History of life
Main article: Timeline of evolution
The chemical evolution from self-catalytic chemical reactions to life (see Origin of life) is not a part of biological evolution, but it is unclear at which point such increasingly complex sets of reactions became what we would consider, today, to be living organisms.
Precambrian stromatolites in the Siyeh Formation, Glacier National Park. In 2002, William Schopf of UCLA published a controversial paper in the journal Nature arguing that formations such as this possess 3.5 billion year old fossilized algae microbes. If true, they would be the earliest known life on earth.Not much is known about the earliest developments in life. However, all existing organisms share certain traits, including cellular structure and genetic code. Most scientists interpret this to mean all existing organisms share a common ancestor, which had already developed the most fundamental cellular processes, but there is no scientific consensus on the relationship of the three domains of life (Archaea, Bacteria, Eukaryota) or the origin of life. Attempts to shed light on the earliest history of life generally focus on the behavior of macromolecules, particularly RNA, and the behavior of complex systems.
The emergence of oxygenic photosynthesis (around 3 billion years ago) and the subsequent emergence of an oxygen-rich, non-reducing atmosphere can be traced through the formation of banded iron deposits, and later red beds of iron oxides. This was a necessary prerequisite for the development of aerobic cellular respiration, believed to have emerged around 2 billion years ago.
In the last billion years, simple multicellular plants and animals began to appear in the oceans. Soon after the emergence of the first animals, the Cambrian explosion (a period of unrivaled and remarkable, but brief, organismal diversity documented in the fossils found at the Burgess Shale) saw the creation of all the major body plans, or phyla, of modern animals. This event is now believed to have been triggered by the development of the Hox genes. About 500 million years ago, plants and fungi colonized the land, and were soon followed by arthropods and other animals, leading to the development of land ecosystems with which we are familiar.
The evolutionary process may be exceedingly slow. Fossil evidence indicates that the diversity and complexity of modern life has developed over much of the history of the earth. Geological evidence indicates that the Earth is approximately 4.6 billion years old. Studies on guppies by David Reznick at the University of California, Riverside, however, have shown that the rate of evolution through natural selection can proceed 10 thousand to 10 million times faster than what is indicated in the fossil record.[29]. Such comparative studies however are invariably biased by disparities in the time scales over which evolutionary change is measured in the laboratory, field experiments, and the fossil record.
The ancestry of living organisms has traditionally been reconstructed from morphology, but is increasingly supplemented with phylogenetic—the reconstruction of phylogenies by the comparison of genetic (usually DNA) sequence.[30] Biologist Gogarten suggests that "the original metaphor of a tree no longer fits the data from recent genome research", and that therefore "biologists [should] use the metaphor of a mosaic to describe the different histories combined in individual genomes and use [the] metaphor of a net to visualize the rich exchange and cooperative effects of HGT among microbes".[31]
Mechanisms of evolution
Evolution consists of two basic types of processes: those that introduce new genetic variation into a population, and those that affect the frequencies of existing variation. Paleontologist Stephen J. Gould once phrased this succinctly as "variation proposes and selection disposes."[33]
These mechanisms of evolution have all been observed in the present and in evidence of their existence in the past. Their study is being used to guide the development of new medicines and other health aids such as the current effort to prevent a H5N1 (i.e. bird flu) pandemic. [34]
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Mutation
Main article: Mutation
Mutation occurs because of "copy errors" that occur during DNA replication.Genetic variation arises due to random mutations that occur at a certain rate in the genomes of all organisms. Mutations are permanent, transmissible changes to the genetic material (usually DNA or RNA) of a cell, and can be caused by: "copying errors" in the genetic material during cell division; by exposure to radiation, chemicals, or viruses. In multicellular organisms, mutations can be subdivided into germline mutations that occur in the gametes and thus can be passed on to progeny, and somatic mutations that often lead to the malfunction or death of a cell and can cause cancer.
Mutations that are not affected by natural selection are called neutral mutations. Their frequency in the population is governed by mutation rate, genetic drift and selective pressure on linked alleles. It is understood that a species' genome, in the absence of selection, undergoes a steady accumulation of neutral mutations.
