Evolution theory
explanation for the appearance of life and human beings on earth
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.
Life on Earth originated and then evolved from a universal common ancestor approximately 3.7 billion years ago. Repeated speciation and the divergence of life can be inferred from shared sets of biochemical and morphological traits, or by shared DNA sequences. These homologous traits and sequences are more similar among species that share a more recent common ancestor, and can be used to reconstruct evolutionary histories, using both existing species and the fossil record. Existing patterns of biodiversity have been shaped both by speciation and by extinction.
Charles Darwin was the first to formulate a scientific argument for the theory of evolution by means of natural selection. Evolution by natural selection is a process that is inferred from three facts about populations: 1) more offspring are produced than can possibly survive, 2) traits vary among individuals, leading to differential rates of survival and reproduction, and 3) trait differences are heritable. Thus, when members of a population die they are replaced by the progeny of parents that were better adapted to survive and reproduce in the environment in which natural selection took place. This process creates and preserves traits that are seemingly fitted for the functional roles they perform. Natural selection is the only known cause of adaptation, but not the only known cause of evolution. Other, nonadaptive causes of evolution include mutation and genetic drift.
In the early 20th century, genetics was integrated with Darwin's theory of evolution by natural selection through the discipline of population genetics. The importance of natural selection as a cause of evolution was accepted into other branches of biology. Moreover, previously held notions about evolution, such as orthogenesis and "progress" became obsolete. Scientists continue to study various aspects of evolution by forming and testing hypotheses, constructing scientific theories, using observational data, and performing experiments in both the field and the laboratory. Biologists agree that descent with modification is one of the most reliably established facts in science. Discoveries in evolutionary biology have made a significant impact not just within the traditional branches of biology, but also in other academic disciplines (e.g., anthropology and psychology) and on society at large.
History of evolutionary thought
The proposal that one type of animal could descend from an animal of another type goes back to some of the first pre-Socratic Greek philosophers, such as Anaximander and Empedocles. In contrast to these materialistic views, Aristotle understood all natural things, not only living things, as being imperfect actualisations of different fixed natural possibilities, known as "forms", "ideas", or (in Latin translations) "species". This was part of his teleological understanding of nature in which all things have an intended role to play in a divine cosmic order. Variations of this idea became the standard understanding of the Middle Ages, and were integrated into Christian learning, but Aristotle did not demand that real types of animals corresponded one-for-one with exact metaphysical forms, and specifically gave examples of how new types of living things could come to be.
In the 17th century the new method of modern science rejected Aristotle's approach, and sought explanations of natural phenomena in terms of laws of nature which were the same for all visible things, and did not need to assume any fixed natural categories, nor any divine cosmic order. But this new approach was slow to take root in the biological sciences, which became the last bastion of the concept of fixed natural types. John Ray used one of the previously more general terms for fixed natural types, "species", to apply to animal and plant types, but unlike Aristotle he strictly identified each type of living thing as a species, and proposed that each species can be defined by the features that perpetuate themselves each generation. These species were designed by God, but showing differences caused by local conditions. The biological classification introduced by Carolus Linnaeus in 1735 also viewed species as fixed according to a divine plan.
Other naturalists of this time speculated on evolutionary change of species over time according to natural laws. Maupertuis wrote in 1751 of natural modifications occurring during reproduction and accumulating over many generations to produce new species. Buffon suggested that species could degenerate into different organisms, and Erasmus Darwin proposed that all warm-blooded animals could have descended from a single micro-organism (or "filament"). The first fully-fledged evolutionary scheme was Lamarck's "transmutation" theory of 1809 which envisaged spontaneous generation continually producing simple forms of life developed greater complexity in parallel lineages with an inherent progressive tendency, and that on a local level these lineages adapted to the environment by inheriting changes caused by use or disuse in parents. (The latter process was later called Lamarckism.) These ideas were condemned by establishment naturalists as speculation lacking empirical support. In particular Georges Cuvier insisted that species were unrelated and fixed, their similarities reflecting divine design for functional needs. In the meantime, Ray's ideas of benevolent design had been developed by William Paley into a natural theology which proposed complex adaptations as evidence of divine design, and was admired by Charles Darwin.
