Evolution

2007 Schools Wikipedia Selection. Related subjects: Evolution and reproduction

In biology, evolution is change in the heritable traits of a population over successive generations, as determined by shifts in the allele frequencies of genes. Over time, this process can result in speciation, the development of new species from existing ones. All contemporary organisms on earth are related to each other through common descent, the products of cumulative evolutionary changes over billions of years. Evolution is thus the source of the vast diversity of life on Earth, including the many extinct species attested to in the fossil record.

The basic mechanisms that produce evolutionary change are natural selection (which includes ecological, sexual, and kin selection) and genetic drift; these two mechanisms act on the genetic variation created by mutation, genetic recombination, and gene flow. Natural selection is the process by which individual organisms with favorable traits are more likely to survive and reproduce. If those traits are heritable, they are passed to the organisms' offspring, with the result that beneficial heritable traits become more common in the next generation. Given enough time, this passive process can result in varied adaptations to changing environmental conditions.

The modern understanding of evolution is based on the theory of natural selection, which was first set out in a joint presentation in 1858 of a pair of papers by Charles Darwin and Alfred Russel Wallace and popularized in Darwin's 1859 book The Origin of Species. In the 1930s, Darwinian natural selection was combined with the theory of Mendelian heredity to form the modern evolutionary synthesis, also known as "Neo- Darwinism". The modern synthesis describes evolution as a change in the frequency of alleles within a population from one generation to the next. With its enormous explanatory and predictive power, this theory has become the central organizing principle of modern biology, relating directly to topics such as the origin of antibiotic resistance in bacteria, eusociality in insects, and the staggering biodiversity of Earth's ecosystem.

Although there is overwhelming scientific consensus supporting the validity of evolution, it has been at the centre of many social and religious controversies since its inception because of its implications for the origins of humankind.

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Evolution

Mechanisms and processes

Adaptation Genetic drift Gene flow Mutation Selection Speciation

Research and history

Evidence History Modern synthesis Social effect

Evolutionary biology fields

Ecological genetics Evolutionary development Human evolution Molecular evolution Phylogenetics Population genetics Evo-devo

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Study of evolution

History of evolutionary thought

The idea of biological evolution has existed since ancient times, notably among Greek philosophers such as Anaximander and Epicurus and Indian philosophers such as Patañjali. However, scientific theories of evolution were not proposed until the 18th and 19th centuries, by scientists such as Jean-Baptiste Lamarck and Charles Darwin.

The transmutation of species was accepted by many scientists before 1859, but Charles Darwin's On The Origin of Species by Means of Natural Selection provided the first convincing exposition of a mechanism by which evolutionary change could occur: natural selection. After many years of working in private on his theory, Darwin was motivated to publish his work on evolution when he received a letter from Alfred Russel Wallace in which Wallace revealed his own, independent discovery of natural selection. Accordingly, Wallace is sometimes given shared credit for originating the theory.

The publication of Darwin's book sparked a great deal of scientific and social debate. Although the occurrence of biological evolution of some sort came to be widely accepted by scientists, Darwin's specific ideas about evolution—that it occurred gradually, through natural selection—were actively attacked and contested. Additionally, while Darwin was able to observe variation, and to infer natural selection and thereby adaptation, he was unable to explain how variation might arise or be altered over generations.

Work on plant hybridity by a contemporary of Darwin's, Gregor Mendel, revealed that certain traits in peas occurred in discrete forms (that is, they were either one distinct trait or another, such as "round" or "wrinkled") and were inherited in a well-defined and predictable manner. When Mendel's work was "rediscovered" in 1901, it was initially interpreted as supporting an anti-Darwinian "jumping", saltationist form of evolution, and contradicting the biometricians' gradualism.

However, the simple version of the theory of 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 reconcilable with the data of the biometricians by the work of statistician and population geneticist R.A. Fisher in the 1930s. Following this, the work of population geneticists and zoologists in the 1930s and 1940s synthesized Darwinian evolution with genetics, creating the modern evolutionary synthesis. Genes were then still theoretical entities, and many paleontologists and embryologists were inclined to dismiss them as being of no, or minor, importance, but subsequent advancements have made genetics a key aspect of evolutionary biology.

