Punctuated equilibrium

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Punctuated_equilibrium 

 

 

 

The punctuated equilibrium model (top) consists of morphological stability followed by rare bursts of evolutionary change via rapid cladogenesis. It is contrasted (below) to phyletic gradualism, the more gradual, continuous model of evolution. On diagram we see equilibrium states separated by a jump phase.

In evolutionary biology, punctuated equilibrium (also called punctuated equilibria) is a theory that proposes that once a species appears in the fossil record, the population will become stable, showing little evolutionary change for most of its geological history. This state of little or no morphological change is called stasis. When significant evolutionary change occurs, the theory proposes that it is generally restricted to rare and geologically rapid events of branching speciation called cladogenesis. Cladogenesis is the process by which a species splits into two distinct species, rather than one species gradually transforming into another.

Punctuated equilibrium is commonly contrasted against phyletic gradualism, the idea that evolution generally occurs uniformly and by the steady and gradual transformation of whole lineages (called anagenesis). In this view, evolution is seen as generally smooth and continuous.

In 1972, paleontologists Niles Eldredge and Stephen Jay Gould published a landmark paper developing their theory and called it punctuated equilibria. Their paper built upon Ernst Mayr's model of geographic speciation, I. Michael Lerner's theories of developmental and genetic homeostasis, and their own empirical research. Eldredge and Gould proposed that the degree of gradualism commonly attributed to Charles Darwin is virtually nonexistent in the fossil record, and that stasis dominates the history of most fossil species.

History

Punctuated equilibrium originated as a logical consequence of Ernst Mayr's concept of genetic revolutions by allopatric and especially peripatric speciation as applied to the fossil record. Although the sudden appearance of species and its relationship to speciation was proposed and identified by Mayr in 1954, historians of science generally recognize the 1972 Eldredge and Gould paper as the basis of the new paleobiological research program. Punctuated equilibrium differs from Mayr's ideas mainly in that Eldredge and Gould placed considerably greater emphasis on stasis, whereas Mayr was concerned with explaining the morphological discontinuity (or "sudden jumps") found in the fossil record. Mayr later complimented Eldredge and Gould's paper, stating that evolutionary stasis had been "unexpected by most evolutionary biologists" and that punctuated equilibrium "had a major impact on paleontology and evolutionary biology."

A year before their 1972 Eldredge and Gould paper, Niles Eldredge published a paper in the journal Evolution which suggested that gradual evolution was seldom seen in the fossil record and argued that Ernst Mayr's standard mechanism of allopatric speciation might suggest a possible resolution.

The Eldredge and Gould paper was presented at the Annual Meeting of the Geological Society of America in 1971. The symposium focused its attention on how modern microevolutionary studies could revitalize various aspects of paleontology and macroevolution. Tom Schopf, who organized that year's meeting, assigned Gould the topic of speciation. Gould recalls that "Eldredge's 1971 publication [on Paleozoic trilobites] had presented the only new and interesting ideas on the paleontological implications of the subject—so I asked Schopf if we could present the paper jointly." According to Gould "the ideas came mostly from Niles, with yours truly acting as a sounding board and eventual scribe. I coined the term punctuated equilibrium and wrote most of our 1972 paper, but Niles is the proper first author in our pairing of Eldredge and Gould." In his book Time Frames Eldredge recalls that after much discussion the pair "each wrote roughly half. Some of the parts that would seem obviously the work of one of us were actually first penned by the other—I remember for example, writing the section on Gould's snails. Other parts are harder to reconstruct. Gould edited the entire manuscript for better consistency. We sent it in, and Schopf reacted strongly against it—thus signaling the tenor of the reaction it has engendered, though for shifting reasons, down to the present day."

John Wilkins and Gareth Nelson have argued that French architect Pierre Trémaux proposed an "anticipation of the theory of punctuated equilibrium of Gould and Eldredge."

Evidence from the fossil record

The fossil record includes well documented examples of both phyletic gradualism and punctuational evolution. As such, much debate persists over the prominence of stasis in the fossil record. Before punctuated equilibrium, most evolutionists considered stasis to be rare or unimportant. The paleontologist George Gaylord Simpson, for example, believed that phyletic gradual evolution (called horotely in his terminology) comprised 90% of evolution. More modern studies, including a meta-analysis examining 58 published studies on speciation patterns in the fossil record showed that 71% of species exhibited stasis, and 63% were associated with punctuated patterns of evolutionary change. According to Michael Benton, "it seems clear then that stasis is common, and that had not been predicted from modern genetic studies." A paramount example of evolutionary stasis is the fern Osmunda claytoniana. Based on paleontological evidence it has remained unchanged, even at the level of fossilized nuclei and chromosomes, for at least 180 million years.

