In biology, evolution is the process by which novel traits arise in populations and are passed on from generation to generation. Its action over large stretches of time explains the origin of new species and ultimately the vast diversity of the biological world. Contemporary species are related to each other through common descent, products of evolution and speciation over billions of years. The phylogenetic tree on the right represents these relationships for the three major domains of life.

The understanding of evolution is based on the theory of natural selection, which was first set out in a joint 1858 paper by Charles Darwin and Alfred Russel Wallace, and achieved a wider readership in Darwin's 1859 book, On The Origin of Species. Natural selection is the idea that individual organisms which possess variations giving them advantageous heritable traits are more likely to survive and reproduce and, in doing so, increase the frequency of such traits in subsequent generations.

In the 1930s scientists combined Darwinian natural selection with the theory of Mendelian heredity to create the modern evolutionary synthesis (often simply called the modern synthesis). The modern synthesis understands evolution to be a change in the frequency of alleles within a population from one generation to the next. The mechanisms that produce these changes are the basic mechanisms of population genetics: natural selection and genetic drift acting on genetic variation created by mutation, sex, and gene flow. This theory has become the central organizing principle of modern biology. It helps biologists understand topics as diverse as the origin of antibiotic resistance in bacteria, eusociality in insects, and the staggering biodiversity of the living world.

Because of its potential implications for the origins of humankind, the evolutionary theory has been at the center of many social and religious controversies since it was first introduced.

History of evolutionary thought

The idea of biological evolution has existed since ancient times, notably among Greek philosophers such as Epicurus and Anaximander, however, the modern theory was not established until the 18th and 19th centuries, by scientists such as Jean-Baptiste Lamarck and Charles Darwin. Transmutation of species was accepted by many scientists before 1859, but the publication of Charles Darwin's On The Origin of Species by Means of Natural Selection provided the first cogent mechanism by which evolutionary change could occur: his theory of natural selection. Darwin was motivated to publish his work on evolution after receiving a letter from Alfred Russel Wallace, in which Wallace revealed his own discovery of natural selection. Accordingly, Wallace is sometimes given shared credit for originating the theory that evolution could be explained through natural selection.

Darwin's theory, although it succeeded in profoundly shaking scientific opinion about the development of life, could not explain the source of variation in traits within a species, and Darwin's proposal of a hereditary mechanism (pangenesis) was not compelling to biologists. Although the occurrence of evolution of some sort became a widely-accepted scientific belief, Darwin's specific ideas about evolution — that it occurred gradually by natural and sexual selection — were actively attacked and rejected. From the end of the 19th century through the early-20th century, forms of neo-Lamarckism, "progressive" evolution (orthogenesis), and an evolution which worked by "jumps" (saltationism, as opposed to gradualism) became popular, although a form of neo-Darwinism (led by August Weismann) also enjoyed some minor success. The biometric school of evolutionary theory resulting from the work of Darwin's cousin, Francis Galton, emerged as well, using statistical approaches to biology which emphasized gradualism and some aspects of natural selection.

When Gregor Mendel's work on the nature of inheritance in the late 19th century was "rediscovered" in 1900, it was interpreted as supporting an anti-Darwinian "jumping" form of evolution. The convinced Mendelians (William Bateson and Charles Benedict Davenport) and biometricians (Walter Frank Raphael Weldon and Karl Pearson) became embroiled in a bitter debate, with Mendelians charging that the biometricians did not understand biology, and biometricians arguing that most biological traits exhibited continuous variation rather than the "jumps" expected by the early Mendelian theory. However the simple version of the early Mendelians soon gave way to the classical genetics of Thomas Hunt Morgan and his school, which thoroughly grounded and articulated the applications of Mendelian laws to biology. Eventually, it was shown that a rigorous statistical approach to Mendelism was reconcileable with the data of the biometricians by the work of biologist and statistician R.A. Fisher in the 1930s. Following this, the work of population geneticists and zoologists in the 1930s and 1940s created a model of Darwinian evolution compatible with the science of genetics, which became known as the modern evolutionary synthesis.

In the 1940s, following up on Griffith's experiment, Avery, McCleod and McCarty definitively identified deoxyribonucleic acid (DNA) as the "transforming principle" responsible for transmitting genetic information. In 1953, Francis Crick and James Watson published their famous paper on the structure of DNA, based on the research of Rosalind Franklin and Maurice Wilkins. These developments ignited the era of molecular biology and transformed the understanding of evolution into a molecular process: the mutation of segments of DNA.