The most significant recent developments in evolutionary biology have been the improved understanding of and advances in genetics. In the 1940s, following up on Griffith's experiment, Avery, MacLeod and McCarty definitively identified DNA (deoxyribonucleic acid) as the "transforming principle" responsible for transmitting genetic information. In 1953, Francis Crick and James D. 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 (see molecular evolution): the mutation of segments of DNA. George C. Williams' 1966 Adaptation and natural selection: A Critique of some Current Evolutionary Thought and Richard Dawkins' The Selfish Gene marked a departure from the idea of groups or organisms as units of selection toward the modern gene-centered view of evolution. In the mid-1970s, Motoo Kimura formulated the neutral theory of molecular evolution, a significant departure from the consensus view of evolution, as it considered genetic drift, rather than natural selection to be the predominant mode of evolution.

Debates over various aspects of how evolution occurs have continued. Two prominent debates are 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, as well as the absence of change or stasis that is observed over significant intervals of time; and also the Neutralist-Selectionist debate.

Academic disciplines

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

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

Evolutionary developmental biology (informally, evo-devo) is a field of biology that compares the developmental processes of different animals in an attempt to determine the ancestral relationship between organisms and how developmental processes evolved. The discovery of genes regulating development in model organisms allowed for comparisons to be made with genes and genetic networks of related organisms.

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

Evidence of evolution

Evolution has left numerous records that reveal the history of different species. Fossils, together with the comparative anatomy of present-day plants and animals, constitute the morphological, or anatomical, record. By comparing the anatomies of both modern and extinct species, paleontologists can infer the lineages of those species. Important fossil evidence includes the connection of distinct classes of organisms by so-called " transitional" species, such as the Archaeopteryx, which provided early evidence for intermediate species between dinosaurs and birds, and the recently-discovered Tiktaalik, which clarifies the development from fish to animals with four limbs.

The development of molecular genetics, and particularly of DNA sequencing, has allowed biologists to study the record of evolution left in organisms' genetic structures. The degrees of similarity and difference in the DNA sequences of modern species allows geneticists to reconstruct their lineages. It is from DNA sequence comparisons that figures such as the 95% genotypic similarity between humans and chimpanzees are obtained.

Additional evidence of ancestry includes idiosyncratic structures present in certain organisms, such as the panda's " thumb", which indicate how an organism's evolutionary lineage constrains its adaptive development. Vestigial structures such as the vestigial limbs on pythons or the degenerate eyes of blind cave-dwelling fish are also evidences of evolutionary development.

Other evidence used to demonstrate evolutionary lineages includes the geographical distribution of species. For instance, monotremes, such as platypus, and most marsupials, like kangaroos or koalas, 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 Earth. For instance, paleoclimatology attests to periodic ice ages during which the world's climate was much cooler, and these are often found to match up with the spread of species which are better-equipped to deal with the cold, such as the woolly mammoth.

Morphological evidence

Fossils are critical evidence for estimating when various lineages originated. Since fossilization of an organism is an uncommon occurrence, usually requiring hard parts (like teeth, bone or pollen), the fossil record is traditionally thought to provide only sparse and intermittent information about ancestral lineages. Fossilization of organisms without hard body parts is rare, but happens under unusual circumstances, such as rapid burial, low oxygen environments, or microbial action.

The fossil record provides several types of data important to the study of evolution. First, the fossil record contains the earliest known examples of life itself, as well as the earliest occurrences of individual lineages. For example, the first complex animals date from the early Cambrian period, approximately 520 million years ago. Second, the records of individual species yield information regarding the patterns and rates of evolution, showing for example if species evolve into new species (speciation) gradually and incrementally, or in relatively brief intervals of geologic time. Thirdly, the fossil record is a document of large scale patterns and events in the history of life, many of which have influenced the evolutionary history of numerous lineages. For example, mass extinctions frequently resulted in the loss of entire groups of species, such as the non-avian dinosaurs, while leaving others relatively unscathed. Recently, molecular biologists have used the time since divergence of related lineages to calibrate the rate at which mutations accumulate, and at which the genomes of different lineages evolve.

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. The appendages on bat wings, for example, are very structurally similar to human hands, and may constitute a vestigial structure. Other examples include the presence of hip bones in whales and snakes. Such structures may exist with little or no function in a more current organism, yet have a clear function in an ancestral species of the same. Examples of vestigial structures in humans include wisdom teeth, the coccyx and the vermiform appendix.

