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Monday, September 9, 2019

Atom

From Wikipedia, the free encyclopedia

Helium atom
Helium atom ground state.
An illustration of the helium atom, depicting the nucleus (pink) and the electron cloud distribution (black). The nucleus (upper right) in helium-4 is in reality spherically symmetric and closely resembles the electron cloud, although for more complicated nuclei this is not always the case. The black bar is one angstrom (10−10 m or 100 pm).
Classification
Smallest recognized division of a chemical element
Properties
Mass range1.67×10−27 to 4.52×10−25 kg
Electric chargezero (neutral), or ion charge
Diameter range62 pm (He) to 520 pm (Cs) (data page)
ComponentsElectrons and a compact nucleus of protons and neutrons

An atom is the smallest constituent unit of ordinary matter that constitutes a chemical element. Every solid, liquid, gas, and plasma is composed of neutral or ionized atoms. Atoms are extremely small; typical sizes are around 100 picometers (1×10−10 m, a ten-millionth of a millimeter, or 1/254,000,000 of an inch). They are so small that accurately predicting their behavior using classical physics – as if they were billiard balls, for example – is not possible. This is due to quantum effects. Current atomic models now use quantum principles to better explain and predict this behavior.

Every atom is composed of a nucleus and one or more electrons bound to the nucleus. The nucleus is made of one or more protons and a number of neutrons. Only the most common variety of hydrogen has no neutrons. Protons and neutrons are called nucleons. More than 99.94% of an atom's mass is in the nucleus. The protons have a positive electric charge whereas the electrons have a negative electric charge. The neutrons have no electric charge. If the number of protons and electrons are equal, then the atom is electrically neutral. If an atom has more or fewer electrons than protons, then it has an overall negative or positive charge, respectively. These atoms are called ions.

The electrons of an atom are attracted to the protons in an atomic nucleus by the electromagnetic force. The protons and neutrons in the nucleus are attracted to each other by the nuclear force. This force is usually stronger than the electromagnetic force that repels the positively charged protons from one another. Under certain circumstances, the repelling electromagnetic force becomes stronger than the nuclear force. In this case, the nucleus shatters and leaves behind different elements. This is a kind of nuclear decay. All electrons, nucleons, and nuclei alike are subatomic particles. The behavior of electrons in atoms is closer to a wave than a particle.

The number of protons in the nucleus, called the atomic number, defines to which chemical element the atom belongs. For example, each copper atom contains 29 protons. The number of neutrons defines the isotope of the element. Atoms can attach to one or more other atoms by chemical bonds to form chemical compounds such as molecules or crystals. The ability of atoms to associate and dissociate is responsible for most of the physical changes observed in nature. Chemistry is the discipline that studies these changes.

History of atomic theory

Atoms in philosophy

The idea that matter is made up of discrete units is a very old idea, appearing in many ancient cultures such as Greece and India. The word atomos, meaning "uncuttable", was coined by the ancient Greek philosophers Leucippus and his pupil Democritus (c. 460 – c. 370 BC). Democritus taught that atoms were infinite in number, uncreated, and eternal, and that the qualities of an object result from the kind of atoms that compose it. Democritus's atomism was refined and elaborated by the later philosopher Epicurus (341–270 BC). During the Early Middle Ages, atomism was mostly forgotten in western Europe, but survived among some groups of Islamic philosophers. During the twelfth century, atomism became known again in western Europe through references to it in the newly-rediscovered writings of Aristotle.

In the fourteenth century, the rediscovery of major works describing atomist teachings, including Lucretius's De rerum natura and Diogenes Laërtius's Lives and Opinions of Eminent Philosophers, led to increased scholarly attention on the subject. Nonetheless, because atomism was associated with the philosophy of Epicureanism, which contradicted orthodox Christian teachings, belief in atoms was not considered acceptable. The French Catholic priest Pierre Gassendi (1592–1655) revived Epicurean atomism with modifications, arguing that atoms were created by God and, though extremely numerous, are not infinite. Gassendi's modified theory of atoms was popularized in France by the physician François Bernier (1620–1688) and in England by the natural philosopher Walter Charleton (1619–1707). The chemist Robert Boyle (1627–1691) and the physicist Isaac Newton (1642–1727) both defended atomism and, by the end of the seventeenth century, it had become accepted by portions of the scientific community.

First evidence-based theory

Various atoms and molecules as depicted in John Dalton's A New System of Chemical Philosophy (1808).
 
In the early 1800s, John Dalton used the concept of atoms to explain why elements always react in ratios of small whole numbers (the law of multiple proportions). For instance, there are two types of tin oxide: one is 88.1% tin and 11.9% oxygen and the other is 78.7% tin and 21.3% oxygen (tin(II) oxide and tin dioxide respectively). This means that 100g of tin will combine either with 13.5g or 27g of oxygen. 13.5 and 27 form a ratio of 1:2, a ratio of small whole numbers. This common pattern in chemistry suggested to Dalton that elements react in multiples of discrete units — in other words, atoms. In the case of tin oxides, one tin atom will combine with either one or two oxygen atoms.

Dalton also believed atomic theory could explain why water absorbs different gases in different proportions. For example, he found that water absorbs carbon dioxide far better than it absorbs nitrogen. Dalton hypothesized this was due to the differences between the masses and configurations of the gases' respective particles, and carbon dioxide molecules (CO2) are heavier and larger than nitrogen molecules (N2).

Brownian motion

In 1827, botanist Robert Brown used a microscope to look at dust grains floating in water and discovered that they moved about erratically, a phenomenon that became known as "Brownian motion". This was thought to be caused by water molecules knocking the grains about. In 1905, Albert Einstein proved the reality of these molecules and their motions by producing the first statistical physics analysis of Brownian motion. French physicist Jean Perrin used Einstein's work to experimentally determine the mass and dimensions of atoms, thereby conclusively verifying Dalton's atomic theory.

Discovery of the electron

The Geiger–Marsden experiment Left: Expected results: alpha particles passing through the plum pudding model of the atom with negligible deflection. Right: Observed results: a small portion of the particles were deflected by the concentrated positive charge of the nucleus.
 
The physicist J.J. Thomson measured the mass of cathode rays, showing they were made of particles, but were around 1800 times lighter than the lightest atom, hydrogen. Therefore, they were not atoms, but a new particle, the first subatomic particle to be discovered, which he originally called "corpuscle" but was later named electron, after particles postulated by George Johnstone Stoney in 1874. He also showed they were identical to particles given off by photoelectric and radioactive materials. It was quickly recognized that they are the particles that carry electric currents in metal wires, and carry the negative electric charge within atoms. Thomson was given the 1906 Nobel Prize in Physics for this work. Thus he overturned the belief that atoms are the indivisible, ultimate particles of matter. Thomson also incorrectly postulated that the low mass, negatively charged electrons were distributed throughout the atom in a uniform sea of positive charge. This became known as the plum pudding model.

Discovery of the nucleus

In 1909, Hans Geiger and Ernest Marsden, under the direction of Ernest Rutherford, bombarded a metal foil with alpha particles to observe how they scattered. They expected all the alpha particles to pass straight through with little deflection, because Thomson's model said that the charges in the atom are so diffuse that their electric fields could not affect the alpha particles much. However, Geiger and Marsden spotted alpha particles being deflected by angles greater than 90°, which was supposed to be impossible according to Thomson's model. To explain this, Rutherford proposed that the positive charge of the atom is concentrated in a tiny nucleus at the center of the atom.