Theoretical mechanisms

Punctuational change

When Eldredge and Gould published their 1972 paper, allopatric speciation was considered the "standard" model of speciation. This model was popularized by Ernst Mayr in his 1954 paper "Change of genetic environment and evolution," and his classic volume Animal Species and Evolution (1963).

Allopatric speciation suggests that species with large central populations are stabilized by their large volume and the process of gene flow. New and even beneficial mutations are diluted by the population's large size and are unable to reach fixation, due to such factors as constantly changing environments. If this is the case, then the transformation of whole lineages should be rare, as the fossil record indicates. Smaller populations on the other hand, which are isolated from the parental stock, are decoupled from the homogenizing effects of gene flow. In addition, pressure from natural selection is especially intense, as peripheral isolated populations exist at the outer edges of ecological tolerance. If most evolution happens in these rare instances of allopatric speciation then evidence of gradual evolution in the fossil record should be rare. This hypothesis was alluded to by Mayr in the closing paragraph of his 1954 paper:

Rapidly evolving peripherally isolated populations may be the place of origin of many evolutionary novelties. Their isolation and comparatively small size may explain phenomena of rapid evolution and lack of documentation in the fossil record, hitherto puzzling to the palaeontologist.

Although punctuated equilibrium generally applies to sexually reproducing organisms, some biologists have applied the model to non-sexual species like viruses, which cannot be stabilized by conventional gene flow. As time went on biologists like Gould moved away from wedding punctuated equilibrium to allopatric speciation, particularly as evidence accumulated in support of other modes of speciation. Gould, for example, was particularly attracted to Douglas Futuyma's work on the importance of reproductive isolating mechanisms.

Stasis

Many hypotheses have been proposed to explain the putative causes of stasis. Gould was initially attracted to I. Michael Lerner's theories of developmental and genetic homeostasis. However this hypothesis was rejected over time, as evidence accumulated against it. Other plausible mechanisms which have been suggested include: habitat tracking, stabilizing selection, the Stenseth-Maynard Smith stability hypothesis, constraints imposed by the nature of subdivided populations, normalizing clade selection, and koinophilia.

Evidence for stasis has also been corroborated from the genetics of sibling species, species which are morphologically indistinguishable, but whose proteins have diverged sufficiently to suggest they have been separated for millions of years. Fossil evidence of reproductively isolated extant species of sympatric Olive Shells (Amalda sp.) also confirm morphological stasis in multiple lineages over three million years.

According to Gould, "stasis may emerge as the theory's most important contribution to evolutionary science." Philosopher Kim Sterelny in clarifying the meaning of stasis adds, "In claiming that species typically undergo no further evolutionary change once speciation is complete, they are not claiming that there is no change at all between one generation and the next. Lineages do change. But the change between generations does not accumulate. Instead, over time, the species wobbles about its phenotypic mean. Jonathan Weiner's The Beak of the Finch describes this very process."

Hierarchical evolution

Punctuated equilibrium has also been cited as contributing to the hypothesis that species are Darwinian individuals, and not just classes, thereby providing a stronger framework for a hierarchical theory of evolution.

Common misconceptions

Much confusion has arisen over what proponents of punctuated equilibrium actually argued, what mechanisms they advocated, how fast the punctuations were, what taxonomic scale their theory applied to, how revolutionary their claims were intended to be, and how punctuated equilibrium related to other ideas like saltationism, quantum evolution, and mass extinction.

Saltationism

Alternative explanations for the punctuated pattern of evolution observed in the fossil record. Both macromutation and relatively rapid episodes of gradual evolution could give the appearance of instantaneous change, since 10,000 years seldom registers in the geological record.

