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In biology, evolution is the change in a population's inherited traits from generation to generation. These traits are the expression of genes that are copied and passed on to offspring during reproduction. Mutations and other random changes in these genes can produce new or altered traits, resulting in heritable differences (genetic variation) between organisms. New traits can also come from transfer of genes between populations, as in horizontal gene transfer or breeding between species. Evolution occurs when these differences become more common or rare in a population, either randomly through genetic drift or nonrandomly through natural selection.

Natural selection is inheritable traits that are helpful for survival and reproduction becoming more common and harmful traits becoming more rare. This occurs because organisms with these advantageous traits produce more offspring, thus passing more copies of the traits on to the next generation. Over very long periods of time, adaptations are produced by a combination of the continuous production of small, random changes in traits, followed by natural selection of the variants best-suited for their environment.

A species is a group of animals that can reproduce with one another. However, when a species is separated into different populations that are prevented from interbreeding, mutations and genetic drift, combined with different environments selecting for and against different traits, result in these populations accumulating differences over time and eventually becoming two separate new species. The similarities between all organisms suggest that all known species are descended from a single ancestral species, through this process of gradual divergence.

The theory of evolution by natural selection was first proposed by Charles Darwin and Alfred Russel Wallace and put forth in detail in Darwin's 1859 book On the Origin of Species. In the 1930s, Darwinian natural selection was combined with Mendelian inheritance to form the modern evolutionary synthesis. With its enormous explanatory and predictive power, this theory has become the central organizing principle of modern biology, providing a unifying explanation for the diversity of life on Earth.

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History of evolutionary thought

Evolutionary ideas such as common descent and the transmutation of species have existed since at least the 6th century BC, when they were expounded by the Greek philosopher Anaximander. As biological knowledge grew in the 18th century, a variety of such ideas developed, beginning with Pierre Maupertuis in 1745.

The first convincing exposition of a mechanism by which evolutionary change could occur was not made until 1858, when Charles Darwin and Alfred Russel Wallace jointly proposed the theory of evolution by natural selection to the Linnean Society of London in separate papers. Shortly after, Darwin's publication of The Origin of Species provided detailed support for the theory and led to increasingly wide acceptance of the occurrence of evolution. However, Darwin's specific ideas about evolution, such as gradualism and natural selection, were strongly contested at first. Lamarckists argued that transmutation of species occurred as parents passed on adaptations acquired during their lifetimes. Eventually, when experiments failed to support it, this popular rival theory was abandoned in favor of Darwinism.

However, Darwin could not account for how traits were passed down from generation to generation. A mechanism was provided in 1865 by Gregor Mendel, whose research revealed that distinct traits were inherited in a well-defined and predictable manner. When Mendel's work was rediscovered in 1900, disagreements over the rate of evolution predicted by early geneticists and biometricians led to a rift between the Mendelian and Darwinian models of evolution. This contradiction was reconciled in the 1930s through the work of biologists such as Ronald Fisher. The end result was a combination of Darwinian natural selection with Mendelian inheritance, the modern evolutionary synthesis, or "Neo-Darwinism".

In the 1940s, the identification of DNA as the genetic material by Oswald Avery and colleagues, and the subsequent publication of the structure of DNA by James Watson and Francis Crick in 1953, demonstrated the physical basis for inheritance. Since then, genetics and molecular biology have become increasingly important in evolutionary biology.

Heredity

Inheritance in organisms occurs through discrete traits, which are one particular characteristic of the organism. In humans for example, eye color is an inherited character and a person could inherit the trait of having brown eyes from one of their parents. Inherited traits are controlled by genes and the set of genes within an organism is called its genotype. Most hereditary traits are inherited through Mendelian inheritance, where offspring have the trait of either one or the other of their parents, but not a mixture of the two traits.

The complete set of observable traits of an organism, its phenotype, comes from the interaction of its genotype with the environment. As a result, not every aspect of an organism's phenotype is inherited. For example, the characteristic of a person having a suntanned skin is the result of the interaction between their genotype and sunlight, and a suntan is not hereditary. However, people differ in their genotype and thus have different responses to sunlight; the most striking examples being people with the inherited trait of albinism, who do not tan at all and are therefore highly sensitive to sunburn.

Genes are the physical basis of inherited traits and are defined as regions within DNA molecules. DNA is made of a backbone of alternating sugars and phosphate groups, attached to each sugar is one of four types of molecules called bases. Genes are distinguished by their differing sequences of bases; these sequences encode the genetic information. This information is read using the genetic code; a gene's DNA sequence specifies a corresponding sequence of the amino acids within a protein. When genes are used by an organism, the DNA is transcribed into RNA and then this RNA is translated into protein. Within cells, the long strands of DNA associate with proteins to form structures called chromosomes. A specific location within the DNA in a chromosome is known as a locus, with a variant of a DNA sequence at a given locus called an allele. These DNA sequences can change through mutations, producing new alleles. If these mutations happen within a gene, they may affect the traits that the genes control and alter the phenotype of the organism. This simple correspondence between a mutation and a trait works in many cases, although complex traits such as disease resistance are controlled by multiple interacting genes.