George C. Williams' 1966 Adaptation and natural selection: A Critique of some Current Evolutionary Thought marked a departure from the idea of group selection towards the modern notion of the gene as the unit of selection. In the mid-1970s, Motoo Kimura formulated the neutral theory of molecular evolution, firmly establishing the importance of genetic drift as a major mechanism of evolution.

Debates have continued within the field. One prominent public debate was over the theory of punctuated equilibrium, proposed in 1972 by paleontologists Niles Eldredge and Stephen Jay Gould to explain the paucity of gradual transitions between species in the fossil record.

The big recent development in evolutionary biology has been the improved resolution in our understanding of genetics.

Overview of evolution

Evidence of evolution

The process of evolution has left behind numerous records which reveal the history of different species. While the best-known of these are the fossils, fossils are only a small part of the overall physical record of evolution. Fossils, taken together with the comparative anatomy of present-day plants and animals, constitute the morphological record. By comparing the anatomies of both modern and extinct species, biologists can reconstruct the lineages of those species with some accuracy. Using fossil evidence, for instance, the connection between dinosaurs and birds has been established by way of so-called "transitional" species such as Archaeopteryx.

The development of genetics has allowed biologists to study the genetic record of evolution as well. Although we cannot obtain the DNA sequences of most extinct species, the degree of similarity and difference among modern species allows geneticists to reconstruct lineages with greater accuracy. It is from genetic comparisons that claims such as the 95% similarity between humans and chimpanzees come from, for instance.

Other evidence used to demonstrate evolutionary lineages includes the geographical distribution of species. For instance, monotremes and most marsupials are found only in Australia, showing that their common ancestor with placental mammals lived before the submerging of the ancient land bridge between Australia and Asia.

Scientists correlate all of the above evidence – drawn from paleontology, anatomy, genetics, and geography – with other information about the history of the earth. For instance, paleoclimatology attests to periodic ice ages during which the climate was much cooler; and these are found to match up with the spread of species such as the woolly mammoth which are better-equipped to deal with cold.

Morphological evidence

Fossil evidence of prehistoric organisms has been found all over the Earth. The age of fossils are typically synchronized with the geologic context in which they are found; many of their absolute ages can be verified with radiometric dating. Some fossils bear a resemblance to organisms alive today, while others are radically different. Fossils have been used to determine at what time a lineage developed, and transitional fossils can be used to demonstrate continuity between two different lineages. Paleontologists investigate evolution largely through analysis of fossils.

Phylogenetics, the study of the ancestry of species, has revealed that structures with similar internal organization may perform divergent functions. Vertebrate limbs are a common example of such homologous structures. Bat wings, for example, are very similar to hands. A vestigial organ or structure may exist with little or no purpose in one organism, though they have a clear purpose in other species. The human wisdom teeth and appendix are common examples.

Genetic sequence evidence

Comparison of the genetic sequence of organisms reveals that phylogenetically close organisms have a higher degree of sequence similarity than organisms that are phylogenetically distant. For example, neutral human DNA sequences are approximately 1.2% divergent (based on substitutions) from those of their nearest genetic relative, the chimpanzee, 1.6% from gorillas, and 6.6% from baboons. Sequence comparison is considered a measure robust enough to be used to correct erroneous assumptions in the phylogenetic tree in instances where other evidence is scarce.

Further evidence for common descent comes from genetic detritus such as pseudogenes, regions of DNA which are orthologous to a gene in a related organism, but are no longer active and appear to be undergoing a steady process of degeneration.

Since metabolic processes do not leave fossils, research into the evolution of the basic cellular processes is done largely by comparison of existing organisms. Many lineages diverged when new metabolic processes appeared, and it is theoretically possible to determine when certain metabolic processes appeared by comparing the traits of the descendants of a common ancestor.

The New York Times report Still Evolving, Human Genes Tell New Story based on A Map of Recent Positive Selection in the Human Genome states the International HapMap Project is "providing the strongest evidence yet that humans are still evolving" and details some of that evidence.

Genetic sequence evidence literally provides a picture of "the missing link" between humans and other apes.

Evidence from studies of complex iteratation

"It has taken more than five decades, but the electronic computer is now powerful enough to simulate evolution" assisting bioinformatics in its attempt to solve biological problems.

Computer science allows the iteration of self changing complex systems to be studied, allowing a mathematically exact understanding of the nature of the processes behind evolution; providing evidence for the hidden causes of known evolutionary events. The evolution of specific cellular mechanisms like spliceosomes that can turn the cell's genome into a vast workshop of billions of interchangeable parts that can create tools that create tools that create tools that create us can be studied for the first time in an exact way.