Not all mutations are created equal; simple point mutations (substitutions) or SNPs (Single Nucleotide Polymorphisms), which comprise a major class of genetic variation, and insertions and deletions (indels) usually can only alter the function or regulation (spatial and temporal expression; levels of expression) of existing genes.
On the other hand, gene duplications, which may occur via a number of mechanisms, are believed to be one major source of raw material for evolving new genes as tens to hundreds of genes are duplicated in animal genomes every million years[35]. Most genes belong to larger "families" of genes derived from a common ancestral gene (two genes from a species that are in the same family are dubbed "paralogs"). Another mechanism causing gene duplication is intergenic recombination, particularly 'exon shuffling', i.e., an abberant recombination that joins the 'upstream' part of one gene with the 'downstream' part of another. Genome duplications result in the duplication of every gene in the genome. This mechanism has been the driving force in the Teleostei genome evolution, where up to four genome duplications are thought to have happened, resulting in species with more than 250 chromosomes.
Finally, large chromosomal rearrangements (like the fusion of two chromosomes in the chimp/human common ancestor that produced human chromosome 2) do not necessarily change gene function, but do generally result in reproductive isolation, and, by definition, speciation (since "species" (in sexual organisms) are usually defined by the ability to interbreed).
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Recombination
Main article: Evolution of sex
In asexual organisms, variants in genes on the same chromosome will always be inherited together - they are linked, by virtue of being on the same DNA molecule. However, sexual organisms, in the production of gametes, shuffle linked alleles on homologous chromosomes inherited from the parents via meiotic recombination. This shuffling allows independent assortment of alleles (mutations) in genes to be propagated in the population independently. This allows bad mutations to be purged and beneficial mutations to be retained more efficiently than in asexual populations.
However, the meitoic recombination rate is not very high - on the order of one crossover (recombination event between homomolgous chromosomes) per chromosome arm per generation. Therefore, linked alleles are not perfectly shuffled away from each other, but tend to be inherited together. This tendency may be measured by comparing the co-occurrence of two alleles, usually quantified as linkage disequilibrium (LD). A set of alleles that are often co-propagated is called a haplotype. Strong haplotype blocks can be a product of strong positive selection.
Recombination is mildly mutagenic, which is one of the proposed reasons why it occurs with limited frequency. Recombination also breaks up gene combinations that have been successful in previous generations, and hence should be opposed by selection. However, recombination could be favoured by negative frequency-dependent selection (this is when rare variants increase in frequency) because it leads to more individuals with new and rare gene combinations being produced.
When alleles cannot be separated by recombination (for example in mammalian Y chromosomes), we see a reduction in effective population size, known as the Hill Robertson effect, and the successive establishment of bad mutations, known as Muller's ratchet.
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Gene flow and Population structure
Main article: Population genetics
Map of the world showing distribution of camelids. Solid black lines indicate possible migration routes.Gene flow (also called gene admixture or simply migration) is the exchange of genetic variation between populations, when geography and culture are not obstacles. Ernst Mayr thought that gene flow is likely to be homogenising, and therefore counteract selective adaptation. Where there are obstacles to gene flow, the situation is termed reproductive isolation and is considered to be necessary for speciation.
The free movement of alleles through a population may also be impeded by population structure. For example, most real-world populations are not actually fully interbreeding; geographic proximity has a strong influence on the movement of alleles within the population.
An example of the effect of population structure is the so-called founder effect, resulting from a migration or population bottleneck, in which a population temporarily has very few individuals, and therefore loses a lot of genetic variation. In this case, a single, rare allele may suddenly increase very rapidly in frequency within a specific population if it happened to be prevalent in a small number of "founder" individuals. The frequency of the allele in the resulting population can be much higher than otherwise expected, especially for deleterious, disease-causing alleles. Since population size has a profound effect on the relative strengths of genetic drift and natural selection, changes in population size can alter the dynamics of these processes considerably.
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Drift
Main article: Genetic drift
Genetic drift describes changes in allele frequency from one generation to the next due to sampling variance. The frequency of an allele in the offspring generation will vary according to a probability distribution of the frequency of the allele in the parent generation. Thus, over time, allele frequencies will tend to "drift" upward or downward, eventually becoming "fixed" - that is, going to 0% or 100% frequency. Fluctuations in allele frequency between successive generations may result in some alleles disappearing from the population. Two separate populations that begin with the same allele frequencies therefore might drift by random fluctuation into two divergent populations with different allele sets (for example, alleles present in one population could be absent in the other, or vice versa).