The punctuational nature of punctuated equilibrium has engendered perhaps the most confusion over Eldredge and Gould's theory. Gould's sympathetic treatment of Richard Goldschmidt, the controversial geneticist who advocated the idea of "hopeful monsters," led some biologists to conclude that Gould's punctuations were occurring in single-generation jumps. This interpretation has frequently been used by creationists to characterize the weakness of the paleontological record, and to portray contemporary evolutionary biology as advancing neo-saltationism. In an often quoted remark, Gould stated, "Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists—whether through design or stupidity, I do not know—as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abundant between larger groups." Although there exist some debate over how long the punctuations last, supporters of punctuated equilibrium generally place the figure between 50,000 and 100,000 years.

Quantum evolution

Quantum evolution was a controversial hypothesis advanced by Columbia University paleontologist George Gaylord Simpson, who was regarded by Gould as "the greatest and most biologically astute paleontologist of the twentieth century." Simpson's conjecture was that according to the geological record, on very rare occasions evolution would proceed very rapidly to form entirely new families, orders, and classes of organisms. This hypothesis differs from punctuated equilibrium in several respects. First, punctuated equilibrium was more modest in scope, in that it was addressing evolution specifically at the species level. Simpson's idea was principally concerned with evolution at higher taxonomic groups. Second, Eldredge and Gould relied upon a different mechanism. Where Simpson relied upon a synergistic interaction between genetic drift and a shift in the adaptive fitness landscape, Eldredge and Gould relied upon ordinary speciation, particularly Ernst Mayr's concept of allopatric speciation. Lastly, and perhaps most significantly, quantum evolution took no position on the issue of stasis. Although Simpson acknowledged the existence of stasis in what he called the bradytelic mode, he considered it (along with rapid evolution) to be unimportant in the larger scope of evolution. In his Major Features of Evolution Simpson stated, "Evolutionary change is so nearly the universal rule that a state of motion is, figuratively, normal in evolving populations. The state of rest, as in bradytely, is the exception and it seems that some restraint or force must be required to maintain it." Despite such differences between the two models, earlier critiques—from such eminent commentators as Sewall Wright as well as Simpson himself—have argued that punctuated equilibrium is little more than quantum evolution relabeled.

Multiple meanings of gradualism

Punctuated equilibrium is often portrayed to oppose the concept of gradualism, when it is actually a form of gradualism. This is because even though evolutionary change appears instantaneous between geological sedimentary layers, change is still occurring incrementally, with no great change from one generation to the next. To this end, Gould later commented that "Most of our paleontological colleagues missed this insight because they had not studied evolutionary theory and either did not know about allopatric speciation or had not considered its translation to geological time. Our evolutionary colleagues also failed to grasp the implication(s), primarily because they did not think at geological scales".

Richard Dawkins dedicated a chapter in The Blind Watchmaker to correcting, in his view, the wide confusion regarding rates of change. His first point is to argue that phyletic gradualism—understood in the sense that evolution proceeds at a single uniform rate of speed, called "constant speedism" by Dawkins—is a "caricature of Darwinism" and "does not really exist". His second argument, which follows from the first, is that once the caricature of "constant speedism" is dismissed, we are left with one logical alternative, which Dawkins terms "variable speedism". Variable speedism may also be distinguished one of two ways: "discrete variable speedism" and "continuously variable speedism". Eldredge and Gould, proposing that evolution jumps between stability and relative rapidity, are described as "discrete variable speedists", and "in this respect they are genuinely radical." They assert that evolution generally proceeds in bursts, or not at all. "Continuously variable speedists", on the other hand, advance that "evolutionary rates fluctuate continuously from very fast to very slow and stop, with all intermediates. They see no particular reason to emphasize certain speeds more than others. In particular, stasis, to them, is just an extreme case of ultra-slow evolution. To a punctuationist, there is something very special about stasis." Dawkins therefore commits himself here to an empirical claim about the geological record, in contrast to his earlier claim that "The paleontological evidence can be argued about, and I am not qualified to judge it." It is this particular commitment that Eldredge and Gould have aimed to overturn.

Criticism

Richard Dawkins regards the apparent gaps represented in the fossil record to document migratory events rather than evolutionary events. According to Dawkins, evolution certainly occurred but "probably gradually" elsewhere. However, the punctuational equilibrium model may still be inferred from both the observation of stasis and examples of rapid and episodic speciation events documented in the fossil record.

