Evolution

Evolution is change in the heritable characteristics of biological populations over successive generations.[1][2] These characteristics are the expressions of genes that are passed on from parent to offspring during reproduction. Different characteristics tend to exist within any given population as a result of mutation, genetic recombination and other sources of genetic variation.[3] Evolution occurs when evolutionary processes such as natural selection (including sexual selection) and genetic drift act on this variation, resulting in certain characteristics becoming more common or rare within a population.[4] It is this process of evolution that has given rise to biodiversity at every level of biological organisation, including the levels of species, individual organisms and molecules.[5][6]

The scientific theory of evolution by natural selection was conceived independently by Charles Darwin and Alfred Russel Wallace in the mid-19th century and was set out in detail in Darwin's book On the Origin of Species (1859).[7] Evolution by natural selection was first demonstrated by the observation that more offspring are often produced than can possibly survive. This is followed by three observable facts about living organisms: (1) traits vary among individuals with respect to their morphology, physiology and behaviour (phenotypic variation), (2) different traits confer different rates of survival and reproduction (differential fitness) and (3) traits can be passed from generation to generation (heritability of fitness).[8] Thus, in successive generations members of a population are more likely to be replaced by the progenies of parents with favourable characteristics that have enabled them to survive and reproduce in their respective environments. In the early 20th century, other competing ideas of evolution such as mutationism and orthogenesis were refuted as the modern synthesis reconciled Darwinian evolution with classical genetics, which established adaptive evolution as being caused by natural selection acting on Mendelian genetic variation.[9]

All life on Earth shares a last universal common ancestor (LUCA)[10][11][12] that lived approximately 3.5–3.8 billion years ago.[13] The fossil record includes a progression from early biogenic graphite,[14] to microbial mat fossils,[15][16][17] to fossilised multicellular organisms. Existing patterns of biodiversity have been shaped by repeated formations of new species (speciation), changes within species (anagenesis) and loss of species (extinction) throughout the evolutionary history of life on Earth.[18] Morphological and biochemical traits are more similar among species that share a more recent common ancestor, and can be used to reconstruct phylogenetic trees.[19][20]

Evolutionary biologists have continued to study various aspects of evolution by forming and testing hypotheses as well as constructing theories based on evidence from the field or laboratory and on data generated by the methods of mathematical and theoretical biology. Their discoveries have influenced not just the development of biology but numerous other scientific and industrial fields, including agriculture, medicine and computer science.[21]

Contents
 * 1History of evolutionary thought
 * 1.1Classical times
 * 1.2Medieval
 * 1.3Pre-Darwinian
 * 1.4Darwinian revolution
 * 1.5Pangenesis and heredity
 * 1.6The 'modern synthesis'
 * 1.7Further syntheses
 * 2Heredity
 * 3Variation
 * 3.1Mutation
 * 3.2Sex and recombination
 * 3.3Gene flow
 * 4Mechanisms
 * 4.1Natural selection
 * 4.1.1Genetic hitchhiking
 * 4.2Genetic drift
 * 4.3Gene flow
 * 4.4Mutation bias
 * 5Outcomes
 * 5.1Adaptation
 * 5.2Coevolution
 * 5.3Cooperation
 * 5.4Speciation
 * 5.5Extinction
 * 6Evolutionary history of life
 * 6.1Origin of life
 * 6.2Common descent
 * 6.3Evolution of life
 * 7Applications
 * 8Social and cultural responses
 * 9See also
 * 10References
 * 11Bibliography
 * 12Further reading
 * 13External links

History of evolutionary thought
Main article: History of evolutionary thought

Further information: History of speciation

Classical times
The proposal that one type of organism could descend from another type goes back to some of the first pre-Socratic Greek philosophers, such as Anaximander and Empedocles.[23] Such proposals survived into Roman times. The poet and philosopher Lucretius followed Empedocles in his masterwork De rerum natura (On the Nature of Things).[24][25]

Medieval
In contrast to these materialistic views, Aristotelianism considered all natural things as actualisations of fixed natural possibilities, known as forms.[26][27] This was part of a medieval teleological understanding of nature in which all things have an intended role to play in a divine cosmic order. Variations of this idea became the standard understanding of the Middle Ages and were integrated into Christian learning, but Aristotle did not demand that real types of organisms always correspond one-for-one with exact metaphysical forms and specifically gave examples of how new types of living things could come to be.[28]

Pre-Darwinian
In the 17th century, the new method of modern science rejected the Aristotelian approach. It sought explanations of natural phenomena in terms of physical laws that were the same for all visible things and that did not require the existence of any fixed natural categories or divine cosmic order. However, this new approach was slow to take root in the biological sciences, the last bastion of the concept of fixed natural types. John Ray applied one of the previously more general terms for fixed natural types, "species", to plant and animal types, but he strictly identified each type of living thing as a species and proposed that each species could be defined by the features that perpetuated themselves generation after generation.[29] The biological classification introduced by Carl Linnaeus in 1735 explicitly recognised the hierarchical nature of species relationships, but still viewed species as fixed according to a divine plan.[30]

