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Biological evolution is the change in a population's inherited traits from generation to generation. These traits are encoded as genes that are copied and passed on to offspring during reproduction. Mutations and other random changes in these genes can produce new or altered traits, resulting in differences between organisms. Evolution occurs when these different traits become more common or rare in a population. This happens randomly through genetic drift, and based on the reproductive value of traits through natural selection.

Under natural selection, organisms with traits that help them to survive and reproduce tend to have more offspring. In doing so, they will pass more copies of inheritable beneficial traits on to the next generation. This leads to advantageous traits becoming more common in each generation, while disadvantageous traits become rarer. Over time, this process can result in varied adaptations to environmental conditions. As differences in and between populations accumulate, new species may evolve. Similarities in cellular processes suggest that all known species are descended from a single ancestral gene pool through this process of gradual divergence.

The theory of evolution by natural selection was first put forth in detail in Charles Darwin's 1859 book On the Origin of Species. In the 1930s, Darwinian natural selection was combined with Mendelian inheritance to form the modern evolutionary synthesis. With its enormous explanatory and predictive power, this theory has become the central organizing principle of modern biology, providing a unifying explanation for the diversity of life on Earth.

History of evolutionary thought

Although the idea of evolution has existed since classical antiquity, being first discussed by Greek philosophers such as Anaximander, the first convincing exposition of a mechanism by which evolutionary change could occur was not proposed until Charles Darwin and Alfred Russel Wallace jointly presented the theory of evolution by natural selection to the Linnean Society of London in separate papers in 1858. Shortly after, the publication of Darwin's On the Origin of Species popularized and provided detailed support for the theory.

However, Darwin had no working mechanism for inheritance. This was provided in 1865 by Gregor Mendel, whose research revealed that distinct traits were inherited in a well-defined and predictable manner.

In the 1930s, Darwinian natural selection and Mendelian inheritance were combined to form the modern evolutionary synthesis. In the 1940s, 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. Since then, the role of genetics in evolutionary biology has become increasingly central.

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 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, the concepts involved were found to have wide applicability, and it was found that most complex traits were polygenetic and not controlled by single-unit characters. Mendel's ideas replaced the notion of "blending inheritance" prevalent at the time Darwin wrote "On the Origin of Species", and answered the long-standing problem of the persistence of variation within populations.

Later research gave a physical basis to the notion of genes, and eventually identified DNA as the heritable material, with genes re-defined and functioning as discrete regions 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. Another epigenetic mechanism is via microRNA and RNA interference, which serve regulatory roles in gene transcription and translation.

Non-DNA based forms of heritable variation exist, such as transmission of the secondary structures of prions or 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 Mendelian framework, which avoids any connection between environmental signals and the production of heritable variation. However, the processes that produce these variations are rather rare, often reversible, and leave the genetic information intact.

Variation

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 genes. Mutations in genetic material, migration between populations (gene flow), and the reshuffling of genes during sexual reproduction (genetic recombination) create variation in organisms. In some organisms, like bacteria and plants, variation is also produced by the mixing of genetic material between different species in horizontal gene transfer and hybridization. Genetic drift and natural selection act on this variation by increasing or decreasing the frequency of traits: genetic drift does so randomly, while natural selection does so based on whether a trait increases fitness (reproductive success).

The heritable portion of an individual's apparent traits, or phenotype, is primarily the result of the specific genetic makeup, or genotype, encoded on DNA molecules called chromosomes. Thus, the variation in heritable traits within a population reflects the variation in genetic makeup. A specific location on a chromosome is known as a locus; a variant of a DNA sequence at a given locus is an allele. The modern evolutionary synthesis defines evolution as the change over time in the relative frequencies of alleles in a population.

Genetic variation is often the result of a new mutation in a single individual (usually point mutations, insertions, or deletions); 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. All evolutionary forces act by driving this change in allele frequency in one direction or another. Variation disappears when an allele 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. Most sites in the complete DNA sequence, or genome, of a species are identical in all individuals in the population. Consequently, relatively small genotypic changes can lead to dramatic phenotypic ones. Sites with more than one allele are called polymorphic, or segregating, sites. Polymorphism leads to distinct groups of traits arising within the same species, such as different hair colors or sexes. Interactions between a genotype and the environment may also affect the phenotype, as reflected in developmental and phenotypic plasticity.