Molecular evidence

Comparison of the DNA sequences allows organisms to be grouped by sequence similarity, and the resulting phylogenetic trees are typically congruent with traditional taxonomy, and are often used to strengthen or correct taxonomic classifications. 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. 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. Genetic sequence evidence thus allows inference and quantification of genetic relatedness between humans and other apes. The sequence of the 16S rRNA gene, a vital gene encoding a part of the ribosome, was used to find the broad phylogenetic relationships between all extant life. The analysis, originally done by Carl Woese, resulted in the three-domain system, arguing for two major splits in the early evolution of life. The first split led to modern Bacteria and the subsequent split led to modern Archaea and Eukaryote.

The proteomic evidence also supports the universal ancestry of life. Vital proteins, such as the ribosome, DNA polymerase, and RNA polymerase are found in the most primitive bacteria to the most complex mammals. The core part of the protein is conserved across all lineages of life, serving similar functions. Higher organisms have evolved additional protein subunits, largely affecting the regulation and protein-protein interaction of the core. Other overarching similarities between all lineages of extant organisms, such as DNA, RNA, amino acids, and the lipid bilayer, give support to the theory of common descent. The chirality of DNA, RNA, and amino acids is conserved across all known life. As there is no functional advantage to right or left handed molecular chirality, the simplest hypothesis is that the choice was made randomly in the early beginnings of life and passed on to all extant life through common descent.

There is also a large body of molecular evidence for a number of different mechanisms for large evolutionary changes, among them genome and gene duplication, horizontal gene transfer, recombination, and endosymbiosis. These mechanisms have been, or are being incorporated into the Modern Evolutionary Synthesis :

1. Gene and genome duplication facilitates rapid evolution by providing substantial quantities of genetic material under weak or no selective constraints.
2. Horizontal gene transfer, the process in which an organism transfers genetic material (i.e. DNA) to another cell that is not its offspring, allows for large sudden evolutionary leaps in a species by incorporating beneficial genes evolved in another species.
3. Recombination is both capable of reassorting large numbers of different alleles, and establishing reproductive isolation.
4. The Endosymbiotic theory explains the origin of mitochondria and plastids (e.g. chloroplasts), which are organelles of eukaryotic cells, as the incorporation of an ancient prokaryotic cell into ancient eukaryotic cell. Rather than evolving eukaryotic organelles slowly, this theory offers a mechanism for a large evolutionary changes by incorporating the genetic material and biochemical composition of a separate species. This evolutionary mechanism has been observed. Hatena, a protist, is an extant organism that is undergoing endosymbiotic evolution.

Further evidence for reconstructing ancestral lineages comes from junk DNA such as pseudogenes, i.e., 'dead' genes, which steadily accumulate mutations.

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 or by detecting their physical manifestations. As an example, the appearance of oxygen in the earth's atmosphere is linked to the evolution of photosynthesis.

Theoretical evidence

Mathematical models of evolution, pioneered by the likes of Sewall Wright, Ronald Fisher and J. B. S. Haldane and extended via diffusion theory by Motoo Kimura, allow predictions about the genetic structure of evolving populations. Direct examination of the genetic structure of modern populations via DNA sequencing has recently allowed verification of many of these predictions. For example, the "Out of Africa" theory of human origins, which states that modern humans developed in Africa and a small sub-population migrated out (undergoing a population bottleneck), implies that modern populations should show the signatures of this migration pattern. Specifically, post-bottleneck populations (Europeans and Asians) should show lower overall genetic diversity and a more uniform distribution of allele frequencies compared to the African population. Both of these predictions are borne out by actual data from a number of studies.

Ancestry of organisms

In biology, the theory of universal common descent proposes that all organisms on Earth are descended from a common ancestor or ancestral gene pool.

Evidence for common descent is inferred from traits shared between all living organisms. In Darwin's day, the evidence of shared traits was based solely on visible observation of morphologic similarities, such as the fact that all birds, even those which do not fly, have wings. Today, there is strong evidence from genetics that all organisms have a common ancestor. 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 many of these traits seems arbitrary.

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. However, a great deal of information about the early Earth has been destroyed by geological processes over the course of time.

History of life

The chemical evolution (or abiogenesis) from self-catalytic chemical reactions to life (see Origin of life) is not a part of biological evolution, but it is unclear at which point such increasingly complex sets of reactions became what we would consider, today, to be living organisms.