Discovery of isotopes

While experimenting with the products of radioactive decay, in 1913 radiochemist Frederick Soddy discovered that there appeared to be more than one type of atom at each position on the periodic table. The term isotope was coined by Margaret Todd as a suitable name for different atoms that belong to the same element. J.J. Thomson created a technique for isotope separation through his work on ionized gases, which subsequently led to the discovery of stable isotopes.

Bohr model

The Bohr model of the atom, with an electron making instantaneous "quantum leaps" from one orbit to another. This model is obsolete.

In 1913 the physicist Niels Bohr proposed a model in which the electrons of an atom were assumed to orbit the nucleus but could only do so in a finite set of orbits, and could jump between these orbits only in discrete changes of energy corresponding to absorption or radiation of a photon. This quantization was used to explain why the electrons orbits are stable (given that normally, charges in acceleration, including circular motion, lose kinetic energy which is emitted as electromagnetic radiation, see synchrotron radiation) and why elements absorb and emit electromagnetic radiation in discrete spectra.

Later in the same year Henry Moseley provided additional experimental evidence in favor of Niels Bohr's theory. These results refined Ernest Rutherford's and Antonius Van den Broek's model, which proposed that the atom contains in its nucleus a number of positive nuclear charges that is equal to its (atomic) number in the periodic table. Until these experiments, atomic number was not known to be a physical and experimental quantity. That it is equal to the atomic nuclear charge remains the accepted atomic model today.

Chemical bonding explained

Chemical bonds between atoms were now explained, by Gilbert Newton Lewis in 1916, as the interactions between their constituent electrons. As the chemical properties of the elements were known to largely repeat themselves according to the periodic law, in 1919 the American chemist Irving Langmuir suggested that this could be explained if the electrons in an atom were connected or clustered in some manner. Groups of electrons were thought to occupy a set of electron shells about the nucleus.

Further developments in quantum physics

The Stern–Gerlach experiment of 1922 provided further evidence of the quantum nature of atomic properties. When a beam of silver atoms was passed through a specially shaped magnetic field, the beam was split in a way correlated with the direction of an atom's angular momentum, or spin. As this spin direction is initially random, the beam would be expected to deflect in a random direction. Instead, the beam was split into two directional components, corresponding to the atomic spin being oriented up or down with respect to the magnetic field.

In 1925 Werner Heisenberg published the first consistent mathematical formulation of quantum mechanics (Matrix Mechanics). One year earlier, in 1924, Louis de Broglie had proposed that all particles behave to an extent like waves and, in 1926, Erwin Schrödinger used this idea to develop a mathematical model of the atom (Wave Mechanics) that described the electrons as three-dimensional waveforms rather than point particles. 

A consequence of using waveforms to describe particles is that it is mathematically impossible to obtain precise values for both the position and momentum of a particle at a given point in time; this became known as the uncertainty principle, formulated by Werner Heisenberg in 1927. In this concept, for a given accuracy in measuring a position one could only obtain a range of probable values for momentum, and vice versa. This model was able to explain observations of atomic behavior that previous models could not, such as certain structural and spectral patterns of atoms larger than hydrogen. Thus, the planetary model of the atom was discarded in favor of one that described atomic orbital zones around the nucleus where a given electron is most likely to be observed.

Discovery of the neutron

The development of the mass spectrometer allowed the mass of atoms to be measured with increased accuracy. The device uses a magnet to bend the trajectory of a beam of ions, and the amount of deflection is determined by the ratio of an atom's mass to its charge. The chemist Francis William Aston used this instrument to show that isotopes had different masses. The atomic mass of these isotopes varied by integer amounts, called the whole number rule. The explanation for these different isotopes awaited the discovery of the neutron, an uncharged particle with a mass similar to the proton, by the physicist James Chadwick in 1932. Isotopes were then explained as elements with the same number of protons, but different numbers of neutrons within the nucleus.

Fission, high-energy physics and condensed matter

In 1938, the German chemist Otto Hahn, a student of Rutherford, directed neutrons onto uranium atoms expecting to get transuranium elements. Instead, his chemical experiments showed barium as a product. A year later, Lise Meitner and her nephew Otto Frisch verified that Hahn's result were the first experimental nuclear fission. In 1944, Hahn received the Nobel prize in chemistry. Despite Hahn's efforts, the contributions of Meitner and Frisch were not recognized.

In the 1950s, the development of improved particle accelerators and particle detectors allowed scientists to study the impacts of atoms moving at high energies. Neutrons and protons were found to be hadrons, or composites of smaller particles called quarks. The standard model of particle physics was developed that so far has successfully explained the properties of the nucleus in terms of these sub-atomic particles and the forces that govern their interactions.

Structure

Subatomic particles

Though the word atom originally denoted a particle that cannot be cut into smaller particles, in modern scientific usage the atom is composed of various subatomic particles. The constituent particles of an atom are the electron, the proton and the neutron; all three are fermions. However, the hydrogen-1 atom has no neutrons and the hydron ion has no electrons. 

The electron is by far the least massive of these particles at 9.11×10−31 kg, with a negative electrical charge and a size that is too small to be measured using available techniques. It was the lightest particle with a positive rest mass measured, until the discovery of neutrino mass. Under ordinary conditions, electrons are bound to the positively charged nucleus by the attraction created from opposite electric charges. If an atom has more or fewer electrons than its atomic number, then it becomes respectively negatively or positively charged as a whole; a charged atom is called an ion. Electrons have been known since the late 19th century, mostly thanks to J.J. Thomson.

Protons have a positive charge and a mass 1,836 times that of the electron, at 1.6726×10−27 kg. The number of protons in an atom is called its atomic number. Ernest Rutherford (1919) observed that nitrogen under alpha-particle bombardment ejects what appeared to be hydrogen nuclei. By 1920 he had accepted that the hydrogen nucleus is a distinct particle within the atom and named it proton.

Neutrons have no electrical charge and have a free mass of 1,839 times the mass of the electron, or 1.6749×10−27 kg. Neutrons are the heaviest of the three constituent particles, but their mass can be reduced by the nuclear binding energy. Neutrons and protons (collectively known as nucleons) have comparable dimensions—on the order of 2.5×10−15 m—although the 'surface' of these particles is not sharply defined. The neutron was discovered in 1932 by the English physicist James Chadwick.

In the Standard Model of physics, electrons are truly elementary particles with no internal structure. However, both protons and neutrons are composite particles composed of elementary particles called quarks. There are two types of quarks in atoms, each having a fractional electric charge. Protons are composed of two up quarks (each with charge +2/3) and one down quark (with a charge of −1/3). Neutrons consist of one up quark and two down quarks. This distinction accounts for the difference in mass and charge between the two particles.

The quarks are held together by the strong interaction (or strong force), which is mediated by gluons. The protons and neutrons, in turn, are held to each other in the nucleus by the nuclear force, which is a residuum of the strong force that has somewhat different range-properties (see the article on the nuclear force for more). The gluon is a member of the family of gauge bosons, which are elementary particles that mediate physical forces.

Nucleus

The binding energy needed for a nucleon to escape the nucleus, for various isotopes
 
All the bound protons and neutrons in an atom make up a tiny atomic nucleus, and are collectively called nucleons. The radius of a nucleus is approximately equal to 1.07 3A fm, where A is the total number of nucleons. This is much smaller than the radius of the atom, which is on the order of 105 fm. The nucleons are bound together by a short-ranged attractive potential called the residual strong force. At distances smaller than 2.5 fm this force is much more powerful than the electrostatic force that causes positively charged protons to repel each other.

Atoms of the same element have the same number of protons, called the atomic number. Within a single element, the number of neutrons may vary, determining the isotope of that element. The total number of protons and neutrons determine the nuclide. The number of neutrons relative to the protons determines the stability of the nucleus, with certain isotopes undergoing radioactive decay.