Mutation

Genetic variation arises due to random mutations that occur at a certain rate in the genomes of all organisms. Mutations are transmissible changes to the genetic material (usually DNA or RNA) of a cell or virus, 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, while deletions and insertions of 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.

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 the same family that coexist within the same genome are called gene paralogs). Genome duplications and chromosome duplications also appear to have served a significant role in evolution.

Large chromosomal rearrangements do not necessarily change gene function, but do generally result in reproductive isolation, and therefore cause speciation. 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 chimpanzee lineage, so that extant chimpanzees retain two separate chromosomes.

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 meiotic recombination rate is not very high - on the order of one crossover (recombination event between homologous 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

Gene flow is the exchange of genetic variation between populations, most commonly of the same species. Examples of intraspecial gene flow include the migration of organisms and the exchange of pollen between populations.

However, gene flow can also occur between different species. Suppose that two closely-related species have acquired adaptations suitable for different environments. In this situation, hybrids can form along the border between those environments and bacteria can share plasmids (small rings of DNA) coding for beneficial traits even between very distantly-related species. As well, viruses can become incorporated into the genome, and can take DNA between hosts, allowing transfer of genes even across biological domains.

Migration into or out of a population may be responsible for a marked change in allele frequencies; that is, the number of individual members carrying a particular variant of a gene can change because of migration. Immigration may result in the addition of new genetic material to the established gene pool of a particular species or population, and conversely emigration may result in the removal of genetic material. As reproductive isolation is a necessary condition for speciation, gene flow within a species may delay speciation by partially homogenizing two otherwise diverging populations.

Physical barriers to gene flow are usually, but not always, natural. They may include impassable mountain ranges, oceans, vast deserts or something so simple as the Great Wall of China, which has hindered the natural flow of plant genes, with samples of the same species from different sides of the wall having been shown to be genetically different.

Hybridization

Depending on how far two species have diverged since their last common ancestor, it may still be possible for them to mate and produce viable offspring. For example, horses and donkeys can be mated to produce mules and hinnys (named based on which species is the mother: with a few genes, the copy used depends on the parent from which it comes. Mules and hinnys are largely infertile, though a few rare cases of successful mating with a donkey have been seen. However, as donkeys and horses have different numbers of chromosomes, the pairing up of chromosomes during meiosis, the process that produces eggs and sperm, usually fails to provide a viable set of chromosomes due to mispairing, so most potential offspring of mules and hinnies simply fail to develop very far, aborting shortly after fertilisation.

However, two more closely-related species may, in some cases, regularly interbreed, with natural selection strongly discriminating against the hybrids and thus keeping the populations distinct. This has been noted in, among other species, toads, butterflies, clams, and mussels. Selection against hybrids may be accompanied by reinforcement (emergence of traits that increase reluctance to mate outside the species), and/or character displacement. In rare cases, hybrids may be well adapted to a zone between the extremes favoured by the two parents, and may fill that zone.

Hybridization, however, rarely leads to new species in the animal kingdom, with notable exceptions among birds. However, it is a common and important method of producing new species in plants, where polyploidy, having more than two copies of each chromosome, is much more tolerated than in animals (where it is usually lethal). This allows hybrids to simply double their total number of chromosomes (not a particularly unusual circumstance in plants), and gain the ability to reproduce. One classic example is spelt wheat and common wheat:

The basic precursors of wheat are all diploid, having two chromosomes with two copies each. The first hybridisation produced wild emmer, T. dicoccoides from T. urartu and some unknown wild goatgrass similar to Aegilops searsii or Ae. speltoides. This produced a plant with four chromosomes, but only one copy of each. In one such hybrid, by chance, a chromosomal duplication occured, allowing it to reproduce freely. As grasses are generally self-fertile, it could then reproduce freely. Domestication developed this hybrid into emmer and durum wheat. Finally, either emmer or durum wheat hybridized with the wild grass Aegilops tauschii within farmer's fields, and, with another chromosomal duplication event, produced the ancestor of spelt wheat (Triticum spelta) and common wheat (Triticum aestivum). All of these hybrids have been reproduced experimentally.