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 behaviour of macromolecules, particularly RNA, and the behaviour 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 evolutionary process may be exceedingly slow. Fossil evidence indicates that the diversity and complexity of modern life has developed over much of the history of the earth. Geological evidence indicates that the Earth is approximately 4.57 billion years old. Studies on guppies by David Reznick at the University of California, Riverside, however, have shown that the rate of evolution through natural selection can proceed 10 thousand to 10 million times faster than what is indicated in the fossil record. Such comparative studies however are invariably biased by disparities in the time scales over which evolutionary change is measured in the laboratory, field experiments, and the fossil record.

The ancestry of living organisms has traditionally been reconstructed from morphology, but is increasingly supplemented with phylogenetic — the reconstruction of phylogenies by the comparison of genetic (usually DNA) sequence. Biologist Gogarten suggests that "the original metaphor of a tree no longer fits the data from recent genome research", and that 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".

Modern synthesis

Charles Darwin was able to observe variation, infer natural selection and thereby adaptation, but didn't know the basis of heritability. He couldn't explain how organisms might change over generations. It also seemed that when two individuals were crossed, their traits must be blended in the progeny, so that eventually all variation would be lost.

The blending problem was solved when the population geneticists R.A. Fisher, Sewall Wright, and J. B. S. Haldane, married Darwinian evolutionary theory to population genetic theory, which was based on Mendelian genetics (genes as discrete units of heredity).

The problem of what the mechanisms might be was solved in principle with the identification of DNA as the genetic material by Oswald Avery and colleagues, and the articulation of the double-helical structure of DNA by James Watson and Francis Crick provided a physical basis for the notion that genes were encoded in DNA.

Heredity

Gregor Mendel's work provided the first firm basis to the idea that heredity occurred in discrete units. He noticed several traits in peas that occur in only one of two forms (e.g., the peas were either "round" or "wrinkled"), and was able to show that the traits were: heritable (passed from parent to offspring); discrete (i.e., if one parent had round peas and the other wrinkled, the progeny were not intermediate, but either round or wrinkled); and were distributed to progeny in a well-defined and predictable manner ( Mendelian inheritance). His research laid the foundation for the concept of discrete heritable traits, known today as genes. After Mendel's work was "rediscovered" in 1900, it was discovered that the concepts could have wide applicability, and that most complex traits were polygenetic and not controlled by single unit characters.

Later research gave a physical basis to the notion of genes, and eventually identified DNA as the genetic material, and identified genes as discrete elements within DNA. DNA is not perfectly copied, and rare mistakes ( mutations) in genes can affect traits that the genes control (e.g., pea shape).

A gene can have modifications such as DNA methylation, which do not change the nucleotide sequence of a gene, but do result in the epigenetic inheritance of a change in the expression of that gene in a trait.

Non-DNA based forms of heritable variation exist, such transmission of the secondary structures of prions, and structural inheritance of patterns in the rows of cilia in protozoans such as Paramecium and Tetrahymena. 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. However, the processes that produce these variations leave the genetic information intact and are often reversible, and are rather rare.

Variation

Evolutionary changes are the product of evolutionary forces acting on genetic variation. In natural populations, there is a certain amount of phenotypic variation (e.g., what makes you appear different from your neighbour). This phenotypic variation is the result of variants in gene sequences among the individuals of a population. There may be one or more functional variants of a gene or locus, and these variants are called alleles. Most sites in the genome (i.e., complete DNA sequence) of a species are identical in all individuals in the population; sites with more than one allele are called polymorphic or segregating sites.

All genetic variation begins as a new mutation in a single individual; in subsequent generations the frequency of that variant may fluctuate in the population, becoming more or less prevalent relative to other alleles at the site. This change in allele frequency is the commonly accepted definition of evolution, and all evolutionary forces act by driving allele frequency in one direction or another. Variation disappears when it reaches the point of fixation — when it either reaches a frequency of zero and disappears from the population, or reaches a frequency of one and replaces the ancestral allele entirely.

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. Paleontologist Stephen J. Gould once phrased this succinctly as "variation proposes and selection disposes."

Mutation

Genetic variation arises due to random mutations that occur at a certain rate in the genomes of all organisms. Mutations 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; 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 can 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 by mutation rate, genetic drift and selective pressure on linked alleles. It is understood that most of a species' genome, in the absence of selection, undergoes a steady accumulation of neutral mutations.