The critical break from the concept of fixed species in biology began with the theory of evolution by natural selection, which was formulated by Charles Darwin. Partly influenced by An Essay on the Principle of Population by Thomas Robert Malthus, Darwin noted that population growth would lead to a "struggle for existence" where favorable variations could prevail as others perished. Each generation, many offspring fail to survive to an age of reproduction because of limited resources. This could explain the diversity of animals and plants from a common ancestry through the working of natural laws working the same for all types of thing. Darwin was developing his theory of "natural selection" from 1838 onwards until Alfred Russel Wallace sent him a similar theory in 1858. Both men presented their separate papers to the Linnean Society of London. At the end of 1859, Darwin's publication of On the Origin of Species explained natural selection in detail and in a way that lead to an increasingly wide acceptance of Darwinian evolution. Thomas Henry Huxley applied Darwin's ideas to humans, using paleontology and comparative anatomy to provide strong evidence that humans and apes shared a common ancestry. Some were disturbed by this since it implied that humans did not have a special place in the universe.
Precise mechanisms of reproductive heritability and the origin of new traits remained a mystery. Towards this end, Darwin developed his provisional theory of pangenesis. In 1865 Gregor Mendel reported that traits were inherited in a predictable manner through the independent assortment and segregation of elements (later known as genes). Mendel's laws of inheritance eventually supplanted most of Darwin's pangenesis theory. August Weismann made the important distinction between germ cells (sperm and eggs) and somatic cells of the body, demonstrating that heredity passes through the germ line only. Hugo de Vries connected Darwin's pangenesis theory to Wiesman's germ/soma cell distinction and proposed that Darwin's pangenes were concentrated in the cell nucleus and when expressed they could move into the cytoplasm to change the cells structure. De Vries was also one of the researchers who made Mendel's work well-known, believing that Mendelian traits corresponded to the transfer of heritable variations along the germline.[36] To explain how new variants originate, De Vries developed a mutation theory that led to a temporary rift between those who accepted Darwinian evolution and biometricians who allied with de Vries.[21][37][38] At the turn of the 20th century, pioneers in the field of population genetics, such as J.B.S. Haldane, Sewall Wright, and Ronald Fisher, set the foundations of evolution onto a robust statistical philosophy. The false contradiction between Darwin's theory, genetic mutations, and Mendelian inheritance was thus reconciled.
In the 1920s and 1930s a modern evolutionary synthesis connected natural selection, mutation theory, and Mendelian inheritance into a unified theory that applied generally to any branch of biology. The modern synthesis was able to explain patterns observed across species in populations, through fossil transitions in palaeontology, and even complex cellular mechanisms in developmental biology. The publication of the structure of DNA by James Watson and Francis Crick in 1953 demonstrated a physical basis for inheritance.[41] Molecular biology improved our understanding of the relationship between genotype and phenotype. Advancements were also made in phylogenetic systematics, mapping the transition of traits into a comparative and testable framework through the publication and use of evolutionary trees. In 1973, evolutionary biologist Theodosius Dobzhansky penned that "nothing in biology makes sense except in the light of evolution", because it has brought to light the relations of what first seemed disjointed facts in natural history into a coherent explanatory body of knowledge that describes and predicts many observable facts about life on this planet.
Since then, the modern synthesis has been further extended to explain biological phenomena across the full and integrative scale of the biological hierarchy, from genes to species. This extension has been dubbed "eco-evo-devo".
Heredity
Evolution in organisms occurs through changes in heritable traits – particular characteristics of an organism. In humans, for example, eye colour is an inherited characteristic and an individual might inherit the "brown-eye trait" 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 behaviour of an organism is called its phenotype. These traits come from the interaction of its genotype with the environment. As a result, many aspects of an organism's phenotype are not inherited. For example, suntanned skin comes from the interaction between a person's genotype and sunlight; thus, suntans are not passed on to people's children. However, some people tan more easily than others, due to differences in their genotype; a striking example are people with the inherited trait of albinism, who do not tan at all and are very sensitive to sunburn.