The proton, the electron, and the neutron are classified as fermions. Fermions obey the Pauli exclusion principle which prohibits identical fermions, such as multiple protons, from occupying the same quantum state at the same time. Thus, every proton in the nucleus must occupy a quantum state different from all other protons, and the same applies to all neutrons of the nucleus and to all electrons of the electron cloud.

A nucleus that has a different number of protons than neutrons can potentially drop to a lower energy state through a radioactive decay that causes the number of protons and neutrons to more closely match. As a result, atoms with matching numbers of protons and neutrons are more stable against decay. However, with increasing atomic number, the mutual repulsion of the protons requires an increasing proportion of neutrons to maintain the stability of the nucleus, which slightly modifies this trend of equal numbers of protons to neutrons.

Illustration of a nuclear fusion process that forms a deuterium nucleus, consisting of a proton and a neutron, from two protons. A positron (e+)—an antimatter electron—is emitted along with an electron neutrino.
 
The number of protons and neutrons in the atomic nucleus can be modified, although this can require very high energies because of the strong force. Nuclear fusion occurs when multiple atomic particles join to form a heavier nucleus, such as through the energetic collision of two nuclei. For example, at the core of the Sun protons require energies of 3–10 keV to overcome their mutual repulsion—the coulomb barrier—and fuse together into a single nucleus. Nuclear fission is the opposite process, causing a nucleus to split into two smaller nuclei—usually through radioactive decay. The nucleus can also be modified through bombardment by high energy subatomic particles or photons. If this modifies the number of protons in a nucleus, the atom changes to a different chemical element.

If the mass of the nucleus following a fusion reaction is less than the sum of the masses of the separate particles, then the difference between these two values can be emitted as a type of usable energy (such as a gamma ray, or the kinetic energy of a beta particle), as described by Albert Einstein's mass–energy equivalence formula, , where is the mass loss and is the speed of light. This deficit is part of the binding energy of the new nucleus, and it is the non-recoverable loss of the energy that causes the fused particles to remain together in a state that requires this energy to separate.

The fusion of two nuclei that create larger nuclei with lower atomic numbers than iron and nickel—a total nucleon number of about 60—is usually an exothermic process that releases more energy than is required to bring them together. It is this energy-releasing process that makes nuclear fusion in stars a self-sustaining reaction. For heavier nuclei, the binding energy per nucleon in the nucleus begins to decrease. That means fusion processes producing nuclei that have atomic numbers higher than about 26, and atomic masses higher than about 60, is an endothermic process. These more massive nuclei can not undergo an energy-producing fusion reaction that can sustain the hydrostatic equilibrium of a star.

Electron cloud

A potential well, showing, according to classical mechanics, the minimum energy V(x) needed to reach each position x. Classically, a particle with energy E is constrained to a range of positions between x1 and x2.
 
The electrons in an atom are attracted to the protons in the nucleus by the electromagnetic force. This force binds the electrons inside an electrostatic potential well surrounding the smaller nucleus, which means that an external source of energy is needed for the electron to escape. The closer an electron is to the nucleus, the greater the attractive force. Hence electrons bound near the center of the potential well require more energy to escape than those at greater separations. 

Electrons, like other particles, have properties of both a particle and a wave. The electron cloud is a region inside the potential well where each electron forms a type of three-dimensional standing wave—a wave form that does not move relative to the nucleus. This behavior is defined by an atomic orbital, a mathematical function that characterises the probability that an electron appears to be at a particular location when its position is measured. Only a discrete (or quantized) set of these orbitals exist around the nucleus, as other possible wave patterns rapidly decay into a more stable form. Orbitals can have one or more ring or node structures, and differ from each other in size, shape and orientation.

Oganesson. An illustration of all the Subshells/orbitals of the Oganesson atom. Blue is for the S-subshell, pink is for the P-subshell, red is for the D-subshell, and green is for the F-subshell.
 
Wave functions of the first five atomic orbitals. The three 2p orbitals each display a single angular node that has an orientation and a minimum at the center.
 
Each atomic orbital corresponds to a particular energy level of the electron. The electron can change its state to a higher energy level by absorbing a photon with sufficient energy to boost it into the new quantum state. Likewise, through spontaneous emission, an electron in a higher energy state can drop to a lower energy state while radiating the excess energy as a photon. These characteristic energy values, defined by the differences in the energies of the quantum states, are responsible for atomic spectral lines.
 
The amount of energy needed to remove or add an electron—the electron binding energy—is far less than the binding energy of nucleons. For example, it requires only 13.6 eV to strip a ground-state electron from a hydrogen atom, compared to 2.23 million eV for splitting a deuterium nucleus. Atoms are electrically neutral if they have an equal number of protons and electrons. Atoms that have either a deficit or a surplus of electrons are called ions. Electrons that are farthest from the nucleus may be transferred to other nearby atoms or shared between atoms. By this mechanism, atoms are able to bond into molecules and other types of chemical compounds like ionic and covalent network crystals.

Properties

Nuclear properties

By definition, any two atoms with an identical number of protons in their nuclei belong to the same chemical element. Atoms with equal numbers of protons but a different number of neutrons are different isotopes of the same element. For example, all hydrogen atoms admit exactly one proton, but isotopes exist with no neutrons (hydrogen-1, by far the most common form, also called protium), one neutron (deuterium), two neutrons (tritium) and more than two neutrons. The known elements form a set of atomic numbers, from the single proton element hydrogen up to the 118-proton element oganesson. All known isotopes of elements with atomic numbers greater than 82 are radioactive, although the radioactivity of element 83 (bismuth) is so slight as to be practically negligible.

About 339 nuclides occur naturally on Earth, of which 254 (about 75%) have not been observed to decay, and are referred to as "stable isotopes". However, only 90 of these nuclides are stable to all decay, even in theory. Another 164 (bringing the total to 254) have not been observed to decay, even though in theory it is energetically possible. These are also formally classified as "stable". An additional 34 radioactive nuclides have half-lives longer than 80 million years, and are long-lived enough to be present from the birth of the solar system. This collection of 288 nuclides are known as primordial nuclides. Finally, an additional 51 short-lived nuclides are known to occur naturally, as daughter products of primordial nuclide decay (such as radium from uranium), or else as products of natural energetic processes on Earth, such as cosmic ray bombardment (for example, carbon-14).

For 80 of the chemical elements, at least one stable isotope exists. As a rule, there is only a handful of stable isotopes for each of these elements, the average being 3.2 stable isotopes per element. Twenty-six elements have only a single stable isotope, while the largest number of stable isotopes observed for any element is ten, for the element tin. Elements 43, 61, and all elements numbered 83 or higher have no stable isotopes.

Stability of isotopes is affected by the ratio of protons to neutrons, and also by the presence of certain "magic numbers" of neutrons or protons that represent closed and filled quantum shells. These quantum shells correspond to a set of energy levels within the shell model of the nucleus; filled shells, such as the filled shell of 50 protons for tin, confers unusual stability on the nuclide. Of the 254 known stable nuclides, only four have both an odd number of protons and odd number of neutrons: hydrogen-2 (deuterium), lithium-6, boron-10 and nitrogen-14. Also, only four naturally occurring, radioactive odd–odd nuclides have a half-life over a billion years: potassium-40, vanadium-50, lanthanum-138 and tantalum-180m. Most odd–odd nuclei are highly unstable with respect to beta decay, because the decay products are even–even, and are therefore more strongly bound, due to nuclear pairing effects.