For example, Christoph Adami et. al. make this point in Evolution of biological complexity:

To make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition identifies genomic complexity with the amount of information a sequence stores about its environment. We investigate the evolution of genomic complexity in populations of digital organisms and monitor in detail the evolutionary transitions that increase complexity. We show that, because natural selection forces genomes to behave as a natural "Maxwell Demon," within a fixed environment, genomic complexity is forced to increase.

For example, David J. Earl and Michael W. Deem make this point in Evolvability is a selectable trait:

Not only has life evolved, but life has evolved to evolve. That is, correlations within protein structure have evolved, and mechanisms to manipulate these correlations have evolved in tandem. The rates at which the various events within the hierarchy of evolutionary moves occur are not random or arbitrary but are selected by Darwinian evolution. Sensibly, rapid or extreme environmental change leads to selection for greater evolvability. This selection is not forbidden by causality and is strongest on the largest-scale moves within the mutational hierarchy. Many observations within evolutionary biology, heretofore considered evolutionary happenstance or accidents, are explained by selection for evolvability. For example, the vertebrate immune system shows that the variable environment of antigens has provided selective pressure for the use of adaptable codons and low-fidelity polymerases during somatic hypermutation. A similar driving force for biased codon usage as a result of productively high mutation rates is observed in the hemagglutinin protein of influenza A.

"Computer simulations of the evolution of linear sequences have demonstrated the importance of recombination of blocks of sequence rather than point mutagenesis alone. Repeated cycles of point mutagenesis, recombination, and selection should allow in vitro molecular evolution of complex sequences, such as proteins." Evolutionary molecular engineering, also called directed evolution or in vitro molecular evolution involves the iterated cycle of mutation, multiplication with recombination, and selection of the fittest of individual molecules (proteins, DNA, and RNA). Natural evolution can be relived showing us possible paths from catalytic cycles based on proteins to based on RNA to based on DNA.

Ancestry of organisms

In biology, the theory of universal common descent proposes that all organisms on Earth are descended from a common ancestor or ancestral gene pool (which is called having "common descent").

Evidence for common descent may be found in traits shared between all living organisms. In Darwin's day, the evidence of shared traits was based solely on visible observation of morphologic similarities, such as the fact that all birds — even those which do not fly — have wings. Today, there is strong evidence from Genetics that evolution occurs and that it does so by natural selection. For example, every living cell makes use of nucleic acids as its genetic material, and uses the same twenty amino acids as the building blocks for proteins. All organisms use the same genetic code (with some extremely rare and minor deviations) to translate nucleic acid sequences into proteins. The universality of these traits strongly suggests common ancestry, because the selection of these traits seems somewhat arbitrary.

The evolutionary process can be exceedingly slow. Fossil evidence indicates that the diversity and complexity of modern life has developed over much of the age of the earth. Geological evidence indicates that the Earth is approximately 4.6 billion years old.

Studies on guppies by David Reznick at the University of California, Riverside, however, have shown that the rate of evolution through natural selection can proceed 10 thousand to 10 million times faster than what is indicated in the fossil record.

Information about the early development of life includes input from the fields of geology and planetary science. These sciences provide information about the history of the Earth and the changes produced by life. A great deal of information about the early Earth has been destroyed by geological processes over the course of time.

History of life

The emergence of oxygenic photosynthesis (around 3 billion years ago) and the subsequent emergence of an oxygen-rich, non-reducing atmosphere can be traced through the formation of banded iron deposits, and later red beds of iron oxides. This was a necessary prerequisite for the development of aerobic cellular respiration, believed to have emerged around 2 billion years ago.

In the last billion years, simple multicellular plants and animals began to appear in the oceans. Soon after the emergence of the first animals, the Cambrian explosion (a period of unrivaled and remarkable, but brief, organismal diversity documented in the fossils found at the Burgess Shale) saw the creation of all the major body plans, or phyla, of modern animals. This event is now believed to have been triggered by the development of the Hox genes. About 500 million years ago, plants and fungi colonized the land, and were soon followed by arthropods and other animals, leading to the development of land ecosystems with which we are familiar.

