History of evolutionary thought
Evolutionary ideas such as common descent and the transmutation of species have existed since at least the 6th century BCE, when they were expounded by the Greek philosopher Anaximander.[14] Others who considered such ideas included the Greek philosopher Empedocles, the Roman philosopher-poet Lucretius, the Afro-Arab biologist Al-Jahiz,[15] the Persian philosopher Ibn Miskawayh, the Brethren of Purity,[16] and the Chinese philosopher Zhuangzi.[17] As biological knowledge grew in the 18th century, evolutionary ideas were set out by a few natural philosophers including Pierre Maupertuis in 1745 and Erasmus Darwin in 1796.[18] The ideas of the biologist Jean-Baptiste Lamarck about transmutation of species had wide influence. Charles Darwin formulated his idea of natural selection in 1838 and was still developing his theory in 1858 when Alfred Russel Wallace sent him a similar theory, and both were presented to the Linnean Society of London in separate papers.[19] At the end of 1859 Darwin's publication of On the Origin of Species explained natural selection in detail and presented evidence leading to increasingly wide acceptance of the occurrence of evolution.
Debate about the mechanisms of evolution continued, and Darwin could not explain the source of the heritable variations which would be acted on by natural selection. Like Lamarck, he thought that parents passed on adaptations acquired during their lifetimes,[20] a theory which was subsequently dubbed Lamarckism.[21] In the 1880s August Weismann's experiments indicated that changes from use and disuse were not heritable, and Lamarckism gradually fell from favour.[22][23] More significantly, Darwin could not account for how traits were passed down from generation to generation. In 1865 Gregor Mendel found that traits were inherited in a predictable manner.[24] When Mendel's work was rediscovered in 1900s, disagreements over the rate of evolution predicted by early geneticists and biometricians led to a rift between the Mendelian and Darwinian models of evolution.
Yet it was the rediscovery of Gregor Mendel’s pioneering work on the fundamentals of genetics (of which Darwin and Wallace were unaware) by Hugo de Vries and others in the early 1900s that provided the impetus for a better understanding of how variation occurs in plant and animal traits. That variation is the main fuel used by natural selection to shape the wide variety of adaptive traits observed in organic life. Even though Hugo de Vries and other early geneticists rejected gradual natural selection, their rediscovery of and subsequent work on genetics eventually provided a solid basis on which the theory of evolution stood even more convincingly than when it was originally proposed.[25]
The apparent contradiction between Darwin’s theory of evolution by natural selection and Mendel’s work was reconciled in the 1920s and 1930s by evolutionary biologists such as J.B.S. Haldane, Sewall Wright, and particularly Ronald Fisher, who set the foundations for the establishment of the field of population genetics. The end result was a combination of evolution by natural selection and Mendelian inheritance, the modern evolutionary synthesis.[26] In the 1940s, the identification of DNA as the genetic material by Oswald Avery and colleagues and the subsequent publication of the structure of DNA by James Watson and Francis Crick in 1953, demonstrated the physical basis for inheritance. Since then, genetics and molecular biology have become core parts of evolutionary biology and have revolutionized the field of phylogenetics.[12]
In its early history, evolutionary biology primarily drew in scientists from traditional taxonomically oriented disciplines, whose specialist training in particular organisms addressed general questions in evolution. As evolutionary biology expanded as an academic discipline, particularly after the development of the modern evolutionary synthesis, it began to draw more widely from the biological sciences.[12] Currently the study of evolutionary biology involves scientists from fields as diverse as biochemistry, ecology, genetics and physiology, and evolutionary concepts are used in even more distant disciplines such as psychology, medicine, philosophy and computer science. In the 21st century, current research in evolutionary biology deals with several areas where the modern evolutionary synthesis may need modification or extension, such as assessing the relative importance of various ideas on the unit of selection and evolvability and how to fully incorporate the findings of evolutionary developmental biology.[27][28]
Heredity
Evolution in organisms occurs through changes in heritable traits – particular characteristics of an organism. In humans, for example, eye color is an inherited characteristic, which individuals can inherit from one of their parents.[29] Inherited traits are controlled by genes and the complete set of genes within an organism's genome is called its genotype.[30]
The complete set of observable traits that make up the structure and behavior of an organism is called its phenotype. These traits come from the interaction of its genotype with the environment.[31] As a result, not every aspect of an organism's phenotype is inherited. Suntanned skin results from the interaction between a person's genotype and sunlight; thus, suntans are not passed on to people's children. However, people have different responses to sunlight, arising from differences in their genotype; a striking example is individuals with the inherited trait of albinism, who do not tan and are highly sensitive to sunburn.[32]