Mass

The large majority of an atom's mass comes from the protons and neutrons that make it up. The total number of these particles (called "nucleons") in a given atom is called the mass number. It is a positive integer and dimensionless (instead of having dimension of mass), because it expresses a count. An example of use of a mass number is "carbon-12," which has 12 nucleons (six protons and six neutrons). 

The actual mass of an atom at rest is often expressed using the unified atomic mass unit (u), also called dalton (Da). This unit is defined as a twelfth of the mass of a free neutral atom of carbon-12, which is approximately 1.66×10−27 kg. Hydrogen-1 (the lightest isotope of hydrogen which is also the nuclide with the lowest mass) has an atomic weight of 1.007825 u. The value of this number is called the atomic mass. A given atom has an atomic mass approximately equal (within 1%) to its mass number times the atomic mass unit (for example the mass of a nitrogen-14 is roughly 14 u). However, this number will not be exactly an integer except in the case of carbon-12 (see below). The heaviest stable atom is lead-208, with a mass of 207.9766521 u.

As even the most massive atoms are far too light to work with directly, chemists instead use the unit of moles. One mole of atoms of any element always has the same number of atoms (about 6.022×1023). This number was chosen so that if an element has an atomic mass of 1 u, a mole of atoms of that element has a mass close to one gram. Because of the definition of the unified atomic mass unit, each carbon-12 atom has an atomic mass of exactly 12 u, and so a mole of carbon-12 atoms weighs exactly 0.012 kg.

Shape and size

Atoms lack a well-defined outer boundary, so their dimensions are usually described in terms of an atomic radius. This is a measure of the distance out to which the electron cloud extends from the nucleus. However, this assumes the atom to exhibit a spherical shape, which is only obeyed for atoms in vacuum or free space. Atomic radii may be derived from the distances between two nuclei when the two atoms are joined in a chemical bond. The radius varies with the location of an atom on the atomic chart, the type of chemical bond, the number of neighboring atoms (coordination number) and a quantum mechanical property known as spin. On the periodic table of the elements, atom size tends to increase when moving down columns, but decrease when moving across rows (left to right). Consequently, the smallest atom is helium with a radius of 32 pm, while one of the largest is caesium at 225 pm.

When subjected to external forces, like electrical fields, the shape of an atom may deviate from spherical symmetry. The deformation depends on the field magnitude and the orbital type of outer shell electrons, as shown by group-theoretical considerations. Aspherical deviations might be elicited for instance in crystals, where large crystal-electrical fields may occur at low-symmetry lattice sites. Significant ellipsoidal deformations have been shown to occur for sulfur ions and chalcogen ions in pyrite-type compounds. 

Atomic dimensions are thousands of times smaller than the wavelengths of light (400–700 nm) so they cannot be viewed using an optical microscope. However, individual atoms can be observed using a scanning tunneling microscope. To visualize the minuteness of the atom, consider that a typical human hair is about 1 million carbon atoms in width. A single drop of water contains about 2 sextillion (2×1021) atoms of oxygen, and twice the number of hydrogen atoms. A single carat diamond with a mass of 2×10−4 kg contains about 10 sextillion (1022) atoms of carbon. If an apple were magnified to the size of the Earth, then the atoms in the apple would be approximately the size of the original apple.

Radioactive decay

This diagram shows the half-life (T½) of various isotopes with Z protons and N neutrons.
 
Every element has one or more isotopes that have unstable nuclei that are subject to radioactive decay, causing the nucleus to emit particles or electromagnetic radiation. Radioactivity can occur when the radius of a nucleus is large compared with the radius of the strong force, which only acts over distances on the order of 1 fm.

The most common forms of radioactive decay are:
  • Alpha decay: this process is caused when the nucleus emits an alpha particle, which is a helium nucleus consisting of two protons and two neutrons. The result of the emission is a new element with a lower atomic number.
  • Beta decay (and electron capture): these processes are regulated by the weak force, and result from a transformation of a neutron into a proton, or a proton into a neutron. The neutron to proton transition is accompanied by the emission of an electron and an antineutrino, while proton to neutron transition (except in electron capture) causes the emission of a positron and a neutrino. The electron or positron emissions are called beta particles. Beta decay either increases or decreases the atomic number of the nucleus by one. Electron capture is more common than positron emission, because it requires less energy. In this type of decay, an electron is absorbed by the nucleus, rather than a positron emitted from the nucleus. A neutrino is still emitted in this process, and a proton changes to a neutron.
  • Gamma decay: this process results from a change in the energy level of the nucleus to a lower state, resulting in the emission of electromagnetic radiation. The excited state of a nucleus which results in gamma emission usually occurs following the emission of an alpha or a beta particle. Thus, gamma decay usually follows alpha or beta decay.
Other more rare types of radioactive decay include ejection of neutrons or protons or clusters of nucleons from a nucleus, or more than one beta particle. An analog of gamma emission which allows excited nuclei to lose energy in a different way, is internal conversion—a process that produces high-speed electrons that are not beta rays, followed by production of high-energy photons that are not gamma rays. A few large nuclei explode into two or more charged fragments of varying masses plus several neutrons, in a decay called spontaneous nuclear fission

Each radioactive isotope has a characteristic decay time period—the half-life—that is determined by the amount of time needed for half of a sample to decay. This is an exponential decay process that steadily decreases the proportion of the remaining isotope by 50% every half-life. Hence after two half-lives have passed only 25% of the isotope is present, and so forth.

Magnetic moment

Elementary particles possess an intrinsic quantum mechanical property known as spin. This is analogous to the angular momentum of an object that is spinning around its center of mass, although strictly speaking these particles are believed to be point-like and cannot be said to be rotating. Spin is measured in units of the reduced Planck constant (ħ), with electrons, protons and neutrons all having spin ½ ħ, or "spin-½". In an atom, electrons in motion around the nucleus possess orbital angular momentum in addition to their spin, while the nucleus itself possesses angular momentum due to its nuclear spin.

The magnetic field produced by an atom—its magnetic moment—is determined by these various forms of angular momentum, just as a rotating charged object classically produces a magnetic field. However, the most dominant contribution comes from electron spin. Due to the nature of electrons to obey the Pauli exclusion principle, in which no two electrons may be found in the same quantum state, bound electrons pair up with each other, with one member of each pair in a spin up state and the other in the opposite, spin down state. Thus these spins cancel each other out, reducing the total magnetic dipole moment to zero in some atoms with even number of electrons.

In ferromagnetic elements such as iron, cobalt and nickel, an odd number of electrons leads to an unpaired electron and a net overall magnetic moment. The orbitals of neighboring atoms overlap and a lower energy state is achieved when the spins of unpaired electrons are aligned with each other, a spontaneous process known as an exchange interaction. When the magnetic moments of ferromagnetic atoms are lined up, the material can produce a measurable macroscopic field. Paramagnetic materials have atoms with magnetic moments that line up in random directions when no magnetic field is present, but the magnetic moments of the individual atoms line up in the presence of a field.

The nucleus of an atom will have no spin when it has even numbers of both neutrons and protons, but for other cases of odd numbers, the nucleus may have a spin. Normally nuclei with spin are aligned in random directions because of thermal equilibrium. However, for certain elements (such as xenon-129) it is possible to polarize a significant proportion of the nuclear spin states so that they are aligned in the same direction—a condition called hyperpolarization. This has important applications in magnetic resonance imaging.

Energy levels

These electron's energy levels (not to scale) are sufficient for ground states of atoms up to cadmium (5s2 4d10) inclusively. Do not forget that even the top of the diagram is lower than an unbound electron state.
 
