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In biology, evolution is the process whereby the frequencies of traits within populations of organisms can change over time. 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 at 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 proposed 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 (see Creation-evolution controversy).
History of evolutionary thought
- Main article: History of evolutionary thought
The idea of biological evolution has existed since ancient times, notably among Hellenists such as Epicurus and Anaximander, but the modern theory was not established until the 18th and 19th centuries, by scientists such as Jean-Baptiste Lamarck and Charles Darwin. While transmutation of species was accepted by a sizeable number of scientists before 1859, it was the publication of Charles Darwin's On The Origin of Species by Means of Natural Selection which 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. As such, Wallace is sometimes given shared credit for the theory natural selection.
Darwin's theory, though it succeeded in profoundly shaking scientific opinion regarding 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. Though 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, though a form of neo-Darwinism (led by August Weismann) enjoyed some minor success as well. 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 regarding the nature of inheritance in the late 19th century was "rediscovered" in 1900, it was interpreted as potentially 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 the Mendelians charging that the biometricians did not understand biology, and the 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 in 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 was able to create 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 (see molecular evolution).
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 of the most prominent public debates 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.
Overview of evolution
Evidence of evolution
- Main article: 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.
Fossils are important for estimating when various lineages developed. Since fossilization on an organism is an uncommon occurrence, usually requiring hard parts (like bone) and death near a site where soft sediments are being gently deposited, the fossil record only provides sparse and intermittent information about the evolution of life. Fossil evidence of organisms without hard body parts, such as shell, bone, and teeth, is sparse but exists in the form of ancient microfossils and the fossilization of ancient burrows, (trace fossils), and rarer examples of soft-bodied organisms.
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.
Ancestry of organisms
- See also: 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, the occurrence of evolution has been strongly confirmed by genetics. 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. (See Timeline of evolution.)
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
- Main article: Timeline of evolution
Not much is known about the earliest developments in life. However, all existing organisms share certain traits, including cellular structure, and genetic code. Most scientists interpret this to mean all existing organisms share a common ancestor, which had already developed the most fundamental cellular processes, but there is no scientific consensus on the relationship of the three domains of life (Archaea, Bacteria, Eukaryota) or the origin of life. Attempts to shed light on the earliest history of life generally focus on the behavior of macromolecules, particularly RNA, and the behavior of complex systems.
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 materialism: "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" (Menand 2001: 121).
Nevertheless, many critiques of the modern evolutionary thought involve misunderstandings of the theory itself, or of science in general.
Evolution and devolution
One of the most common misunderstandings of the theory 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 - it was made by Social Darwinists who thought the subjugation of the poor and minority groups was favored by evolution.
Evolution does involve "progression," however, one one interpretation of that term since the earliest lifeforms were much simpler than many of the species existing today. In that sense, there clearly has been a gradual progression over time from simple organisms to complex - and in some cases intelligent - lifeforms. However, the theory provides no guarantee that any particular organism existing today will become more intelligent, more complex, bigger, or stronger in the future. In fact, evolution can favor lower intelligence, lower complexity, and so on if those traits become a selective disadvantage in the organism's environment. Moreover,
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.
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. (See entropy for a more precise discussion.)
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.
Second, as James Clerk Maxwell argued, the second law is not deterministic, it is probabilistic (see 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 (Menand 2001: 197-199).
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.
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 antibodies 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:
- Common descent of all organisms from a single ancestor or ancestral gene pool.
- Manifestation of novel traits in a lineage.
- 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
- Main article: Theory
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 hypotheses can be generated and tested through controlled experiments, or be verified through empirical observation. In this scientific sense, "facts" are 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.
Scholars in a number of academic disciplines and subdisciplines document the fact of evolution, and contribute to explaining its occurrence. 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.
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 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.
- Main article: Modern evolutionary 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.
Gregor Mendel first proposed a gene-based theory of inheritance, discretizing the elements responsible for heritable traits into the fundamental units we now call genes, and laying out a mathematical framework for the segregation and inheritance of variants of a gene, which we now refer to as alleles.
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.
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. 
- Main article: 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 (see below).
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.
- Main article: Evolution of sex
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 (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 includes horizontal gene transfer, antigenic shift, and reassortment. 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." 
- Main article Population genetics
An important facet of evolution occurs through changes in population structure. The movement of populations and changes in their sizes can have profound impacts on evolution over and above those governed by selection and drift.
Migration can result in admixture leading to the introduction of new genetic variation, or it may result in geographic isolation which may in turn lead to reproductive isolation or speciation.
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 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.
- Main article: Genetic 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 that are present in one have been lost in the other).
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
- Main article: Natural selection
Natural selection comes from differences in survival and reproduction as a result of the environment. Differential mortality is the survival rate of individuals to their reproductive age. Differential fertility is the total genetic contribution to the next generation. Note that, whereas mutations and genetic drift are random, natural selection is not, as it preferentially selects for different mutations based on differential fitnesses. For example, rolling dice is random, but always picking the higher number on two rolled dice is not random. The central role of natural selection in evolutionary theory has given rise to a strong connection between that field and the study of ecology.
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.
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 understandings 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
Speciation is the creation of two or more species from one. This may take place by various mechanisms. Allopatric speciation occurs in populations that become isolated geographically, such as by habitat fragmentation or migration. Sympatric speciation occurs when new species emerge in the same geographic area. Ernst Mayr's peripatric speciation is a type of speciation that exists in between the extremes of allopatry and sympatry. Peripatric speciation is a critical underpinning of the theory of punctuated equilibrium.