Some molecular features of cells can influence traits in a heritable manner without changing the DNA sequence of an organism. These "epigenetic" features change over the course of reproduction and development of organisms, but there have been notable observations of multigenerational inheritance — how these are involved in evolution is at the moment highly speculative. Because they are generally dynamic, most epigenetic features are not considered to "evolve" in the long term manner of DNA changes, but they may play a role in adaptation by allowing reversible changes to phenotype.

Variation

An individual's phenotype results from the interaction of their genotype with the environment. Thus, the variation in phenotypes within a population reflects the variation in this population's genotypes. The modern evolutionary synthesis defines evolution as the change over time in the relative frequencies of alleles in a population. The frequency of these variants may fluctuate in the population, becoming more or less prevalent relative to other alleles of that gene. All evolutionary forces act by driving these changes in allele frequency in one direction or another. Variation disappears when an allele reaches the point of fixation — when it either disappears from the population, or when it replaces the ancestral allele entirely.

Variation comes from mutations in genetic material, migration between populations (gene flow), and the reshuffling of genes during sexual reproduction. In some organisms, variation is also produced by the mixing of genetic material between different species through horizontal gene transfer in bacteria, and hybridization in plants. Despite all the processes that introduce variation, most sites in the genome of a species are identical in all individuals of this species. However, even relatively small changes in genotype can lead to dramatic changes in phenotype, with chimpanzees and humans only differing in about 5% of their genomes.

Mutation

Genetic variation arises due to random mutations that occur in the genomes of all organisms. Mutations are transmissible changes in genetic material, and are often caused by external factors such as radiation and mutagenic chemicals, as well as errors that occur during meiosis or DNA replication. Viruses and mobile DNA sequences such as transposons, are another cause of mutations. Individual genes can be affected by two different types of mutations. In point mutations, a single base pair is altered. This change in a single base pair may or may not affect the function of the gene. The other type of mutations are the deletion and insertion of base pairs. These changes often cause a loss of the gene's function, as they cause a shift in reading frame and thus change many amino acid codons simultaneously.

In multicellular organisms, mutations can be classified into germline mutations that occur in the gametes and thus can be passed onto offspring, and somatic mutations that can trigger cell death, or cause cancer. These somatic mutations are not inherited and therefore have no effect on evolutionary processes. Due to the damaging effects that mutations can have on cells, organisms have evolved multiple mechanisms such as DNA repair that reduce mutation rates. However, the optimal mutation rate for an organism is a trade-off between short-term costs, such as the energy expended on DNA repair and the effects of deleterious mutations, and the long-term benefits of advantageous mutations. Organisms such as bacteria can even increase their mutation rate in response to stress, leading to the evolution of novel alleles that counter the source of stress.

Most genes belong to larger families of genes that are derived though mutation from one or more ancestral genes. Novel genes can be produced either through duplication and mutation of an ancestral gene, or the recombination of protein domains to form a new combination of these structural modules. Gene duplications, which may occur through a number of mechanisms, are believed to be one major source of raw material for evolving new genes, as tens to hundreds of genes are duplicated in animal genomes every million years. At a higher level, the duplication of entire genomes to produce polyploid organisms also appears to have been important in evolution, particularly in vertebrates and in plants. Another possible advantage of gene duplication is that overlapping or redundant function in families of genes can allow retention of alleles that would otherwise have deleterious effects, thus increasing genetic diversity.

Changes in chromosome number may also involve the breakage and rearrangement of genes in chromosomes. Large chromosomal rearrangements do not necessarily change gene function, but can result in reproductive isolation. An example of chromosomal rearrangements is the fusion of two chromosomes in the Homo genus that produced human chromosome 2; this fusion did not occur in the chimpanzee lineage, and chimpanzees retain two separate chromosomes. However, chromosomal rearrangements do not appear to have driven the divergence of the human and chimpanzee lineages. The major role of such chromosomal rearrangements in speciation may be to reduce recombination, thus preventing separation of linked alleles and accelerating divergence.

Recombination

In asexual organisms, genes will be inherited together, they are linked, as they have no opportunity to mix with genes from other organisms during reproduction. However, the offspring of sexual organisms contain a random mixture of their parents' chromosomes, which is the result of a process called independent assortment. Sexual organisms can also exchange DNA between two matching chromosomes in a process called genetic recombination. This shuffling of genetic material between chromosomes allows even alleles of genes that are close together in the genome to be inherited independently. However, the recombination rate is not very high and in humans is approximately one recombination event per 1,000,000 base pairs. Therefore, alleles close together on a chromosome are not often shuffled away from each other, but tend to be inherited together. This tendency is measured by comparing the co-occurrence of two alleles, their linkage disequilibrium. A set of alleles that are often inherited together is called a haplotype and this co-inheritance can indicate that the locus is under positive selection (see below).