The potential energy of an electron in an atom is negative, its dependence of its position reaches the minimum (the most absolute value) inside the nucleus, and vanishes when the distance from the nucleus goes to infinity, roughly in an inverse proportion to the distance. In the quantum-mechanical model, a bound electron can only occupy a set of states centered on the nucleus, and each state corresponds to a specific energy level. An energy level can be measured by the amount of energy needed to unbind the electron from the atom, and is usually given in units of electronvolts (eV). The lowest energy state of a bound electron is called the ground state, i.e. stationary state, while an electron transition to a higher level results in an excited state. The electron's energy raises when n increases because the (average) distance to the nucleus increases. Dependence of the energy on is caused not by electrostatic potential of the nucleus, but by interaction between electrons. 

For an electron to transition between two different states, e.g. ground state to first excited state, it must absorb or emit a photon at an energy matching the difference in the potential energy of those levels, according to the Niels Bohr model, what can be precisely calculated by the Schrödinger equation. Electrons jump between orbitals in a particle-like fashion. For example, if a single photon strikes the electrons, only a single electron changes states in response to the photon; see Electron properties

The energy of an emitted photon is proportional to its frequency, so these specific energy levels appear as distinct bands in the electromagnetic spectrum. Each element has a characteristic spectrum that can depend on the nuclear charge, subshells filled by electrons, the electromagnetic interactions between the electrons and other factors.

An example of absorption lines in a spectrum
 
When a continuous spectrum of energy is passed through a gas or plasma, some of the photons are absorbed by atoms, causing electrons to change their energy level. Those excited electrons that remain bound to their atom spontaneously emit this energy as a photon, traveling in a random direction, and so drop back to lower energy levels. Thus the atoms behave like a filter that forms a series of dark absorption bands in the energy output. (An observer viewing the atoms from a view that does not include the continuous spectrum in the background, instead sees a series of emission lines from the photons emitted by the atoms.) Spectroscopic measurements of the strength and width of atomic spectral lines allow the composition and physical properties of a substance to be determined.

Close examination of the spectral lines reveals that some display a fine structure splitting. This occurs because of spin–orbit coupling, which is an interaction between the spin and motion of the outermost electron. When an atom is in an external magnetic field, spectral lines become split into three or more components; a phenomenon called the Zeeman effect. This is caused by the interaction of the magnetic field with the magnetic moment of the atom and its electrons. Some atoms can have multiple electron configurations with the same energy level, which thus appear as a single spectral line. The interaction of the magnetic field with the atom shifts these electron configurations to slightly different energy levels, resulting in multiple spectral lines. The presence of an external electric field can cause a comparable splitting and shifting of spectral lines by modifying the electron energy levels, a phenomenon called the Stark effect.

If a bound electron is in an excited state, an interacting photon with the proper energy can cause stimulated emission of a photon with a matching energy level. For this to occur, the electron must drop to a lower energy state that has an energy difference matching the energy of the interacting photon. The emitted photon and the interacting photon then move off in parallel and with matching phases. That is, the wave patterns of the two photons are synchronized. This physical property is used to make lasers, which can emit a coherent beam of light energy in a narrow frequency band.

Valence and bonding behavior

Valency is the combining power of an element. It is equal to number of hydrogen atoms that atom can combine or displace in forming compounds. The outermost electron shell of an atom in its uncombined state is known as the valence shell, and the electrons in that shell are called valence electrons. The number of valence electrons determines the bonding behavior with other atoms. Atoms tend to chemically react with each other in a manner that fills (or empties) their outer valence shells. For example, a transfer of a single electron between atoms is a useful approximation for bonds that form between atoms with one-electron more than a filled shell, and others that are one-electron short of a full shell, such as occurs in the compound sodium chloride and other chemical ionic salts. However, many elements display multiple valences, or tendencies to share differing numbers of electrons in different compounds. Thus, chemical bonding between these elements takes many forms of electron-sharing that are more than simple electron transfers. Examples include the element carbon and the organic compounds.

The chemical elements are often displayed in a periodic table that is laid out to display recurring chemical properties, and elements with the same number of valence electrons form a group that is aligned in the same column of the table. (The horizontal rows correspond to the filling of a quantum shell of electrons.) The elements at the far right of the table have their outer shell completely filled with electrons, which results in chemically inert elements known as the noble gases.

States

Graphic illustrating the formation of a Bose–Einstein condensate
 
Quantities of atoms are found in different states of matter that depend on the physical conditions, such as temperature and pressure. By varying the conditions, materials can transition between solids, liquids, gases and plasmas. Within a state, a material can also exist in different allotropes. An example of this is solid carbon, which can exist as graphite or diamond. Gaseous allotropes exist as well, such as dioxygen and ozone

At temperatures close to absolute zero, atoms can form a Bose–Einstein condensate, at which point quantum mechanical effects, which are normally only observed at the atomic scale, become apparent on a macroscopic scale. This super-cooled collection of atoms then behaves as a single super atom, which may allow fundamental checks of quantum mechanical behavior.

Identification

Scanning tunneling microscope image showing the individual atoms making up this gold (100) surface. The surface atoms deviate from the bulk crystal structure and arrange in columns several atoms wide with pits between them.
 
The scanning tunneling microscope is a device for viewing surfaces at the atomic level. It uses the quantum tunneling phenomenon, which allows particles to pass through a barrier that would normally be insurmountable. Electrons tunnel through the vacuum between two planar metal electrodes, on each of which is an adsorbed atom, providing a tunneling-current density that can be measured. Scanning one atom (taken as the tip) as it moves past the other (the sample) permits plotting of tip displacement versus lateral separation for a constant current. The calculation shows the extent to which scanning-tunneling-microscope images of an individual atom are visible. It confirms that for low bias, the microscope images the space-averaged dimensions of the electron orbitals across closely packed energy levels—the Fermi level local density of states.

An atom can be ionized by removing one of its electrons. The electric charge causes the trajectory of an atom to bend when it passes through a magnetic field. The radius by which the trajectory of a moving ion is turned by the magnetic field is determined by the mass of the atom. The mass spectrometer uses this principle to measure the mass-to-charge ratio of ions. If a sample contains multiple isotopes, the mass spectrometer can determine the proportion of each isotope in the sample by measuring the intensity of the different beams of ions. Techniques to vaporize atoms include inductively coupled plasma atomic emission spectroscopy and inductively coupled plasma mass spectrometry, both of which use a plasma to vaporize samples for analysis.

A more area-selective method is electron energy loss spectroscopy, which measures the energy loss of an electron beam within a transmission electron microscope when it interacts with a portion of a sample. The atom-probe tomograph has sub-nanometer resolution in 3-D and can chemically identify individual atoms using time-of-flight mass spectrometry.

Spectra of excited states can be used to analyze the atomic composition of distant stars. Specific light wavelengths contained in the observed light from stars can be separated out and related to the quantized transitions in free gas atoms. These colors can be replicated using a gas-discharge lamp containing the same element. Helium was discovered in this way in the spectrum of the Sun 23 years before it was found on Earth.

Origin and current state

Baryonic matter forms about 4% of the total energy density of the observable Universe, with an average density of about 0.25 particles/m3 (mostly protons and electrons). Within a galaxy such as the Milky Way, particles have a much higher concentration, with the density of matter in the interstellar medium (ISM) ranging from 105 to 109 atoms/m3. The Sun is believed to be inside the Local Bubble, so the density in the solar neighborhood is only about 103 atoms/m3. Stars form from dense clouds in the ISM, and the evolutionary processes of stars result in the steady enrichment of the ISM with elements more massive than hydrogen and helium. 