Dawkins also emphasizes that punctuated equilibrium has been "oversold by some journalists", but partly due to Eldredge and Gould's "later writings". Dawkins contends that the hypothesis "does not deserve a particularly large measure of publicity". It is a "minor gloss," an "interesting but minor wrinkle on the surface of neo-Darwinian theory," and "lies firmly within the neo-Darwinian synthesis".

In his book Darwin's Dangerous Idea, philosopher Daniel Dennett is especially critical of Gould's presentation of punctuated equilibrium. Dennett argues that Gould alternated between revolutionary and conservative claims, and that each time Gould made a revolutionary statement—or appeared to do so—he was criticized, and thus retreated to a traditional neo-Darwinian position. Gould responded to Dennett's claims in The New York Review of Books, and in his technical volume The Structure of Evolutionary Theory.

English professor Heidi Scott argues that Gould's talent for writing vivid prose, his use of metaphor, and his success in building a popular audience of nonspecialist readers altered the "climate of specialized scientific discourse" favorably in his promotion of punctuated equilibrium. While Gould is celebrated for the color and energy of his prose, as well as his interdisciplinary knowledge, critics such as Scott, Richard Dawkins, and Daniel Dennett have concerns that the theory has gained undeserved credence among non-scientists because of Gould's rhetorical skills. Philosopher John Lyne and biologist Henry Howe believed punctuated equilibrium's success has much more to do with the nature of the geological record than the nature of Gould's rhetoric. They state, a "re-analysis of existing fossil data has shown, to the increasing satisfaction of the paleontological community, that Eldredge and Gould were correct in identifying periods of evolutionary stasis which are interrupted by much shorter periods of evolutionary change."

Some critics jokingly referred to the theory of punctuated equilibrium as "evolution by jerks", which reportedly prompted punctuationists to describe phyletic gradualism as "evolution by creeps."

Darwin's theory

The sudden appearance of most species in the geologic record and the lack of evidence of substantial gradual change in most species—from their initial appearance until their extinction—has long been noted, including by Charles Darwin who appealed to the imperfection of the record as the favored explanation. When presenting his ideas against the prevailing influences of catastrophism and progressive creationism, which envisaged species being supernaturally created at intervals, Darwin needed to forcefully stress the gradual nature of evolution in accordance with the gradualism promoted by his friend Charles Lyell. He privately expressed concern, noting in the margin of his 1844 Essay, "Better begin with this: If species really, after catastrophes, created in showers world over, my theory false."

It is often incorrectly assumed that he insisted that the rate of change must be constant, or nearly so, but even the first edition of On the Origin of Species states that "Species of different genera and classes have not changed at the same rate, or in the same degree. In the oldest tertiary beds a few living shells may still be found in the midst of a multitude of extinct forms... The Silurian Lingula differs but little from the living species of this genus". Lingula is among the few brachiopods surviving today but also known from fossils over 500 million years old. In the fourth edition (1866) of On the Origin of Species Darwin wrote that "the periods during which species have undergone modification, though long as measured in years, have probably been short in comparison with the periods during which they retain the same form." Thus punctuationism in general is consistent with Darwin's conception of evolution.

According to early versions of punctuated equilibrium, "peripheral isolates" are considered to be of critical importance for speciation. However, Darwin wrote, "I can by no means agree ... that immigration and isolation are necessary elements.... Although isolation is of great importance in the production of new species, on the whole I am inclined to believe that largeness of area is still more important, especially for the production of species which shall prove capable of enduring for a long period, and of spreading widely."

The importance of isolation in forming species had played a significant part in Darwin's early thinking, as shown in his Essay of 1844. But by the time he wrote the Origin he had downplayed its importance. He explained the reasons for his revised view as follows:

Throughout a great and open area, not only will there be a greater chance of favourable variations, arising from the large number of individuals of the same species there supported, but the conditions of life are much more complex from the large number of already existing species; and if some of these species become modified and improved, others will have to be improved in a corresponding degree, or they will be exterminated. Each new form, also, as soon as it has been improved, will be able to spread over the open and continuous area, and will thus come into competition with many other forms ... the new forms produced on large areas, which have already been victorious over many competitors, will be those that will spread most widely, and will give rise to the greatest number of new varieties and species. They will thus play a more important role in the changing history of the organic world.

Thus punctuated equilibrium is incongruous with some of Darwin's ideas regarding the specific mechanisms of evolution, but generally accords with Darwin's theory of evolution by natural selection.