Heritable traits are passed from one generation to the next via DNA, a molecule that encodes genetic information.[30] DNA is a natural 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 specifying a sentence. 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. A specific location 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.[33][34] The study of such complex traits is a major area of current genetic research. Another interesting but unsolved question in genetics is if epigenetics is important in evolution, this is where heritable changes occur in organisms without there being any changes to the sequences of their genes.[35]
Variation
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.[34] The modern evolutionary synthesis defines evolution as the change over time in this genetic variation. The frequency of one particular allele will fluctuate, becoming more or less prevalent relative to other forms of that gene. Evolutionary forces act by driving these changes in allele frequency in one direction or another. Variation disappears when an allele reaches the point of fixation — when it either disappears from the population or replaces the ancestral allele entirely.[36]
Variation comes from mutations in genetic material, migration between populations (gene flow), and the reshuffling of genes through sexual reproduction. Variation also comes from exchanges of genes between different species; for example, through horizontal gene transfer in bacteria, and hybridization in plants.[37] Despite the constant introduction of variation through these processes, most of the genome of a species is identical in all individuals of that species.[38] However, even relatively small changes in genotype can lead to dramatic changes in phenotype: chimpanzees and humans differ in only about 5% of their genomes.[39]
Mutation
Random mutations constantly occur in the genomes of organisms; these mutations create genetic variation. Mutations are changes in the DNA sequence of a cell's genome and are caused by radiation, viruses, transposons and mutagenic chemicals, as well as errors that occur during meiosis or DNA replication.[40][41][42] These mutagens produce several different types of change in DNA sequences; these can either have no effect, alter the product of a gene, or prevent the gene from functioning. Studies in the fly Drosophila melanogaster suggest that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70 percent of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial.[43] Due to the damaging effects that mutations can have on cells, organisms have evolved mechanisms such as DNA repair to remove mutations.[40] Therefore, the optimal mutation rate for a species is a trade-off between costs of a high mutation rate, such as deleterious mutations, and the metabolic costs of maintaining systems to reduce the mutation rate, such as DNA repair enzymes.[44] Viruses that use RNA as their genetic material have rapid mutation rates,[45] which can be an advantage since these viruses will evolve constantly and rapidly, and thus evade the defensive responses of e.g. the human immune system.[46]
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.[47] Extra copies of genes are a major source of the raw material needed for new genes to evolve.[48] This is important because most new genes evolve within gene families from pre-existing genes that share common ancestors.[49] For example, the human eye uses four genes to make structures that sense light: three for color vision and one for night vision; all four are descended from a single ancestral gene.[50] New genes can be created 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 this increases redundancy; with one gene in the pair acquiring a new function while the other copy still performs its original function.[51][52] Other types of mutation occasionally can even create entirely new genes from previously noncoding DNA.[53][54] The creation 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.[55][56] When new genes are assembled from shuffling pre-existing parts, domains act as modules with simple independent functions, which can be mixed together creating new combinations with new and complex functions.[57] 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.[58]
Changes in chromosome number may involve even larger mutations, where segments of the DNA within chromosomes break and then rearrange. For example, two chromosomes in the Homo genus fused to produce human chromosome 2; this fusion did not occur in the lineage of the other apes, and they retain these separate chromosomes.[59] In evolution, the most important role of such chromosomal rearrangements may be to accelerate the divergence of a population into new species by making populations less likely to interbreed, and thereby preserving genetic differences between these populations.[60]
Sequences of DNA that can move about the genome, such as transposons, make up a major fraction of the genetic material of plants and animals, and may have been important in the evolution of genomes.[61] For example, more than a million copies of the Alu sequence are present in the human genome, and these sequences have now been recruited to perform functions such as regulating gene expression.[62] Another effect of these mobile DNA sequences is that when they move within a genome, they can mutate or delete existing genes and thereby produce genetic diversity.[41]
Sex and recombination
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.[63] 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.[64] Sex usually increases genetic variation and may increase the rate of evolution.[65][66] However, asexuality is advantageous in some environments as it can evolve in previously-sexual animals.[67] Here, asexuality might allow the two sets of alleles in their genome to diverge and gain different functions.[68]