Heritable traits are known to be passed from one generation to the next via DNA, a molecule that encodes genetic information. DNA is a long polymer composed of four types of bases. The sequence of bases along a particular DNA molecule specify the genetic information, in a manner similar to a sequence of letters spelling out a sentence. Before a cell divides, the DNA is copied, so that each of the resulting two cells will inherit the DNA sequence. Portions of a DNA molecule that specify a single functional unit are called genes; different genes have different sequences of bases. Within cells, the long strands of DNA form condensed structures called chromosomes. The specific location of a DNA sequence within a chromosome is known as a locus. If the DNA sequence at a locus varies between individuals, the different forms of this sequence are called alleles. DNA sequences can change through mutations, producing new alleles. If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the organism. However, while this simple correspondence between an allele and a trait works in some cases, most traits are more complex and are controlled by multiple interacting genes.
Recent findings have confirmed important examples of heritable changes that cannot be explained by changes to the sequence of nucleotides in the DNA. These phenomena are classed as epigenetic inheritance systems. DNA methylation marking chromatin, self-sustaining metabolic loops, gene silencing by RNA interference and the three dimensional conformation of proteins (such as prions) are areas where epigenetic inheritance systems have been discovered at the organismic level. Developmental biologists suggest that complex interactions in genetic networks and communication among cells can lead to heritable variations that may underlay some of the mechanics in developmental plasticity and canalization. Heritability may also occur at even larger scales. For example, ecological inheritance through the process of niche construction is defined by the regular and repeated activities of organisms in their environment. This generates a legacy of effects that modify and feed back into the selection regime of subsequent generations. Descendants inherit genes plus environmental characteristics generated by the ecological actions of ancestors. Other examples of heritability in evolution that are not under the direct control of genes include the inheritance of cultural traits and symbiogenesis.
An individual organism's phenotype results from both its genotype and the influence from the environment it has lived in. A substantial part of the variation in phenotypes in a population is caused by the differences between their genotypes.[54] The modern evolutionary synthesis defines evolution as the change over time in this genetic variation. The frequency of one particular allele will become more or less prevalent relative to other forms of that gene. Variation disappears when a new allele reaches the point of fixation — when it either disappears from the population or replaces the ancestral allele entirely.[62]
Natural selection will only cause evolution if there is enough genetic variation in a population. Before the discovery of Mendelian genetics, one common hypothesis was blending inheritance. But with blending inheritance, genetic variance would be rapidly lost, making evolution by natural selection implausible. The Hardy-Weinberg principle provides the solution to how variation is maintained in a population with Mendelian inheritance. The frequencies of alleles (variations in a gene) will remain constant in the absence of selection, mutation, migration and genetic drift.[63]
Variation comes from mutations in genetic material, reshuffling of genes through sexual reproduction and migration between populations (gene flow). Despite the constant introduction of new variation through mutation and gene flow, most of the genome of a species is identical in all individuals of that species.[64] However, even relatively small differences in genotype can lead to dramatic differences in phenotype: for example, chimpanzees and humans differ in only about 5% of their genomes.
MutationMutations are changes in the DNA sequence of a cell's genome. When mutations occur, they can either have no effect, alter the product of a gene, or prevent the gene from functioning. Based on studies in the fly Drosophila melanogaster, it has been suggested that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70% of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial.[66]
Mutations can involve large sections of a chromosome becoming duplicated (usually by genetic recombination), which can introduce extra copies of a gene into a genome.[67] Extra copies of genes are a major source of the raw material needed for new genes to evolve.[68] This is important because most new genes evolve within gene families from pre-existing genes that share common ancestors.[69] For example, the human eye uses four genes to make structures that sense light: three for colour vision and one for night vision; all four are descended from a single ancestral gene.[70]
New genes can be generated from an ancestral gene when a duplicate copy mutates and acquires a new function. This process is easier once a gene has been duplicated because it increases the redundancy of the system; one gene in the pair can acquire a new function while the other copy continues to perform its original function.[71][72] Other types of mutations can even generate entirely new genes from previously noncoding DNA.[73][74]
The generation of new genes can also involve small parts of several genes being duplicated, with these fragments then recombining to form new combinations with new functions.[75][76] When new genes are assembled from shuffling pre-existing parts, domains act as modules with simple independent functions, which can be mixed together to produce new combinations with new and complex functions.[77] For example, polyketide synthases are large enzymes that make antibiotics; they contain up to one hundred independent domains that each catalyze one step in the overall process, like a step in an assembly line.