Horizontal gene transfer

Horizontal gene transfer (HGT), which is also known as "Lateral gene transfer" (LGT), is any process in which an organism transfers genetic material to another cell that is not its offspring. By contrast, vertical transfer occurs when an organism receives genetic material from its ancestor (e.g. its parent or a species from which it evolved) or passes genetic material to its offspring. Most thinking in genetics has focused on the more prevalent vertical transfer, but there is a recent awareness that horizontal gene transfer is a significant phenomenon. Artificial horizontal gene transfer is a form of genetic engineering.

Horizontal gene transfer is common among bacteria, even very distantly-related ones. This process is thought to be a significant cause of increased drug resistance; when one bacterial cell acquires resistance, it can quickly transfer the resistance genes to many species. Enteric bacteria appear to exchange genetic material with each other within the gut in which they live.

Analysis of DNA sequences suggests that horizontal gene transfer has also occurred within eukaryotes, from their chloroplast and mitochondrial genome to their nuclear genome. As stated in the endosymbiotic theory, chloroplasts and mitochondria probably originated as bacterial endosymbionts of a progenitor to the eukaryotic cell. Horizontal transfer of genes from bacteria to some fungi, especially the yeast Saccharomyces cerevisiae has been well documented. There is also recent evidence that the adzuki bean beetle has somehow acquired genetic material from its (non-beneficial) endosymbiont Wolbachia; however this claim is disputed and the evidence is not conclusive.

Horizontal gene transfer complicates the inference of the phylogeny of life, since genetic information can be passed to other organisms and other species in addition to being passed from parent to offspring, leading to connections between possibly distant branches.

Mechanisms

Selection and adaptation

Natural selection, one of the processes that drives evolution, results from the difference in reproductive success between individuals in a population. It has often been called a "self-evident" mechanism because it necessarily follows from the following facts:

• Natural, heritable variation exists within populations and among species
• Organisms are superfecund (produce more offspring than can possibly survive)
• Organisms in a population vary in their ability to survive and reproduce
• In any generation, successful reproducers necessarily pass their heritable traits to the next generation, while unsuccessful reproducers do not.

If these traits increase the evolutionary fitness of the individuals that carry them, then those individuals will be more likely to survive and reproduce than other organisms in the population, thus passing more copies of those heritable traits on to the next generation. The corresponding decrease in fitness for deleterious traits results in their becoming rarer. In time, this can result in adaptation: the gradual accumulation of new traits that generally result in a population of organisms becoming better suited to its environment and ecological niche. It is important to note that not all characteristics of an organism are necessarily adaptations, as many traits are present in organisms simply by virtue of ancestry or developmental constraints.

A special case of natural selection is sexual selection: selection for any trait whose presence is directly correlated with mating success due to preferential mate choice. Traits that evolved via sexual selection are particularly prominent among males of animal species. Despite the fact that such traits may decrease the survival of individual males (e.g. cumbersome antlers, mating calls or bright colors that attract predators, male-male fighting over access to mates), reproductive success is usually higher in males that show robust, sexually selected phenotypes.

Natural selection of trait frequencies within a population can be subcategorized into three different modes: directional selection (a shift in the mean trait value over time); disruptive selection (selection for extreme trait values on both ends, or "tails" of the distribution, often resulting in a bimodal distribution and selection against the mean); and stabilizing selection (also called purifying selection — selection against extreme trait values on both ends, and a decrease in variance around the mean.)

Through the process of natural selection, organisms generally become better suited to their environments. Adaptation is often thought of as any evolutionary process that increases the fitness of the individual — however, under such a loose definition all natural selection would be considered adaptive. More strictly speaking, an adaptation is a specifically defined trait that not only enhances performance of some function, but also evolved under selection to perform that function (in other words, historical function must be the same as the current utility). Many traits that appear to be adaptations are in fact exaptations. Note that adaptation is context-sensitive; a trait that increases fitness in one environment may decrease it in another.

