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Sunday, May 19, 2019

Introduction to evolution

From Wikipedia, the free encyclopedia

The "Paleontological Tree of the Vertebrates," from the 5th edition of The Evolution of Man (London, 1910) by Ernst Haeckel. The evolutionary history of species has been described as a tree, with many branches arising from a single trunk.
 
Evolution is the process of change in all forms of life over generations, and evolutionary biology is the study of how evolution occurs. Biological populations evolve through genetic changes that correspond to changes in the organisms' observable traits. Genetic changes include mutations, which are caused by damage or replication errors in organisms' DNA. As the genetic variation of a population drifts randomly over generations, natural selection gradually leads traits to become more or less common based on the relative reproductive success of organisms with those traits. 

The age of the Earth is about 4.54 billion years. The earliest undisputed evidence of life on Earth dates at least from 3.5 billion years ago. Evolution does not attempt to explain the origin of life (covered instead by abiogenesis), but it does explain how early lifeforms evolved into the complex ecosystem that we see today. Based on the similarities between all present-day organisms, all life on Earth is assumed to have originated through common descent from a last universal ancestor from which all known species have diverged through the process of evolution.

All individuals have hereditary material in the form of genes received from their parents, which they pass on to any offspring. Among offspring there are variations of genes due to the introduction of new genes via random changes called mutations or via reshuffling of existing genes during sexual reproduction. The offspring differs from the parent in minor random ways. If those differences are helpful, the offspring is more likely to survive and reproduce. This means that more offspring in the next generation will have that helpful difference and individuals will not have equal chances of reproductive success. In this way, traits that result in organisms being better adapted to their living conditions become more common in descendant populations. These differences accumulate resulting in changes within the population. This process is responsible for the many diverse life forms in the world. 

The modern understanding of evolution began with the 1859 publication of Charles Darwin's On the Origin of Species. In addition, Gregor Mendel's work with plants helped to explain the hereditary patterns of genetics. Fossil discoveries in paleontology, advances in population genetics and a global network of scientific research have provided further details into the mechanisms of evolution. Scientists now have a good understanding of the origin of new species (speciation) and have observed the speciation process in the laboratory and in the wild. Evolution is the principal scientific theory that biologists use to understand life and is used in many disciplines, including medicine, psychology, conservation biology, anthropology, forensics, agriculture and other social-cultural applications.

Simple overview

The main ideas of evolution may be summarized as follows:
  • Life forms reproduce and therefore have a tendency to become more numerous.
  • Factors such as predation and competition work against the survival of individuals.
  • Each offspring differs from their parent(s) in minor, random ways.
  • If these differences are beneficial, the offspring is more likely to survive and reproduce.
  • This makes it likely that more offspring in the next generation will have beneficial differences and fewer will have detrimental differences.
  • These differences accumulate over generations, resulting in changes within the population.
  • Over time, populations can split or branch off into new species.
  • These processes, collectively known as evolution, are responsible for the many diverse life forms seen in the world.

Natural selection

Charles Darwin proposed the theory of evolution by natural selection.

In the 19th century, natural history collections and museums were popular. The European expansion and naval expeditions employed naturalists, while curators of grand museums showcased preserved and live specimens of the varieties of life. Charles Darwin was an English graduate educated and trained in the disciplines of natural history. Such natural historians would collect, catalogue, describe and study the vast collections of specimens stored and managed by curators at these museums. Darwin served as a ship's naturalist on board HMS Beagle, assigned to a five-year research expedition around the world. During his voyage, he observed and collected an abundance of organisms, being very interested in the diverse forms of life along the coasts of South America and the neighboring Galápagos Islands.

Darwin noted that orchids have complex adaptations to ensure pollination, all derived from basic floral parts.
 
Darwin gained extensive experience as he collected and studied the natural history of life forms from distant places. Through his studies, he formulated the idea that each species had developed from ancestors with similar features. In 1838, he described how a process he called natural selection would make this happen.

The size of a population depends on how much and how many resources are able to support it. For the population to remain the same size year after year, there must be an equilibrium, or balance between the population size and available resources. Since organisms produce more offspring than their environment can support, not all individuals can survive out of each generation. There must be a competitive struggle for resources that aid in survival. As a result, Darwin realised that it was not chance alone that determined survival. Instead, survival of an organism depends on the differences of each individual organism, or "traits," that aid or hinder survival and reproduction. Well-adapted individuals are likely to leave more offspring than their less well-adapted competitors. Traits that hinder survival and reproduction would disappear over generations. Traits that help an organism survive and reproduce would accumulate over generations. Darwin realised that the unequal ability of individuals to survive and reproduce could cause gradual changes in the population and used the term natural selection to describe this process.

Observations of variations in animals and plants formed the basis of the theory of natural selection. For example, Darwin observed that orchids and insects have a close relationship that allows the pollination of the plants. He noted that orchids have a variety of structures that attract insects, so that pollen from the flowers gets stuck to the insects' bodies. In this way, insects transport the pollen from a male to a female orchid. In spite of the elaborate appearance of orchids, these specialised parts are made from the same basic structures that make up other flowers. In his book, Fertilisation of Orchids (1862), Darwin proposed that the orchid flowers were adapted from pre-existing parts, through natural selection.

Darwin was still researching and experimenting with his ideas on natural selection when he received a letter from Alfred Russel Wallace describing a theory very similar to his own. This led to an immediate joint publication of both theories. Both Wallace and Darwin saw the history of life like a family tree, with each fork in the tree’s limbs being a common ancestor. The tips of the limbs represented modern species and the branches represented the common ancestors that are shared amongst many different species. To explain these relationships, Darwin said that all living things were related, and this meant that all life must be descended from a few forms, or even from a single common ancestor. He called this process descent with modification.

Darwin published his theory of evolution by natural selection in On the Origin of Species in 1859. His theory means that all life, including humanity, is a product of continuing natural processes. The implication that all life on Earth has a common ancestor has met with objections from some religious groups. Their objections are in contrast to the level of support for the theory by more than 99 percent of those within the scientific community today.

Natural selection is commonly equated with survival of the fittest, but this expression originated in Herbert Spencer's Principles of Biology in 1864, five years after Charles Darwin published his original works. Survival of the fittest describes the process of natural selection incorrectly, because natural selection is not only about survival and it is not always the fittest that survives.