Supplemental modes of rapid evolution

Recent work in developmental biology has identified dynamical and physical mechanisms of tissue morphogenesis that may underlie abrupt morphological transitions during evolution. Consequently, consideration of mechanisms of phylogenetic change that have been found in reality to be non-gradual is increasingly common in the field of evolutionary developmental biology, particularly in studies of the origin of morphological novelty. A description of such mechanisms can be found in the multi-authored volume Origination of Organismal Form (MIT Press; 2003).

Language change

In linguistics, R. M. W. Dixon has proposed a punctuated equilibrium model for language histories, with reference particularly to the prehistory of the indigenous languages of Australia and his objections to the proposed Pama–Nyungan language family there. Although his model has raised considerable interest, it does not command majority support within linguistics.

Separately, recent work using computational phylogenetic methods claims to show that punctuational bursts play an important factor when languages split from one another, accounting for anywhere from 10 to 33% of the total divergence in vocabulary.

Mythology

Punctuational evolution has been argued to explain changes in folktales and mythology over time.

Microevolution

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Microevolution 

Microevolution is the change in allele frequencies that occurs over time within a population. This change is due to four different processes: mutation, selection (natural and artificial), gene flow and genetic drift. This change happens over a relatively short (in evolutionary terms) amount of time compared to the changes termed macroevolution.

Population genetics is the branch of biology that provides the mathematical structure for the study of the process of microevolution. Ecological genetics concerns itself with observing microevolution in the wild. Typically, observable instances of evolution are examples of microevolution; for example, bacterial strains that have antibiotic resistance.

Microevolution may lead to speciation, which provides the raw material for macroevolution.

Difference from macroevolution

Macroevolution is guided by sorting of interspecific variation ("species selection"), as opposed to sorting of intraspecific variation in microevolution. Species selection may occur as (a) effect-macroevolution, where organism-level traits (aggregate traits) affect speciation and extinction rates, and (b) strict-sense species selection, where species-level traits (e.g. geographical range) affect speciation and extinction rates. Macroevolution does not produce evolutionary novelties, but it determines their proliferation within the clades in which they evolved, and it adds species-level traits as non-organismic factors of sorting to this process.

Four processes

Mutation

Duplication of part of a chromosome

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. Errors are introduced particularly often in the process of DNA replication, in the polymerization of the second strand. These errors can also be induced by the organism itself, by cellular processes such as hypermutation. Mutations can affect the phenotype of an organism, especially if they occur within the protein coding sequence of a gene. Error rates are usually very low—1 error in every 10–100 million bases—due to the proofreading ability of DNA polymerases. (Without proofreading error rates are a thousandfold higher; because many viruses rely on DNA and RNA polymerases that lack proofreading ability, they experience higher mutation rates.) Processes that increase the rate of changes in DNA are called mutagenic: mutagenic chemicals promote errors in DNA replication, often by interfering with the structure of base-pairing, while UV radiation induces mutations by causing damage to the DNA structure. Chemical damage to DNA occurs naturally as well, and cells use DNA repair mechanisms to repair mismatches and breaks in DNA—nevertheless, the repair sometimes fails to return the DNA to its original sequence.

In organisms that use chromosomal crossover to exchange DNA and recombine genes, errors in alignment during meiosis can also cause mutations. Errors in crossover are especially likely when similar sequences cause partner chromosomes to adopt a mistaken alignment making some regions in genomes more prone to mutating in this way. These errors create large structural changes in DNA sequence—duplications, inversions or deletions of entire regions, or the accidental exchanging of whole parts between different chromosomes (called translocation).

Mutation can result in 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. Due to the damaging effects that mutations can have on cells, organisms have evolved mechanisms such as DNA repair to remove mutations. 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. Viruses that use RNA as their genetic material have rapid mutation rates, 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.

Mutations can involve large sections of DNA becoming duplicated, usually through genetic recombination. These duplications are a major source of raw material for evolving new genes, with tens to hundreds of genes duplicated in animal genomes every million years. Most genes belong to larger families of genes of shared ancestry. Novel genes are produced by several methods, commonly through the duplication and mutation of an ancestral gene, or by recombining parts of different genes to form new combinations with new functions.

