and in a frame moving relative to the unprimed frame at velocity v, the fields are denoted with primes. In addition, the fields parallel to the velocity v are denoted by while the fields perpendicular to v are denoted as . In these two frames moving at relative velocity v, the E-fields and B-fields are related by:^[2]

where

is called the Lorentz factor and c is the speed of light in free space. The inverse transformations are the same except v → −v.

An equivalent, alternative expression is:^[3]

where v̂ is the velocity unit vector.

If one of the fields is zero in one frame of reference, that doesn't necessarily mean it is zero in all other frames of reference. This can be seen by, for instance, making the unprimed electric field zero in the transformation to the primed electric field. In this case, depending on the orientation of the magnetic field, the primed system could see an electric field, even though there is none in the unprimed system.

This does not mean two completely different sets of events are seen in the two frames, but that the same sequence of events is described in two different ways (see Moving magnet and conductor problem below).

If a particle of charge q moves with velocity u with respect to frame S, then the Lorentz force in frame S is:

In frame S', the Lorentz force is:

If S and S' have aligned axes then:^[4]

A derivation for the transformation of the Lorentz force for the particular case u = 0 is given here.^[5] A more general one can be seen here.^[6]

Component by component, for relative motion along the x-axis, this works out to be the following:

The transformations in this form can be made more compact by introducing the electromagnetic tensor (defined below), which is a covariant tensor.

The D and H fields

For the electric displacement D and magnetic intensity H, using the constitutive relations and the result for c²:

gives

Analogously for E and B, the D and H form the electromagnetic displacement tensor.

The φ and A fields

An alternative simpler transformation of the EM field uses the electromagnetic potentials - the electric potential φ and magnetic potential A:^[7]

where is the parallel component of A to the direction of relative velocity between frames v, and is the perpendicular component. These transparently resemble the characteristic form of other Lorentz transformations (like time-position and energy-momentum), while the transformations of E and B above are slightly more complicated. The components can be collected together as:

The ρ and J fields

Analogously for the charge density ρ and current density J,^[7]

Collecting components together:

Non-relativistic approximations

For speeds v ≪ c, the relativistic factor γ ≈ 1, which yields:

so that there is no need to distinguish between the spatial and temporal coordinates in Maxwell's equations.

Relationship between electricity and magnetism

“	One part of the force between moving charges we call the magnetic force. It is really one aspect of an electrical effect.	”
—Richard Feynman[8]

Deriving magnetism from electrostatics

The chosen reference frame determines if an electromagnetic phenomenon is viewed as an effect of electrostatics or magnetism. Authors usually derive magnetism from electrostatics when special relativity and charge invariance are taken into account. The Feynman Lectures on Physics (vol. 2, ch. 13-6) uses this method to derive the "magnetic" force on a moving charge next to a current-carrying wire. See also Haskell^[9] and Landau.^[10]

Fields intermix in different frames

The above transformation rules show that the electric field in one frame contributes to the magnetic field in another frame, and vice versa.^[11] This is often described by saying that the electric field and magnetic field are two interrelated aspects of a single object, called the electromagnetic field. Indeed, the entire electromagnetic field can be encoded in a single rank-2 tensor called the electromagnetic tensor; see below.

Moving magnet and conductor problem

A famous example of the intermixing of electric and magnetic phenomena in different frames of reference is called the "moving magnet and conductor problem", cited by Einstein in his 1905 paper on Special Relativity.
If a conductor moves with a constant velocity through the field of a stationary magnet, eddy currents will be produced due to a magnetic force on the electrons in the conductor. In the rest frame of the conductor, on the other hand, the magnet will be moving and the conductor stationary. Classical electromagnetic theory predicts that precisely the same microscopic eddy currents will be produced, but they will be due to an electric force.^[12]

Covariant formulation in vacuum

The laws and mathematical objects in classical electromagnetism can be written in a form which is manifestly covariant. Here, this is only done so for vacuum (or for the microscopic Maxwell equations, not using macroscopic descriptions of materials such as electric permittivity), and uses SI units.

This section uses Einstein notation, including Einstein summation convention. See also Ricci calculus for a summary of tensor index notations, and raising and lowering indices for definition of superscript and subscript indices, and how to switch between them. The Minkowski metric tensor η here has metric signature (+ − − −).

