Evolution

File:PhylogeneticTree.jpg

A phylogenetic tree of all living things, based on rRNA gene data, showing the separation of the three domains, bacteria, archaea, and eukaryotes, as described initially by Carl Woese.

This article is about evolution in the field of life science. For other uses, see Evolution (disambiguation).

In biology, evolution is the process by which populations of organisms acquire and pass on novel traits from generation to generation, affecting the overall makeup of the population and even leading to the emergence of new species. The terms organic evolution or biological evolution are often used to distinguish this meaning from other usages.

The development of the modern theory of evolution began with the introduction of the concept of natural selection in a joint 1858 paper by Charles Darwin and Alfred Russel Wallace. This theory achieved a wider readership in Darwin's 1859 book, The Origin of Species. Darwin and Wallace proposed that evolution occurs because a heritable trait that increases an individual's chance of successfully reproducing will become more common, by inheritance, from one generation to the next, and likewise a heritable trait that decreases an individual's chance of reproducing will become rarer. This work was groundbreaking, and overturned other evolutionary theories, such as that advanced by Jean Baptiste Lamarck. Because of its potential implications for the origins of humankind, the theory has been at the center of many social and religious controversies since its first inception (see Creation-evolution controversy).

In the 1930s, scientists combined Darwinian natural selection with the re-discovered theory of Mendelian heredity to create the modern synthesis, now one of the fundamental scientific theories of biology. In the modern synthesis, "evolution" is defined as a change in the frequency of alleles within a population from one generation to the next. The basic mechanisms that produce these changes are natural selection, genetic drift, and genetic variation. The primary sources of genetic variation are mutation, sex, and gene flow.^[2]

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 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 98-99% similarity between humans and chimpanzees come from, for instance.^[3]

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

Fossils are important for estimating when various lineages developed. As fossilization on an organism is an uncommon occurrence, usually requiring hard parts (like bone) and death near a site where sediments are being 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 and a few soft-bodied organisms.

Fossil evidence of prehistoric organisms has been found all over the Earth. The age of fossils can often be deduced from the geologic context in which they are found; and their absolute age 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.

Phylogeny, 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.^[4] 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.^[5]

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.

History of evolutionary thought

Image 6:Charles Darwin in 1854, 5 years before he published The Origin of Species.

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 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 of evolution.

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 most biologists. It was not until the late 19th and early 20th centuries that these mechanisms were established.

File:Stephen Jay Gould.png

Image 7: Stephen Jay Gould, who, along with Niles Eldredge, proposed the theory of punctuated equilibrium in 1972.

When Gregor Mendel's work regarding the nature of inheritance in the late 19th century was "rediscovered" in 1900, it led to a storm of conflict between Mendelians (Charles Benedict Davenport) and biometricians (Walter Frank Raphael Weldon and Karl Pearson), who insisted that the great majority of traits important to evolution must show continuous variation that was not explainable by Mendelian analysis. Eventually, the two models were reconciled and merged, primarily through the work of the biologist and statistician R.A. Fisher. This combined approach, applying a rigorous statistical model to Mendel's theories of inheritance via genes, became known in the 1930s and 1940s 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 transitional forms between phyla in the fossil record.

Social and religious controversies

Image 8: A satirical image of Charles Darwin as an ape from 1871 reflects part of the social controversy over whether humans and apes share a common lineage.

Main articles: Social implications of the theory of evolution and Creation-evolution controversy

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 primates, have been independently argued as repellent notions by generations of detractors.

Others also intepreted 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 has made it an especially tenacious issue with religious traditions. It has prominently been seen as opposing a "literal" interpretation of the account of the origins of humankind as described in Genesis, the first book of the Bible. In many 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.

Science of evolution

Science: fact and theory

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.

Evolution as fact and theory

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, or several new, species. In this sense, evolution occurs whenever a new strain of bacterium evolves that is resistant to antibodies that had been lethal to prior strains.