Recombination in sexual organisms allows disadvantageous mutations to be purged and beneficial mutations to be retained more efficiently than in asexual organisms. In addition, recombination can lead to more individuals with new and advantageous gene combinations being produced. These benefits can be identified by looking at the effects of situations where alleles cannot be separated by recombination, such as in mammalian Y chromosomes. In these circumstances, there is a reduction in effective population size called the Hill-Robertson effect, which causes the accumulation of deleterious mutations. These positive effects of recombination are balanced by the facts that it can cause mutations (as it involves the breaking and rejoining of the DNA strands) and it can also separate gene combinations that have been successful in previous generations. The optimal rate of recombination for a species is therefore a trade-off between these conflicting factors.

Mechanisms of evolution

There are many basic mechanisms of evolutionary change: natural selection, genetic drift, and others like gene flow from migration. Gene flow is the transfer of genetic material within and between populations, genetic drift is the random sampling of a generation's genes during reproduction, which causes random changes in the frequency of alleles, and natural selection is the non-random propagation of genes that favor survival and reproduction. The relative importance of these three forces in driving evolution is variable. The importance of natural selection and genetic drift depends on the effective population size, which is the number of organisms capable of breeding, as well as the strength of selection. Natural selection probably predominates in large populations, while genetic drift dominates in small populations. As a result, changing population size can dramatically influence the course of evolution. Population bottlenecks, where the population shrinks in size temporarily to a small number of individuals and therefore loses much genetic variation, result in a more uniform population and the loss of most rare variation. Bottlenecks may also result from alterations in gene flow such as decreased migration, founder effects, or population subdivision.

Natural selection

Natural selection results from the difference in reproductive success between individuals in a population and causes adaptation. It has often been called a "self-evident" mechanism because it necessarily follows from the following facts:

• Natural, heritable variation exists within populations and among species
• Organisms are superfecund (produce more offspring than can possibly survive)
• Organisms in a population vary in their ability to survive and reproduce
• In any generation, successful reproducers pass their heritable traits to the next generation, while unsuccessful reproducers do not.

The central concept of natural selection is the evolutionary fitness of an organism. This is a measure of the organism's genetic contribution to the next generation. However, this is not the same as the total number of the organism's offspring: instead fitness measures the proportion of subsequent generations that carry the organism's genes. Consequently, if an allele produces a trait that increases fitness, with each generation this allele will become more common within a population. Examples of traits that can increase fitness are enhanced survival, and increased fecundity. Conversely, a decrease in fitness caused by a deleterious allele results in this allele becoming rarer. Importantly, the fitness of an allele is not a fixed characteristic, if the environment changes, previously neutral and harmful traits may become beneficial and previously beneficial traits become deleterious.

Natural selection within a population can be subcategorized into three different modes: directional selection (a shift in the mean trait value over time); disruptive selection (selection for extreme trait values on both ends, or "tails" of the distribution, often resulting in a bimodal distribution and selection against the mean); and stabilizing selection (also called purifying selection — selection against extreme trait values on both ends, and a decrease in variance around the mean.)

A special case of natural selection is sexual selection: selection for any trait whose presence is directly correlated with mating success due to preferential mate choice. Traits that evolved via sexual selection are particularly prominent among males of animal species. Despite the fact that such traits may decrease the survival of individual males (e.g. cumbersome antlers, mating calls or bright colors that attract predators, male-male fighting over access to mates), reproductive success is usually higher in males that show hard to fake, sexually selected traits.

An active area of current research is the level of selection, with natural selection being proposed to work at the level of genes, cells, individual organisms, groups of organisms and even species. None of these models are mutually-exclusive and selection may act on multiple levels simultaneously. In the gene-centered view of evolution, which is the lowest level of selection, intragenomic conflict is caused by "replicators" such as transposons that can multiply within genomes, while group selection may allow the evolution of co-operation, as discussed below.

Genetic drift

Genetic drift is the change in allele frequency from one generation to the next that occurs because alleles in the offspring generation are a random sample of alleles in the parent generation, and are thus subject to sampling error. As a result, in the absence of selection on the alleles, allele frequencies tend to "drift" upward or downward in a random walk, until they eventually become fixed - that is, going to 0% or 100% frequency. The time for an allele to become fixed in the population by genetic drift (that is, for all individuals in the population to carry that allele) depends on population size, with smaller populations requiring a shorter time for fixation. Fluctuations in allele frequency between generations may therefore eliminate some alleles from a population due to chance alone. Two separate populations that began with the same allele frequencies can therefore drift apart by random fluctuation into two divergent populations with different sets of alleles.