Source of variation

Darwin's theory of natural selection laid the groundwork for modern evolutionary theory, and his experiments and observations showed that the organisms in populations varied from each other, that some of these variations were inherited, and that these differences could be acted on by natural selection. However, he could not explain the source of these variations. Like many of his predecessors, Darwin mistakenly thought that heritable traits were a product of use and disuse, and that features acquired during an organism's lifetime could be passed on to its offspring. He looked for examples, such as large ground feeding birds getting stronger legs through exercise, and weaker wings from not flying until, like the ostrich, they could not fly at all. This misunderstanding was called the inheritance of acquired characters and was part of the theory of transmutation of species put forward in 1809 by Jean-Baptiste Lamarck. In the late 19th century this theory became known as Lamarckism. Darwin produced an unsuccessful theory he called pangenesis to try to explain how acquired characteristics could be inherited. In the 1880s August Weismann's experiments indicated that changes from use and disuse could not be inherited, and Lamarckism gradually fell from favor.

The missing information needed to help explain how new features could pass from a parent to its offspring was provided by the pioneering genetics work of Gregor Mendel. Mendel's experiments with several generations of pea plants demonstrated that inheritance works by separating and reshuffling hereditary information during the formation of sex cells and recombining that information during fertilisation. This is like mixing different hands of playing cards, with an organism getting a random mix of half of the cards from one parent, and half of the cards from the other. Mendel called the information factors; however, they later became known as genes. Genes are the basic units of heredity in living organisms. They contain the information that directs the physical development and behavior of organisms. 

Genes are made of DNA. DNA is a long molecule made up of individual molecules called nucleotides. Genetic information is encoded in the sequence of nucleotides, that make up the DNA, just as the sequence of the letters in words carries information on a page. The genes are like short instructions built up of the "letters" of the DNA alphabet. Put together, the entire set of these genes gives enough information to serve as an "instruction manual" of how to build and run an organism. The instructions spelled out by this DNA alphabet can be changed, however, by mutations, and this may alter the instructions carried within the genes. Within the cell, the genes are carried in chromosomes, which are packages for carrying the DNA. It is the reshuffling of the chromosomes that results in unique combinations of genes in offspring. Since genes interact with one another during the development of an organism, novel combinations of genes produced by sexual reproduction can increase the genetic variability of the population even without new mutations. The genetic variability of a population can also increase when members of that population interbreed with individuals from a different population causing gene flow between the populations. This can introduce genes into a population that were not present before.

Evolution is not a random process. Although mutations in DNA are random, natural selection is not a process of chance: the environment determines the probability of reproductive success. Evolution is an inevitable result of imperfectly copying, self-replicating organisms reproducing over billions of years under the selective pressure of the environment. The outcome of evolution is not a perfectly designed organism. The end products of natural selection are organisms that are adapted to their present environments. Natural selection does not involve progress towards an ultimate goal. Evolution does not strive for more advanced, more intelligent, or more sophisticated life forms. For example, fleas (wingless parasites) are descended from a winged, ancestral scorpionfly, and snakes are lizards that no longer require limbs—although pythons still grow tiny structures that are the remains of their ancestor's hind legs. Organisms are merely the outcome of variations that succeed or fail, dependent upon the environmental conditions at the time. 

Rapid environmental changes typically cause extinctions. Of all species that have existed on Earth, 99.9 percent are now extinct. Since life began on Earth, five major mass extinctions have led to large and sudden drops in the variety of species. The most recent, the Cretaceous–Paleogene extinction event, occurred 66 million years ago.

Genetic drift

Genetic drift is a cause of allelic frequency change within populations of a species. Alleles are different variations of specific genes. They determine things like hair color, skin tone, eye color and blood type; in other words, all the genetic traits that vary between individuals. Genetic drift does not introduce new alleles to a population, but it can reduce variation within a population by removing an allele from the gene pool. Genetic drift is caused by random sampling of alleles. A truly random sample is a sample in which no outside forces affect what is selected. It is like pulling marbles of the same size and weight but of different colors from a brown paper bag. In any offspring, the alleles present are samples of the previous generations alleles, and chance plays a role in whether an individual survives to reproduce and to pass a sample of their generation onward to the next. The allelic frequency of a population is the ratio of the copies of one specific allele that share the same form compared to the number of all forms of the allele present in the population.

Genetic drift affects smaller populations more than it affects larger populations.

Hardy–Weinberg principle

The Hardy–Weinberg principle states that under certain idealized conditions, including the absence of selection pressures, a large population will have no change in the frequency of alleles as generations pass. A population that satisfies these conditions is said to be in Hardy–Weinberg equilibrium. In particular, Hardy and Weinberg showed that dominant and recessive alleles do not automatically tend to become more and less frequent respectively, as had been thought previously.

The conditions for Hardy-Weinberg equilibrium include that there must be no mutations, immigration, or emigration, all of which can directly change allelic frequencies. Additionally, mating must be totally random, with all males (or females in some cases) being equally desirable mates. This ensures a true random mixing of alleles. A population that is in Hardy–Weinberg equilibrium is analogous to a deck of cards; no matter how many times the deck is shuffled, no new cards are added and no old ones are taken away. Cards in the deck represent alleles in a population’s gene pool.

In practice, no population can be in perfect Hardy-Weinberg equilibrium. The population's finite size, combined with natural selection and many other effects, cause the allelic frequencies to change over time.

Population bottleneck

Model of population bottleneck illustrates how alleles can be lost
 
A population bottleneck occurs when the population of a species is reduced drastically over a short period of time due to external forces. In a true population bottleneck, the reduction does not favor any combination of alleles; it is totally random chance which individuals survive. A bottleneck can reduce or eliminate genetic variation from a population. Further drift events after the bottleneck event can also reduce the population's genetic diversity. The lack of diversity created can make the population at risk to other selective pressures.

A common example of a population bottleneck is the Northern elephant seal. Due to excessive hunting throughout the 19th century, the population of the northern elephant seal was reduced to 30 individuals or less. They have made a full recovery, with the total number of individuals at around 100,000 and growing. The effects of the bottleneck are visible, however. The seals are more likely to have serious problems with disease or genetic disorders, because there is almost no diversity in the population.

Founder effect

In the founder effect, small new populations contain different allele frequencies from the parent population.
 