Individual genes can be affected by point mutations, also known as SNPs, in which a single base pair is altered. The substitution of a single base pair may or may not affect the function of the gene (see mutation) while deletions and insertions of a single or several base pairs usually results in a non-functional gene.

Mobile elements, transposons, make up a major fraction of the genomes of plants and animals and appear to have played a significant role in the evolution of genomes. These mobile insertional elements can jump within a genome and alter existing genes and gene networks to produce evolutionary change and diversity.

On the other hand, gene duplications, which may occur via a number of mechanisms, are believed to be one major source of raw material for evolving new genes as tens to hundreds of genes are duplicated in animal genomes every million years. 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"). Another mechanism causing gene duplication is intergenic recombination, particularly ' exon shuffling', i.e., an aberrant recombination that joins the 'upstream' part of one gene with the 'downstream' part of another. Genome duplications and chromosome duplications also appear to have served a significant role in evolution. Genome duplication has been the driving force in the Teleostei genome evolution, where up to four genome duplications are thought to have happened, resulting in species with more than 250 chromosomes.

Large chromosomal rearrangements do not necessarily change gene function, but do generally result in reproductive isolation, and, by definition, speciation ( species (in sexual organisms) are usually defined by the ability to interbreed). An example of this mechanism is the fusion of two chromosomes in the homo genus that produced human chromosome 2; this fusion did not occur in the chimp lineage, resulting in two separate chromosomes in extant chimps.

Selection and adaptation

Natural selection comes from differences in survival and reproduction . 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.
• Purifying or stabilizing selection maintains a common trait in the population by decreasing the frequency of harmful mutations and weeding them out of the population. " Living fossils" are arguably the product of stabilizing selection, as their form and traits have remained virtually identical over a long period. It is argued that stabilizing selection is the most common form of natural selection.
• Artificial selection refers to purposeful breeding of a species to produce a more desirable and “perfect” breed. Humans have directed artificial selection in the breeding of both animals and plants, with examples ranging from agriculture (crops and livestock) to pets and horticulture. However, because humans are only part of the environment, the fractions of change in a species due to natural or artificial means can be difficult to determine. Artificial selection within human populations is a controversial enterprise known as eugenics.
• 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 anaemia 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 beneficial allele is selected for, and linked alleles, which can be neutral or beneficial, are pushed towards fixation along with the beneficial allele.

Through the process of natural selection, organisms 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 adaptationary changes. The belief in a teleological evolution of this sort is known as orthogenesis, and is not supported by the scientific understanding of evolution. One example of this misconception is the erroneous belief humans will evolve more fingers in the future on account of their increased use of machines such as computers. In reality, this would only occur if more fingers offered a significantly higher rate of reproductive success than those not having them, which seems very unlikely at the current time.

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

Recombination

In asexual organisms, variants in genes on the same chromosome will always be inherited together — they are linked, by virtue of being on the same DNA molecule. However, sexual organisms, in the production of gametes, shuffle linked alleles on homologous chromosomes inherited from the parents via meiotic recombination. This shuffling allows independent assortment of alleles (mutations) in genes 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.

However, the meitoic recombination rate is not very high - on the order of one crossover (recombination event between homomolgous chromosomes) per chromosome arm per generation. Therefore, linked alleles are not perfectly shuffled away from each other, but tend to be inherited 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 can be a product of strong positive selection.

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), there is an observable 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 and Population structure

Gene flow (also called gene admixture or simply migration) is the exchange of genetic variation between populations, when geography and culture are not obstacles. Ernst Mayr thought that gene flow is likely to be homogenising, and therefore counteract selective adaptation. Where there are obstacles to gene flow, the situation is termed reproductive isolation and is considered to be necessary for speciation.

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.

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

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 even in the absence of selection upon the alleles, allele frequencies will tend to "drift" upward or downward, eventually becoming "fixed" - that is, going to 0% or 100% frequency. Thus, fluctuations in allele frequency between successive generations may result in some alleles disappearing from the population due to chance alone. Two separate populations that begin with the same allele frequencies therefore might drift apart by random fluctuation into two divergent populations with different allele sets (for example, alleles present in one population could be absent in the other, or vice versa).

The consequence of genetic drift depends strongly on the size of the population (generally abbreviated as N): drift is important in small mating populations (see Founder effect and Population bottleneck), 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 predominant 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.