Although natural selection is responsible for adaptation, the relative importance of the two forces of natural selection and genetic drift in driving evolutionary change in general is an area of current research in evolutionary biology. These investigations were prompted by the neutral theory of molecular evolution, which proposed that most evolutionary changes are the result the fixation of neutral mutations that do not affect the fitness of an organism. Hence, in this model, most genetic changes in a population are the result of constant mutation pressure and random genetic drift.

Gene flow

Gene flow is the exchange of genes between populations, most commonly of the same species. Examples of gene flow within a species include the migration and then breeding of organisms, or the exchange of pollen. Gene transfer between species includes the formation of hybrid organisms and horizontal gene transfer.

Migration into or out of a population can change allele frequencies. Immigration may add new genetic material to the established gene pool of a population. Conversely, emigration may remove genetic material. As reproductive isolation is required for speciation, gene flow may delay speciation by homogenizing two diverging populations. Gene flow is hindered by mountain ranges, oceans and deserts or even man-made structures such as the Great Wall of China, which has hindered the flow of plant genes.

Depending on how far two species have diverged since their last common ancestor, it may still be possible for them to produce viable offspring, as with horses and donkeys mating to produce mules. Such hybrids are generally infertile, due to mispairings of chromosomes during meiosis. In this case, closely-related species may regularly interbreed, but hybrids will be selected against and the populations will remain distinct. However, viable hybrids can also be formed and these new species can either have properties intermediate between their parent species, or a radically different phenotype. Hybridization rarely leads to new species in animals, although this has been seen in the tree frog Hyla versicolor. Hybridization is however an important means of speciation in plants, since polyploidy (having more than two copies of each chromosome) is tolerated in plants more readily than in animals. Polyploidy is important in hybrids as it allows reproduction, with the two different sets of chromosomes each being able to pair with an identical partner during meiosis. Polypolids also have more genetic diversity, which allows them to resist the effects of inbreeding.

Horizontal gene transfer is the transfer of genetic material from one organism to another organism that is not its offspring. Horizontal gene transfer is common among bacteria, even between very distantly-related species. In medicine, this contributes to the spread of antibiotic resistance, as when one bacteria acquires resistance genes it can transfer them to many other species. Horizontal transfer of genes from bacteria to eukaryotes such as the yeast Saccharomyces cerevisiae and the adzuki bean beetle Callosobruchus chinensis may also have occurred. Viruses can also carry DNA between organisms, allowing transfer of genes even across biological domains.

Horizontal gene transfer has also occurred within eukaryotes, from their chloroplast and mitochondrial genome to their nuclear genome. According to endosymbiotic theory, chloroplasts and mitochondria probably originated as bacterial endosymbionts of a progenitor to the eukaryotic cell. Horizontal gene transfer complicates phylogenetics, since it produces genetic connections between distantly-related species.

Outcomes of evolution

The outcomes of evolution are generally divided into macroevolution, which is evolution that occurs at or above the level of species and microevolution, which refers to smaller evolutionary changes (typically described as changes in allele frequencies) within a species or population. Within the modern evolutionary synthesis, in most cases macroevolution is thought of as the compounded effects of microevolution. Thus, the distinction between micro- and macroevolution is not a fundamental one - the major difference between them is simply of the time involved. However, in some cases speciation events may involve the rapid development of genuinely novel characteristics, such as hybrid genomes and changes in development, and here micro- and macroevolution can be distinct.

Adaptation

As a result of natural selection, organisms undergo adaptation, which is the gradual accumulation of new traits that cause a population of organisms to become better suited to surviving and reproducing in their particular environment. Adaptations are defined traits that not only enhance a specific function, but also evolved to perform that function. These adaptations are the result of gradual modifications of existing traits and this adaptation process can cause either the gain of a new feature or the loss of an ancestral feature. Bacterial adaptation to antibiotic selection shows both these types of adaptation, with mutations causing antibiotic resistance either by modifying the target of the drug, or causing the loss of the transporters that allow the drug into the cell.

However, many traits that appear to be adaptations are in fact exaptations that originally had one function, but were later co-opted for something else. For example, the forelimbs of penguins were wings before they evolved into flippers. Additionally, adaptation has no objective or absolute value: a trait that increases fitness in one environment may decrease it in another. As an example, light pigmentation is an advantageous adaptation for camouflage in light-colored habitats, but disadvantageous in dark-colored environments.