Other naturalists of this time speculated on the evolutionary change of species over time according to natural laws. In 1751, Pierre Louis Maupertuis wrote of natural modifications occurring during reproduction and accumulating over many generations to produce new species.[31] Georges-Louis Leclerc, Comte de Buffon suggested that species could degenerate into different organisms, and Erasmus Darwin proposed that all warm-blooded animals could have descended from a single microorganism (or "filament").[32] The first full-fledged evolutionary scheme was Jean-Baptiste Lamarck's "transmutation" theory of 1809,[33] which envisaged spontaneous generation continually producing simple forms of life that developed greater complexity in parallel lineages with an inherent progressive tendency, and postulated that on a local level, these lineages adapted to the environment by inheriting changes caused by their use or disuse in parents.[34][35] (The latter process was later called Lamarckism.)[34][36][37][38] These ideas were condemned by established naturalists as speculation lacking empirical support. In particular, Georges Cuvier insisted that species were unrelated and fixed, their similarities reflecting divine design for functional needs. In the meantime, Ray's ideas of benevolent design had been developed by William Paley into the Natural Theology or Evidences of the Existence and Attributes of the Deity (1802), which proposed complex adaptations as evidence of divine design and which was admired by Charles Darwin.[39][40][41]

Darwinian revolution
The crucial break from the concept of constant typological classes or types in biology came with the theory of evolution through natural selection, which was formulated by Charles Darwin in terms of variable populations. Darwin used the expression "descent with modification" rather than "evolution".[42] Partly influenced by An Essay on the Principle of Population (1798) by Thomas Robert Malthus, Darwin noted that population growth would lead to a "struggle for existence" in which favourable variations prevailed as others perished. In each generation, many offspring fail to survive to an age of reproduction because of limited resources. This could explain the diversity of plants and animals from a common ancestry through the working of natural laws in the same way for all types of organism.[43][44][45][46] Darwin developed his theory of "natural selection" from 1838 onwards and was writing up his "big book" on the subject when Alfred Russel Wallace sent him a version of virtually the same theory in 1858. Their separate papers were presented together at an 1858 meeting of the Linnean Society of London.[47] At the end of 1859, Darwin's publication of his "abstract" as On the Origin of Species explained natural selection in detail and in a way that led to an increasingly wide acceptance of Darwin's concepts of evolution at the expense of alternative theories. Thomas Henry Huxley applied Darwin's ideas to humans, using paleontology and comparative anatomy to provide strong evidence that humans and apes shared a common ancestry. Some were disturbed by this since it implied that humans did not have a special place in the universe.[48]

Pangenesis and heredity
The mechanisms of reproductive heritability and the origin of new traits remained a mystery. Towards this end, Darwin developed his provisional theory of pangenesis.[49] In 1865, Gregor Mendel reported that traits were inherited in a predictable manner through the independent assortment and segregation of elements (later known as genes). Mendel's laws of inheritance eventually supplanted most of Darwin's pangenesis theory.[50] August Weismann made the important distinction between germ cells that give rise to gametes (such as sperm and egg cells) and the somatic cells of the body, demonstrating that heredity passes through the germ line only. Hugo de Vries connected Darwin's pangenesis theory to Weismann's germ/soma cell distinction and proposed that Darwin's pangenes were concentrated in the cell nucleus and when expressed they could move into the cytoplasm to change the cell's structure. De Vries was also one of the researchers who made Mendel's work well known, believing that Mendelian traits corresponded to the transfer of heritable variations along the germline.[51] To explain how new variants originate, de Vries developed a mutation theory that led to a temporary rift between those who accepted Darwinian evolution and biometricians who allied with de Vries.[35][52][53] In the 1930s, pioneers in the field of population genetics, such as Ronald Fisher, Sewall Wright and J. B. S. Haldane set the foundations of evolution onto a robust statistical philosophy. The false contradiction between Darwin's theory, genetic mutations, and Mendelian inheritance was thus reconciled.[54]

The 'modern synthesis'
Main article: Modern synthesis (20th century)

In the 1920s and 1930s the so-called modern synthesis connected natural selection and population genetics, based on Mendelian inheritance, into a unified theory that applied generally to any branch of biology. The modern synthesis explained patterns observed across species in populations, through fossil transitions in palaeontology, and complex cellular mechanisms in developmental biology.[35][55] The publication of the structure of DNA by James Watson and Francis Crick with contribution of Rosalind Franklin in 1953 demonstrated a physical mechanism for inheritance.[56] Molecular biology improved understanding of the relationship between genotype and phenotype. Advancements were also made in phylogenetic systematics, mapping the transition of traits into a comparative and testable framework through the publication and use of evolutionary trees.[57][58] In 1973, evolutionary biologist Theodosius Dobzhansky penned that "nothing in biology makes sense except in the light of evolution," because it has brought to light the relations of what first seemed disjointed facts in natural history into a coherent explanatory body of knowledge that describes and predicts many observable facts about life on this planet.[59]