Genetic drift

Genetic drift is the change in allele frequency from one generation to the next that occurs because alleles in the offspring generation are a random sample of alleles in the parent generation, and are thus subject to sampling error. Over time, even in the absence of selection on the alleles, allele frequencies tend to "drift" upward or downward, until they eventually becoming "fixed" - that is, going to 0% or 100% frequency. Fluctuations in allele frequency between successive generations may thus 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 effect of genetic drift depends strongly on the size of the population: drift is 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. Natural selection is predominant in large populations, while genetic drift is 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 — smaller populations require a shorter time for fixation.

Similarly, changing population size can dramatically influence the course of evolution. Population bottlenecks, where the population shrinks in size temporarily to a small number of individuals and therefore loses much genetic variation, result in a more uniform population and the loss of most rare variation. Bottlenecks may also result from migration or population subdivision.

Common descent

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 20 amino acids as the building blocks for proteins. The universality of these traits strongly suggests common ancestry, because the selection of many of these traits seems arbitrary.

In the Origin of Species, Darwin built his case for the truth of shared ancestry of all organisms by pointing out a number of facts that were not new to science: 1.) organisms have geographic distributions that cannot be explained by local ecology or adaptation alone. 2.) The diversity of life is not a diversity of completely unique organisms, but a diversity of organisms that share traits and similarities with one another (see homology). 3.) Many organisms have vestigial traits or even behaviors that have no clear purpose in their modern bearers. 4.) All of life, as Linneaus and others have always recognized, can be naturally classified into a hierarchy of nested groups. This last point in particular is strongly consistent with a shared evolutionary history of all organisms that live today and ever lived.

Evolution has also left numerous signs of the histories of different species. Fossils, along with the comparative anatomy of present-day organisms, constitute the morphological, or anatomical, record. By comparing the anatomies of both modern and extinct species, paleontologists can infer the lineages of those species.

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 96% genotypic similarity between humans and chimpanzees are obtained.

Other evidence used to demonstrate evolutionary lineages includes the geographical distribution of species. For instance, marsupials are found only in Australia and South America, showing that their common ancestor with placental mammals lived before the breakup of Gondwana and the freezing over of Antarctica.

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 homology

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 provides only sparse and intermittent information about ancestral lineages.

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 whether, for example, speciation occurs 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. For example, mass extinctions frequently resulted in the loss of entire groups of species, 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. Vestigial structures are idiosyncratic anatomical features such as the panda's "thumb", which indicate how an organism's evolutionary lineage constrains its adaptive development. Other examples of vestigial structures include the degenerate eyes of blind cave-dwelling fish, and 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. Examples of vestigial structures in humans include wisdom teeth, the coccyx and the vermiform appendix.

These anatomical similarities in extant and fossil organisms can give evidence of the relationships between different groups of organisms. 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.

Molecular homology

By comparing the genetic and/or protein sequences of species, we can discern their evolutionary relationships. The resultant phylogenetic trees are typically congruent with traditional taxonomy, and are often used to either 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. This 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 eukaryotes.

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. For example, the appearance of oxygen in the earth's atmosphere is linked to the evolution of photosynthesis.

The proteomic evidence also supports the universal ancestry of life. Vital proteins, such as the ribosome, DNA polymerase, and RNA polymerase, are found in everything from 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 by early organisms and passed on to all extant life through common descent. Further evidence for reconstructing ancestral lineages comes from junk DNA such as pseudogenes, "dead" genes which steadily accumulate mutations.

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, which facilitates rapid evolution by providing substantial quantities of genetic material under weak or no selective constraints; horizontal gene transfer, the process of transferring genetic material to another cell that is not an organism's offspring, allowing for species to acquire beneficial genes from each other; recombination, capable of reassorting large numbers of different alleles and of establishing reproductive isolation; and endosymbiosis, the incorporation of genetic material and biochemical composition of a separate species, a process observed in organisms such as the protist hatena and used to explain the origin of organelles such as mitochondria and plastids as the absorption of ancient prokaryotic cells into ancient eukaryotic ones.