As adaptation occurs through the gradual modification of existing structures, structures with similar internal organization may have very different functions in related organisms. This is the result of a single ancestral structure being adapted to function in different ways. Vertebrate limbs are a common example of such homologous structures. The bones within bat wings, for example, are structurally similar to both human hands and seal flippers, due to the common descent of these structures from an ancestor that also had 5 digits at the end of each forelimb. Other idiosyncratic anatomical features, such as the panda's "thumb", indicate that an organism's evolutionary lineage can limit what adaptions are possible.

During adaption, some structures may lose their original function and become vestigial structures. Such structures may have little or no function in a current species, yet have a clear function in ancestral species, or other closely-related species. Examples include the non-functional remains of eyes in blind cave-dwelling fish, wings in flightless birds, and the presence of hip bones in whales and snakes. Examples of vestigial structures in humans include wisdom teeth, the coccyx, and the vermiform appendix.

An area of current investigation in evolutionary developmental biology is the developmental basis of adaptations. This research addresses the origin and evolution of embryonic development; how modifications of development and developmental processes produce novel features, and the role of developmental plasticity in evolution. These studies have shown that evolution can alter developmental processes to create new structures, such as embryonic bone structures that develop into the jaw in other animals instead forming the ossicles of the middle ear in mammals. It is also possible for structures that have been lost in evolution to reappear due to changes in developmental genes, such as a mutation in chickens causing embryos to grow teeth similar to those of crocodiles. In addition, developmental programs can be conserved in extremely diverse organisms, such as eye development genes that are common to jellyfish, insects, and mammals.

Complexity

Evolution has produced some remarkably complex organisms, but this feature is hard to measure in biology, with properties such as gene content, the number of cell types or morphology all being used to assess an organism's complexity. The observation that complex organisms can be produced from simpler ones has led to the common idea of evolution being progressive and leading towards what are viewed as "higher organisms". If this were generally true, evolution would possess an active trend towards complexity. As shown to the right, in this type of process the value of the most common amount of complexity would increase over time. Indeed, some computer models have suggested that the generation of complex organisms is an inescapable feature of evolution.

However, the idea of a general trend towards complexity in evolution can also be explained through a passive process. This involves an increase in variance but the most common value does not change. Thus, the maximum level of complexity increases over time, but only as an indirect product of there being more organisms in total. In this hypothesis, the apparent trend towards complex organisms is an illusion resulting from concentrating on the small number of large, complex organisms that inhabit the right-hand tail of the complexity distribution and ignoring simpler and much more common organisms. This passive model emphasises that the overwhelming majority of species are microscopic prokaryotes, which comprise about half the world's biomass. constitute the vast majority of Earth's biodiversity. Consequently, microscopic life dominates Earth, and large organisms only appear more diverse due to sampling bias.

Co-evolution and cooperation

A major part of the environment of living organisms are other organisms, such as predators, prey or their siblings. Interactions between organisms can produce both conflict and co-operation. When the interaction is between species, the evolution of one species can exert a selective pressure on a second species. This second species can then adapt and, in turn, exert a new selective pressure on the first species. This mutually-reinforcing selection produces co-evolution. In co-evolution, pairs of organisms such as mutualists, a pathogen and a host, or a predator and its prey undergo matched adaptations. An example is the production of tetrodotoxin in the rough-skinned newt and the co-evolution of the common garter snake. The co-evolution between this predator-prey pair is an example of an evolutionary arms race and has produced very high levels of toxin in the newt and correspondingly high levels of toxin resistance in the snake. Extreme co-evolutionary adaptations also occur between plants and their mutualist mycorrhizal fungi; here the fungi actually grow inside plant cells and exchange nutrients with their hosts, while sending signals that suppress the plant immune system.

However, not all interactions involve conflict. One of the most striking features of the natural world is that genes, cells, and organisms cooperate to form higher-order entities. For example, cells in animals sacrifice their reproduction to increase the fitness of the entire organism. Here, cells respond to specific signals that instruct them to either grow or kill themselves. If cells ignore these signals their uncontrolled growth can cause cancer. Generally, mathematical models incorporating only mutation and natural selection have been used to model adaptation and evolution. However, incorporation of game theory can aid the generation of reliable models. Cooperation is now seen as a fundamental property needed for evolution to construct new levels of organization. That selfish replicators could sacrifice their own reproductive potential to cooperate seems paradoxical in a competitive world, however a number of mechanisms can generate cooperation, such as kin selection and group selection, as well as direct, indirect and network reciprocity. The ubiquity of cooperation in the natural world reveals that cooperation is a common outcome of evolution.

Speciation

Speciation is the process where a species diverges into two descendant species. These speciation events have been observed multiple times in both plants and animals, under controlled laboratory conditions and in nature. Since the pair of species produced by speciation are equally descended from the ancestral form, it is incorrect to view one daughter species as the "original" and the other the "new" species. However, this mistake is a common misconception about evolution, and gives rise to ideas such that if humans evolved from monkeys, monkeys should no longer exist. However, humans did not evolve from monkeys — instead humans share a common ancestor with monkeys that was neither human nor monkey.