Many aspects of genetic drift depend on the size of the population (generally abbreviated as N). This is especially important in small mating populations (see Founder effect), where chance fluctuations from generation to generation can be large. The relative importance of natural selection and genetic drift in determining the fate of new mutations also depends on the population size and the strength of selection: when N times s (population size times strength of selection) is small, genetic drift predominates. When N times s is large, selection predominates. Thus, natural selection is 'more efficient' in large populations, or equivalently, genetic drift is stronger in small populations. Finally, the time for an allele to become fixed in the population by genetic drift (that is, for all individuals in the population to carry that allele) depends on population size, with smaller populations requiring a shorter time to fixation.
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Horizontal gene transfer
One source of genetic variation is horizontal gene transfer, the movement of genetic material across species boundaries, which can include horizontal gene transfer, antigenic shift, reassortment, and hybridization. Viruses can transfer genes between species via transduction, [36]. Bacteria can incorporate genes from other dead bacteria or plasmids via transformation, exchange genes with living bacteria via conjugation, and can have plasmids "set up residence separate from the host's genome" [37].
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Selection and adaptation
Main articles: Natural selection and Adaptation
A peacock's tail is the canonical example of sexual selectionNatural selection comes from differences in survival and reproduction . Differential mortality is the survival rate of individuals to their reproductive age. Differential fertility is the total genetic contribution to the next generation. Note that, whereas mutations and genetic drift are random, natural selection is not, as it preferentially selects for different mutations based on differential fitnesses. For example, rolling dice is random, but always picking the higher number on two rolled dice is not random. The central role of natural selection in evolutionary theory has given rise to a strong connection between that field and the study of ecology.
Natural selection can be subdivided into two categories:
Ecological selection occurs when organisms that survive and reproduce increase the frequency of their genes in the gene pool over those that do not survive.
Sexual selection occurs when organisms which are more attractive to the opposite sex because of their features reproduce more and thus increase the frequency of those features in the gene pool.
Natural selection also operates on mutations in several different ways:
Positive or directional selection increases the frequency of a beneficial mutation, or pushes the mean in either direction.
Purifying or stabilizing selection maintains a common trait in the population by decreasing the frequency of harmful mutations and weeding them out of the population. "Living fossils" are arguably the product of stabilizing selection, as their form and traits have remained virtually identical over a long period of time. It is argued that stabilizing selection is the most common form of natural selection.
Artificial selection refers to purposeful breeding of a species to produce a more desirable and “perfect” breed. Humans have directed artificial selection in the breeding of both animals and plants, with examples ranging from agriculture (crops and livestock) to pets and horticulture. However, because humans are only part of the environment, the fractions of change in a species due to natural or artificial means can be difficult to determine. Artificial selection within human populations is a controversial enterprise known as eugenics.
Balancing selection maintains variation within a population through a number of mechanisms, including:
Heterozygote advantage or overdominance, where the heterozygote is more fit than either of the homozygous forms (exemplified by human sickle cell anemia conferring resistance to malaria)
Frequency-dependent selection, where rare variants either have increased fitness or decreased fitness, because of their rarity.
Disruptive selection favors both extremes, and results in a bimodal distribution of gene frequency. The mean may or may not shift.
Selective sweeps describe the affect of selection acting on linked alleles. It comes in two forms:
Background selection occurs when a deleterious mutation is selected against, and linked mutations are eliminated along with the deleterious variant, resulting in lower genetic polymorphism in the surrounding region.
Genetic hitchhiking occurs when a beneficial allele is selected for, and linked alleles, which can be neutral or beneficial, are pushed towards fixation along with the beneficial allele.
Through the process of natural selection, organisms become better adapted to their environments. Adaptation is any evolutionary process that increases the fitness of the individual, or sometimes the trait that confers increased fitness, e.g. a stronger prehensile tail or greater visual acuity. Note that adaptation is context-sensitive; a trait that increases fitness in one environment may decrease it in another.