Horizontal gene transfer

Horizontal gene transfer (HGT) (or Lateral gene transfers) is any process in which an organism transfers genetic material (i.e. DNA) to another organism that is not its offspring. This mechanism allows for the transfer of genetic material between unrelated organisms of the same species or of different species.

Many mechanisms for horizontal gene transfer have been observed, such as antigenic shift, reassortment, and hybridization. Viruses can transfer genes between species via transduction. Bacteria can incorporate genes from other dead bacteria or plasmids via transformation, exchange genes with living bacteria via conjugation, and can have plasmids "set up residence separate from the host's genome".

HGT has been shown to result in the spread of antibiotic resistance across bacterial populations. Furthermore, findings indicate that HGT has been a major mechanism for prokaryotic and eukaryotic evolution.

HGT complicates the inference of the phylogeny of life, as the original metaphor of a tree of life no longer fits. Rather, since genetic information is passed to other organisms and other species in addition to being passed from parent to offspring, "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."

Speciation and extinction

Speciation is the process by which new biological species arise. 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. An example of rapid sympatric speciation can be eloquently represented in the triangle of U; where new species of Brassica sp. have been made by the fusing of separate genomes from related plants.

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.

Misunderstandings about modern evolutionary biology

Although the modern synthesis is a central theory in science, many misunderstandings about ideas of modern synthesis prevail among some within the general population. These misunderstandings have hindered acceptance of modern synthesis, most notably in the United States. Some of the most common misunderstandings are outlined in this section.

Distinctions between theory and fact

Stephen Jay Gould explained that "evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts do not go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's, but apples did not suspend themselves in mid-air, pending the outcome. And humans evolved from ape-like ancestors whether they did so by Darwin's proposed mechanism or by some other yet to be discovered."

The modern synthesis, like its Mendelian and Darwinian antecedents, is a scientific theory. A theory is an attempt to identify and describe relationships between phenomena or things, and generates falsifiable predictions which can be tested through controlled experiments and empirical observation. Speculative or conjectural explanations tend to be called hypotheses, and well tested explanations, theories. Fact tends to mean a datum, an observation, i.e., a fact is obtained by a fairly direct observation. However, a fact does not mean absolute certainty; in science, fact can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." A theory is obtained by inference from a body of facts. A related concept is a scientific law. It is common to encounter reference to the "law of natural selection" or the "laws of evolution." For example, see the article on physical law. Fact and theory denote the epistemological status of knowledge: how the knowledge was obtained, what sort of knowledge it is.

In this scientific sense, "facts" are what theories attempt to explain. So, for scientists, "theory" and "fact" do not stand in opposition, but rather exist in a reciprocal relationship; for example, it is a "fact" that apples have fallen to the ground the last billion times they were dropped and the "theory" which explains this is the current theory of gravitation. In the same way, heritable variation, natural selection, and response to selection (e.g. in domesticated plants and animals) are "facts", and the generalization or extrapolation beyond these phenomena, and the explanation for them, is the "theory of evolution".

Evolution and devolution

One of the most common misunderstandings of evolution is that one species can be "more highly evolved" than another, that evolution is necessarily progressive and/or leads to greater "complexity", or that its converse is " devolution". Evolution provides no assurance that later generations are more intelligent or complex than earlier generations. The claim that evolution results in progress is not part of modern evolutionary theory; it derives from earlier belief systems which were held around the time Darwin formulated his ideas.

In many cases evolution does involve "progression" towards more complexity, since the earliest lifeforms were extremely simple compared to many of the species existing today, and there was nowhere to go but up. However, there is no guarantee that any particular organism existing today will become more intelligent, more complex, bigger, or stronger in the future. In fact, natural selection will only favour this kind of "progression" if it increases chance of survival, i.e. the ability to live long enough to raise offspring to sexual maturity. The same mechanism can actually favour lower intelligence, lower complexity, and so on if those traits become a selective advantage in the organism's environment. One way of understanding the apparent "progression" of lifeforms over time is to remember that the earliest life began as maximally simple forms. Evolution caused life to become more complex, since becoming simpler wasn't advantageous. Once individual lineages have attained sufficient complexity, however, simplifications ( specialization) are as likely as increased complexity. This can be seen in many parasite species, for example, which have evolved simpler forms from more complex ancestors.