Field tensor and 4-current

The above relativistic transformations suggest the electric and magnetic fields are coupled together, in a mathematical object with 6 components: an antisymmetric second-rank tensor, or a bivector. This is called the electromagnetic field tensor, usually written as F^μν. In matrix form:^[13]

where c the speed of light - in natural units c = 1.

There is another way of merging the electric and magnetic fields into an antisymmetric tensor, by replacing E/c → B and B → − E/c, to get the dual tensor G^μν.

In the context of special relativity, both of these transform according to the Lorentz transformation according to

,

where Λ^α_ν is the Lorentz transformation tensor for a change from one reference frame to another. The same tensor is used twice in the summation.

The charge and current density, the sources of the fields, also combine into the four-vector

called the four-current.

Maxwell's equations in tensor form

Using these tensors, Maxwell's equations reduce to:^[13]

Maxwell's equations (Covariant formulation)

where the partial derivatives may be written in various ways, see 4-gradient. The first equation listed above corresponds to both Gauss's Law (for β = 0) and the Ampère-Maxwell Law (for β = 1, 2, 3). The second equation corresponds to the two remaining equations, Gauss's law for magnetism (for β = 0) and Faraday's Law ( for β = 1, 2, 3).

These tensor equations are manifestly-covariant, meaning the equations can be seen to be covariant by the index positions. This short form of writing Maxwell's equations illustrates an idea shared amongst some physicists, namely that the laws of physics take on a simpler form when written using tensors.

By lowering the indices on F^αβ to obtain F_αβ (see raising and lowering indices):

the second equation can be written in terms of F_αβ as:

where is the contravariant Levi-Civita symbol. Notice the cyclic permutation of indices in this equation: .
Another covariant electromagnetic object is the electromagnetic stress-energy tensor, a covariant rank-2 tensor which includes the Poynting vector, Maxwell stress tensor, and electromagnetic energy density.

4-potential[edit]

The EM field tensor can also be written^[14]

where

is the four-potential and

is the four-position.

Using the 4-potential in the Lorenz gauge, an alternative manifestly-covariant formulation can be found in a single equation (a generalization of an equation due to Bernhard Riemann by Arnold Sommerfeld, known as the Riemann–Sommerfeld equation,^[15] or the covariant form of the Maxwell equations^[16]):

Maxwell's equations (Covariant Lorenz gauge formulation)

where is the d'Alembertian operator, or four-Laplacian. For a more comprehensive presentation of these topics, see Covariant formulation of classical electromagnetism.

How spacetime is built by quantum entanglement

A collaboration of physicists and a mathematician has made a significant step toward unifying general relativity and quantum mechanics by explaining how spacetime emerges from quantum entanglement in a more fundamental theory. The paper announcing the discovery by Hirosi Ooguri, a Principal Investigator at the University of Tokyo's Kavli IPMU, with Caltech mathematician Matilde Marcolli and graduate students Jennifer Lin and Bogdan Stoica, will be published in Physical Review Letters as an Editors' Suggestion "for the potential interest in the results presented and on the success of the paper in communicating its message, in particular to readers from other fields."

Physicists and mathematicians have long sought a Theory of Everything (ToE) that unifies general relativity and quantum mechanics. General relativity explains gravity and large-scale phenomena such as the dynamics of stars and galaxies in the universe, while quantum mechanics explains microscopic phenomena from the subatomic to molecular scales.

The holographic principle is widely regarded as an essential feature of a successful Theory of Everything. The holographic principle states that gravity in a three-dimensional volume can be described by quantum mechanics on a two-dimensional surface surrounding the volume. In particular, the three dimensions of the volume should emerge from the two dimensions of the surface. However, understanding the precise mechanics for the emergence of the volume from the surface has been elusive.

Now, Ooguri and his collaborators have found that quantum entanglement is the key to solving this question. Using a quantum theory (that does not include gravity), they showed how to compute energy density, which is a source of gravitational interactions in three dimensions, using quantum entanglement data on the surface. This is analogous to diagnosing conditions inside of your body by looking at X-ray images on two-dimensional sheets. This allowed them to interpret universal properties of quantum entanglement as conditions on the energy density that should be satisfied by any consistent quantum theory of gravity, without actually explicitly including gravity in the theory. The importance of quantum entanglement has been suggested before, but its precise role in emergence of spacetime was not clear until the new paper by Ooguri and collaborators.