Speciation and extinction

Speciation is the irreversible process by which a pre-existing species lineage diverges into two descendant (or "daughter") species lineages, which then become reproductively isolated. Speciation is always described and understood as a binary (two-part) split in genealogy. Because a pair of sister species are equally descended from the ancestral form, it is incorrect to view one daughter species as the "original" species and the other as the "new" one.

In sexually reproducing organisms, speciation results from two important events: 1.) the evolution of reproductive isolating mechanisms, resulting in 2.) genealogical divergence. The most common mode of speciation in animals is allopatric speciation, which occurs in populations that initially become isolated geographically, such as by habitat fragmentation or migration. Simply by virtue of being geographically separated, selection and drift will act independently in the isolated populations, and will proceed to reproductive incompatibility if the separation is maintained long enough. Sympatric speciation is species divergence without geographic isolation, and it is typically controversial since even a small amount of gene flow may be sufficient to homogenize a potentially diverging species. General models of sympatric speciation require the evolution of stable polymorphisms associated with non-random assortative mating, in order for reproductive isolation to evolve. An example of rapid sympatric speciation can be clearly observed in the triangle of U, where new species of Brassica sp. have been made by the fusing of separate genomes from related plants, although this type of speciation may be more accurately described as speciation by polyploidization.

Ernst Mayr's peripatric speciation is a type of speciation that exists as a result of character displacement on hybrid-zone boundaries between two adjoining populations. Peripatric speciation is a critical underpinning of the theory of punctuated equilibrium.

One common misconception about evolution is the idea that if humans evolved from monkeys, monkeys should no longer exist. However, biologists have never claimed that humans evolved from monkeys — only that humans and monkeys, like all organisms, share a common ancestor (that was neither human nor monkey).Common misconceptions like this indicate a misunderstanding of speciation, which involves two subsets of a population cladogenetically splitting apart, rather than an entire species simply turning into a new one.

Extinction is the disappearance of species (i.e., gene pools). The moment of extinction is generally defined as occurring at the death of the last individual of that species. Extinction is not an unusual event on a geological time scale — species regularly appear through 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 all terrestrial vertebrate species. In the Cretaceous-Tertiary extinction event, many forms of life perished (including approximately 50% of all genera), the most commonly mentioned among them being the non-avian dinosaurs. The Holocene extinction event is a current mass extinction, involving the rapid extinction of tens or hundreds of thousands of species each year. Scientists consider human activities to be the primary cause of the ongoing extinction event, as well as the related influence of climate change.

History of life

The origin of life from self-catalytic chemical reactions is not a part of biological evolution, but rather of pre-evolutionary abiogenesis. However, disputes over what defines life make the point at which such increasingly complex sets of reactions became true organisms unclear. Not much is yet known about the earliest developments in life. There is no scientific consensus regarding the relationship of the three domains of organisms (Archaea, Bacteria, and Eukaryota) or regarding the precise reactions involved in abiogenesis. Attempts to shed light on the origin of life generally focus on the behavior of macromolecules—particularly RNA—and the behavior of complex systems.

Fossil evidence indicates that the diversity and complexity of modern life has developed over much of the 4.57 billion year history of Earth. Oxygenic photosynthesis emerged around 3 billion years ago, and the subsequent emergence of an oxygen-rich atmosphere made the development of aerobic cellular respiration possible 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 geologically brief period of remarkable biological diversity, originated 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 (mya), plants and fungi colonized the land, and were soon followed by arthropods and other animals. Amphibians first appeared around 300 mya, followed by reptiles, then mammals around 200 mya and birds around 100 mya. The human genus arose around 2 mya, while the earliest modern humans lived 200 thousand years ago.

Modern research

Academic disciplines

Scholars in a number of academic disciplines continue to document examples 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 contributions to current understanding of evolutionary mechanisms. 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.

The capability of evolution through selection to produce biological processes and networks optimized for a particular environment has greatly interested mathematicians, scientists and engineers. There has been some recent success in implementing these ideas for artificial uses, including genetic algorithms, which can find the solution to a multi-dimensional problem more quickly than standard software produced by human intelligent designers, and the use of evolutionary fitness landscapes to optimize the design of a system Evolutionary optimization techniques are particularly useful in situations in which it is easy to determine the quality of a single solution, but hard to go through all possible solutions one by one.