The founder effect occurs when a small group from one population splits off and forms a new population, often through geographic isolation. This new population's allelic frequency is probably different from the original population's, and will change how common certain alleles are in the populations. The founders of the population will determine the genetic makeup, and potentially the survival, of the new population for generations.

One example of the founder effect is found in the Amish migration to Pennsylvania in 1744. Two of the founders of the colony in Pennsylvania carried the recessive allele for Ellis–van Creveld syndrome. Because the Amish tend to be religious isolates, they interbreed, and through generations of this practice the frequency of Ellis–van Creveld syndrome in the Amish people is much higher than the frequency in the general population.

Modern synthesis

The modern evolutionary synthesis is based on the concept that populations of organisms have significant genetic variation caused by mutation and by the recombination of genes during sexual reproduction. It defines evolution as the change in allelic frequencies within a population caused by genetic drift, gene flow between sub populations, and natural selection. Natural selection is emphasised as the most important mechanism of evolution; large changes are the result of the gradual accumulation of small changes over long periods of time.

The modern evolutionary synthesis is the outcome of a merger of several different scientific fields to produce a more cohesive understanding of evolutionary theory. In the 1920s, Ronald Fisher, J.B.S. Haldane and Sewall Wright combined Darwin's theory of natural selection with statistical models of Mendelian genetics, founding the discipline of population genetics. In the 1930s and 1940s, efforts were made to merge population genetics, the observations of field naturalists on the distribution of species and sub species, and analysis of the fossil record into a unified explanatory model. The application of the principles of genetics to naturally occurring populations, by scientists such as Theodosius Dobzhansky and Ernst Mayr, advanced the understanding of the processes of evolution. Dobzhansky's 1937 work Genetics and the Origin of Species helped bridge the gap between genetics and field biology by presenting the mathematical work of the population geneticists in a form more useful to field biologists, and by showing that wild populations had much more genetic variability with geographically isolated subspecies and reservoirs of genetic diversity in recessive genes than the models of the early population geneticists had allowed for. Mayr, on the basis of an understanding of genes and direct observations of evolutionary processes from field research, introduced the biological species concept, which defined a species as a group of interbreeding or potentially interbreeding populations that are reproductively isolated from all other populations. Both Dobzhansky and Mayr emphasised the importance of subspecies reproductively isolated by geographical barriers in the emergence of new species. The paleontologist George Gaylord Simpson helped to incorporate paleontology with a statistical analysis of the fossil record that showed a pattern consistent with the branching and non-directional pathway of evolution of organisms predicted by the modern synthesis.

Evidence for evolution

During the second voyage of HMS Beagle, naturalist Charles Darwin collected fossils in South America, and found fragments of armor which he thought were like giant versions of the scales on the modern armadillos living nearby. On his return, the anatomist Richard Owen showed him that the fragments were from gigantic extinct glyptodons, related to the armadillos. This was one of the patterns of distribution that helped Darwin to develop his theory.

Scientific evidence for evolution comes from many aspects of biology and includes fossils, homologous structures, and molecular similarities between species' DNA.

Fossil record

Research in the field of paleontology, the study of fossils, supports the idea that all living organisms are related. Fossils provide evidence that accumulated changes in organisms over long periods of time have led to the diverse forms of life we see today. A fossil itself reveals the organism's structure and the relationships between present and extinct species, allowing paleontologists to construct a family tree for all of the life forms on Earth.

Modern paleontology began with the work of Georges Cuvier. Cuvier noted that, in sedimentary rock, each layer contained a specific group of fossils. The deeper layers, which he proposed to be older, contained simpler life forms. He noted that many forms of life from the past are no longer present today. One of Cuvier’s successful contributions to the understanding of the fossil record was establishing extinction as a fact. In an attempt to explain extinction, Cuvier proposed the idea of "revolutions" or catastrophism in which he speculated that geological catastrophes had occurred throughout the Earth’s history, wiping out large numbers of species. Cuvier's theory of revolutions was later replaced by uniformitarian theories, notably those of James Hutton and Charles Lyell who proposed that the Earth’s geological changes were gradual and consistent. However, current evidence in the fossil record supports the concept of mass extinctions. As a result, the general idea of catastrophism has re-emerged as a valid hypothesis for at least some of the rapid changes in life forms that appear in the fossil records. 

A very large number of fossils have now been discovered and identified. These fossils serve as a chronological record of evolution. The fossil record provides examples of transitional species that demonstrate ancestral links between past and present life forms. One such transitional fossil is Archaeopteryx, an ancient organism that had the distinct characteristics of a reptile (such as a long, bony tail and conical teeth) yet also had characteristics of birds (such as feathers and a wishbone). The implication from such a find is that modern reptiles and birds arose from a common ancestor.

Comparative anatomy

The comparison of similarities between organisms of their form or appearance of parts, called their morphology, has long been a way to classify life into closely related groups. This can be done by comparing the structure of adult organisms in different species or by comparing the patterns of how cells grow, divide and even migrate during an organism's development.

Taxonomy

Taxonomy is the branch of biology that names and classifies all living things. Scientists use morphological and genetic similarities to assist them in categorising life forms based on ancestral relationships. For example, orangutans, gorillas, chimpanzees, and humans all belong to the same taxonomic grouping referred to as a family—in this case the family called Hominidae. These animals are grouped together because of similarities in morphology that come from common ancestry (called homology).

A bat is a mammal and its forearm bones have been adapted for flight.
 
Strong evidence for evolution comes from the analysis of homologous structures: structures in different species that no longer perform the same task but which share a similar structure. Such is the case of the forelimbs of mammals. The forelimbs of a human, cat, whale, and bat all have strikingly similar bone structures. However, each of these four species' forelimbs performs a different task. The same bones that construct a bat's wings, which are used for flight, also construct a whale's flippers, which are used for swimming. Such a "design" makes little sense if they are unrelated and uniquely constructed for their particular tasks. The theory of evolution explains these homologous structures: all four animals shared a common ancestor, and each has undergone change over many generations. These changes in structure have produced forelimbs adapted for different tasks.

The bird and the bat wing are examples of convergent evolution.
 
However, anatomical comparisons can be misleading, as not all anatomical similarities indicate a close relationship. Organisms that share similar environments will often develop similar physical features, a process known as convergent evolution. Both sharks and dolphins have similar body forms, yet are only distantly related—sharks are fish and dolphins are mammals. Such similarities are a result of both populations being exposed to the same selective pressures. Within both groups, changes that aid swimming have been favored. Thus, over time, they developed similar appearances (morphology), even though they are not closely related.