Misconceptions about modern evolutionary biology

Many critics of evolution claim that the theory robs life and the universe of any transcendental meaning. Indeed, one of the great strengths of evolution by natural selection is that it has no need for a supernatural intelligence or any intelligent design. As Louis Menand has pointed out, what was radical about Darwin's theory of speciation through natural selection was not the notion of evolution — a concept people espoused before Darwin, and a word that does not appear in The Origin of Species — but his presentation of a natural method by which this might take place: "Darwin wanted to establish... that the species — including human beings — were created by, and evolve according to, processes that are entirely natural, chance-generated, and blind" .

Nevertheless, many critiques of modern evolutionary thought involve misunderstandings of the theory itself, or of science in general.

Evolution and devolution

One of the most common misunderstandings of evolution is that one species can be "more highly evolved" than another, that evolution is necessarily progressive, or that its converse is "devolution". Evolution provides no assurance that later generations are more intelligent, complex, or morally worthy than earlier generations. The claim that evolution results in moral progress is not part of modern evolutionary theory – that claim is associated with Social Darwinism, which held that the subjugation of the poor, and of minority groups, was favored by evolution.

In many cases evolution does involve "progression" towards more complexity, since the earliest lifeforms were clearly much simpler than many of the species existing today. In that sense, there clearly has been a gradual movement over time from simple organisms to complex – and in some cases intelligent – lifeforms. However, there is no guarantee that any particular organism existing today will become more intelligent, more complex, bigger, or stronger in the future. In fact, natural selection will only favor this kind of "progression" if it increases chance of survival. The same mechanism can actually favor lower intelligence, lower complexity, and so on if those traits become a selective advantage in the organism's environment.

Speciation

Another misunderstanding is the claim that speciation – the origin of new species – has never been directly observed. This is a misunderstanding of both science and evolution. First, scientific discovery does not occur solely through reproducible experiments; the principle of uniformitarianism allows natural scientists to infer causes through their empirical effects. Second, Darwin provided a compellingly large amount of evidence to support his theory. Moreover, since the publication of On the Origin of Species scientists have confirmed Darwin's hypothesis by data gathered from sources that did not exist in his day, such as DNA similarity among species and new fossil discoveries.

A variation of this assertion is that "microevolution" has been observed and "macroevolution" has not been observed. Some creationists redefine macroevolution as a change from one "kind" to another. One of Darwin's key insights was to view species statistically – that is, a "species" is not a homogeneous and immutable thing; rather, it consists of a mass of individuals that vary in form from one another and from their offspring. This view was substantiated with the development of Mendelian genetics, which distinguishes different species in terms of differences in the frequencies of particular genes. "Microevolution" and "macroevolution" both refer fundamentally to the same thing, changes in gene frequencies. The difference between them is primarily one of scale; that is, qualitative differences between species is the result of quantitative differences in gene frequencies. Commonly, macroevolution is defined as microevolution over a longer timescale. Some scientists, such as Stephen Jay Gould, use the term macroevolution to instead describe evolutionary processes that occur at the level of species or above.

Evidence of the mechanisms for the larger scales of time comes from evidence of the mechanisms for the smaller scales of time. The differences between macroevolution and microevolution are a result of this change of scale and do not necessitate mechanisms of change other than those already found in microevolution.

Entropy

Another misconception is the claim that evolution violates the second law of thermodynamics. The second law holds that in a closed system, entropy will tend to increase or stay the same. The misconception is that entropy means "disorder" and evolution means an increase in order (thus, a decrease in entropy). This is a misunderstanding of both entropy and evolution. "Entropy" does not mean "disorder" in a generic way (any set of objects may be ordered in any number of ways; disorder from one perspective may be order from another). Secondly, entropy refers specifically to differences in useable energy; an example of which is temperature differences.

What appears to be a violation of the second law is not evolution (meaning, the development of new species of life) but rather life itself. But the existence of life does not violate the second law of thermodynamics for two reasons. First, the second law of thermodynamics applies only to a closed system. Earth is not a closed system because it receives an energy input from the sun. However much life may proliferate on earth, the energy of the sun does dissipate over time.

The second law is not deterministic, it is probabilistic as is shown in statistical mechanics. For example, molecules within a container move at different velocities; the temperature of the contents is an average. The more time passes, the greater the probability that differences in temperature within the chamber will even out. This fact does not mean that at any given moment there is a small chance that differences in temperature will increase. As Louis Menand has observed, Darwin's theory of natural selection operates in an analogous fashion: at any given moment most of the members of a species vary little from the average form. Nevertheless, at any given moment there are deviations from the average, and it is the natural selection of specific deviations that leads to a new species. In other words, Darwin applied the same statistical approach to biology that Maxwell applied to physics .