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 (See Image 5).
Social and religious controversies
There has been constant controversy surrounding the ideas presented by The Origin of Species since it was first printed in 1859. Since the early twentieth century, however, the idea that biological evolution of some form occurred and is responsible for speciation has been almost completely uncontested within the scientific community.
Most controversy over the theory has come because of its philosophical, cosmological, and religious implications, and supporters as well as detractors have interpreted it as generally indicating that human beings are, like all animals, evolved, and that this account of the origins of humankind is squarely at odds with many religious interpretations. The idea that humans are "merely" animals, and are genetically very closely related to other primates, has been independently argued as a repellent notion by generations of detractors.
Others also interpreted the truth of the theory to imply varying types of social changes — one prominent example is the idea of eugenics, formulated by Darwin's cousin Francis Galton, which argues for the improvement of human heredity by means of political policies. Others have found different political interpretations which have been used as arguments both for and against the theory.
The questions raised about the relation of evolution to the origins of humans have made it an especially tenacious issue with some origin beliefs. It is viewed by some Judeo-Christians as contradicting their beliefs on the origins of humankind as described in the book of Genesis. In some countries — notably in the United States — this has led to what has been called the creation-evolution controversy, which has focused primarily on struggles over 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 controversies.
Notes and references
- ↑ Darwin, Charles November 24 1859. On the Origin of Species by means of Natural Selection or the Preservation of Favoured Races in the Struggle for Life. London: John Murray, Albemarle Street. 502 pages. Reprinted: Gramercy (May 22, 1995). ISBN 0517123207
- ↑ Understanding Evolution, from California's Berkeley University. " 
- ↑ Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69–87. Britten RJ (2002) Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proc Natl Acad Sci U S A 99: 13633–13635.
- ↑ Two sources: 'Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees'. and 'Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes' " "
- ↑ Pseudogene evolution and natural selection for a compact genome. ""
- ↑ Evaluation of the Rate of Evolution in Natural Populations of Guppies (Poecilia reticulata) ""
- ↑ The use of evolutionary principles to guide disease diagnosis and drug development with respect to bird flu (i.e. H5N1 virus) 
- Zimmer, Carl. Evolution: The Triumph of an Idea. Perennial (October 1, 2002). ISBN 0060958502
- Larson, Edward J. Evolution: The Remarkable History of a Scientific Theory (Modern Library Chronicles). Modern Library (May 4, 2004). ISBN 0679642889
- Mayr, Ernst. What Evolution Is. Basic Books (October, 2002). ISBN 0465044263
- Menand, Louis. 2001 The Metaphysical Club. New York: Farar, Straus and Giraux. ISBN0374199639
- Gigerenzer, Gerd, et al., The empire of chance: how probability changed science and everyday life (New York: Cambridge University Press, 1989).
- Smith, D. C. 1988. Heritable divergence of Rhagoletis pomonella host races by seasonal asynchrony. Nature 336: 66-67.
- Williams, G.C. (1966). Adaptation and Natural Selection: A Critique of some Current Evolutionary Thought . Princeton, N.J.: Princeton University Press.
- Sean B. Carroll, 2005, Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom, W. W. Norton & Company. ISBN 0393060160
- Natalia S. Gavrilova & Leonid A. Gavrilov, 2002, Evolution of Aging, In: David J. Ekerdt (ed.) Encyclopedia of Aging, New York, Macmillan Reference USA, 2002, vol.2, 458-467.ISBN 0028654722
- Bill Bryson, A Short History of Nearly Everything, Black Swan Books (2004), ISBN 0-552-99704-8
- Talk.Origins Archive — see also talk.origins
- Understanding Evolution from University of California, Berkeley
- National Academies Evolution Resources
- EvoWiki — A wiki whose goal is to promote general evolution education, and provide mainstream scientific responses to the arguments of antievolutionists.
- Evolution by Natural Selection — An introduction to the logic of evolution by natural selection
- Evolution — Provided by PBS.
- Everything you wanted to know about evolution — Provided by New Scientist.
- International Journal of Organic Evolution
- Howstuffworks.com — How Evolution Works
- Charles Darwin's writings
- Evolution News from Genome News Network (GNN)
- National Academy Press: Teaching About Evolution and the Nature of Science
- Evolution for beginners
- RMCybernetics - AI Evolution can create emergent behavior in a computer program.
- NPR - Science Friday: links to museums, articles and books.
- "Evolution: Fact and Theory" by Richard E. Lenski
- Evolution by level Book reviews of books on evolution by knowledge level.
- Evolution Simulators
- Isolated species evolves to interact more efficiently with its environment (java applet)
- Evolution in a predator-prey relationship (java applet)
|Basic topics in evolutionary biology||(edit)|
|Processes of evolution: evidence - macroevolution - microevolution - speciation|
|Mechanisms: selection - genetic drift - gene flow - mutation - phenotypic plasticity|
|Modes: anagenesis - catagenesis - cladogenesis|
|History: History of evolutionary thought - Charles Darwin - The Origin of Species - modern evolutionary synthesis|
|Subfields: population genetics - ecological genetics - human evolution - molecular evolution - phylogenetics - systematics - evo-devo|
|List of evolutionary biology topics | Timeline of evolution | Timeline of human evolution|
|This page uses Creative Commons Licensed content from Wikipedia (view authors).|