In asexual organisms, genes are inherited together, or linked, as they cannot mix with genes of other organisms during reproduction. In contrast, the offspring of sexual organisms contain random mixtures of their parents' chromosomes that are produced through independent assortment. In a related process called homologous recombination, sexual organisms exchange DNA between two matching chromosomes.[79] Recombination and reassortment do not alter allele frequencies, but instead change which alleles are associated with each other, producing offspring with new combinations of alleles.[80] Sex usually increases genetic variation and may increase the rate of evolution.
Gene flow is the exchange of genes between populations and between species.[83] It can therefore be a source of variation that is new to a population or to a species. Gene flow can be caused by the movement of individuals between separate populations of organisms, as might be caused by the movement of mice between inland and coastal populations, or the movement of pollen between heavy metal tolerant and heavy metal sensitive populations of grasses.
Gene transfer between species includes the formation of hybrid organisms and horizontal gene transfer. Horizontal gene transfer is the transfer of genetic material from one organism to another organism that is not its offspring; this is most common among bacteria.[84] In medicine, this contributes to the spread of antibiotic resistance, as when one bacteria acquires resistance genes it can rapidly transfer them to other species. Horizontal transfer of genes from bacteria to eukaryotes such as the yeast Saccharomyces cerevisiae and the adzuki bean beetle Callosobruchus chinensis has occurred. An example of larger-scale transfers are the eukaryotic bdelloid rotifers, which have received a range of genes from bacteria, fungi and plants. Viruses can also carry DNA between organisms, allowing transfer of genes even across biological domains.
Large-scale gene transfer has also occurred between the ancestors of eukaryotic cells and bacteria, during the acquisition of chloroplasts and mitochondria. It is possible that eukaryotes themselves originated from horizontal gene transfers between bacteria and archaea.
From a Neo-Darwinian perspective, evolution occurs when there are changes in the frequencies of alleles within a population of interbreeding organisms. For example, the allele for black colour in a population of moths becoming more common. Mechanisms that can lead to changes in allele frequencies include natural selection,genetic drift, genetic hitchhiking, mutation and gene flow.
Evolution by means of natural selection is the process by which genetic mutations that enhance reproduction become and remain, more common in successive generations of a population. It has often been called a "self-evident" mechanism because it necessarily follows from three simple facts:
Heritable variation exists within populations of organisms.
Organisms produce more offspring than can survive.
These offspring vary in their ability to survive and reproduce.
These conditions produce competition between organisms for survival and reproduction. Consequently, organisms with traits that give them an advantage over their competitors pass these advantageous traits on, while traits that do not confer an advantage are not passed on to the next generation.[91]
The central concept of natural selection is the evolutionary fitness of an organism.[92] Fitness is measured by an organism's ability to survive and reproduce, which determines the size of its genetic contribution to the next generation.[92] However, fitness is not the same as the total number of offspring: instead fitness is indicated by the proportion of subsequent generations that carry an organism's genes. For example, if an organism could survive well and reproduce rapidly, but its offspring were all too small and weak to survive, this organism would make little genetic contribution to future generations and would thus have low fitness.