Embryology

In some cases, anatomical comparison of structures in the embryos of two or more species provides evidence for a shared ancestor that may not be obvious in the adult forms. As the embryo develops, these homologies can be lost to view, and the structures can take on different functions. Part of the basis of classifying the vertebrate group (which includes humans), is the presence of a tail (extending beyond the anus) and pharyngeal slits. Both structures appear during some stage of embryonic development but are not always obvious in the adult form.

Because of the morphological similarities present in embryos of different species during development, it was once assumed that organisms re-enact their evolutionary history as an embryo. It was thought that human embryos passed through an amphibian then a reptilian stage before completing their development as mammals. Such a reenactment, often called recapitulation theory, is not supported by scientific evidence. What does occur, however, is that the first stages of development are similar in broad groups of organisms. At very early stages, for instance, all vertebrates appear extremely similar, but do not exactly resemble any ancestral species. As development continues, specific features emerge from this basic pattern.

Vestigial structures

Homology includes a unique group of shared structures referred to as vestigial structures. Vestigial refers to anatomical parts that are of minimal, if any, value to the organism that possesses them. These apparently illogical structures are remnants of organs that played an important role in ancestral forms. Such is the case in whales, which have small vestigial bones that appear to be remnants of the leg bones of their ancestors which walked on land. Humans also have vestigial structures, including the ear muscles, the wisdom teeth, the appendix, the tail bone, body hair (including goose bumps), and the semilunar fold in the corner of the eye.

Biogeography

Four of the Galápagos finch species, produced by an adaptive radiation that diversified their beaks for different food sources
 
Biogeography is the study of the geographical distribution of species. Evidence from biogeography, especially from the biogeography of oceanic islands, played a key role in convincing both Darwin and Alfred Russel Wallace that species evolved with a branching pattern of common descent. Islands often contain endemic species, species not found anywhere else, but those species are often related to species found on the nearest continent. Furthermore, islands often contain clusters of closely related species that have very different ecological niches, that is have different ways of making a living in the environment. Such clusters form through a process of adaptive radiation where a single ancestral species colonises an island that has a variety of open ecological niches and then diversifies by evolving into different species adapted to fill those empty niches. Well-studied examples include Darwin's finches, a group of 13 finch species endemic to the Galápagos Islands, and the Hawaiian honeycreepers, a group of birds that once, before extinctions caused by humans, numbered 60 species filling diverse ecological roles, all descended from a single finch like ancestor that arrived on the Hawaiian Islands some 4 million years ago. Another example is the Silversword alliance, a group of perennial plant species, also endemic to the Hawaiian Islands, that inhabit a variety of habitats and come in a variety of shapes and sizes that include trees, shrubs, and ground hugging mats, but which can be hybridised with one another and with certain tarweed species found on the west coast of North America; it appears that one of those tarweeds colonised Hawaii in the past, and gave rise to the entire Silversword alliance.

Molecular biology

A section of DNA
 
Every living organism (with the possible exception of RNA viruses) contains molecules of DNA, which carries genetic information. Genes are the pieces of DNA that carry this information, and they influence the properties of an organism. Genes determine an individual's general appearance and to some extent their behavior. If two organisms are closely related, their DNA will be very similar. On the other hand, the more distantly related two organisms are, the more differences they will have. For example, brothers are closely related and have very similar DNA, while cousins share a more distant relationship and have far more differences in their DNA. Similarities in DNA are used to determine the relationships between species in much the same manner as they are used to show relationships between individuals. For example, comparing chimpanzees with gorillas and humans shows that there is as much as a 96 percent similarity between the DNA of humans and chimps. Comparisons of DNA indicate that humans and chimpanzees are more closely related to each other than either species is to gorillas.

The field of molecular systematics focuses on measuring the similarities in these molecules and using this information to work out how different types of organisms are related through evolution. These comparisons have allowed biologists to build a relationship tree of the evolution of life on Earth. They have even allowed scientists to unravel the relationships between organisms whose common ancestors lived such a long time ago that no real similarities remain in the appearance of the organisms.

Artificial selection

The results of artificial selection: a Chihuahua mix and a Great Dane
 
Artificial selection is the controlled breeding of domestic plants and animals. Humans determine which animal or plant will reproduce and which of the offspring will survive; thus, they determine which genes will be passed on to future generations. The process of artificial selection has had a significant impact on the evolution of domestic animals. For example, people have produced different types of dogs by controlled breeding. The differences in size between the Chihuahua and the Great Dane are the result of artificial selection. Despite their dramatically different physical appearance, they and all other dogs evolved from a few wolves domesticated by humans in what is now China less than 15,000 years ago.

Artificial selection has produced a wide variety of plants. In the case of maize (corn), recent genetic evidence suggests that domestication occurred 10,000 years ago in central Mexico. Prior to domestication, the edible portion of the wild form was small and difficult to collect. Today The Maize Genetics Cooperation • Stock Center maintains a collection of more than 10,000 genetic variations of maize that have arisen by random mutations and chromosomal variations from the original wild type.

In artificial selection the new breed or variety that emerges is the one with random mutations attractive to humans, while in natural selection the surviving species is the one with random mutations useful to it in its non-human environment. In both natural and artificial selection the variations are a result of random mutations, and the underlying genetic processes are essentially the same. Darwin carefully observed the outcomes of artificial selection in animals and plants to form many of his arguments in support of natural selection. Much of his book On the Origin of Species was based on these observations of the many varieties of domestic pigeons arising from artificial selection. Darwin proposed that if humans could achieve dramatic changes in domestic animals in short periods, then natural selection, given millions of years, could produce the differences seen in living things today.

Coevolution

Coevolution is a process in which two or more species influence the evolution of each other. All organisms are influenced by life around them; however, in coevolution there is evidence that genetically determined traits in each species directly resulted from the interaction between the two organisms.

An extensively documented case of coevolution is the relationship between Pseudomyrmex, a type of ant, and the acacia, a plant that the ant uses for food and shelter. The relationship between the two is so intimate that it has led to the evolution of special structures and behaviors in both organisms. The ant defends the acacia against herbivores and clears the forest floor of the seeds from competing plants. In response, the plant has evolved swollen thorns that the ants use as shelter and special flower parts that the ants eat. Such coevolution does not imply that the ants and the tree choose to behave in an altruistic manner. Rather, across a population small genetic changes in both ant and tree benefited each. The benefit gave a slightly higher chance of the characteristic being passed on to the next generation. Over time, successive mutations created the relationship we observe today.