Organization

When they consider rocks that just sit there, some people may think it is obvious that matter cannot organize itself. Matter, in fact, organizes itself in numerous ways. Crystals such as diamonds and snowflakes can and do self-organize. Likewise proteins fold in very specific ways based on their chemical makeup. Amino acids are the building blocks of proteins. While the chemical conditions on the relatively young Earth 3.5 billion years ago, when life evolved, are still being debated, the spontaneous synthesis of amino acids has been shown for a wide range of conditions, in such settings as the Miller-Urey experiment.

Information

Misunderstanding the nature of information, some assert that evolution cannot create information, that information is a manifestation of intelligence. Physical information exists regardless of the presence of an intelligence, and evolution allows for new information whenever a novel mutation or gene duplication occurs and is kept. It does not need to be beneficial nor visually apparent to be "information." However, even if those were requirements they would be satisfied with the appearance of nylon-eating bacteria , which required new enzymes to digest a material that never existed until the modern age.

"It wasn't a highly competent design because the bacteria weren't extracting a lot of energy from the process, just enough to get by. And it was based on a simply frame shift reading of a gene that had other uses. But with a simple frame shift of a gene that was already there, it could now "eat" nylon. Future mutations, perhaps point mutations inside that gene, could conceivably heighten the energy gain of the nylon decomp process, and allow the bacteria to truly feast and reproduce faster and more plentifully on just nylon, thus leading perhaps in time to an irreducibly complex arrangement between bacteria who live solely on nylon and a man-made fiber produced only by man."

Science of evolution

The word "evolution" has been used to refer both to a fact and a theory, and it is important to understand both these different meanings of evolution, and the relationship between fact and theory in science.

Status of evolution in science

When "evolution" is used to describe a fact, it refers to the observations that populations of one species of organism do, over time, change into new species. In this sense, evolution occurs whenever a new species of bacterium evolves that is resistant to antibiotics that had been lethal to prior strains.

When "evolution" is used to describe a theory, it refers to an explanation for why and how evolution (for example, in the sense of "speciation") occurs. An example of evolution as theory is the modern synthesis of Darwin and Wallace's theory of natural selection and Mendel's principles of genetics. This theory has three major aspects:

1. Common descent of all organisms from a single ancestor or ancestral gene pool.
2. Manifestation of novel traits in a lineage.
3. Mechanisms that cause some traits to persist while others perish.

When people provide evidence for evolution, in some cases they are providing evidence that evolution occurs; in other cases they are providing evidence that a given theory is the best explanation yet as to why and how evolution occurs.

Distinctions between theory and fact

The modern synthesis, like its Mendelian and Darwinian antecedents, is a scientific theory. In plain English, people use the word "theory" to signify "conjecture", "speculation", or "opinion." In this sense, "theories" are opposed to "facts" — parts of the world, or claims about the world, that are real or true regardless of what people think. In scientific terminology however, a theory is a model of the world (or some portion of it) from which falsifiable predictions can be generated and tested through controlled experiments, or be verified through empirical observation. In this scientific sense, "facts" exist only as parts of theories – they are things, or relationships between things, that theories must take for granted in order to make predictions, or that theories predict. In other words, for scientists "theory" and "fact" do not stand in opposition, but rather exist in a reciprocal relationship – for example, it is a "fact" that every apple ever dropped on earth (under normal, controlled conditions) has been observed to fall towards the center of the planet in a straight line, and the "theory" which explains these observations is the current theory of gravitation. In this same sense evolution is an observed fact and the modern synthesis is currently the most powerful theory explaining evolution. Within the science of biology, modern synthesis has completely replaced earlier accepted explanations for the origin of species, including Lamarckism and creationism.

Academic disciplines

Scholars in a number of academic disciplines continue to document examples of evolution, contributing to a deeper understanding of the underlying mechanisms. Every subdiscipline within biology both informs and is informed by knowledge of the theory and details of evolution (examples: population genetics, ecological genetics, human evolution, molecular evolution, phylogenetics, systematics, evo-devo). Mathematics (example bioinformatics), physics, chemistry and others all make important foundational contributions. 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 itself and human civilization upon it.

Evolutionary biology

At first it was an interdisciplinarity 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 use those organisms as systems 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.

Evolutionary developmental biology

Evolutionary developmental biology is an emergent subfield of evolutionary biology that looks at genes of related and unrelated organisms. By comparing the explicit nucleotide sequences of DNA/RNA, it is possible to trace and experimentally determine the timelines of species development. For example, gene sequences support the conclusion that chimpanzees are the closest primate ancestor to humans, and that arthropods (e.g., insects) and vertebrates (e.g., humans) have a common biological ancestor.

