Evolution Totally Explained

In biology, evolution is the change in the inherited traits of a population from generation to generation. These traits are the expression of genes that are copied and passed on to offspring during reproduction. Mutations in these genes can produce new or altered traits, resulting in heritable differences (genetic variation) between organisms. New traits can also come from transfer of genes between populations, as in migration, or between species, in horizontal gene transfer. Evolution occurs when these heritable differences become more common or rare in a population, either non-randomly through natural selection or randomly through genetic drift.
   Natural selection is a process that causes heritable traits that are helpful for survival and reproduction to become more common, and harmful traits to become more rare. This occurs because organisms with advantageous traits pass on more copies of these heritable traits to the next generation. Over many generations, adaptations occur through a combination of successive, small, random changes in traits, and natural selection of those variants best-suited for their environment. In contrast, genetic drift produces random changes in the frequency of traits in a population. Genetic drift arises from the role chance plays in whether a given individual will survive and reproduce.
   One definition of a species is a group of organisms that can reproduce with one another and produce fertile offspring. However, when a species is separated into populations that are prevented from interbreeding, mutations, genetic drift, and the selection of novel traits cause the accumulation of differences over generations and the emergence of new species. The similarities between organisms suggest that all known species are descended from a common ancestor (or ancestral gene pool) through this process of gradual divergence.
   The theory of evolution by natural selection was proposed roughly simultaneously by both Charles Darwin and Alfred Russel Wallace, and set out in detail in Darwin's 1859 book On the Origin of Species. It encountered initial resistance from religious authorities who believed humans were divinely set apart from the animal kingdom. In the 1930s, Darwinian natural selection was combined with Mendelian inheritance to form the modern evolutionary synthesis,

Heredity

Inheritance in organisms occurs through discrete traits – particular characteristics of an organism. In humans, for example, eye color is an inherited characteristic, which individuals can inherit from one of their parents. Inherited traits are controlled by genes and the complete set of genes within an organism's genome is called its genotype.
The complete set of observable traits that make up the structure and behavior of an organism is called its phenotype. These traits come from the interaction of its genotype with the environment. As a result, not every aspect of an organism's phenotype is inherited. Suntanned skin results from the interaction between a person's genotype and sunlight; thus, a suntan isn't hereditary. However, people have different responses to sunlight, arising from differences in their genotype; a striking example is individuals with the inherited trait of albinism, who don't tan and are highly sensitive to sunburn. Genes are regions within DNA molecules that contain genetic information.

Variation

Because an individual's phenotype results from the interaction of their genotype with the environment, the variation in phenotypes in a population reflects the variation in these organisms' genotypes. The frequency of one particular allele will fluctuate, becoming more or less prevalent relative to other forms of that gene. Evolutionary forces act by driving these changes in allele frequency in one direction or another. Variation disappears when an allele reaches the point of fixation — when it either disappears from the population or replaces the ancestral allele entirely.
Variation comes from mutations in genetic material, migration between populations (gene flow), and the reshuffling of genes through sexual reproduction. Variation also comes from exchanges of genes between different species; for example, through horizontal gene transfer in bacteria, and hybridization in plants. Despite the constant introduction of variation through these processes, most of the genome of a species is identical in all individuals of that species. However, even relatively small changes in genotype can lead to dramatic changes in phenotype: chimpanzees and humans differ in only about 5% of their genomes.

Mutation

Genetic variation comes from random mutations that occur in the genomes of organisms. Mutations are changes in the DNA sequence of a cell's genome and are caused by radiation, viruses, transposons and mutagenic chemicals, as well as errors that occur during meiosis or DNA replication. These mutagens produce several different types of change in DNA sequences; these can either have no effect, alter the product of a gene, or prevent the gene from functioning. Studies in the fly Drosophila melanogaster suggest that about 70 percent of mutations are deleterious, and the remainder are either neutral or have a weak beneficial effect. Due to the damaging effects that mutations can have on cells, organisms have evolved mechanisms such as DNA repair to remove mutations.
   Large sections of DNA can also be duplicated, which is a major source of raw material for evolving new genes, with tens to hundreds of genes duplicated in animal genomes every million years. Most genes belong to larger families of genes of shared ancestry. Novel genes are produced either through duplication and mutation of an ancestral gene, or by recombining parts of different genes to form new combinations with new functions. For example, the human eye uses four genes to make structures that sense light: three for color vision and one for night vision; all four arose from a single ancestral gene. An advantage of duplicating a gene (or even an (entire genome) is that overlapping or redundant functions in multiple genes allows alleles to be retained that would otherwise be harmful, thus increasing genetic diversity.
   Changes in chromosome number may also involve the breakage and rearrangement of DNA within chromosomes. For example, two chromosomes in the Homo genus fused to produce human chromosome 2; this fusion didn't occur in the chimpanzee lineage and chimpanzees retain these separate chromosomes. In evolution, the most important role of such chromosomal rearrangements may be to accelerate the divergence of a population into new species by preserving genetic differences within populations.
   Sequences of DNA that can move about the genome, such as transposons, make up a major fraction of the genetic material of plants and animals, and may have been important in the evolution of genomes. For example, more than a million copies of the Alu sequence are present in the human genome, and these sequences have now been recruited to perform functions such as regulating gene expression. Another effect of these mobile DNA sequences is that when they move within a genome, they can mutate or delete existing genes and thereby produce genetic diversity.