Here, domains act as modules, each with a particular and independent function, that can be mixed together to produce genes encoding new proteins with novel properties. For example, the human eye uses four genes to make structures that sense light: three for color vision and one for night vision; all four arose from a single ancestral gene. Another advantage of duplicating a gene (or even an entire genome) is that this increases redundancy; this allows one gene in the pair to acquire a new function while the other copy performs the original function. Other types of mutation occasionally create new genes from previously noncoding DNA.

Selection

Selection is the process by which heritable traits that make it more likely for an organism to survive and successfully reproduce become more common in a population over successive generations.

It is sometimes valuable to distinguish between naturally occurring selection, natural selection, and selection that is a manifestation of choices made by humans, artificial selection. This distinction is rather diffuse. Natural selection is nevertheless the dominant part of selection.

Natural selection of a population for dark coloration.

The natural genetic variation within a population of organisms means that some individuals will survive more successfully than others in their current environment. Factors which affect reproductive success are also important, an issue which Charles Darwin developed in his ideas on sexual selection.

Natural selection acts on the phenotype, or the observable characteristics of an organism, but the genetic (heritable) basis of any phenotype which gives a reproductive advantage will become more common in a population (see allele frequency). Over time, this process can result in adaptations that specialize organisms for particular ecological niches and may eventually result in the speciation (the emergence of new species).

Natural selection is one of the cornerstones of modern biology. The term was introduced by Darwin in his groundbreaking 1859 book On the Origin of Species, in which natural selection was described by analogy to artificial selection, a process by which animals and plants with traits considered desirable by human breeders are systematically favored for reproduction. The concept of natural selection was originally developed in the absence of a valid theory of heredity; at the time of Darwin's writing, nothing was known of modern genetics. The union of traditional Darwinian evolution with subsequent discoveries in classical and molecular genetics is termed the modern evolutionary synthesis. Natural selection remains the primary explanation for adaptive evolution.

Genetic drift

Ten simulations of random genetic drift of a single given allele with an initial frequency distribution 0.5 measured over the course of 50 generations, repeated in three reproductively synchronous populations of different sizes. In general, alleles drift to loss or fixation (frequency of 0.0 or 1.0) significantly faster in smaller populations.

Genetic drift is the change in the relative frequency in which a gene variant (allele) occurs in a population due to random sampling. That is, the alleles in the offspring in the population are a random sample of those in the parents. And chance has a role in determining whether a given individual survives and reproduces. A population's allele frequency is the fraction or percentage of its gene copies compared to the total number of gene alleles that share a particular form.

Genetic drift is an evolutionary process which leads to changes in allele frequencies over time. It may cause gene variants to disappear completely, and thereby reduce genetic variability. In contrast to natural selection, which makes gene variants more common or less common depending on their reproductive success, the changes due to genetic drift are not driven by environmental or adaptive pressures, and may be beneficial, neutral, or detrimental to reproductive success.

The effect of genetic drift is larger in small populations, and smaller in large populations. Vigorous debates wage among scientists over the relative importance of genetic drift compared with natural selection. Ronald Fisher held the view that genetic drift plays at the most a minor role in evolution, and this remained the dominant view for several decades. In 1968 Motoo Kimura rekindled the debate with his neutral theory of molecular evolution which claims that most of the changes in the genetic material are caused by genetic drift. The predictions of neutral theory, based on genetic drift, do not fit recent data on whole genomes well: these data suggest that the frequencies of neutral alleles change primarily due to selection at linked sites, rather than due to genetic drift by means of sampling error.

Gene flow

Gene flow is the exchange of genes between populations, which are usually of the same species. 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.

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. 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. The importance of hybridization in developing new species of animals is unclear, although cases have been seen in many types of animals, with the gray tree frog being a particularly well-studied example.

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. 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. Polyploid hybrids also have more genetic diversity, which allows them to avoid inbreeding depression in small populations.

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. 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 may also have occurred. 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. 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 prokaryotes, during the acquisition of chloroplasts and mitochondria.

Gene flow is the transfer of alleles from one population to another.

Migration into or out of a population may be responsible for a marked change in allele frequencies. Immigration may also result in the addition of new genetic variants to the established gene pool of a particular species or population.

There are a number of factors that affect the rate of gene flow between different populations. One of the most significant factors is mobility, as greater mobility of an individual tends to give it greater migratory potential. Animals tend to be more mobile than plants, although pollen and seeds may be carried great distances by animals or wind.