Physical anthropology

Physical anthropology emerged in the late 1800s 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 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 object of study of, physical anthropologists. In addition to studying skeletal remains, they began to study genetic variation among human populations (i.e. population genetics); thus, some physical anthropologists began calling themselves biological anthropologists.

Modern synthesis

The current understanding of the mechanistics of evolution differs considerably from the theory first outlined by Charles Darwin. Importantly, advances in genetics pioneered by Gregor Mendel led to a sophisticated understanding of the basis of variation and the mechanisms of inheritance. In addition natural selection has come to be seen as only one of a number of forces acting in evolution. A notable milestone in this regard was the formulation of the neutral theory of molecular evolution by Motoo Kimura.

Heredity

Later research identified the molecule DNA as the genetic material, through which traits are passed from parent to offspring, and identified genes as discrete elements within DNA. Though largely faithfully maintained within organisms, DNA is both variable across individuals and subject to a process of change or mutation.

Non-DNA based forms of heritable variation exist, which may change the way in which genes are expressed or maintained. The processes that produce these variations leave the genetic information intact and are often reversible. This is called epigenetic inheritance and may include phenomena such as DNA methylation, prions, and structural inheritance. Investigations continue into whether these mechanisms allow for the production of specific beneficial heritable variation in response to environmental signals. If this were shown to be the case, then some instances of evolution would lie outside of the typical Darwinian framework, which avoids any connection between environmental signals and the production of heritable variation.

Many organisms reproduce by sexual reproduction, which involves meiotic recombination followed by independent assortment of chromosomes and the joining of the gametes - usually egg and sperm.

Mechanisms of evolution

Evolution consists of two basic types of processes: those that introduce new genetic variation into a population, and those that affect the frequencies of existing variation. "Variation proposes and selection disposes."

The mechanisms of evolution include mutation, linkage, heterozygosity, recombination, gene flow, population structure, drift, natural selection, and adaptation.

These mechanisms of evolution have all been observed in the present and in evidence of their existence in the past. Their study is being used to guide the development of new medicines and other health aids such as the current effort to prevent a H5N1 (i.e. bird flu) pandemic.

Mutation

The ultimate source of all genetic variation is mutations. They are permanent, transmissible changes to the genetic material (usually DNA or RNA) of a cell, and can be caused by "copying errors" in the genetic material during cell division and by exposure to radiation, chemicals, or viruses. In multicellular organisms, mutations can be subdivided into germline mutations that occur in the gametes and thus can be passed on to progeny, and somatic mutations that often lead to the malfunction or death of a cell and can cause cancer.

Mutations that are not affected by natural selection are called neutral mutations. Their frequency in the population is governed entirely by genetic drift and gene flow. It is understood that a species' genome, in the absence of selection, undergoes a steady accumulation of neutral mutations. The probable mutation effect is the proposition that a gene that is not under selection will be destroyed by accumulated mutations. This is an aspect of genome degradation.

Not all mutations are created equal; simple point mutations (substitutions), which comprise the vast majority of genetic variation, usually can only alter the function or level of expression of existing genes. Gene duplications, which may occur via a number of mechanisms, are believed to be the major mechanism for the introduction of new genes; most genes belong to larger "families" of genes derived from a common ancestral gene (two genes from a species that are in the same family are dubbed "paralogs"). Finally, large chromosomal rearrangements (like the fusion of two chromosomes in the chimp/human common ancestor that produced human chromosome 2) almost invariably result in a speciation event.

Linkage and heterozygosity

Genetic variation cannot move perfectly freely through the population from one generation to the next. Deviations from a random distribution of alleles (a population where alleles are truly independently assorted and gametes randomly joined) may appear in the form of decreased heterozygosity - that is, the fraction of the population which has one copy of each allele. Low heterozygosity may result from inbreeding populations. High heterozygosity is usually a product of some forms of balancing selection.

A second significant restraint on alleles appears in the form of genetic linkage, where alleles that are nearby on a chromosome tend to be propagated together. This tendency may be measured by comparing the co-occurrence of two alleles, usually quantified as linkage disequilibrium (LD). A set of alleles that are often co-propagated is called a haplotype. Strong haplotype blocks are associated with high LD, and can be a product of strong positive selection or rapid demographic changes.