Another clear case of evolution as fact involves the hawthorn fly, Rhagoletis pomonella. Different populations of hawthorn fly feed on different fruits. A new population spontaneously emerged in North America in the 19th century some time after apples, a non-native species, were introduced. The apple feeding population normally feeds only on apples and not on the historically preferred fruit of hawthorns. Likewise the current hawthorn feeding population does not normally feed on apples. A current area of scientific research is the investigation of whether or not the apple feeding race may further evolve into a new species. Some evidence, such as the fact that six out of thirteen alozyme loci are different, that hawthorn flies mature later in the season, and take longer to mature, than apple flies, and that there is little evidence of interbreeding (researchers have documented a 4-6%hybridization rate) suggests that this is indeed ocurring.^[6] (see Berlocher and Bush 1982, Berlocher and Feder 2002, Bush 1969, McPheron et. al. 1988, Prokopy et. al. 1988, Smith 1988)

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.

The meaning of, and relationship between, fact and theory in science

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 popular 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 a fact and modern synthesis is currently the most powerful theory explaining evolution, variation and speciation. Within the science of biology, modern synthesis has completely replaced earlier accepted explanations for the origin of species, including Lamarckism and creationism.

Who studies evolution?

Scholars in a number of academic disciplines and subdisciplines document the fact of evolution, and contribute to the theory of evolution.

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 revelaed temporal and spacial 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.

Evolutionary biology

Evolutionary biology is a subfield of biology concerned with the origin and descent of species, as well as their change over time.

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 experimentally determine and trace 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.

Ancestry of organisms

File:ChimpThinker.jpg

A chimpanzee, man's closest living relative.

See also: Common descent

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, the theory 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.^[7]

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

Pre-Cambrian stromatolites in the Siyeh Formation, Glacier National Park. In 2002, William Schopf of UCLA published a controversial paper in the journal Nature arguing that formations such as this possess 3.5 billion year old fossilized algae microbes.^[1] If true, they would be the earliest known life on earth.

Main article: Timeline of evolution

The chemical evolution from self-catalytic chemicals to life (see Origin of life) is not a part of biological 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 (Archea, 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.

The 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

Gregor Mendel first proposed a gene-based theory of inheritance, discretizing the elements responsible for heritable traints 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.

Sexual reproduction

In addition to passing genetic material from parent to offspring, nearly all organisms employ sex to exchange genetic material. This, combined with meiotic recombination, allows genetic variation to be propagated through an interbreeding population. These mechanisms allow individual variations to be propagated more or less independently, so that the population as a whole can retain beneficial variation and eliminate harmful variation (rather than both of these effects competing within a single asexual organism). However, these mechanisms are not perfect, and so some variation is co-propagated as a result of linkage, producing some odd effects (see Muller's ratchet).

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.

There are three known processes that affect the survival of a characteristic (or, more specifically, the frequency of an allele):

• Natural selection
• Changes in population structure
• Genetic drift

These basic 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 ^[8]

Variation

Without genetic variation, populations cannot evolve. The two principle sources of genetic variation are mutations and gene flow.

Other forms of genetic variation due to gene transfer include horizontal gene transfer, antigenic shift, and reassortment.

Viruses can transfer genes between species [9]. Bacteria can incorporate genes from other dead bacteria, exchange genes with living bacteria, and can have plasmids "set up residence seperate from the host's genome" [10]. "Genes that move between species play by rules that microbial experts are just beginning to discern" [11].

Mutation

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.

Gene flow

Gene flow (or gene admixture) 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.

Drift

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.

Population structure

An important facet of evolution occurs through changes in population structure. The movement of populations and changes in their size 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.

Selection and adaptation

Natural selection

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:

• Purifying or background selection eliminates deleterious mutations from a population.
• Directional selection increases the frequency of a beneficial mutation.
• 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 have a higher fitness, because of thier rarity.
• Stabilizing selection favors average characteristics in a population, thus reducing gene variation but retaining the mean.
• Disruptive selection favors both extremes, and results in a bimodal distribution of gene frequency. The mean may or may not shift.

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 theory 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

File:800px-Allosaurus1.jpg

An allosaurus skeleton.

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).

Misconceptions

The vast majority of criticism and controversy involving evolution stems from misconceptions perpetuated by those with little background in biology and science:

• Evolution has never been observed.

Speciation as well as novel behavior and adaptations have been observed; also many predictions evolution has made, from the fossil record to DNA heredity between species and "kinds" has agreed with evolutionary theory.