Quantum entanglement is a phenomenon whereby quantum states such as spin or polarization of particles at different locations cannot be described independently. Measuring (and hence acting on) one particle must also act on the other, something that Einstein called "spooky action at distance." The work of Ooguri and collaborators shows that this quantum entanglement generates the extra dimensions of the gravitational theory.

"It was known that quantum entanglement is related to deep issues in the unification of general relativity and quantum mechanics, such as the black hole information paradox and the firewall paradox," says Hirosi Ooguri. "Our paper sheds new light on the relation between quantum entanglement and the microscopic structure of spacetime by explicit calculations. The interface between quantum gravity and information science is becoming increasingly important for both fields. I myself am collaborating with information scientists to pursue this line of research further."

More information: Locality of Gravitational Systems from Entanglement of Conformal Field Theories, Physical Review Letters, 2015.

Provided by University of Tokyo

Molecular evolution

From Wikipedia, the free encyclopedia

Molecular evolution is a 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 to explain patterns in these changes. Major topics in molecular evolution concern the rates and impacts of single nucleotide changes, neutral evolution vs. natural selection, origins of new genes, the genetic nature of complex traits, the genetic basis of speciation, evolution of development, and ways that evolutionary forces influence genomic and phenotypic changes.

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 or virus. Mutations result from errors in DNA replication during cell division 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. 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 transversions (purine ↔ pyrimidine)^[1] and are less likely to alter amino acid 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.

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 orthologous genomic regions 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 sequence 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 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 is close to a threshold value of 1 / the effective population size 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.^[2] 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 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, 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.

Selection can operate at the gene level at the expense of organismal fitness, resulting in 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. (See Intragenomic conflict.)

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 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 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 ^[3] 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.

DNA transposons are cut and paste transposable elements which excise DNA and move it to alternate sections of the genome.

non-LTR retrotransposons

LTR retrotransposons

Helitrons

Alu elements comprise over XX % of the human genome. They are short non-autonomous repeat sequences.

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^[4] whereas the Adders-tongue fern Ophioglossum reticulatum has up to 1260 chromosomes.^[5] Cilliate 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 was created from a fusion of two chimpanzee chromosomes and still contains central telomeres as well as a vestigial second centromere. 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.^[6]

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 are more likely to recombine due to increased physical distance over the coding sequence. As such, long introns may facilitate ectopic recombination, 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.

In gene duplication, a gene sequence is copied to create redundancy. Duplicated gene sequences can then mutate to develop new functions or to specialize so that each 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 genes 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.

Novel genes can also arise from previously non-coding DNA.^[7] For instance, Levine and colleagues reported the origin of five new genes in the D. melanogaster genome from noncoding DNA.^[8][9] Similar de novo origin of genes has been also shown in other organisms such as yeast,^[10] rice^[11] and humans.^[12] De novo genes may evolve from transcripts that are already expressed at low levels.^[13] Mutation of a stop codon to a regular codon or a frameshift may cause an extended protein that includes a previously non-coding sequence.

Molecular phylogenetics

Molecular systematics is a product of the traditional field of systematics and molecular genetics. It uses DNA, RNA, or protein sequences 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 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.

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.^[14]
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.^[15] Biases in codon usage are usually explained with reference to the ability of even weak selection to shape molecular evolution.^[16]

Neutralist hypotheses emphasize the importance of mutation, purifying selection and random genetic drift.^[17] The introduction of the neutral theory by Kimura,^[18] quickly followed by King and Jukes' own findings,^[19] 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.^[20][21][22]

Mutationists hypotheses emphasize random drift and biases in mutation patterns.^[23] 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.^[24]

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, cryptic species) and (ii) one lineage, multiple morphologies (e.g. phenotypic plasticity, multiple life-cycle stages). Neutral evolution possibly could explain the incongruences in some cases.^[25]

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, systematics, and evolutionary biology.