Recombination

This haplotype structure is the result of limited rates of recombination combined with drift or selection. It is the random assortment of chromosomes and meiotic recombination that allow mutations that have arisen on the same chromosome to be propagated in the population independently. This allows bad mutations to be purged and beneficial mutations to be retained more efficiently than in asexual populations.

Recombination is mildly mutagenic, which is one of the proposed reasons why it occurs with limited frequency. Recombination also breaks up gene combinations that have been successful in previous generations, and hence should be opposed by selection. However, recombination could be favoured by negative frequency-dependent selection (this is when rare variants increase in frequency) because it leads to more individuals with new and rare gene combinations being produced.

When alleles cannot be separated by recombination (for example in mammalian Y chromosomes), we see a reduction in effective population size, known as the Hill Robertson effect, and the successive establishment of bad mutations, known as Muller's ratchet.

Gene flow

Gene flow (also called gene admixture or simply migration) is introduction of variation into a population from an outside population. It is the only mechanism whereby two populations can become closer genetically while increasing their variation. Migration of one population into an area occupied by a second population can result in gene flow. Gene flow operates when geography and culture are not obstacles. When gene flow is impeded by non-geographic obstacles, the situation is termed reproductive isolation and is considered to be the hallmark of speciation.

One source of genetic variation is gene transfer, the movement of genetic material across species boundaries, which can include horizontal gene transfer, antigenic shift, reassortment, and hybridization. Viruses can transfer genes between species . Bacteria can incorporate genes from other dead bacteria, exchange genes with living bacteria, and can have plasmids "set up residence separate from the host's genome" . "Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of phylogenetic 'domains'. Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes."

Biologist Gogarten suggests "the original metaphor of a tree no longer fits the data from recent genome research" therefore "biologists [should] use the metaphor of a mosaic to describe the different histories combined in individual genomes and use [the] metaphor of a net to visualize the rich exchange and cooperative effects of HGT among microbes."

"Using single genes as phylogenetic markers, it is difficult to trace organismal phylogeny in the presence of HGT [horizontal gene transfer]. Combining the simple coalescence model of cladogenesis with rare HGT [horizontal gene transfer] events suggest there was no single last common ancestor that contained all of the genes ancestral to those shared among the three domains of life. Each contemporary molecule has its own history and traces back to an individual molecule cenancestor. However, these molecular ancestors were likely to be present in different organisms at different times."

Population structure

Populations may also shrink or grow over time, producing "bottlenecks" or "explosions" respectively. Since population size has a profound effect on the relative strengths of genetic drift and natural selection, changes in population size can alter the dynamics of these processes considerably. Such changes may also produce dramatic and dangerous crashes in the level of genetic variation in the population, or allow rapid increases in standing genetic variation.

The free movement of alleles through a population may also be impeded by population structure. For example, most real-world populations are not actually fully interbreeding; geographic proximity has a strong influence on the movement of alleles within the population. Many models of evolution rely on simplifying assumptions of constant population size and fully interbreeding populations for mathematical convenience.

An example of the effect of population structure is the so-called founder effect, resulting from a migration and population bottleneck. In this case, a single, rare allele may suddenly increase very rapidly in frequency within a specific population if it happened to be prevalent in a small number of "founder" individuals. The frequency of the allele in the resulting population can be much higher than otherwise expected, especially for deleterious, disease-causing alleles.

Drift

Genetic drift describes changes in allele frequency from one generation to the next due to sampling variance. The frequency of an allele in the offspring generation will vary according to a probability distribution of the frequency of the allele in the parent generation. Thus, over time, allele frequencies will tend to "drift" upward or downward, eventually becoming "fixed" - that is, going to 0% or 100% frequency. Fluctuations in allele frequency between successive generations may result in some alleles disappearing from the population. Two separate populations that begin with the same allele frequencies therefore might drift by random fluctuation into two divergent populations with different allele sets (for example, alleles present in one population could be absent in the other, or vice versa).

Many aspects of genetic drift depend on the size of the population (generally abbreviated as N). This is especially important in small mating populations, where chance fluctuations from generation to generation can be large. The relative importance of natural selection and genetic drift in determining the fate of new mutations also depends on the population size and the strength of selection: when N times s (population size times strength of selection) is small, genetic drift predominates. When N times s is large, selection predominates. Thus, natural selection is 'more efficient' in large populations, or equivalently, genetic drift is stronger in small populations. Finally, 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 to fixation.