Maintained gene flow between two populations can also lead to a combination of the two gene pools, reducing the genetic variation between the two groups. It is for this reason that gene flow strongly acts against speciation, by recombining the gene pools of the groups, and thus, repairing the developing differences in genetic variation that would have led to full speciation and creation of daughter species.

For example, if a species of grass grows on both sides of a highway, pollen is likely to be transported from one side to the other and vice versa. If this pollen is able to fertilise the plant where it ends up and produce viable offspring, then the alleles in the pollen have effectively been able to move from the population on one side of the highway to the other.

Origin and extended use of the term

Origin

The term microevolution was first used by botanist Robert Greenleaf Leavitt in the journal Botanical Gazette in 1909, addressing what he called the "mystery" of how formlessness gives rise to form.

..The production of form from formlessness in the egg-derived individual, the multiplication of parts and the orderly creation of diversity among them, in an actual evolution, of which anyone may ascertain the facts, but of which no one has dissipated the mystery in any significant measure. This microevolution forms an integral part of the grand evolution problem and lies at the base of it, so that we shall have to understand the minor process before we can thoroughly comprehend the more general one...

However, Leavitt was using the term to describe what we would now call developmental biology; it was not until Russian Entomologist Yuri Filipchenko used the terms "macroevolution" and "microevolution" in 1927 in his German language work, Variabilität und Variation, that it attained its modern usage. The term was later brought into the English-speaking world by Filipchenko's student Theodosius Dobzhansky in his book Genetics and the Origin of Species (1937).

Use in creationism

In young Earth creationism and baraminology a central tenet is that evolution can explain diversity in a limited number of created kinds which can interbreed (which they call "microevolution") while the formation of new "kinds" (which they call "macroevolution") is impossible. This acceptance of "microevolution" only within a "kind" is also typical of old Earth creationism.

Scientific organizations such as the American Association for the Advancement of Science describe microevolution as small scale change within species, and macroevolution as the formation of new species, but otherwise not being different from microevolution. In macroevolution, an accumulation of microevolutionary changes leads to speciation. The main difference between the two processes is that one occurs within a few generations, whilst the other takes place over thousands of years (i.e. a quantitative difference). Essentially they describe the same process; although evolution beyond the species level results in beginning and ending generations which could not interbreed, the intermediate generations could.

Opponents to creationism argue that changes in the number of chromosomes can be accounted for by intermediate stages in which a single chromosome divides in generational stages, or multiple chromosomes fuse, and cite the chromosome difference between humans and the other great apes as an example. Creationists insist that since the actual divergence between the other great apes and humans was not observed, the evidence is circumstantial.

Describing the fundamental similarity between macro and microevolution in his authoritative textbook "Evolutionary Biology," biologist Douglas Futuyma writes,

One of the most important tenets of the theory forged during the Evolutionary Synthesis of the 1930s and 1940s was that "macroevolutionary" differences among organisms - those that distinguish higher taxa - arise from the accumulation of the same kinds of genetic differences that are found within species. Opponents of this point of view believed that "macroevolution" is qualitatively different from "microevolution" within species, and is based on a totally different kind of genetic and developmental patterning... Genetic studies of species differences have decisively disproved [this] claim. Differences between species in morphology, behavior, and the processes that underlie reproductive isolation all have the same genetic properties as variation within species: they occupy consistent chromosomal positions, they may be polygenic or based on few genes, they may display additive, dominant, or epistatic effects, and they can in some instances be traced to specifiable differences in proteins or DNA nucleotide sequences. The degree of reproductive isolation between populations, whether prezygotic or postzygotic, varies from little or none to complete. Thus, reproductive isolation, like the divergence of any other character, evolves in most cases by the gradual substitution of alleles in populations.

— Douglas Futuyma, "Evolutionary Biology" (1998), pp.477-8

Contrary to the claims of some antievolution proponents, evolution of life forms beyond the species level (i.e. speciation) has indeed been observed and documented by scientists on numerous occasions. In creation science, creationists accepted speciation as occurring within a "created kind" or "baramin", but objected to what they called "third level-macroevolution" of a new genus or higher rank in taxonomy. There is ambiguity in the ideas as to where to draw a line on "species", "created kinds", and what events and lineages fall within the rubric of microevolution or macroevolution.