Up to 95% of the Milky Way's baryonic matter are concentrated inside stars, where conditions are unfavorable for atomic matter. The total baryonic mass is about 10% of the mass of the galaxy; the remainder of the mass is an unknown dark matter. High temperature inside stars makes most "atoms" fully ionized, that is, separates all electrons from the nuclei. In stellar remnants—with exception of their surface layers—an immense pressure make electron shells impossible.

Formation

Electrons are thought to exist in the Universe since early stages of the Big Bang. Atomic nuclei forms in nucleosynthesis reactions. In about three minutes Big Bang nucleosynthesis produced most of the helium, lithium, and deuterium in the Universe, and perhaps some of the beryllium and boron.

Ubiquitousness and stability of atoms relies on their binding energy, which means that an atom has a lower energy than an unbound system of the nucleus and electrons. Where the temperature is much higher than ionization potential, the matter exists in the form of plasma—a gas of positively charged ions (possibly, bare nuclei) and electrons. When the temperature drops below the ionization potential, atoms become statistically favorable. Atoms (complete with bound electrons) became to dominate over charged particles 380,000 years after the Big Bang—an epoch called recombination, when the expanding Universe cooled enough to allow electrons to become attached to nuclei.

Since the Big Bang, which produced no carbon or heavier elements, atomic nuclei have been combined in stars through the process of nuclear fusion to produce more of the element helium, and (via the triple alpha process) the sequence of elements from carbon up to iron.

Isotopes such as lithium-6, as well as some beryllium and boron are generated in space through cosmic ray spallation. This occurs when a high-energy proton strikes an atomic nucleus, causing large numbers of nucleons to be ejected. 

Elements heavier than iron were produced in supernovae through the r-process and in AGB stars through the s-process, both of which involve the capture of neutrons by atomic nuclei. Elements such as lead formed largely through the radioactive decay of heavier elements.

Earth

Most of the atoms that make up the Earth and its inhabitants were present in their current form in the nebula that collapsed out of a molecular cloud to form the Solar System. The rest are the result of radioactive decay, and their relative proportion can be used to determine the age of the Earth through radiometric dating. Most of the helium in the crust of the Earth (about 99% of the helium from gas wells, as shown by its lower abundance of helium-3) is a product of alpha decay.

There are a few trace atoms on Earth that were not present at the beginning (i.e., not "primordial"), nor are results of radioactive decay. Carbon-14 is continuously generated by cosmic rays in the atmosphere. Some atoms on Earth have been artificially generated either deliberately or as by-products of nuclear reactors or explosions. Of the transuranic elements—those with atomic numbers greater than 92—only plutonium and neptunium occur naturally on Earth. Transuranic elements have radioactive lifetimes shorter than the current age of the Earth and thus identifiable quantities of these elements have long since decayed, with the exception of traces of plutonium-244 possibly deposited by cosmic dust. Natural deposits of plutonium and neptunium are produced by neutron capture in uranium ore.

The Earth contains approximately 1.33×1050 atoms. Although small numbers of independent atoms of noble gases exist, such as argon, neon, and helium, 99% of the atmosphere is bound in the form of molecules, including carbon dioxide and diatomic oxygen and nitrogen. At the surface of the Earth, an overwhelming majority of atoms combine to form various compounds, including water, salt, silicates and oxides. Atoms can also combine to create materials that do not consist of discrete molecules, including crystals and liquid or solid metals. This atomic matter forms networked arrangements that lack the particular type of small-scale interrupted order associated with molecular matter.

Rare and theoretical forms

Superheavy elements

While isotopes with atomic numbers higher than lead (82) are known to be radioactive, an "island of stability" has been proposed for some elements with atomic numbers above 103. These superheavy elements may have a nucleus that is relatively stable against radioactive decay. The most likely candidate for a stable superheavy atom, unbihexium, has 126 protons and 184 neutrons.

Exotic matter

Each particle of matter has a corresponding antimatter particle with the opposite electrical charge. Thus, the positron is a positively charged antielectron and the antiproton is a negatively charged equivalent of a proton. When a matter and corresponding antimatter particle meet, they annihilate each other. Because of this, along with an imbalance between the number of matter and antimatter particles, the latter are rare in the universe. The first causes of this imbalance are not yet fully understood, although theories of baryogenesis may offer an explanation. As a result, no antimatter atoms have been discovered in nature. However, in 1996 the antimatter counterpart of the hydrogen atom (antihydrogen) was synthesized at the CERN laboratory in Geneva.

Other exotic atoms have been created by replacing one of the protons, neutrons or electrons with other particles that have the same charge. For example, an electron can be replaced by a more massive muon, forming a muonic atom. These types of atoms can be used to test the fundamental predictions of physics.

Sunday, September 8, 2019

Human evolutionary genetics

From Wikipedia, the free encyclopedia
 
Human evolutionary genetics studies how one human genome differs from another human genome, the evolutionary past that gave rise to the human genome, and its current effects. Differences between genomes have anthropological, medical, historical and forensic implications and applications. Genetic data can provide important insights into human evolution.

Origin of apes

The taxonomic relationships of hominoids.
 
Biologists classify humans, along with only a few other species, as great apes (species in the family Hominidae). The living Hominidae include two distinct species of chimpanzee (the bonobo, Pan paniscus, and the common chimpanzee, Pan troglodytes), two species of gorilla (the western gorilla, Gorilla gorilla, and the eastern gorilla, Gorilla graueri), and two species of orangutan (the Bornean orangutan, Pongo pygmaeus, and the Sumatran orangutan, Pongo abelii). The great apes with the family Hylobatidae of gibbons form the superfamily Hominoidea of apes.

Apes, in turn, belong to the primate order (>400 species), along with the Old World monkeys, the New World monkeys, and others. Data from both mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) indicate that primates belong to the group of Euarchontoglires, together with Rodentia, Lagomorpha, Dermoptera, and Scandentia. This is further supported by Alu-like short interspersed nuclear elements (SINEs) which have been found only in members of the Euarchontoglires.

Phylogenetics

A phylogenetic tree is usually derived from DNA or protein sequences from populations. Often, mitochondrial DNA or Y chromosome sequences are used to study ancient human demographics. These single-locus sources of DNA do not recombine and are almost always inherited from a single parent, with only one known exception in mtDNA. Individuals from closer geographic regions generally tend to be more similar than individuals from regions farther away. Distance on a phylogenetic tree can be used approximately to indicate:
  1. Genetic distance. The genetic difference between humans and chimpanzees is less than 2%, or three times larger than the variation among modern humans (estimated at 0.6%).
  2. Temporal remoteness of the most recent common ancestor. The mitochondrial most recent common ancestor of modern humans is estimated to have lived roughly 160,000 years ago, the latest common ancestors of humans and chimpanzees roughly 5 to 6 million years ago.

Speciation of humans and the African apes

The separation of humans from their closest relatives, the non-human apes (chimpanzees and gorillas), has been studied extensively for more than a century. Five major questions have been addressed:
  • Which apes are our closest ancestors?
  • When did the separations occur?
  • What was the effective population size of the common ancestor before the split?
  • Are there traces of population structure (subpopulations) preceding the speciation or partial admixture succeeding it?
  • What were the specific events (including fusion of chromosomes 2a and 2b) prior to and subsequent to the separation?