Recombination allows even alleles that are close together in a strand of DNA to be inherited independently. However, the rate of recombination is low (approximately two events per chromosome per generation). As a result, genes close together on a chromosome may not always be shuffled away from each other, and genes that are close together tend to be inherited together, a phenomenon known as linkage.[69] This tendency is measured by finding how often two alleles occur together on a single chromosome, which is called their linkage disequilibrium. A set of alleles that is usually inherited in a group is called a haplotype. This can be important when one allele in a particular haplotype is strongly beneficial: natural selection can drive a selective sweep that will also cause the other alleles in the haplotype to become more common in the population; this effect is called genetic hitchhiking.[70]
When alleles cannot be separated by recombination – such as in mammalian Y chromosomes, which pass intact from fathers to sons – harmful mutations accumulate.[71][72] By breaking up allele combinations, sexual reproduction allows the removal of harmful mutations and the retention of beneficial mutations.[73] In addition, recombination and reassortment can produce individuals with new and advantageous gene combinations. These positive effects are balanced by the fact that sex reduces an organism's reproductive rate, can cause mutations and may separate beneficial combinations of genes.[73] The reasons for the evolution of sexual reproduction are therefore unclear and this question is still an active area of research in evolutionary biology,[74][75] that has prompted ideas such as the Red Queen hypothesis.[76]
Population genetics
From a genetic viewpoint, evolution is a generation-to-generation change in the frequencies of alleles within a population that shares a common gene pool.[77] A population is a localized group of individuals belonging to the same species. For example, all of the moths of the same species living in an isolated forest represent a population. A single gene in this population may have several alternate forms, which account for variations between the phenotypes of the organisms. An example might be a gene for coloration in moths that has two alleles: black and white. A gene pool is the complete set of alleles for a gene in a single population; the allele frequency measures the fraction of the gene pool composed of a single allele (for example, what fraction of moth coloration genes are the black allele). Evolution occurs when there are changes in the frequencies of alleles within a population of interbreeding organisms; for example, the allele for black color in a population of moths becoming more common.
To understand the mechanisms that cause a population to evolve, it is useful to consider what conditions are required for a population not to evolve. The Hardy-Weinberg principle states that the frequencies of alleles (variations in a gene) in a sufficiently large population will remain constant if the only forces acting on that population are the random reshuffling of alleles during the formation of the sperm or egg, and the random combination of the alleles in these sex cells during fertilization.[78] Such a population is said to be in Hardy-Weinberg equilibrium; it is not evolving.[79]
Gene flow
Gene flow is the exchange of genes between populations, which are usually of the same species.[81] Examples of gene flow within a species include the migration and then breeding of organisms, or the exchange of pollen. Gene transfer between species includes the formation of hybrid organisms and horizontal gene transfer.
Migration into or out of a population can change allele frequencies, as well as introducing genetic variation into a population. Immigration may add new genetic material to the established gene pool of a population. Conversely, emigration may remove genetic material. As barriers to reproduction between two diverging populations are required for the populations to become new species, gene flow may slow this process by spreading genetic differences between the populations. Gene flow is hindered by mountain ranges, oceans and deserts or even man-made structures such as the Great Wall of China, which has hindered the flow of plant genes.[82]
Depending on how far two species have diverged since their most recent common ancestor, it may still be possible for them to produce offspring, as with horses and donkeys mating to produce mules.[83] Such hybrids are generally infertile, due to the two different sets of chromosomes being unable to pair up during meiosis. In this case, closely related species may regularly interbreed, but hybrids will be selected against and the species will remain distinct. However, viable hybrids are occasionally formed and these new species can either have properties intermediate between their parent species, or possess a totally new phenotype.[84] The importance of hybridization in creating new species of animals is unclear, although cases have been seen in many types of animals,[85] with the gray tree frog being a particularly well-studied example.[86]
Hybridization is, however, an important means of speciation in plants, since polyploidy (having more than two copies of each chromosome) is tolerated in plants more readily than in animals.[87][88] Polyploidy is important in hybrids as it allows reproduction, with the two different sets of chromosomes each being able to pair with an identical partner during meiosis.[89] Polyploids also have more genetic diversity, which allows them to avoid inbreeding depression in small populations.[90]
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.[91] 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.[92] Horizontal transfer of genes from bacteria to eukaryotes such as the yeast Saccharomyces cerevisiae and the adzuki bean beetle Callosobruchus chinensis may also have occurred.[93][94] An example of larger-scale transfers are the eukaryotic bdelloid rotifers, which appear to have received a range of genes from bacteria, fungi, and plants.[95] Viruses can also carry DNA between organisms, allowing transfer of genes even across biological domains.[96] Large-scale gene transfer has also occurred between the ancestors of eukaryotic cells and prokaryotes, during the acquisition of chloroplasts and mitochondria.[97]