In sexually reproducing organisms, speciation results from reproductive isolation and then genealogical divergence. There are four mechanisms for speciation. The most common in animals is allopatric speciation, which occurs in populations that initially become isolated geographically, such as by habitat fragmentation or migration. Simply by virtue of being geographically separated, selection and drift will act independently in the isolated populations. If isolation is maintained, the separate evolutionary process will eventually produce reproductive incompatibility.

In contrast, the second mode, sympatric speciation, is species divergence without geographic isolation, and its identification is typically controversial, since even a small amount of gene flow may be sufficient to homogenize a potentially diverging species. Generally, models of sympatric speciation in animals require the evolution of stable polymorphisms associated with non-random assortative mating, in order for reproductive isolation to evolve. However, a common mechanism of sympatric speciation in plants appears to the the formation of polyploid species and can involve either a single plant doubling its numbers of chromosomes (an autopolyploid such as cabbage), or two related plants cross-breeding to form an allopolyploid such as wheat.

The third mechanism of speciation is peripatric speciation, which occurs as a result of small populations of organisms becoming isolated in a new environment. Here, the founder effect causes rapid speciation through both rapid genetic drift and selection on a reduced gene pool. In parapatric speciation there is no specific extrinsic barrier to gene flow. The population is continuous, but nonetheless, the population does not mate randomly. Individuals are more likely to mate with their geographic neighbors than with individuals in a different part of the population’s range. In this mode, divergence may happen because of reduced gene flow within the population and varying selection pressures across the population’s range. Peripatric speciation is commonly cited as contributing to punctuated equilibrium, which describes speciation as proceeding in short "bursts" interspersed with long periods of stasis, where species remain relatively unchanged. Here, the majority of the fossil record will correspond to the parental population, with the isolated organisms rarely being preserved and consequently few intermediate forms being fossilized.

Finally, the fourth mechanism of speciation is parapatric speciation, which is similar to peripatric speciation, in that a small population enters a new habitat. However, there in this type of speciation there is no physical separation between these two populations. Instead, speciation results from the evolution of biological mechanisms that reduce gene flow between the two populations. Generally, this occurs when there has been a drastic change in the environment within the original species' habitat. An example of this is the grass genus Anthoxanthum odoratum, which can undergo parapatric speciation in response to localized metal pollution from mines. Here, around the mine, there is selection for resistance to high levels of metals in the soil. Selection against interbreeding with the metal-sensitive parental population produces a change in flowering time of the metal-resistant plants resulting in reproductive isolation. Selection against hybrids between the two populations may result in reinforcement, which is the evolution of traits that promote mating within a species, as well as character displacement, which causes two species to become more distinct.

Extinction

Extinction is the disappearance of entire species. Extinction is not an unusual event on a geological time scale as species regularly appear through speciation, and disappear through extinction. Indeed, virtually all animal and plant species that have ever lived on the earth are now extinct. These extinctions have happened continuously throughout the history of life, although the rate of extinction spikes in occasional mass extinction events. The Permian-Triassic extinction event was the Earth's most severe extinction event, rendering extinct 96% of all species. In the later Cretaceous-Tertiary extinction event, 76% of all species perished, the most commonly mentioned among them being the non-avian dinosaurs. The Holocene extinction event is the mass extinction associated with humanity's expansion across the globe over the last few thousand years and involves the rapid extinction of hundreds of thousands of species and the loss of up to 30% of all species by the mid 21st century. Human activities are probably the cause of the ongoing extinction event, and climate change may further accelerate it in the future.

The role of extinction in evolution depends on which type is considered. The cause of the continuous "low-level" extinction events, which form the majority of known extinctions, are not well understood and may be the result of competition between species for shared resources. This could produce "species selection" as an additional and important level of natural selection. The intermittent mass extinctions are also important, but instead of acting as a selective force they drastically reduce diversity in a non-specific manner and may therefore promote a burst of adaptive radiation in survivors.

Evolutionary history of life

Origin of life

Life must exist before it starts diversifying, and so the origin of life (or abiogenesis) is a necessary precursor for biological evolution. However, understanding that evolution has occurred and investigating how this happens does not require an understanding of the origin of life. Nonetheless, abiogenesis is a subject which is often discussed under the general heading of evolution. The current scientific consensus is that life began from self-catalytic chemical reactions, but disputes over what defines life make the point at which such increasingly-complex sets of reactions became organisms unclear. Not much is certain about the earliest developments in life, the structure of the first living things, or the identity of the last universal common ancestor. Consequently, there is no scientific consensus on what would be involved in abiogenesis but discussions generally focus on self-replicating molecules such as RNA, the behavior of complex systems, and the assembly of protocells.