Evolution does not act in a linear direction towards a pre-defined "goal" — it only responds to various types of adaptionary changes. The belief in a telelogical evolution of this sort is known as orthogenesis, and is not supported by the scientific understanding of evolution. One example of this misconception is the erroneous belief humans will evolve more fingers in the future on account of their increased use of machines such as computers. In reality, this would only occur if more fingers offered a significantly higher rate of reproductive success than those not having them, which seems very unlikely at the current time.
Most biologists believe that adaptation occurs through the accumulation of many mutations of small effect. However, macromutation is an alternative process for adaptation that involves a single, very large scale mutation.
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Speciation and extinction
An Allosaurus skeleton.Speciation is the process by which new biological species arise. This may take place by various mechanisms. Allopatric speciation occurs in populations that become isolated geographically, such as by habitat fragmentation or migration. Sympatric speciation[38][39] occurs when new species emerge in the same geographic area. Ernst Mayr's peripatric speciation is a type of speciation that exists in between the extremes of allopatry and sympatry. Peripatric speciation is a critical underpinning of the theory of punctuated equilibrium. An example of rapid sympatric speciation can be eloquently represented in the triangle of U; where new species of Brassica sp. have been made by the fusing of separate genomes from related plants.
Extinction is the disappearance of species (i.e. gene pools). The moment of extinction generally occurs at the death of the last individual of that species. Extinction is not an unusual event in geological time — species are created by speciation, and disappear through extinction. The Permian-Triassic extinction event was the Earth's most severe extinction event, rendering extinct 90% of all marine species and 70% of terrestrial vertebrate species. In the Cretaceous-Tertiary extinction event many forms of life perished (including approximately 50% of all genera), the most often mentioned among them being the extinction of the non-avian dinosaurs.
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Current Research
See also: Ancestral Reconstruction, Human Genome Project, Bioinformatics, and Evo-devo
Evolution is still an active field of research in the scientific community. Improvements in sequencing methods have resulted in a large increase of sequenced genomes, allowing for the testing and refining of the theory of evolution with respect to whole genome data. Advances in computational hardware and software have allowed for the testing and extrapolation of increasingly advanced evolutionary models. Discoveries in biotechnology have produced methods for the ‘’de novo’’ synthesis of proteins and, potentially, entire genomes, driving evolutionary studies at the molecular level.
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Misunderstandings about modern evolutionary biology
Main article: Creation-evolution controversy
Though the modern synthesis is almost universally accepted within the scientific community, people often find that it introduces concepts which go against their perception of design, purpose, directive principle, or finality in nature. As Louis Menand has pointed out, "Darwin wanted to establish... that the species — including human beings — were created by, and evolve according to, processes that are entirely natural, chance-generated, and blind." [40]
In the resulting controversy, publicity is given to creationist arguments against evolution and natural selection, which generally involve misunderstandings or misconceptions about evolution or about science in general.[41] Some of the most common arguments are examined in this section. More are considered at An Index to Creationist Claims.
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Distinctions between theory and fact
Further information: Scientific Theory
See also: Theory vs. Fact
The modern synthesis, like its Mendelian and Darwinian antecedents, is a scientific theory. A theory is an attempt to identify and describe relationships between phenomena or things, and generates falsifiable predictions which can be tested through controlled experiments and empirical observation. Speculative or conjectural explanations tend to be called hypotheses, and well tested explanations, theories. Fact tends to mean a datum, an observation, i.e., a fact is obtained by a fairly direct observation. In contrast, a theory is obtained by inference from a body of facts. Fact and theory denote the epistemological status of knowledge; how the knowledge was obtained, what sort of knowledge it is.
In this scientific sense, "facts" are what theories attempt to explain. So, for scientists "theory" and "fact" do not stand in opposition, but rather exist in a reciprocal relationship; for example, it is a "fact" that an apple will fall to the ground if it becomes dislodged from a branch and the "theory" which explains this is the current theory of gravitation. In the same way, heritable variation, natural selection, and response to selection (e.g. in domesticated plants and animals) are "facts", and the generalization or extrapolation beyond these phenomena, and the explanation for them, is the "theory of evolution". [42]
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Evolution and devolution
One of the most common misunderstandings of evolution is that one species can be "more highly evolved" than another, that evolution is necessarily progressive and/or leads to greater "complexity", or that its converse is "devolution".[43] Evolution provides no assurance that later generations are more intelligent or complex than earlier generations. The claim that evolution results in progress is not part of modern evolutionary theory; it derives from earlier belief systems which were held around the time Darwin devised his theory of evolution.