• Evolution violates the 2nd law of thermodynamics.

The law explicitly states that the disorder of a system will over time become greater. Since the Earth is not a closed system it receives energy from the Sun; although order can be seen in life on Earth, the amount of disorder the Sun has created during that time far outweighes the order found on Earth. Hence, on the whole disorder has indeed increased.

• There are no transitional fossils.

There are numerous examples of transitional fossils between every major animal group. It should also be noted evolution requires many transitional species, but has no bearing on the frequency of fossilization; which is a relatively rare process. As transitional species populations would be small and short lived they are inherantly less likely to be fossilized.

• The theory of evolution says that life originated, and evolution proceeds, by random chance.

Evolution proceeds by natural selection acting upon random mutations. Natural selection is not random.

• Evolution is only a theory; it hasn't been proved.

See: Fact and theory in science

In the face of explanations and evidence for old misconceptions neo-creationists have come up with more subtle misconceptions:

• Matter cannot organize itself.

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, the building blocks of proteins; have been shown to assemble naturally.

• Evolution cannot create information, which 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 occurs and is kept. It does not need to beneficial nor visually apparent to be "information". However, even if those were requirements they could be satisfied with the appearance of nylon eating bacteria, which required new enzymes to digest a material that never existed until the modern age. [12]

See also

Abiogenesis Altruism in animals Anagenesis Argument from evolution Atavism Behavioral ecology Catagenesis Cladogenesis Convergent evolution Creation-evolution controversy Darwin Awards Endosymbiont Eugenics Evolution of sex Evolutionary algorithm Evolutionary art Evolutionary medicine Evolutionary psychology

Evolutionary tree Experimental evolution Fitness landscape Genetic algorithm Gradualism Instinct Modern evolutionary synthesis Natural science Neutral theory of molecular evolution Niche construction Parallel evolution Quantum evolution Quasispecies model Scientific method Sexual selection Social implications of the theory of evolution Teratogenesis Thermodynamic evolution

Notes and references

1. ^ "Ancient microfossils from Western Australia are again the subject of heated scientific argument: are they the oldest sign of life on Earth, or just a flaw in the rock?" "[13]"
2. ^ Understanding Evolution, from California's Berkeley University. "[14] [15]
3. ^ Li WH, Saunders MA (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.
4. ^ 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' "[16] [17]"
5. ^ Pseudogene evolution and natural selection for a compact genome. "[18]"
6. ^ Reference for emergence of new race of apple maggot flies [[19]]
7. ^ Evaluation of the Rate of Evolution in Natural Populations of Guppies (Poecilia reticulata) "[20]"
8. ^ The use of evolutionary principles to guide disease diagnosis and drug development with respect to bird flu (i.e. H5N1 virus) [21]
9. ^ Understanding Evolution, from California's Berkeley University: "Sex can introduce new gene combinations into a population. This genetic shuffling is another important source of genetic variation."[22]

• Berlocher, S.H. and G.L. Bush. 1982. An electrophoretic analysis of Rhagoletis (Diptera: Tephritidae) phylogeny. Systematic Zoology 31:136-155.
• Berlocher, S.H. and J.L. Feder. 2002. Sympatric speciation in phytophagous insects: moving beyond controversy? Annual Review of Entomology 47:773-815.
• Bush, G.L. 1969. Sympatric host race formation and speciation in frugivorous flies of the genus Rhagoletis (Diptera: Tephritidae). Evolution 23:237-251.
• 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
• Prokopy, R.J., S.R. Diehl and S.S. Cooley. 1988. Behavioral evidence for host races in Rhagoletis pomonella flies. Oecologia 76:138-147.
• 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
• McPheron, B. A., D. C. Smith and S. H. Berlocher. 1988. Genetic differentiation between host races of Rhagoletis pomonella. Nature. 336:64-66.
• 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
• Bill Bryson, A Short History of Nearly Everything, Black Swan Books (2004), ISBN 0-552-99704-8

External links

• Talk.Origins Archive — see also talk.origins
• Understanding Evolution @ 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 the theory 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 Simulators

• Isolated species evolves to interact more efficiently with its environment (java applet)
• Evolution in a predator-prey relationship (java applet)