If an allele increases fitness more than the other alleles of that gene, then with each generation this allele will become more common within the population. These traits are said to be "selected for". Examples of traits that can increase fitness are enhanced survival and increased fecundity. Conversely, the lower fitness caused by having a less beneficial or deleterious allele results in this allele becoming rarer — they are "selected against". Importantly, the fitness of an allele is not a fixed characteristic; if the environment changes, previously neutral or harmful traits may become beneficial and previously beneficial traits become harmful. However, even if the direction of selection does reverse in this way, traits that were lost in the past may not re-evolve in an identical form (see Dollo's law).
A chart showing three types of selection. 1. Disruptive selection 2. Stabilizing selection 3. Directional selection
Natural selection within a population for a trait that can vary across a range of values, such as height, can be categorised into three different types. The first is directional selection, which is a shift in the average value of a trait over time — for example, organisms slowly getting taller.[97] Secondly, disruptive selection is selection for extreme trait values and often results in two different values becoming most common, with selection against the average value. This would be when either short or tall organisms had an advantage, but not those of medium height. Finally, in stabilizing selection there is selection against extreme trait values on both ends, which causes a decrease in variance around the average value and less diversity. This would, for example, cause organisms to slowly become all the same height.
A special case of natural selection is sexual selection, which is selection for any trait that increases mating success by increasing the attractiveness of an organism to potential mates. Traits that evolved through sexual selection are particularly prominent in males of some animal species, despite traits such as cumbersome antlers, mating calls or bright colours that attract predators, decreasing the survival of individual males. This survival disadvantage is balanced by higher reproductive success in males that show these hard to fake, sexually selected traits.
Natural selection most generally makes nature the measure against which individuals and individual traits, are more or less likely to survive. "Nature" in this sense refers to an ecosystem, that is, a system in which organisms interact with every other element, physical as well as biological, in their local environment. Eugene Odum, a founder of ecology, defined an ecosystem as: "Any unit that includes all of the organisms...in a given area interacting with the physical environment so that a flow of energy leads to clearly defined trophic structure, biotic diversity and material cycles (ie: exchange of materials between living and nonliving parts) within the system." Each population within an ecosystem occupies a distinct niche, or position, with distinct relationships to other parts of the system. These relationships involve the life history of the organism, its position in the food chain and its geographic range. This broad understanding of nature enables scientists to delineate specific forces which, together, comprise natural selection.
Natural selection can act at different levels of organisation, such as genes, cells, individual organisms, groups of organisms and species. Selection can act at multiple levels simultaneously. An example of selection occurring below the level of the individual organism are genes called transposons, which can replicate and spread throughout a genome. Selection at a level above the individual, such as group selection, may allow the evolution of co-operation, as discussed below.
Biased mutation
In addition to being a major source of variation, mutation may also function as a mechanism of evolution when there are different probabilities at the molecular level for different mutations to occur, a process known as mutation bias. If two genotypes, for example one with the nucleotide G and another with the nucleotide A in the same position, have the same fitness, but mutation from G to A happens more often than mutation from A to G, then genotypes with A will tend to evolve. Different insertion vs. deletion mutation biases in different taxa can lead to the evolution of different genome sizes. Developmental or mutational biases have also been observed in morphological evolution. For example, according to the phenotype-first theory of evolution, mutations can eventually cause the genetic assimilation of traits that were previously induced by the environment.
Mutation bias effects are superimposed on other processes. If selection would favor either one out of two mutations, but there is no extra advantage to having both, then the mutation that occurs the most frequently is the one that is most likely to become fixed in a population. Mutations leading to the loss of function of a gene are much more common than mutations that produce a new, fully functional gene. Most loss of function mutations are selected against. But when selection is weak, mutation bias towards loss of function can affect evolution. For example, pigments are no longer useful when animals live in the darkness of caves, and tend to be lost. This kind of loss of function can occur because of mutation bias, and/or because the function had a cost, and once the benefit of the function disappeared, natural selection leads to the loss. Loss of sporulation ability in a bacterium during laboratory evolution appears to have been caused by mutation bias, rather than natural selection against the cost of maintaining sporulation ability. When there is no selection for loss of function, the speed at which loss evolves depends more on the mutation rate than it does on the effective population size, indicating that it is driven more by mutation bias than by genetic drift.