Social and religious controversies

Ever since the publication of The Origin of Species in 1859, evolution has been a source of controversy. In general, controversy has centered on the philosophical, 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 is completely uncontested within the scientific community.

As Darwin recognized early on, perhaps the most controversial aspect of evolutionary thought is its applicability to human beings. Specifically, many object to the idea that all diversity in life, including human beings, arose through natural processes without a need for supernatural intervention. Although many religions, such as Catholicism, have reconciled their beliefs with evolution through theistic evolution, creationists object to evolution on the basis that it contradicts their theistic origin beliefs. In some countries — notably the United States — these tensions between scientific and religious teachings have fueled the ongoing creation-evolution controversy, a social and religious conflict especially centering on politics and public education. While other fields of science, such as cosmology and earth science, also conflict with literal interpretations of many religious texts, evolutionary biology has borne the brunt of these debates.

Evolution has been used to support philosophical and ethical views which most contemporary scientists consider to have been 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.

Notes

1. ^ Futuyma, Douglas J. (2005). Evolution. Sunderland, Massachusetts: Sinauer Associates, Inc. ISBN 0-87893-187-2.
2. Lande, R. (1983). "The measurement of selection on correlated characters". Evolution. 37: 1210–1226. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
3. Haldane, J.B.S. (1953). "The measurement of natural selection". Proceedings of the 9th International Congress of Genetics. 1: 480–487.
4. ^ "Mechanisms: the processes of evolution". Understanding Evolution. University of California, Berkeley. Retrieved 2006-07-14.
5. Gould, Stephen J. (2002). The Structure of Evolutionary Theory. Belknap Press. ISBN 0-674-00613-5.
6. Dawkins, Richard (1989). The Selfish Gene. Oxford University Press Press. ISBN 0-674-00613-5.
7. Myers, PZ (2006-06-18). "Ann Coulter: No evidence for evolution?". Pharyngula. scienceblogs.com. Retrieved 2006-11-18.
8. IAP Statement on the Teaching of Evolution Joint statement issued by the national science academies of 67 countries, including the United Kingdom's Royal Society (PDF file)
9. From the American Association for the Advancement of Science, the world's largest general scientific society: 2006 Statement on the Teaching of Evolution (PDF file), AAAS Denounces Anti-Evolution Laws
10. Bowler, Peter J. (1989). The Mendelian Revolution: The Emergence of Hereditarian Concepts in Modern Science and Society. Baltimore: Johns Hopkins University Press.
11. Rincon, Paul (2005). "Evolution takes science honours". BBC News. Retrieved 2006-07-16. According to the BBC, Colin Norman, news editor of Science, said "cientists tend to take for granted that evolution underpins modern biology Evolution is not just something that scientists study as an esoteric enterprise. It has very important implications for public health and for our understanding of who we are" and Dr. Mike Ritchie, of the school of biology at the University of St Andrews, UK said "The big recent development in evolutionary biology has obviously been the improved resolution in our understanding of genetics. Where people have found a gene they think is involved in speciation, I can now go and look how it has evolved in 12 different species of fly, because we've got the genomes of all these species available on the web."
12. Created from: Edwards, KJ (1993). "MOLECULAR STRUCTURE OF THE B-DNA DODECAMER D(CGCAAATTTGCG)2; AN EXAMINATION OF PROPELLER TWIST AND MINOR-GROOVE WATER STRUCTURE AT 2.2 ANGSTROMS RESOLUTION". Protein Data Bank. Retrieved 2007-03-17. {{cite web}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
13. Beisson, J (1965). "Cytoplasmic inheritance of the organization of the cell cortex of Paramecium aurelia". Proceedings of the National Academy of Sciences USA. 53: 275–282. {{cite journal}}: Unknown parameter |coauthor= ignored (|author= suggested) (help)
14. Nelsen, EM. "Non-genic inheritance of cellular handedness". Development. 105: 447–456. Retrieved 2007-03-11. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