In many cases evolution does involve "progression" towards more complexity, since the earliest lifeforms were extremely simple compared to many of the species existing today, and there was nowhere to go but up. However, there is no guarantee that any particular organism existing today will become more intelligent, more complex, bigger, or stronger in the future. In fact, natural selection will only favor this kind of "progression" if it increases chance of survival, i.e. the ability to live long enough to raise offspring to sexual maturity. The same mechanism can actually favor lower intelligence, lower complexity, and so on if those traits become a selective advantage in the organism's environment. One way of understanding the apparent "progression" of lifeforms over time is to remember that the earliest life began as maximally simple forms. Evolution caused life to become more complex, since becoming simpler wasn't advantageous. Once individual lineages have attained sufficient complexity, however, simplifications (specialization) are as likely as increased complexity. This can be seen in many parasite species, for example, which have evolved simpler forms from more complex ancestors.[44]
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Speciation
Main article: Speciation
The existence of several different, but related, finches on the Galápagos Islands is evidence of the occurrence of speciation.It is sometimes claimed that speciation – the origin of new species – has never been directly observed, and thus evolution cannot be called sound science. A variation of this assertion is that "microevolution" has been observed and "macroevolution" has not been observed. Some creationists redefine macroevolution as a change from one "kind" to another (see Created kind), though it is unclear what a "kind" in this context is intended to refer to. This is a misunderstanding of both science and evolution. First, scientific discovery does not occur solely through reproducible experiments; the principle of uniformitarianism allows natural scientists to infer causes through their empirical effects. Moreover, since the publication of On the Origin of Species scientists have confirmed Darwin's hypothesis by data gathered from sources that did not exist in his day, such as DNA similarity among species and new fossil discoveries. Finally, speciation has actually been directly observed. [45] (See the hawthorn fly example, above.)
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Self-organization and entropy
Main article: Self-organization
It is claimed that evolution, by increasing complexity without supernatural intervention, violates the second law of thermodynamics. This law posits that in an idealised isolated system, entropy will tend to increase or stay the same. Entropy is a measure of the amount of energy in a physical system which cannot be used to do mechanical work, and in statistical thermodynamics it is envisioned as a measure of the statistical "disorder" at a microstate level.
The claim ignores the fact that biological systems are not isolated systems. The Sun provides a large amount of energy to the Earth, and this flow of heat results in huge increases in entropy, when compared with decreases associated with decreasing the disorder of biological systems.
In fact, the flow of matter and energy through open systems allows self-organization enabling an increase in complexity without guidance or management. Examples include mineral crystals and snowflakes. Life inherently involves open systems, not isolated systems, as all organisms exchange energy and matter with their environment, and similarly the Earth receives energy from the Sun and emits energy back into space.
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Information
Some assert that evolution cannot create information, or that information can only be created by an intelligence. Physical information exists regardless of the presence of an intelligence, and evolution allows for new information whenever a novel mutation or gene duplication occurs and is kept. It does not need to be beneficial or visually apparent to be "information." However, even if those were requirements they would be satisfied with the appearance of nylon-eating bacteria, [46] which required new enzymes to efficiently digest a material that never existed until the modern age.[47]
Japanese researchers demonstrated that nylon degrading ability can be obtained de novo in laboratory cultures of Pseudomonas aeruginosa strain POA, which initially had no enzymes capable of degrading nylon oligomers. This indicates that the ability of bacteria to digest nylon can evolve if proper artificial selection is applied. [48] Recently, the same group solved the high resolution X-ray crystal structure of the newly evolved nylon-digesting enzyme. [49] Using the structural results, the authors propose "that the amino acid replacements in the catalytic cleft of a preexisting esterase with the beta-lactamase fold resulted in the evolution of the" nylon-digesting enzyme. This hypothesis still needs to be confirmed by detailed mutagenesis studies.
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