Speciation

There are numerous species of cichlids that demonstrate dramatic variations in morphology.

Given the right circumstances, and enough time, evolution leads to the emergence of new species. Scientists have struggled to find a precise and all-inclusive definition of species. Ernst Mayr defined a species as a population or group of populations whose members have the potential to interbreed naturally with one another to produce viable, fertile offspring. (The members of a species cannot produce viable, fertile offspring with members of other species). Mayr's definition has gained wide acceptance among biologists, but does not apply to organisms such as bacteria, which reproduce asexually

Speciation is the lineage-splitting event that results in two separate species forming from a single common ancestral population. A widely accepted method of speciation is called allopatric speciation. Allopatric speciation begins when a population becomes geographically separated. Geological processes, such as the emergence of mountain ranges, the formation of canyons, or the flooding of land bridges by changes in sea level may result in separate populations. For speciation to occur, separation must be substantial, so that genetic exchange between the two populations is completely disrupted. In their separate environments, the genetically isolated groups follow their own unique evolutionary pathways. Each group will accumulate different mutations as well as be subjected to different selective pressures. The accumulated genetic changes may result in separated populations that can no longer interbreed if they are reunited. Barriers that prevent interbreeding are either prezygotic (prevent mating or fertilisation) or postzygotic (barriers that occur after fertilisation). If interbreeding is no longer possible, then they will be considered different species. The result of four billion years of evolution is the diversity of life around us, with an estimated 1.75 million different species in existence today.

Usually the process of speciation is slow, occurring over very long time spans; thus direct observations within human life-spans are rare. However speciation has been observed in present-day organisms, and past speciation events are recorded in fossils. Scientists have documented the formation of five new species of cichlid fishes from a single common ancestor that was isolated fewer than 5,000 years ago from the parent stock in Lake Nagubago. The evidence for speciation in this case was morphology (physical appearance) and lack of natural interbreeding. These fish have complex mating rituals and a variety of colorations; the slight modifications introduced in the new species have changed the mate selection process and the five forms that arose could not be convinced to interbreed.

Mechanism

The theory of evolution is widely accepted among the scientific community, serving to link the diverse specialty areas of biology. Evolution provides the field of biology with a solid scientific base. The significance of evolutionary theory is summarised by Theodosius Dobzhansky as "nothing in biology makes sense except in the light of evolution." Nevertheless, the theory of evolution is not static. There is much discussion within the scientific community concerning the mechanisms behind the evolutionary process. For example, the rate at which evolution occurs is still under discussion. In addition, there are conflicting opinions as to which is the primary unit of evolutionary change—the organism or the gene.

Rate of change

Darwin and his contemporaries viewed evolution as a slow and gradual process. Evolutionary trees are based on the idea that profound differences in species are the result of many small changes that accumulate over long periods. 

Gradualism had its basis in the works of the geologists James Hutton and Charles Lyell. Hutton's view suggests that profound geological change was the cumulative product of a relatively slow continuing operation of processes which can still be seen in operation today, as opposed to catastrophism which promoted the idea that sudden changes had causes which can no longer be seen at work. A uniformitarian perspective was adopted for biological changes. Such a view can seem to contradict the fossil record, which often shows evidence of new species appearing suddenly, then persisting in that form for long periods. In the 1970s paleontologists Niles Eldredge and Stephen Jay Gould developed a theoretical model that suggests that evolution, although a slow process in human terms, undergoes periods of relatively rapid change (ranging between 50,000 and 100,000 years) alternating with long periods of relative stability. Their theory is called punctuated equilibrium and explains the fossil record without contradicting Darwin's ideas.

Unit of change

A common unit of selection in evolution is the organism. Natural selection occurs when the reproductive success of an individual is improved or reduced by an inherited characteristic, and reproductive success is measured by the number of an individual's surviving offspring. The organism view has been challenged by a variety of biologists as well as philosophers. Richard Dawkins proposes that much insight can be gained if we look at evolution from the gene's point of view; that is, that natural selection operates as an evolutionary mechanism on genes as well as organisms. In his 1976 book, The Selfish Gene, he explains:


Others view selection working on many levels, not just at a single level of organism or gene; for example, Stephen Jay Gould called for a hierarchical perspective on selection.

Saturday, May 18, 2019

Introduction to viruses

From Wikipedia, the free encyclopedia

A rotavirus
 
A virus is a biological agent that reproduces inside the cells of living hosts. When infected by a virus, a host cell is forced to produce thousands of identical copies of the original virus at an extraordinary rate. Unlike most living things, viruses do not have cells that divide; new viruses are assembled in the infected host cell. But unlike still simpler infectious agents, viruses contain genes, which gives them the ability to mutate and evolve. Over 5,000 species of viruses have been discovered.

The origins of viruses are unclear: some may have evolved from plasmids—pieces of DNA that can move between cells—while others may have evolved from bacteria. A virus consists of two or three parts: genes, made from either DNA or RNA, long molecules that carry genetic information; a protein coat that protects the genes; and in some viruses, an envelope of fat that surrounds the protein coat and is used, in combination with specific receptors, to enter a new host cell. Viruses vary in shape from the simple helical and icosahedral to more complex structures. Viruses range in size from 20 to 300 nanometres; it would take 33,000 to 500,000 of them, side by side, to stretch to 1 centimetre (0.39 in). 

Viruses spread in many ways. Just as many viruses are very specific as to which host species or tissue they attack, each species of virus relies on a particular method for propagation. Plant viruses are often spread from plant to plant by insects and other organisms, known as vectors. Some viruses of animals, including humans, are spread by exposure to infected bodily fluids. Viruses such as influenza are spread through the air by droplets of moisture when people cough or sneeze. Viruses such as norovirus are transmitted by the faecal–oral route, which involves the contamination of hands, food and water. Rotavirus is often spread by direct contact with infected children. The human immunodeficiency virus, HIV, is transmitted by bodily fluids transferred during sex. Others, such as the Dengue virus, are spread by blood-sucking insects. 