General observations

As discussed before, different parts of the genome show different sequence divergence between different hominoids. It has also been shown that the sequence divergence between DNA from humans and chimpanzees varies greatly. For example, the sequence divergence varies between 0% to 2.66% between non-coding, non-repetitive genomic regions of humans and chimpanzees. The percentage of nucleotides in the human genome (hg38) that had one-to-one exact matches in the chimpanzee genome (pantro6) was 84.38%. Additionally gene trees, generated by comparative analysis of DNA segments, do not always fit the species tree. Summing up:
  • The sequence divergence varies significantly between humans, chimpanzees and gorillas.
  • For most DNA sequences, humans and chimpanzees appear to be most closely related, but some point to a human-gorilla or chimpanzee-gorilla clade.
  • The human genome has been sequenced, as well as the chimpanzee genome. Humans have 23 pairs of chromosomes, while chimpanzees, gorillas, and orangutans have 24. Human chromosome 2 is a fusion of two chromosomes 2a and 2b that remained separate in the other primates.

Divergence times

The divergence time of humans from other apes is of great interest. One of the first molecular studies, published in 1967 measured immunological distances (IDs) between different primates. Basically the study measured the strength of immunological response that an antigen from one species (human albumin) induces in the immune system of another species (human, chimpanzee, gorilla and Old World monkeys). Closely related species should have similar antigens and therefore weaker immunological response to each other's antigens. The immunological response of a species to its own antigens (e.g. human to human) was set to be 1. 

The ID between humans and gorillas was determined to be 1.09, that between humans and chimpanzees was determined as 1.14. However the distance to six different Old World monkeys was on average 2.46, indicating that the African apes are more closely related to humans than to monkeys. The authors consider the divergence time between Old World monkeys and hominoids to be 30 million years ago (MYA), based on fossil data, and the immunological distance was considered to grow at a constant rate. They concluded that divergence time of humans and the African apes to be roughly ~5 MYA. That was a surprising result. Most scientists at that time thought that humans and great apes diverged much earlier (>15 MYA).

The gorilla was, in ID terms, closer to human than to chimpanzees; however, the difference was so slight that the trichotomy could not be resolved with certainty. Later studies based on molecular genetics were able to resolve the trichotomy: chimpanzees are phylogenetically closer to humans than to gorillas. However, some divergence times estimated later (using much more sophisticated methods in molecular genetics) do not substantially differ from the very first estimate in 1967, but a recent paper puts it at 11–14 MYA.

Divergence times and ancestral effective population size

The sequences of the DNA segments diverge earlier than the species. A large effective population size in the ancestral population (left) preserves different variants of the DNA segments (=alleles) for a longer period of time. Therefore, on average, the gene divergence times (tA for DNA segment A; tB for DNA segment B) will deviate more from the time the species diverge (tS) compared to a small ancestral effective population size (right).
 
Current methods to determine divergence times use DNA sequence alignments and molecular clocks. Usually the molecular clock is calibrated assuming that the orangutan split from the African apes (including humans) 12-16 MYA. Some studies also include some old world monkeys and set the divergence time of them from hominoids to 25-30 MYA. Both calibration points are based on very little fossil data and have been criticized.

If these dates are revised, the divergence times estimated from molecular data will change as well. However, the relative divergence times are unlikely to change. Even if we can't tell absolute divergence times exactly, we can be pretty sure that the divergence time between chimpanzees and humans is about sixfold shorter than between chimpanzees (or humans) and monkeys.

One study (Takahata et al., 1995) used 15 DNA sequences from different regions of the genome from human and chimpanzee and 7 DNA sequences from human, chimpanzee and gorilla. They determined that chimpanzees are more closely related to humans than gorillas. Using various statistical methods, they estimated the divergence time human-chimp to be 4.7 MYA and the divergence time between gorillas and humans (and chimps) to be 7.2 MYA.

Additionally they estimated the effective population size of the common ancestor of humans and chimpanzees to be ~100,000. This was somewhat surprising since the present day effective population size of humans is estimated to be only ~10,000. If true that means that the human lineage would have experienced an immense decrease of its effective population size (and thus genetic diversity) in its evolution.

A and B are two different loci. In the upper figure they fit to the species tree. The DNA that is present in today's gorillas diverged earlier from the DNA that is present in today's humans and chimps. Thus both loci should be more similar between human and chimp than between gorilla and chimp or gorilla and human. In the lower graph, locus A has a more recent common ancestor in human and gorilla compared to the chimp sequence. Whereas chimp and gorilla have a more recent common ancestor for locus B. Here the gene trees are incongruent to the species tree.
 
Another study (Chen & Li, 2001) sequenced 53 non-repetitive, intergenic DNA segments from a human, a chimpanzee, a gorilla, and orangutan. When the DNA sequences were concatenated to a single long sequence, the generated neighbor-joining tree supported the Homo-Pan clade with 100% bootstrap (that is that humans and chimpanzees are the closest related species of the four). When three species are fairly closely related to each other (like human, chimpanzee and gorilla), the trees obtained from DNA sequence data may not be congruent with the tree that represents the speciation (species tree). 

The shorter internodal time span (TIN) the more common are incongruent gene trees. The effective population size (Ne) of the internodal population determines how long genetic lineages are preserved in the population. A higher effective population size causes more incongruent gene trees. Therefore, if the internodal time span is known, the ancestral effective population size of the common ancestor of humans and chimpanzees can be calculated.

When each segment was analyzed individually, 31 supported the Homo-Pan clade, 10 supported the Homo-Gorilla clade, and 12 supported the Pan-Gorilla clade. Using the molecular clock the authors estimated that gorillas split up first 6.2-8.4 MYA and chimpanzees and humans split up 1.6-2.2 million years later (internodal time span) 4.6-6.2 MYA. The internodal time span is useful to estimate the ancestral effective population size of the common ancestor of humans and chimpanzees.

A parsimonious analysis revealed that 24 loci supported the Homo-Pan clade, 7 supported the Homo-Gorilla clade, 2 supported the Pan-Gorilla clade and 20 gave no resolution. Additionally they took 35 protein coding loci from databases. Of these 12 supported the Homo-Pan clade, 3 the Homo-Gorilla clade, 4 the Pan-Gorilla clade and 16 gave no resolution. Therefore, only ~70% of the 52 loci that gave a resolution (33 intergenic, 19 protein coding) support the 'correct' species tree. From the fraction of loci which did not support the species tree and the internodal time span they estimated previously, the effective population of the common ancestor of humans and chimpanzees was estimated to be ~52 000 to 96 000. This value is not as high as that from the first study (Takahata), but still much higher than present day effective population size of humans. 

A third study (Yang, 2002) used the same dataset that Chen and Li used but estimated the ancestral effective population of 'only' ~12,000 to 21,000, using a different statistical method.

Genetic differences between humans and other great apes

The alignable sequences within genomes of humans and chimpanzees differ by about 35 million single-nucleotide substitutions. Additionally about 3% of the complete genomes differ by deletions, insertions and duplications.

Since mutation rate is relatively constant, roughly one half of these changes occurred in the human lineage. Only a very tiny fraction of those fixed differences gave rise to the different phenotypes of humans and chimpanzees and finding those is a great challenge. The vast majority of the differences are neutral and do not affect the phenotype.

Molecular evolution may act in different ways, through protein evolution, gene loss, differential gene regulation and RNA evolution. All are thought to have played some part in human evolution.

Gene loss

Many different mutations can inactivate a gene, but few will change its function in a specific way. Inactivation mutations will therefore be readily available for selection to act on. Gene loss could thus be a common mechanism of evolutionary adaptation (the "less-is-more" hypothesis).

80 genes were lost in the human lineage after separation from the last common ancestor with the chimpanzee. 36 of those were for olfactory receptors. Genes involved in chemoreception and immune response are overrepresented. Another study estimated that 86 genes had been lost.