15. Paleontologist Stephen Jay Gould once summarized this as "variation proposes and selection disposes". Gould, SJ (1997-06-12). "Darwinian Fundamentalism". No. 10. New York Review of Books. Retrieved 2007-03-17. {{cite news}}: Text "volume44" ignored (help)
16. Snustad, P (2002). Principles of Genetics, 3rd edition. John Wiley and Sons, Inc. p. 20. ISBN 978-0471441809. {{cite book}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
17. Aminetzach, YT (1992). "Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila". Science. 309 (5735): 764–7. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
18. Carroll S.B,. Grenier J.K., Weatherbee S.D. (2005). From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design. Second Edition. Oxford: Blackwell Publishing. ISBN 1-4051-1950-0.{{cite book}}: CS1 maint: multiple names: authors list (link)
19. Pilcher, Helen R (2003). "Great Wall blocks gene flow". News@Nature. Nature.
20. Duttaroy, Asim K (2006). "Evolution, epigenetics, and maternal nutrition". Retrieved 2007-03-16.
21. Sotka, EE (2006). "The Use of Genetic Clines to Estimate the Dispersal Distances of Marine Larvae" (PDF). Ecology. 87 (5): 1094–1103. Retrieved 2007-03-17. {{cite journal}}: Cite has empty unknown parameter: |1= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
22. Belderok, B (2000). Bread-Making Quality of Wheat: A Century of Breeding in Europe. Springer. p. 3. ISBN 0-7923-6383-3. {{cite book}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
23. ^ Hancock, JF (2003). Plant Evolution and the Origin of Crop Species. ISBN 978-0851996851. {{cite book}}: Unknown parameter |publishing= ignored (help)
24. McFadden, ES (1946). "The Origin of triticum spelta and its free-threshing hexpaloid relatives" (PDF). Journal of Heredity. 37: 81–89. Retrieved 2007-03-16. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
25. Lande, R. (1983). "The measurement of selection on correlated characters". Evolution. 37: 1210–1226. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
26. Haldane, J.B.S. (1953). "The measurement of natural selection". Proceedings of the 9th International Congress of Genetics. 1: 480–487.
27. Oklahoma State - Horizontal Gene Transfer: "Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of phylogenetic 'domains'. Thus determining the phylogenetic history of a species cannot be done conclusively by determining evolutionary trees for single genes."
28. Chimpanzee Sequencing and Analysis Consortium (2005). "Initial sequence of the chimpanzee genome and comparison with the human genome". Nature. 437: 69–87.
29. Varki A, Altheide TK. (2005). "Comparing the human and chimpanzee genomes: searching for needles in a haystack". Genome Res. 15(12): 1746–58.
30. Schweitzer M.H.; et al. (2005). "Soft-tissue vessels and cellular preservation in Tyrannosaurus rex". Science. 307 (5717): 1952–1955. {{cite journal}}: Explicit use of et al. in: |author= (help)
31. Feduccia, Alan (1996). The Origin and Evolution of Birds. New Haven: Yale University Press. ISBN 0-300-06460-8.
32. Daeschler, Edward B., Shubin, Neil H., & Jenkins Jr, Farish A. (2006). "A Devonian tetrapod-like fish and the evolution of the tetrapod body plan". Nature. 440: 757–763. doi:10.1038/nature04639. Retrieved 2006-07-14. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
33. Chen, FC (2001). "Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees". American Journal of Human Genetics. 68: 444–56. Retrieved 2007-03-16. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
34. Cooper, GM (2003). "Quantitative Estimates of Sequence Divergence for Comparative Analysis of Mammalian Genomes". Genome Research. 13: 813–820. Retrieved 2007-03-16. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
35. The picture labeled "Human Chromosome 2 and its analogs in the apes" in the article Williams, Robert. "Comparison of the Human and Great Ape Chromosomes as Evidence for Common Ancestry". Retrieved 2007-03-17. shows how humans have a single chromosome which is two separate chromosomes in the nonhuman apes.
36. Wade, Nicholas (2006-03-07). "Still Evolving, Human Genes Tell New Story". New York Times. Retrieved 2007-03-17.