Speciation

It is sometimes claimed that speciation — the origin of new species — has never been directly observed, and thus evolution cannot be called sound science. 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. 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. Finally, speciation has actually been directly observed. (See the hawthorn fly example.) Further, there are a number of examples of speciation in plants, and differences in ectodysplasin alleles in stickleback fish speciation has developed as a supermodel for studying gene alterations and speciation.

A variation of this assertion, that microevolution has been directly observed and macroevolution has not, is subject to the same counterarguments. However, it is generally accepted that macroevolution uses the same mechanisms of change as those already observed in microevolution.

Entropy and life

It is claimed that evolution, by increasing complexity without supernatural intervention, violates the second law of thermodynamics. This law posits that in an idealised isolated system, entropy will tend to increase or stay the same. Entropy is a measure of the dispersal of energy in a physical system so that it is not available to do mechanical work. The claim ignores the fact that biological systems are not isolated systems. Life inherently involves open systems, not isolated systems, as all organisms exchange energy and matter with their environment, and similarly the Earth receives energy from the Sun and emits energy back into space. Simple calculations show that the Sun-Earth-space system does not violate the second law because the enormous increase in entropy due to the Sun and Earth radiating into space dwarfs the small decrease in entropy caused by the evolution of life.

In statistical thermodynamics entropy has been envisioned as a measure of the statistical "disorder" at a microstate level, leading to the mistaken idea that entropy implies increasing chaos. Misunderstandings also arise from the mistaken idea that the second law applies in some way to information entropy.

The flow of matter and energy allows self-organization, enabling an increase in complexity without guidance or management. Examples of this spontaneous order include mineral crystals, snowflakes, and rain droplets. In the world we observe many cases where the natural course is increasing order.

Self assembly is ubiquitous in biological systems and for nanostructures under equilibrium and some in non-equilibrium conditions. There are numerous examples of entropy driving order and self assembly.

Information

Some assert that evolution cannot create information, or that information can only be created by an 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 or 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 efficiently digest a material that never existed until the modern age.

Japanese researchers demonstrated that nylon degrading ability can be obtained de novo in laboratory cultures of Pseudomonas aeruginosa strain POA, which initially had no enzymes capable of degrading nylon oligomers. This indicates that the ability of bacteria to digest nylon can evolve if proper artificial selection is applied. Recently, the same group solved the high resolution X-ray crystal structure of the newly evolved nylon-digesting enzyme. Using the structural results, the authors propose "that the amino acid replacements in the catalytic cleft of a preexisting esterase with the beta-lactamase fold resulted in the evolution of the" nylon-digesting enzyme. This hypothesis still needs to be confirmed by detailed mutagenesis studies.

Social and religious controversies

Starting with the publication of The Origin of Species in 1859, the modern science of evolution has been a source of nearly constant controversy. In general, controversy has centered on the philosophical, cosmological, social, and religious implications of evolution, not on the science of evolution itself. The proposition that biological evolution occurs through the mechanism of natural selection has been almost completely uncontested within the scientific community for much of the 20th century.

As Darwin recognized early on, perhaps the most controversial aspect of evolutionary thought is its applicability to human beings. The idea that all diversity in life, including human beings, arose through natural processes without a need for supernatural intervention poses difficulties for the belief in purpose inherent in most religious faiths — and especially for the Abrahamic religions. Many religious people are able to reconcile the science of evolution with their faith, or see no real conflict; Judaism and Catholicism are notable as major faith traditions whose adherents generally see no conflict between evolutionary theory and religious belief. The idea that faith and evolution are compatible has been called theistic evolution. Another group of religious people, generally referred to as creationists, consider evolutionary origin beliefs to be incompatible with their faith, their religious texts and their perception of design in nature, and so cannot accept what they call "unguided evolution".

One particularly contentious topic evoked by evolution is the biological status of humanity. Whereas the classical religious view can broadly be characterized as a belief in the great chain of being (in which people are "above" the animals but slightly "below" the angels), the science of evolution shows that humans are animals and share common ancestry with chimpanzees, gibbons, gorillas, and orangutans, which some people find offensive, for, in their opinion, it "degrades" humankind. A related conflict arises when critics combine the religious view of people's superior status with the mistaken notion that evolution is necessarily "progressive". If human beings are superior to animals yet evolved from them, these critics claim, inferior animals would not still exist. Because animals that are inferior creatures do demonstrably exist, those criticising evolution sometimes incorrectly take this as supporting their claim that evolution is false.

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

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