Hair keratin gene KRTHAP1

A gene for type I hair keratin was lost in the human lineage. Keratins are a major component of hairs. Humans still have nine functional type I hair keratin genes, but the loss of that particular gene may have caused the thinning of human body hair. Based on the assumption of a constant molecular clock, the study predicts the gene loss occurred relatively recently in human evolution—less than 240 000 years ago, but both the Vindija Neandertal and the high-coverage Denisovan sequence contain the same premature stop codons as modern humans and hence dating should be greater than 750 000 years ago. 

Myosin gene MYH16

Stedman et al. (2004) stated that the loss of the sarcomeric myosin gene MYH16 in the human lineage led to smaller masticatory muscles. They estimated that the mutation that led to the inactivation (a two base pair deletion) occurred 2.4 million years ago, predating the appearance of Homo ergaster/erectus in Africa. The period that followed was marked by a strong increase in cranial capacity, promoting speculation that the loss of the gene may have removed an evolutionary constraint on brain size in the genus Homo.

Another estimate for the loss of the MYH16 gene is 5.3 million years ago, long before Homo appeared.

Other

  • CASPASE12, a cysteinyl aspartate proteinase. The loss of this gene is speculated to have reduced the lethality of bacterial infection in humans.

Gene addition

Segmental duplications (SDs or LCRs) have had roles in creating new primate genes and shaping human genetic variation.

Human-specific DNA insertions

When the human genome was compared to the genomes of five comparison primate species, including the chimpanzee, gorilla, orangutan, gibbon, and macaque, it was found that there are approximately 20,000 human-specific insertions believed to be regulatory. While most insertions appear to be fitness neutral, a small amount have been identified in positively selected genes showing associations to neural phenotypes and some relating to dental and sensory perception-related phenotypes. These findings hint at the seemingly important role of human-specific insertions in the recent evolution of humans.

Selection pressures

Human accelerated regions are areas of the genome that differ between humans and chimpanzees to a greater extent than can be explained by genetic drift over the time since the two species shared a common ancestor. These regions show signs of being subject to natural selection, leading to the evolution of distinctly human traits. Two examples are HAR1F, which is believed to be related to brain development and HAR2 (a.k.a. HACNS1) that may have played a role in the development of the opposable thumb

It has also been hypothesized that much of the difference between humans and chimpanzees is attributable to the regulation of gene expression rather than differences in the genes themselves. Analyses of conserved non-coding sequences, which often contain functional and thus positively selected regulatory regions, address this possibility.

Sequence divergence between humans and apes

When the draft sequence of the common chimpanzee (Pan troglodytes) genome was published in the summer 2005, 2400 million bases (of ~3160 million bases) were sequenced and assembled well enough to be compared to the human genome. 1.23% of this sequenced differed by single-base substitutions. Of this, 1.06% or less was thought to represent fixed differences between the species, with the rest being variant sites in humans or chimpanzees. Another type of difference, called indels (insertions/deletions) accounted for many fewer differences (15% as many), but contributed ~1.5% of unique sequence to each genome, since each insertion or deletion can involve anywhere from one base to millions of bases.

A companion paper examined segmental duplications in the two genomes, whose insertion and deletion into the genome account for much of the indel sequence. They found that a total of 2.7% of euchromatic sequence had been differentially duplicated in one or the other lineage. 

Percentage sequence divergence between humans and other hominids
Locus Human-Chimp Human-Gorilla Human-Orangutan
Alu elements 2 - -
Non-coding (Chr. Y) 1.68 ± 0.19 2.33 ± 0.2 5.63 ± 0.35
Pseudogenes (autosomal) 1.64 ± 0.10 1.87 ± 0.11 -
Pseudogenes (Chr. X) 1.47 ± 0.17 - -
Noncoding (autosomal) 1.24 ± 0.07 1.62 ± 0.08 3.08 ± 0.11
Genes (Ks) 1.11 1.48 2.98
Introns 0.93 ± 0.08 1.23 ± 0.09 -
Xq13.3 0.92 ± 0.10 1.42 ± 0.12 3.00 ± 0.18
Subtotal for X chromosome 1.16 ± 0.07 1.47 ± 0.08 -
Genes (Ka) 0.8 0.93 1.96

The sequence divergence has generally the following pattern: Human-Chimp < Human-Gorilla << Human-Orangutan, highlighting the close kinship between humans and the African apes. Alu elements diverge quickly due to their high frequency of CpG dinucleotides which mutate roughly 10 times more often than the average nucleotide in the genome. The mutation rate is higher in the male germ line, therefore the divergence in the Y chromosome—which is inherited solely from the father—is higher than in autosomes. The X chromosome is inherited twice as often through the female germ line as through the male germ line and therefore shows slightly lower sequence divergence. The sequence divergence of the Xq13.3 region is surprisingly low between humans and chimpanzees.

Mutations altering the amino acid sequence of proteins (Ka) are the least common. In fact ~29% of all orthologous proteins are identical between human and chimpanzee. The typical protein differs by only two amino acids. The measures of sequence divergence shown in the table only take the substitutional differences, for example from an A (adenine) to a G (guanine), into account. DNA sequences may however also differ by insertions and deletions (indels) of bases. These are usually stripped from the alignments before the calculation of sequence divergence is performed.

Genetic differences between modern humans and Neanderthals

An international group of scientists completed a draft sequence of the Neanderthal genome in May 2010. The results indicate some breeding between modern humans (Homo sapiens) and Neanderthals (Homo neanderthalensis), as the genomes of non-African humans have 1–4% more in common with Neanderthals than do the genomes of subsaharan Africans. Neanderthals and most modern humans share a lactose-intolerant variant of the lactase gene that encodes an enzyme that is unable to break down lactose in milk after weaning. Modern humans and Neanderthals also share the FOXP2 gene variant associated with brain development and with speech in modern humans, indicating that Neanderthals may have been able to speak. Chimps have two amino acid differences in FOXP2 compared with human and Neanderthal FOXP2.

Genetic differences among modern humans

H. sapiens is thought to have emerged about 300,000 years ago. It dispersed throughout Africa, and after 70,000 years ago throughout Eurasia and Oceania. A 2009 study identified 14 "ancestral population clusters", the most remote being the San people of Southern Africa.

With their rapid expansion throughout different climate zones, and especially with the availability of new food sources with the domestication of cattle and the development of agriculture, human populations have been exposed to significant selective pressures since their dispersal. For example, East Asians have been found to be separated from Europids by a number of concentrated alleles suggestive of selection pressures, including variants of the EDAR, ADH1B, ABCC1, and ALDH2genes. The East Asian types of ADH1B in particular are associated with rice domestication and would thus have arisen after the development of rice cultivation roughly 10,000 years ago. Several phenotypical traits of characteristic of East Asians are due to a single mutation of the EDAR gene, dated to c. 35,000 years ago.

As of 2017, the Single Nucleotide Polymorphism Database (dbSNP), which lists SNP and other variants, listed a total of 324 million variants found in sequenced human genomes. Nucleotide diversity, the average proportion of nucleotides that differ between two individuals, is estimated at between 0.1% and 0.4% for contemporary humans (compared to 2% between humans and chimpanzees). This corresponds to genome differences at a few million sites; the 1000 Genomes Project similarly found that "a typical [individual] genome differs from the reference human genome at 4.1 million to 5.0 million sites … affecting 20 million bases of sequence."

In February 2019, scientists discovered evidence, based on genetics studies using artificial intelligence (AI), that suggest the existence of an unknown human ancestor species, not Neanderthal, Denisovan or human hybrid (like Denny (hybrid hominin)), in the genome of modern humans.

Information asymmetry

From Wikipedia, the free encyclopedia https://en.wikipedia.org/wiki/Inf...