Extinction

Extinction is the disappearance of an entire species. Extinction isn't an unusual event, as species regularly appear through speciation, and disappear through extinction. Indeed, virtually all animal and plant species that have lived on earth are now extinct. These extinctions have happened continuously throughout the history of life, although the rate of extinction spikes in occasional mass extinction events. The Cretaceous–Tertiary extinction event, during which the dinosaurs went extinct, is the most well-known, but the earlier Permian-Triassic extinction event was even more severe, with approximately 96 percent of species driven to extinction. Human activities are now the primary cause of the ongoing extinction event; global warming may further accelerate it in the future.
The role of extinction in evolution depends on which type is considered. The causes of the continuous "low-level" extinction events, which form the majority of extinctions, are not well understood and may be the result of competition between species for shared resources. The current scientific consensus is that the complex biochemistry that makes up life came from simpler chemical reactions, but it's unclear how this occurred. Not much is certain about the earliest developments in life, the structure of the first living things, or the identity and nature of any last universal common ancestor or ancestral gene pool. Consequently, there's no scientific consensus on how life began, but proposals include self-replicating molecules such as RNA, and the assembly of simple cells.

Common descent

All organisms on Earth are descended from a common ancestor or ancestral gene pool. Current species are a stage in the process of evolution, with their diversity the product of a long series of speciation and extinction events. The common descent of organisms was first deduced from four simple facts about organisms: First, they've geographic distributions that can't be explained by local adaptation. Second, the diversity of life isn't a set of completely unique organisms, but organisms that share morphological similarities. Third, vestigial traits with no clear purpose resemble functional ancestral traits, and finally, that organisms can be classified using these similarities into a hierarchy of nested groups. By comparing the anatomies of both modern and extinct species, paleontologists can infer the lineages of those species. However, this approach is most successful for organisms that had hard body parts, such as shells, bones or teeth. Further, as prokaryotes such as bacteria and archaea share a limited set of common morphologies, their fossils don't provide information on their ancestry.
More recently, evidence for common descent has come from the study of biochemical similarities between organisms. For example, all living cells use the same nucleic acids and amino acids. The development of molecular genetics has revealed the record of evolution left in organisms' genomes: dating when species diverged through the molecular clock produced by mutations. For example, these DNA sequence comparisons have revealed the close genetic similarity between humans and chimpanzees and shed light on when the common ancestor of these species existed.