Common descent

All organisms on Earth are descended from a common ancestor or ancestral gene pool, which originated from the origin of life. The current set of species on earth are the final products of the process of evolution, with their diversity the product of a long series of speciation and extinction events. In the Origin of Species, Darwin inferred the common descent of organisms from four simple facts. Firstly, organisms have geographic distributions that cannot be explained by local ecology or adaptation alone. Secondly, the diversity of life is not a diversity of completely unique organisms, but a diversity of organisms that show morphological similarities with one another. Thirdly, many organisms have vestigial traits that have no clear purpose in their modern bearers and finally, that all of life, as Linneaus and others had described, can be classified using these similarities into a hierarchy of nested groups. This last point in particular is strongly consistent with a shared evolutionary history of all organisms that live today or have ever lived.

Past species have also left records of their evolutionary history. Fossils, along with the comparative anatomy of present-day organisms, constitute the morphological, or anatomical, record. By comparing the anatomies of both modern and extinct species, paleontologists can infer the lineages of those species. However, this approach is most successful for organisms that had hard body parts, such as shells, bones or teeth. Furthermore, as prokeryotes such as bacteria and archaea share a limited set of common morphologies, comparisons of their fossils do not provide information on their ancestry.

Other evidence for common descent comes from the biochemical similarities between all living organisms. For example, every living cell uses of the same nucleic acids as its genetic material, and all genetic material encodes the same set of amino acids. The development of molecular genetics has also allowed biologists to study the record of evolution left in organisms' genomes and date when the species diverged through the molecular clock produced by mutations. For example, these DNA sequence comparisons have revealed the close genetic similarity between humans and chimpanzees and shed light on when the common ancestor of these species existed.

Evolution of life

Despite the uncertainty on how life began, it is clear that microorganisms were the first organisms to inhabit earth, approximately 3–4 billion years ago. Evolution did not produce rapid changes in morphology, and for about 3 billion years until the Ediacaran period, all organisms were microscopic. Therefore, most of the history of life describes microorganisms and it is only about a billion years ago that simple multicellular plants and animals began to appear in the oceans.

These multicellular forms of life were the eukaryotes and came from ancient bacteria being engulfed by the ancestors of eukaryotic cells, which allowed endosymbiotic associations between the bacteria and the host cell. The engulfed bacteria then evolved into either mitochondria or hydrogenosomes, structures that are still found in all known eukaryotes. Later on, an independent second engulfment of cyanobacterial-like organisms by some mitochondria-containing eukaryotes led to the formation of chloroplasts in algae and plants.

Soon after the emergence of the first animals, the Cambrian explosion, a geologically brief period of remarkable biological diversity, originated the majority of body plans, or phyla, seen in modern animals, as well as a number of unique lineages that subsequently became extinct. Various triggers for the Cambrian explosion have been proposed, including the accumulation of oxygen in the atmosphere from photosynthesis. About 500 million years ago (mya), plants and fungi colonized the land, and were soon followed by arthropods and other animals. Amphibians first appeared around 300 mya, followed by early amniotes, then mammals around 200 mya and birds around 100 mya (both from "reptile"-like lineages). The human genus arose around 2 mya, with the earliest anatomically-modern humans developing in Africa 100–200 thousand years ago. However, despite this apparent progression, the smaller forms of life that evolved early in this process continue to be highly successful and dominate the earth, with the majority of species prokaryotes and the majority of animals insects.

Modern research

Scholars in a number of academic disciplines continue to document examples of evolution, contributing to a deeper understanding of its underlying mechanisms. Every subdiscipline within biology both informs and is informed by knowledge of the details of evolution, such as in ecological genetics, human evolution, molecular evolution, and phylogenetics. Areas of mathematics (such as bioinformatics), physics, chemistry, and other fields all make important contributions to current understanding of evolutionary mechanisms. Even disciplines as far removed as geology and sociology play a part, since the process of biological evolution has coincided in time and space with the development of both the Earth and human civilization.

Evolutionary biology is a subdiscipline of biology concerned with the origin and descent of species, as well as their changes over time. It was originally an interdisciplinary field including scientists from many traditional taxonomically-oriented disciplines. For example, it generally includes scientists who may have a specialist training in particular organisms, such as mammalogy, ornithology, or herpetology, but who use those organisms to answer general questions in evolution. Evolutionary biology as an academic discipline in its own right emerged as a result of the modern evolutionary synthesis in the 1930s and 1940s. It was not until the 1970s and 1980s, however, that a significant number of universities had departments that specifically included the term evolutionary biology in their titles.