37. Voight, BF (2006). "A Map of Recent Positive Selection in the Human Genome". PLoS Biol. 4 (3). doi:10.1371/journal.pbio.0040072. Retrieved 2007-03-17. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)CS1 maint: unflagged free DOI (link), states the International HapMap Project is "providing the strongest evidence yet that humans are still evolving" and details some of that evidence.
38. Petrov, DA (2000). "Pseudogene evolution and natural selection for a compact genome". Journal of Heredity. 91 (3): 221–227. Retrieved 2007-03-16. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
39. Okamoto N, Inouye I. (2005). "A secondary symbiosis in progress". Science. 310 (5746): 287.
40. Okamoto, N (2006). "Hatena arenicola gen. et sp. nov., a Katablepharid Undergoing Probable Plastid Acquisition". Protist. Article in Print. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
41. Hoskin, CJ (2005). "Reinforcement drives rapid allopatric speciation". Nature. 437: 1353–1356. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
42. Savolainen; et al. (May 2006). "Sympatric speciation in palms on an oceanic island". Nature. 441: 210–213. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: year (link)
43. Barluenga; et al. (February 2006). "Sympatric speciation in Nicaraguan crater lake cichlid fish". Nature. 439: 719–723. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: year (link)
44. Isaak, Mark (2005). "Index to Creationist Claims, Claim CC150". The TalkOrigins Archive. Retrieved 2007-03-17.
45. Leakey, Richard (1996). The Sixth Extinction : Patterns of Life and the Future of Humankind. Anchor. ISBN 0-385-46809-1. {{cite book}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
46. Buscher, David (2003). "Interferometric "fitness" and the large optical array". Proceedings of the SPIE. 4838: 110–125. Retrieved 2007-03-17. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help) optimizing the design of a large interferometer array using an evolutionary fitness landscape.
47. An overview of the philosophical, religious, and cosmological controversies by a philosopher who strongly supports evolution is: Daniel Dennett, Darwin's Dangerous Idea: Evolution and the Meanings of Life (New York: Simon & Schuster, 1995). On the scientific and social reception of evolution in the 19th and early 20th centuries, see: Peter J. Bowler, Evolution: The History of an Idea, 3rd. rev. edn. (Berkeley: University of California Press, 2003).
48. AnswersInGenesis.org – Evolution & creation, science & religion, facts & bias
49. Spergel, D. N. (2003). "First-Year Wilkinson Microwave Anisotropy Probe (WMAP) Observations: Determination of Cosmological Parameters". The Astrophysical Journal Supplement Series. 148: 175–194. doi:10.1086/377226. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
50. Wilde, S. A. (2001). "Evidence from detrital zircons for the existence of continental crust and oceans on the Earth 4.4 Gyr ago". Nature. 409: 175–178. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
51. Darwin strongly disagreed with attempts by Herbert Spencer and other to extrapolate evolutionary ideas to all possible subject matters; see Mary Midgley The Myths we Live By Routledge 2004 p62.
52. On the history of eugenics and evolution, see Daniel Kevles, In the Name of Eugenics: Genetics and the Uses of Human Heredity (New York: Knopf, 1985).

References

• Carroll, SB (2005). Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom. W. W. Norton & Company. ISBN 0-393-06016-0.
• Larson, EJ (2004). Evolution: The Remarkable History of a Scientific Theory. Modern Library. ISBN 0-679-64288-9.
• Mayr, E (2002). What Evolution Is. Basic Books. ISBN 0-465-04426-3.
• Williams, GC (1966). Adaptation and Natural Selection: A Critique of some Current Evolutionary Thought. Princeton University Press. ISBN 978-0691023571.
• Zimmer, C (2006). Evolution: The Triumph of an Idea. Academic Internet Publishers. ISBN 978-1428804098.

External links

2. Part 2

• Understanding Evolution from University of California, Berkeley
• National Academies Evolution Resources
• Charles Darwin's writings online
• Everything you wanted to know about evolution (provided by New Scientist)
• Howstuffworks.com — How Evolution Works
• Synthetic Theory Of Evolution: An Introduction to Modern Evolutionary Concepts and Theories
• Evolution News from Genome News Network (GNN)
• Understanding Evolution: History, Theory, Evidence, and Implications Deals heavily with the history of evolutionary thought

Template:Link FA

• Evolution
• Evolutionary biology
• Theories