Evolution of life

Despite the uncertainty on how life began, it's clear that prokaryotes were the first organisms to inhabit Earth, approximately 3–4 billion years ago. No obvious changes in morphology or cellular organization occurred in these organisms over the next few billion years.
   The eukaryotes were the next major innovation in evolution. These came from ancient bacteria being engulfed by the ancestors of eukaryotic cells, in a cooperative association called endosymbiosis. The engulfed bacteria and the host cell then underwent co-evolution, with the bacteria evolving into either mitochondria or hydrogenosomes. An independent second engulfment of cyanobacterial-like organisms led to the formation of chloroplasts in algae and plants.
   The history of life was that of the unicellular eukaryotes, prokaryotes, and archaea until about a billion years ago when multicellular organisms began to appear in the oceans in the Ediacaran period. The evolution of multicellularity occurred in multiple independent events, in organisms as diverse as sponges, brown algae, cyanobacteria, slime moulds and myxobacteria.
   Soon after the emergence of these first multicellular organisms, a remarkable amount of biological diversity appeared over approximately 10 million years, in an event called the Cambrian explosion. Here, the majority of types of modern animals evolved, as well as unique lineages that subsequently became extinct. Various triggers for the Cambrian explosion have been proposed, including the accumulation of oxygen in the atmosphere from photosynthesis. About 500 million years ago, plants and fungi colonized the land, and were soon followed by arthropods and other animals. Amphibians first appeared around 300 million years ago, followed by early amniotes, then mammals around 200 million years ago and birds around 100 million years ago (both from "reptile"-like lineages). However, despite the evolution of these large animals, smaller organisms similar to the types that evolved early in this process continue to be highly successful and dominate the Earth, with the majority of both biomass and species being prokaryotes. Evolutionary thought was further developed by other early thinkers, including the Greek philosopher Empedocles, the Roman philosopher Lucretius, the Arab biologist Al-Jahiz, the Persian philosopher Ibn Miskawayh, and the Brethren of Purity. Also in the Far East, the philosopher Zhuangzi discussed a transformative power of species to adapt to their surroundings. As biological knowledge grew in the 18th century, a variety of such ideas developed, beginning with Pierre Maupertuis in 1745, and with contributions from natural philosophers such as Erasmus Darwin and Jean-Baptiste Lamarck. In 1858, Charles Darwin and Alfred Russel Wallace jointly proposed the theory of evolution by natural selection to the Linnean Society of London in separate papers. Shortly after, Darwin's publication of The Origin of Species provided detailed support for the theory and led to increasingly wide acceptance of the occurrence of evolution.
   Nonetheless, Darwin's specific ideas about evolution, such as gradualism and the mechanisms of natural selection, were strongly contested at first. Lamarckists argued that transmutation of species occurred as parents passed on adaptations acquired during their lifetimes. Eventually, when experiments failed to support it, this idea was abandoned in favor of Darwinism. More significantly, Darwin couldn't account for how traits were passed down from generation to generation. A mechanism was provided in 1865 by Gregor Mendel, who found that traits were inherited in a predictable manner. When Mendel's work was rediscovered in 1900, disagreements over the rate of evolution predicted by early geneticists and biometricians led to a rift between the Mendelian and Darwinian models of evolution.
   This contradiction was reconciled in the 1930s by biologists such as Ronald Fisher. The end result was a combination of evolution by natural selection and Mendelian inheritance, the modern evolutionary synthesis. In the 1940s, the identification of DNA as the genetic material by Oswald Avery and colleagues and the subsequent publication of the structure of DNA by James Watson and Francis Crick in 1953, demonstrated the physical basis for inheritance. Since then, genetics and molecular biology have become core parts of evolutionary biology and have revolutionized the field of phylogenetics.
   In its early history, evolutionary biology primarily drew in scientists from traditional taxonomically-oriented disciplines, whose specialist training in particular organisms addressed general questions in evolution. As evolutionary biology expanded as an academic discipline, particularly after the development of the modern evolutionary synthesis, it began to draw more widely from the biological sciences.
   As Darwin recognized early on, the most controversial aspect of evolutionary thought is its application to humans. Specifically, some people object to the idea that humans arose through natural processes without supernatural intervention. Although many religions and denominations have reconciled their beliefs with evolution through theistic evolution, several denominations contain creationists who object to evolution, as it contradicts their literal interpretation of origin beliefs. In some countries – notably the United States – these tensions between scientific and religious teachings have fueled the ongoing creation–evolution controversy, a religious conflict focusing on politics and public education. While other scientific fields such as cosmology and earth science also conflict with literal interpretations of many religious texts, evolutionary biology has borne the brunt of religious objection.
   Evolution has also attracted controversy because it has been used to support philosophical positions that promote discrimination and racism. 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 those considered "good stock" to reproduce, and the compulsory sterilization, prenatal testing, birth control, and even killing, of those considered bad stock. Another example of an extension of evolutionary theory that's 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. However, contemporary scientists and philosophers consider these ideas to have been neither mandated by evolutionary theory nor supported by data.

Uses in technology

A major technological application of the power of evolution is artificial selection, which is the intentional selection of certain traits in a population of organisms. Humans have used artificial selection for thousands of years in the domestication of plants and animals. More recently, such selection has become a vital part of genetic engineering, with selectable markers such as antibiotic resistance genes being used to manipulate DNA in molecular biology.
As evolution can produce highly optimized processes and networks, it has many applications in computer science. Here, simulations of evolution using evolutionary algorithms and artificial life started with the work of Nils Aall Barricelli in the 1960s, and was extended by Alex Fraser, who published a series of papers on simulation of artificial selection. Artificial evolution became a widely recognized optimization method as a result of the work of Ingo Rechenberg in the 1960s and early 1970s, who used evolution strategies to solve complex engineering problems. Genetic algorithms in particular became popular through the writing of John Holland. As academic interest grew, dramatic increases in the power of computers allowed practical applications. Evolution algorithms are now used to solve multi-dimensional problems more quickly than software produced by human designers, and also to optimize the design of systems.

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