Viral infections can cause disease in humans, animals and even plants. However, they are usually eliminated by the immune system, conferring lifetime immunity to the host for that virus. Antibiotics have no effect on viruses, but antiviral drugs have been developed to treat life-threatening infections. Vaccines that produce lifelong immunity can prevent some viral infections.

Discovery

Scanning electron micrograph of HIV-1 viruses, coloured green, budding from a lymphocyte
 
In 1884 the French microbiologist Charles Chamberland invented a filter, known today as the Chamberland filter or Chamberland–Pasteur filter, that has pores smaller than bacteria. Thus he could pass a solution containing bacteria through the filter and completely remove them from the solution. In the early 1890s the Russian biologist Dmitri Ivanovsky used this filter to study what became known as the tobacco mosaic virus. His experiments showed that extracts from the crushed leaves of infected tobacco plants remain infectious after filtration.

At the same time several other scientists proved that, although these agents (later called viruses) were different from bacteria, they could still cause disease, and they were about one hundredth the size of bacteria. In 1899 the Dutch microbiologist Martinus Beijerinck observed that the agent multiplied only in dividing cells. Having failed to demonstrate its particulate nature, he called it a "contagium vivum fluidum", a "soluble living germ". In the early 20th century the English bacteriologist Frederick Twort discovered viruses that infect bacteria, and the French-Canadian microbiologist Félix d'Herelle described viruses that, when added to bacteria growing on agar, would lead to the formation of whole areas of dead bacteria. Counting these dead areas allowed him to calculate the number of viruses in the suspension.

With the invention of the electron microscope in 1931 by the German engineers Ernst Ruska and Max Knoll came the first images of viruses. In 1935 American biochemist and virologist Wendell Meredith Stanley examined the tobacco mosaic virus and found it to be mostly made from protein. A short time later, this virus was separated into protein and RNA parts. A problem for early scientists was that they did not know how to grow viruses without using live animals. The breakthrough came in 1931, when the American pathologist Ernest William Goodpasture and Alice Miles Woodruff grew influenza and several other viruses in fertilised chickens' eggs. Some viruses could not be grown in chickens' eggs, but this problem was solved in 1949 when John Franklin Enders, Thomas Huckle Weller and Frederick Chapman Robbins grew polio virus in cultures of living animal cells. Over 5,000 species of virus have been discovered.

Origins

Viruses co-exist with life wherever it occurs. They have probably existed since living cells first evolved. The origin of viruses remains unclear because they do not form fossils, so molecular techniques have been the most useful means of hypothesising how they arose. However, these techniques rely on the availability of ancient viral DNA or RNA but most of the viruses that have been preserved and stored in laboratories are less than 90 years old. Molecular methods have only been successful in tracing the ancestry of viruses that evolved in the 20th century. Three main theories speculate on the origins of viruses:
Regressive theory 
Viruses may have once been small cells that parasitised larger cells. Over time, genes not required by their parasitism were lost. The bacteria rickettsia and chlamydia are living cells that, like viruses, can reproduce only inside host cells. They lend credence to this theory, as their dependence on parasitism is likely to have caused the loss of genes that enabled them to survive outside a cell.
Cellular origin theory 
Some viruses may have evolved from bits of DNA or RNA that "escaped" from the genes of a larger organism. The escaped DNA could have come from plasmids—pieces of DNA that can move between cells—while others may have evolved from bacteria.
Coevolution theory 
Viruses may have evolved from complex molecules of protein and DNA at the same time as cells first appeared on earth and would have depended on cellular life for many millions of years.
There are problems with all of these hypotheses: the regressive hypothesis does not explain why even the smallest of cellular parasites do not resemble viruses in any way. The escape hypothesis does not explain the structures of virus particles. The coevolution, or virus-first hypothesis, contravenes the definition of viruses, in that they are dependent on host cells. But viruses are recognised as ancient and to have origins that pre-date the divergence of life into the three domains. This discovery has led modern virologists to reconsider and re-evaluate these three classical hypotheses.

Structure

A simplified diagram of the structure of a virus
 
A virus particle, also known as a virion, consists of genes made from DNA or RNA which are surrounded by a protective coat of protein called a capsid. The capsid is made of many smaller, identical protein molecules which are called capsomers. The arrangement of the capsomers can either be icosahedral (20-sided), helical or more complex. There is an inner shell around the DNA or RNA called the nucleocapsid, which is formed by proteins. Some viruses are surrounded by a bubble of lipid (fat) called an envelope.

Size

Viruses are among the smallest infectious agents, and most of them can only be seen by electron microscopy. Most viruses cannot be seen by light microscopy (in other words, they are sub-microscopic); their sizes range from 20 to 300 nm. They are so small that it would take 30,000 to 750,000 of them, side by side, to stretch to one cm. By contrast bacterial sizes are typically around 1 micrometre (1000 nm) in diameter, and the cells of higher organisms a few tens of micrometres. Some viruses such as megaviruses and pandoraviruses are relatively large. At around 1 micrometer, these viruses, which infect amoebae, were discovered in 2003 and 2013. They are around a thousand times larger than influenza viruses and the discovery of these "giant" viruses astonished scientists.

Genes

Genes are made from DNA (deoxyribonucleic acid) and, in many viruses, RNA (ribonucleic acid). The biological information contained in an organism is encoded in its DNA or RNA. Most organisms use DNA, but many viruses have RNA as their genetic material. The DNA or RNA of viruses consists of either a single strand or a double helix.

Viruses reproduce rapidly because they have only a few genes compared to humans who have 20,000–25,000. For example, influenza virus has only eight genes and rotavirus has eleven. These genes encode structural proteins that form the virus particle, or non-structural proteins, that are only found in cells infected by the virus.

All cells, and many viruses, produce proteins that are enzymes called DNA polymerase and RNA polymerase which make new copies of DNA and RNA. A virus's polymerase enzymes are often much more efficient at making DNA and RNA than the host cell's. However, RNA polymerase enzymes often make mistakes, and this is one of the reasons why RNA viruses often mutate to form new strains.

In some species of RNA virus, the genes are not on a continuous molecule of RNA, but are separated. The influenza virus, for example, has eight separate genes made of RNA. When two different strains of influenza virus infect the same cell, these genes can mix and produce new strains of the virus in a process called reassortment.