Selection and adaptation

Natural selection

Natural selection can be subdivided into two categories:

• Ecological selection occurs when organisms that survive and reproduce increase the frequency of their genes in the gene pool over those that do not survive.
• Sexual selection occurs when organisms which are more attractive to the opposite sex because of their features reproduce more and thus increase the frequency of those features in the gene pool.

Natural selection also operates on mutations in several different ways:

• Positive or directional selection increases the frequency of a beneficial mutation, or pushes the mean in either direction.
• Stabilizing or purifying selection favors average characteristics in a population, thus reducing gene variation but retaining the mean.
• Balancing selection maintains variation within a population through a number of mechanisms, including:
  • Heterozygote advantage or overdominance, where the heterozygote is more fit than either of the homozygous forms (exemplified by human sickle cell anemia conferring resistance to malaria)
  • Frequency-dependent selection, where rare variants either have increased fitness or decreased fitness, because of their rarity.
• Disruptive selection favors both extremes, and results in a bimodal distribution of gene frequency. The mean may or may not shift.
• Selective sweeps describe the affect of selection acting on linked alleles. It comes in two forms:
  • Background selection occurs when a deleterious mutation is selected against, and linked mutations are eliminated along with the deleterious variant, resulting in lower genetic polymorphism in the surrounding region.
  • Genetic hitchhiking occurs when a positive mutation is selected for, and linked mutations are pushed towards fixation along with the positive variant.

Adaptation

Through the process of natural selection, species become better adapted to their environments. Adaptation is any evolutionary process that increases the fitness of the individual, or sometimes the trait that confers increased fitness, e.g. a stronger prehensile tail or greater visual acuity. Note that adaptation is context-sensitive; a trait that increases fitness in one environment may decrease it in another.

Evolution does not act in a linear direction towards a pre-defined "goal" — it only responds to various types of adaptionary changes. The belief in a telelogical evolution of this sort is known as orthogenesis, and is not supported by the scientific understanding of evolution. One example of this misconception is the erroneous belief humans will evolve more fingers in the future on account of their increased use of machines such as computers. In reality, this would only occur if more fingers offered a significantly higher rate of reproductive success than those not having them, which seems very unlikely at the current time.

Most biologists believe that adaptation occurs through the accumulation of many mutations of small effect. However, macromutation is an alternative process for adaptation that involves a single, very large scale mutation.

Speciation and extinction

Extinction is the disappearance of species (i.e. gene pools). The moment of extinction generally occurs at the death of the last individual of that species. Extinction is not an unusual event in geological time — species are created by speciation, and disappear through extinction. The Permian-Triassic extinction event was the Earth's most severe extinction event, rendering extinct 90% of all marine species and 70% of terrestrial vertebrate species. In the Cretaceous-Tertiary extinction event many forms of life perished (including approximately 50% of all genera), the most often mentioned among them being the extinction of the non-avian dinosaurs.

Social and religious controversies

As Darwin recognized early on, perhaps the most controversial aspect of evolutionary thought is its application to human beings. Given that some members of religious groups — especially devotees of the Abrahamic religions — believe evolutionary origin beliefs are incompatible with their faith or religious texts, the debate is often heated and seemingly endless. The idea that all diversity in life, especially human beings, arose through "unguided" natural processes goes against teleological notions present in almost every religious origin story, though many religious people have managed to reconcile the science with their religions.

One especially contentious topic evoked by evolution is the biological status of humanity: whereas the classical religious view is approximated by the great chain of being (where people are "above" the animals but slightly "below" the angels), evolution entails both that humans are animals and have ancestors in common with chimpanzees, gorillas, and orangutans. Many people have found this last view repellent, as, in their opinion, it "degrades" human kind. A related conflict arises when critics combine the religious view of people's status with the mistaken notion that evolution is necessarily "progressive": if human beings are superior to animals but yet evolved from them, these critics claim, inferior animals would not still exist, but they do exist, hence the incorrect inference that evolution is false.

In some countries—notably the United States—these and other tensions between religion and evolution have fuelled what has been called the creation-evolution controversy, which, among other things, has generated struggles over the teaching curriculum. While many other fields of science, such as cosmology and earth science, also conflict with a literal interpretation of religious texts, evolutionary studies have borne the brunt of these debates.

Evolution has been used to support philosophical and ethical choices which most modern scientists argue are neither mandated by evolution nor supported by science. 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 disincentives, such as compulsory sterilization, "euthanasia", and later, prenatal testing, birth control, and genetic engineering, for those of "bad". Another example of an extension of evolutionary theory that is widely regarded as unwarrented 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.