Physical anthropology emerged in the late 19th century as the study of human osteology, and the fossilized skeletal remains of other hominids. At that time, anthropologists debated whether their evidence supported Darwin's claims, because skeletal remains revealed temporal and spatial variation among hominids, but Darwin had not offered an explanation of the specific mechanisms that produce variation. With the recognition of Mendelian genetics and the rise of the modern synthesis, however, evolution became both the fundamental conceptual framework for, and the object of study of, physical anthropologists. In addition to studying skeletal remains, they began to study genetic variation among human populations (population genetics); thus, some physical anthropologists began calling themselves biological anthropologists.

The capability of evolution through selection to produce biological processes and networks optimized for a particular environment has greatly interested mathematicians, scientists and engineers. There has been some recent success in implementing these ideas for artificial uses, including genetic algorithms, which can find the solution to a multi-dimensional problem more quickly than standard software produced by human intelligent designers, and the use of evolutionary fitness landscapes to optimize the design of a system Evolutionary optimization techniques are particularly useful in situations in which it is easy to determine the quality of a single solution, but hard to go through all possible solutions one by one.

Social and religious controversies

Even before the publication of The Origin of Species, the idea that life had evolved was a source of controversy and similar arguments continue to this day. In general, controversy has centered on the philosophical, social, and religious implications of evolution, not on the science of evolution itself; the proposition that biological evolution occurs through the mechanism of natural selection is completely uncontested within the scientific literature.

As Darwin recognized early on, perhaps the most controversial aspect of evolutionary thought is its application to human beings. Specifically, many object to the idea that all diversity in life, including human beings, arose through natural processes without supernatural intervention. Although many religions, such as Catholicism, have reconciled their beliefs with evolution through theistic evolution, creationists object to evolution as it contradicts their theistic origin beliefs. In some countries — notably the United States — these tensions between scientific and religious teachings have fueled the ongoing creation-evolution controversy, a social and religious conflict especially centering on politics and public education. While other scientific fields such as cosmology and earth science also conflict with literal interpretations of many religious texts, evolutionary biology has borne the brunt of these debates.

Evolution has been used to support philosophical and ethical views that most contemporary scientists consider to have been neither mandated by evolution nor supported by data. For example, the eugenic ideas of Francis Galton were developed into arguments that the human gene pool should be improved by selective breeding policies, including incentives for reproduction for those of "good stock" and the compulsory sterilization, prenatal testing, birth control, and even killing, of those of "bad stock". Another example of an extension of evolutionary theory that is now widely regarded as unwarranted is "Social Darwinism", a term given to the 19th century Whig Malthusian theory developed by Herbert Spencer into ideas about "survival of the fittest" in commerce and human societies as a whole, and by others into claims that social inequality, racism, and imperialism were justified.

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Further reading

Introductory reading

• Jones, S., Darwin's Ghost: The Origin of Species Updated (Ballantine Books, 2001) ISBN 0-345-42277-5
• Dawkins, R., The Selfish Gene. (Oxford University Press, USA; 3rd edition, 2006) ISBN 0-199-29114-4
• Gould, SJ, Wonderful Life: The Burgess Shale and the Nature of History. (W. W. Norton & Company, 1990) ISBN 0-393-30700-X
• Carroll, SB., Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom. (W. W. Norton & Company, 2005) ISBN 0-393-06016-0

History of evolutionary thought

• Larson, EJ., Evolution: The Remarkable History of a Scientific Theory. (Modern Library, 2004) ISBN 0-679-64288-9
• Zimmer, C., Evolution: The Triumph of an Idea. (Academic Internet Publishers, 2006) ISBN 0-060-19906-7

Advanced reading

• Williams, GC., Adaptation and Natural Selection: A Critique of some Current Evolutionary Thought. (Princeton University Press, 1966) ISBN 0-691-02357-3
• Futuyma, DJ., Evolution (Sinauer Associates, 2005) ISBN 0-878-93187-2
• Mayr, E., What Evolution Is. (Basic Books, 2002) ISBN 0-465-04426-3
• Coyne, JA. and Orr, HA., Speciation (Sinauer Associates, 2004) ISBN 0-878-93089-2
• Smith, JM. and Szathmary, E., The Major Transitions in Evolution (Oxford University Press, 1997) ISBN 0-198-50294-X

External links

2. Part 2

General information

• Understanding Evolution from University of California, Berkeley
• National Academies Evolution Resources
• Everything you wanted to know about evolution (provided by New Scientist)
• Howstuffworks.com — How Evolution Works
• Synthetic Theory Of Evolution: An Introduction to Modern Evolutionary Concepts and Theories
• Evolution News by the Genome News Network

History of evolutionary thought

• The Complete Work of Charles Darwin Online, Darwin's writings and ancillary texts by other authors
• Understanding Evolution: History, Theory, Evidence, and Implications Deals heavily with the history of thoughts about evolution

Template:Link FA

• Evolution
• Evolutionary biology