Protein synthesis

Diagram of a typical eukaryotic cell, showing subcellular components. Organelles: (1) nucleolus (2) nucleus (3) ribosome (4) vesicle (5) rough endoplasmic reticulum (ER) (6) Golgi apparatus (7) cytoskeleton (8) smooth ER (9) mitochondria (10) vacuole (11) cytoplasm (12) lysosome (13) centrioles within centrosome (14) virus particle shown to approximate scale
 
Proteins are essential to life. Cells produce new protein molecules from amino acid building blocks based on information coded in DNA. Each type of protein is a specialist that usually only performs one function, so if a cell needs to do something new, it must make a new protein. Viruses force the cell to make new proteins that the cell does not need, but are needed for the virus to reproduce. Protein synthesis consists of two major steps: transcription and translation.

Transcription is the process where information in DNA, called the genetic code, is used to produce RNA copies called messenger RNA (mRNA). These migrate through the cell and carry the code to ribosomes where it is used to make proteins. This is called translation because the protein's amino acid structure is determined by the mRNA's code. Information is hence translated from the language of nucleic acids to the language of amino acids.

Some nucleic acids of RNA viruses function directly as mRNA without further modification. For this reason, these viruses are called positive-sense RNA viruses. In other RNA viruses, the RNA is a complementary copy of mRNA and these viruses rely on the cell's or their own enzyme to make mRNA. These are called negative-sense RNA viruses. In viruses made from DNA, the method of mRNA production is similar to that of the cell. The species of viruses called retroviruses behave completely differently: they have RNA, but inside the host cell a DNA copy of their RNA is made with the help of the enzyme reverse transcriptase. This DNA is then incorporated into the host's own DNA, and copied into mRNA by the cell's normal pathways.

Life-cycle

Life-cycle of a typical virus (left to right); following infection of a cell by a single virus, hundreds of offspring are released.
 
When a virus infects a cell, the virus forces it to make thousands more viruses. It does this by making the cell copy the virus's DNA or RNA, making viral proteins, which all assemble to form new virus particles.

There are six basic, overlapping stages in the life cycle of viruses in living cells:
  • Attachment is the binding of the virus to specific molecules on the surface of the cell. This specificity restricts the virus to a very limited type of cell. For example, the human immunodeficiency virus (HIV) infects only human T cells, because its surface protein, gp120, can only react with CD4 and other molecules on the T cell's surface. Plant viruses can only attach to plant cells and cannot infect animals. This mechanism has evolved to favour those viruses that only infect cells in which they are capable of reproducing.
  • Penetration follows attachment; viruses penetrate the host cell by endocytosis or by fusion with the cell.
  • Uncoating happens inside the cell when the viral capsid is removed and destroyed by viral enzymes or host enzymes, thereby exposing the viral nucleic acid.
  • Replication of virus particles is the stage where a cell uses viral messenger RNA in its protein synthesis systems to produce viral proteins. The RNA or DNA synthesis abilities of the cell produce the virus's DNA or RNA.
  • Assembly takes place in the cell when the newly created viral proteins and nucleic acid combine to form hundreds of new virus particles.
  • Release occurs when the new viruses escape or are released from the cell. Most viruses achieve this by making the cells burst, a process called lysis. Other viruses such as HIV are released more gently by a process called budding.

Effects on the host cell

The range of structural and biochemical effects that viruses have on the host cell is extensive. These are called cytopathic effects. Most virus infections eventually result in the death of the host cell. The causes of death include cell lysis (bursting), alterations to the cell's surface membrane and apoptosis (cell "suicide"). Often cell death is caused by cessation of its normal activity due to proteins produced by the virus, not all of which are components of the virus particle.

Some viruses cause no apparent changes to the infected cell. Cells in which the virus is latent and inactive show few signs of infection and often function normally. This causes persistent infections and the virus is often dormant for many months or years. This is often the case with herpes viruses.

Some viruses, such as Epstein-Barr virus, often cause cells to proliferate without causing malignancy; but some other viruses, such as papillomavirus, are an established cause of cancer. When a cell's DNA is damaged by a virus, and if the cell cannot repair itself, this often triggers apoptosis. One of the results of apoptosis is destruction of the damaged DNA by the cell itself. Some viruses have mechanisms to limit apoptosis so that the host cell does not die before progeny viruses have been produced; HIV, for example, does this.

Viruses and diseases

Norovirus. Ten Norovirus particles; this RNA virus causes winter vomiting disease. It is often in the news as a cause of gastro-enteritis on cruise ships and in hospitals.
 
Common human diseases caused by viruses include the common cold, the flu, chickenpox and cold sores. Serious diseases such as Ebola and AIDS are also caused by viruses. Many viruses cause little or no disease and are said to be "benign". The more harmful viruses are described as virulent. Viruses cause different diseases depending on the types of cell that they infect. Some viruses can cause lifelong or chronic infections where the viruses continue to reproduce in the body despite the host's defence mechanisms. This is common in hepatitis B virus and hepatitis C virus infections. People chronically infected with a virus are known as carriers. They serve as important reservoirs of the virus. If there is a high proportion of carriers in a given population, a disease is said to be endemic.

There are many ways in which viruses spread from host to host but each species of virus uses only one or two. Many viruses that infect plants are carried by organisms; such organisms are called vectors. Some viruses that infect animals, including humans, are also spread by vectors, usually blood-sucking insects. However, direct transmission is more common. Some virus infections, such as norovirus and rotavirus, are spread by contaminated food and water, hands and communal objects and by intimate contact with another infected person, while others are airborne (influenza virus). Viruses such as HIV, hepatitis B and hepatitis C are often transmitted by unprotected sex or contaminated hypodermic needles. It is important to know how each different kind of virus is spread to prevent infections and epidemics.

Diseases of plants

Peppers infected by mild mottle virus
 
There are many types of plant virus, but often they only cause a loss of yield, and it is not economically viable to try to control them. Plant viruses are often spread from plant to plant by organisms (vectors). These are normally insects, but some fungi, nematode worms and single-celled organisms have been shown to be vectors. When control of plant virus infections is considered economical (perennial fruits, for example) efforts are concentrated on killing the vectors and removing alternate hosts such as weeds. Plant viruses are harmless to humans and other animals because they can only reproduce in living plant cells.