Further syntheses
Since then, the modern synthesis has been further extended to explain biological phenomena across the full and integrative scale of the biological hierarchy, from genes to species. One extension, known as evolutionary developmental biology and informally called "evo-devo," emphasises how changes between generations (evolution) acts on patterns of change within individual organisms (development).[60][61][62] Since the beginning of the 21st century and in light of discoveries made in recent decades, some biologists have argued for an extended evolutionary synthesis, which would account for the effects of non-genetic inheritance modes, such as epigenetics, parental effects, ecological inheritance and cultural inheritance, and evolvability.[63][64]

Heredity
Further information: Introduction to genetics, Genetics, Heredity, and Reaction norm Evolution in organisms occurs through changes in heritable traits—the inherited characteristics of an organism. In humans, for example, eye colour is an inherited characteristic and an individual might inherit the "brown-eye trait" from one of their parents.[65] Inherited traits are controlled by genes and the complete set of genes within an organism's genome (genetic material) is called its genotype.[66]

The complete set of observable traits that make up the structure and behaviour of an organism is called its phenotype. These traits come from the interaction of its genotype with the environment.[67] As a result, many aspects of an organism's phenotype are not inherited. For example, suntanned skin comes from the interaction between a person's genotype and sunlight; thus, suntans are not passed on to people's children. However, some people tan more easily than others, due to differences in genotypic variation; a striking example are people with the inherited trait of albinism, who do not tan at all and are very sensitive to sunburn.[68]

Heritable traits are passed from one generation to the next via DNA, a molecule that encodes genetic information.[66] DNA is a long biopolymer composed of four types of bases. The sequence of bases along a particular DNA molecule specify the genetic information, in a manner similar to a sequence of letters spelling out a sentence. Before a cell divides, the DNA is copied, so that each of the resulting two cells will inherit the DNA sequence. Portions of a DNA molecule that specify a single functional unit are called genes; different genes have different sequences of bases. Within cells, the long strands of DNA form condensed structures called chromosomes. The specific location of a DNA sequence within a chromosome is known as a locus. If the DNA sequence at a locus varies between individuals, the different forms of this sequence are called alleles. DNA sequences can change through mutations, producing new alleles. If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the organism.[69] However, while this simple correspondence between an allele and a trait works in some cases, most traits are more complex and are controlled by quantitative trait loci (multiple interacting genes).[70][71]

Recent findings have confirmed important examples of heritable changes that cannot be explained by changes to the sequence of nucleotides in the DNA. These phenomena are classed as epigenetic inheritance systems.[72] DNA methylation marking chromatin, self-sustaining metabolic loops, gene silencing by RNA interference and the three-dimensional conformation of proteins (such as prions) are areas where epigenetic inheritance systems have been discovered at the organismic level.[73][74] Developmental biologists suggest that complex interactions in genetic networks and communication among cells can lead to heritable variations that may underlay some of the mechanics in developmental plasticity and canalisation.[75] Heritability may also occur at even larger scales. For example, ecological inheritance through the process of niche construction is defined by the regular and repeated activities of organisms in their environment. This generates a legacy of effects that modify and feed back into the selection regime of subsequent generations. Descendants inherit genes plus environmental characteristics generated by the ecological actions of ancestors.[76] Other examples of heritability in evolution that are not under the direct control of genes include the inheritance of cultural traits and symbiogenesis.[77][78]

Variation
Main article: Genetic variation

Further information: Genetic diversity and Population genetics

An individual organism's phenotype results from both its genotype and the influence from the environment it has lived in. A substantial part of the phenotypic variation in a population is caused by genotypic variation.[71] The modern evolutionary synthesis defines evolution as the change over time in this genetic variation. The frequency of one particular allele will become more or less prevalent relative to other forms of that gene. Variation disappears when a new allele reaches the point of fixation—when it either disappears from the population or replaces the ancestral allele entirely.[79]

Natural selection will only cause evolution if there is enough genetic variation in a population. Before the discovery of Mendelian genetics, one common hypothesis was blending inheritance. But with blending inheritance, genetic variance would be rapidly lost, making evolution by natural selection implausible. The Hardy–Weinberg principle provides the solution to how variation is maintained in a population with Mendelian inheritance. The frequencies of alleles (variations in a gene) will remain constant in the absence of selection, mutation, migration and genetic drift.[80]

Variation comes from mutations in the genome, reshuffling of genes through sexual reproduction and migration between populations (gene flow). Despite the constant introduction of new variation through mutation and gene flow, most of the genome of a species is identical in all individuals of that species.[81] However, even relatively small differences in genotype can lead to dramatic differences in phenotype: for example, chimpanzees and humans differ in only about 5% of their genomes.[82]