Mechanisms
The two main mechanisms that produce evolution are natural selection and genetic drift. Natural selection favors genes that improve capacity for survival and reproduction. Genetic drift is random change in the frequency of alleles, caused by the random sampling of a generation's genes during reproduction. The relative importance of natural selection and genetic drift in a population varies depending on the strength of the selection and the effective population size, which is the number of individuals capable of breeding.[98] Natural selection usually predominates in large populations, while genetic drift dominates in small populations. The dominance of genetic drift in small populations can even lead to the fixation of slightly deleterious mutations.[99] As a result, changing population size can dramatically influence the course of evolution. Population bottlenecks, where the population shrinks temporarily and therefore loses genetic variation, result in a more uniform population.[36]
Natural selection
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.[100]
The central concept of natural selection is the evolutionary fitness of an organism.[101] Fitness is measured by an organism's ability to survive and reproduce, which determines the size of its genetic contribution to the next generation.[101] 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.[102] 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.[101]
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".[3] 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.[2] 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).[103][104]
Natural selection within a population for a trait that can vary across a range of values, such as height, can be categorized 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.[105] 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.[100][106] 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.[107] 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 colors that attract predators, decreasing the survival of individual males.[108] This survival disadvantage is balanced by higher reproductive success in males that show these hard to fake, sexually selected traits.[109]
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."[110] 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.
An active area of research is the unit of selection, with natural selection being proposed to work at the level of genes, cells, individual organisms, groups of organisms and even species.[111][112] None of these are mutually exclusive and selection may act on multiple levels simultaneously.[113] An example of selection occurring below the level of the individual organism are genes called transposons, which can replicate and spread throughout a genome.[114] Selection at a level above the individual, such as group selection, may allow the evolution of co-operation, as discussed below.[115]
Genetic drift
Genetic drift is the change in allele frequency from one generation to the next that occurs because alleles in offspring are a random sample of those in the parents, as well as from the role that chance plays in determining whether a given individual will survive and reproduce. In mathematical terms, alleles are subject to sampling error. As a result, when selective forces are absent or relatively weak, allele frequencies tend to "drift" upward or downward randomly (in a random walk). This drift halts when an allele eventually becomes fixed, either by disappearing from the population, or replacing the other alleles entirely. Genetic drift may therefore eliminate some alleles from a population due to chance alone. Even in the absence of selective forces, genetic drift can cause two separate populations that began with the same genetic structure to drift apart into two divergent populations with different sets of alleles.[116]
The time for an allele to become fixed by genetic drift depends on population size, with fixation occurring more rapidly in smaller populations.[117] The precise measure of population that is important is called the effective population size. The effective population is always smaller than the total population since it takes into account factors such as the level of inbreeding, the number of animals that are too old or young to breed, and the lower probability of animals that live far apart managing to mate with each other.[118]
An example when genetic drift is probably of central importance in determining a trait is the loss of pigments from animals that live in caves, a change that produces no obvious advantage or disadvantage in complete darkness.[119] However, it is usually difficult to measure the relative importance of selection and drift,[120] so the comparative importance of these two forces in driving evolutionary change is an area of current research.[121] These investigations were prompted by the neutral theory of molecular evolution, which proposed that most evolutionary changes are the result of the fixation of neutral mutations that do not have any immediate effects on the fitness of an organism.[122] Hence, in this model, most genetic changes in a population are the result of constant mutation pressure and genetic drift.[123] This form of the neutral theory is now largely abandoned, since it does not seem to fit the genetic variation seen in nature.[124][125] However, a more recent and better-supported version of this model is the nearly neutral theory, where most mutations only have small effects on fitness.
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