Bacteriophages

The structure of a typical bacteriophage
 
Bacteriophages are viruses that infect bacteria and archaea. The International Committee on Taxonomy of Viruses officially recognises 28 genera of bacteriophages that belong to 11 families. They are important in marine ecology: as the infected bacteria burst, carbon compounds are released back into the environment, which stimulates fresh organic growth. Bacteriophages are useful in scientific research because they are harmless to humans and can be studied easily. These viruses can be a problem in industries that produce food and drugs by fermentation and depend on healthy bacteria. Some bacterial infections are becoming difficult to control with antibiotics, so there is a growing interest in the use of bacteriophages to treat infections in humans.

Host resistance

Innate immunity of animals

Animals, including humans, have many natural defences against viruses. Some are non-specific and protect against many viruses regardless of the type. This innate immunity is not improved by repeated exposure to viruses and does not retain a "memory" of the infection. The skin of animals, particularly its surface, which is made from dead cells, prevents many types of viruses from infecting the host. The acidity of the contents of the stomach destroys many viruses that have been swallowed. When a virus overcomes these barriers and enters the host, other innate defences prevent the spread of infection in the body. A special hormone called interferon is produced by the body when viruses are present, and this stops the viruses from reproducing by killing the infected cell and its close neighbours. Inside cells, there are enzymes that destroy the RNA of viruses. This is called RNA interference. Some blood cells engulf and destroy other virus infected cells.

Adaptive immunity of animals

Two rotavirus particles: the one on the right is coated with antibodies which stop its attaching to cells and infecting them
 
Specific immunity to viruses develops over time and white blood cells called lymphocytes play a central role. Lymphocytes retain a "memory" of virus infections and produce many special molecules called antibodies. These antibodies attach to viruses and stop the virus from infecting cells. Antibodies are highly selective and attack only one type of virus. The body makes many different antibodies, especially during the initial infection; however, after the infection subsides, some antibodies remain and continue to be produced, often giving the host lifelong immunity to the virus.

Plant resistance

Plants have elaborate and effective defence mechanisms against viruses. One of the most effective is the presence of so-called resistance (R) genes. Each R gene confers resistance to a particular virus by triggering localised areas of cell death around the infected cell, which can often be seen with the unaided eye as large spots. This stops the infection from spreading. RNA interference is also an effective defence in plants. When they are infected, plants often produce natural disinfectants which destroy viruses, such as salicylic acid, nitric oxide and reactive oxygen molecules.

Resistance to bacteriophages

The major way bacteria defend themselves from bacteriophages is by producing enzymes which destroy foreign DNA. These enzymes, called restriction endonucleases, cut up the viral DNA that bacteriophages inject into bacterial cells.

Prevention and treatment of viral disease in humans and other animals

Vaccines

The structure of DNA showing the position of the nucleosides and the phosphorus atoms that form the "backbone" of the molecule
 
Vaccination is a way of preventing diseases caused by viruses. Vaccines simulate a natural infection and its associated immune response, but do not cause the disease. Their use has resulted in the eradication of smallpox and a dramatic decline in illness and death caused by infections such as polio, measles, mumps and rubella. Vaccines are available to prevent over fourteen viral infections of humans and more are used to prevent viral infections of animals. Vaccines may consist of either live or killed viruses. Live vaccines contain weakened forms of the virus, but these vaccines can be dangerous when given to people with weak immunity. In these people, the weakened virus can cause the original disease. Biotechnology and genetic engineering techniques are used to produce "designer" vaccines that only have the capsid proteins of the virus. Hepatitis B vaccine is an example of this type of vaccine. These vaccines are safer because they can never cause the disease.

Antiviral drugs

Since the mid 1980s, the development of antiviral drugs has increased rapidly, mainly driven by the AIDS pandemic. Antiviral drugs are often nucleoside analogues, which are molecules very similar, but not identical to DNA building blocks. When the replication of virus DNA begins, some of these fake building blocks are incorporated. As soon as that happens, replication stops prematurely—the fake building blocks lack the essential features that allow the addition of further building blocks. Thus, DNA production is halted, and the virus can no longer reproduce. Examples of nucleoside analogues are aciclovir for herpes virus infections and lamivudine for HIV and hepatitis B virus infections. Aciclovir is one of the oldest and most frequently prescribed antiviral drugs.

The structure of the DNA base guanosine and the antiviral drug aciclovir
 
Other antiviral drugs target different stages of the viral life cycle. HIV is dependent on an enzyme called the HIV-1 protease for the virus to become infectious. There is a class of drugs called protease inhibitors, which bind to this enzyme and stop it from functioning.

Hepatitis C is caused by an RNA virus. In 80% of people infected, the disease becomes chronic, and they remain infectious for the rest of their lives unless they are treated. There is an effective treatment that uses the nucleoside analogue drug ribavirin combined with interferon. Treatments for chronic carriers of the hepatitis B virus by a similar strategy using lamivudine and other anti-viral drugs have been developed. In both diseases, the drugs stop the virus from reproducing and the interferon kills any remaining infected cells. 

HIV infections are usually treated with a combination of antiviral drugs, each targeting a different stage in the virus's life-cycle. There are drugs that prevent the virus from attaching to cells, others that are nucleoside analogues and some poison the virus's enzymes that it needs to reproduce. The success of these drugs is proof of the importance of knowing how viruses reproduce.

Role in ecology

Viruses are the most abundant biological entity in aquatic environments—there are about one million of them in a teaspoon of seawater—and they are essential to the regulation of saltwater and freshwater ecosystems. Most of these viruses are bacteriophages, which are harmless to plants and animals. They infect and destroy the bacteria in aquatic microbial communities and this is the most important mechanism of recycling carbon in the marine environment. The organic molecules released from the bacterial cells by the viruses stimulate fresh bacterial and algal growth.

Microorganisms constitute more than 90% of the biomass in the sea. It is estimated that viruses kill approximately 20% of this biomass each day and that there are fifteen times as many viruses in the oceans as there are bacteria and archaea. Viruses are mainly responsible for the rapid destruction of harmful algal blooms, which often kill other marine life. The number of viruses in the oceans decreases further offshore and deeper into the water, where there are fewer host organisms.

Their effects are far-reaching; by increasing the amount of respiration in the oceans, viruses are indirectly responsible for reducing the amount of carbon dioxide in the atmosphere by approximately 3 gigatonnes of carbon per year.

Marine mammals are also susceptible to viral infections. In 1988 and 2002, thousands of harbour seals were killed in E.

Streaming algorithm

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