Macroevolution

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Macroevolution

Macroevolution in the modern sense is evolution that is guided by selection among interspecific variation, as opposed to selection among intraspecific variation in microevolution. This modern definition differs from the original concept, which referred macroevolution to the evolution of taxa above the species level (genera, families, orders etc.).

Origin and changing meaning of the term

Philiptschenko distinguished between microevolution and macroevolution because he rejected natural selection in the sense of Darwin as an explanation for larger evolutionary transitions that give rise to taxa above the species level in the Linnean taxonomy. Accordingly, he restricted Darwinian "microevolution" to evolutionary changes within the boundary of given species that may lead to different races or subspecies at the most. By contrast, he referred "macroevolution" to major evolutionary changes that correspond to taxonomic differences above the species level, which in his opinion would require evolutionary processes different from natural selection. An explanatory model for macroevolution in this sense was the "hopeful monster" concept of geneticist Richard Goldschmidt, who suggested saltational evolutionary changes either due to mutations that affect the rates of developmental processes or due to alterations in the chromosomal pattern. Particularly the latter idea was widely rejected by the modern synthesis and is disproved today, but the hopeful monster concept based on evo-devo explanations found a moderate revival in recent times. As an alternative to saltational evolution, Dobzhansky  suggested that the difference between macroevolution and microevolution reflects essentially a difference in time-scales, and that macroevolutionary changes were simply the sum of microevolutionary changes over geologic time. This view became broadly accepted, and accordingly, the term macroevolution has been used widely as a neutral label for the study of evolutionary changes that take place over a very large time-scale. However, the tenet that large-scale evolutionary patterns were ultimately reducible to microevolution has been challenged by the concept of species selection, which suggests that selection among species is a major evolutionary factor that is independent from and complementary to selection among organisms. Accordingly, the level of selection (or, more generally, of sorting) has become the conceptual basis of a third definition, which defines macroevolution as evolution through selection among interspecific variation.

Macroevolutionary processes

Speciation

According to the modern definition, the evolutionary transition from the ancestral to the daughter species is microevolutionary, because it results from selection (or, more generally, sorting) among varying organisms. However, speciation has also a macroevolutionary aspect, because it produces the interspecific variation species selection operates on. Another macroevolutionary aspect of speciation is the rate at which it successfully occurs, analogous to reproduction success in microevolution.

Species selection

"Species selection operates on variation provided by the largely random process of speciation and favors species that speciate at high rates or survive for long periods and therefore tend to leave many daughter species." Species selection comprises (a) effect-macroevolution, where organism-level traits (aggregate traits) affect speciation and extinction rates (Stanley’s original concept), and (b) strict-sense species selection, where species-level traits (e.g. geographical range) affect speciation and extinction rates. It has been argued that effect macroevolution is reducible to microevolution because both operate through selection on organismic traits, but Grantham demonstrated that effect macroevolution can oppose selection at the organismic level and is therefore not reducible microevolution. Cases in which selection on the same trait has opposing effects at the organismic and the species level have been made in the context of sexual selection, which increases individual fitness but may also increase the extinction risk of the species.

Punctuated equilibrium

Punctuated equilibrium postulates that evolutionary change is concentrated during a geologically short speciation phase, which is followed by evolutionary stasis that persists until the species goes extinct. The prevalence of evolutionary stasis through most of the existence time of species is a major argument for the relevance of species selection in shaping the evolutionary history of clades. However, punctuated equilibrium is neither a macroevolutionary model of speciation, nor is it a prerequisite for species selection.

Examples

Evolutionary faunas

A macroevolutionary benchmark study is Sepkoski's work on marine animal diversity through the Phanerozoic. His iconic diagram of the numbers of marine families from the Cambrian to the Recent illustrates the successive expansion and dwindling of three "evolutionary faunas" that were characterized by differences in origination rates and carrying capacities.

Mass extinctions

The macroevolutionary relevance of environmental changes is most obvious in the case of global mass extinction events. Such events are usually due to massive disturbances of the non-biotic environment that occur too fast for a microevolutionary response through adaptive change. Mass extinctions therefore act nearly excursively through selection among species, i.e., macroevolutionary. In their differential impact on species, mass extinctions introduce a strong non-adaptive aspect to evolution. A classic example in this context is the suggestion that the decline of brachiopods that is apparently mirrored by the rise of bivalves was actually caused by differential survival of these clades during the end-Permian mass extinction.

Stanley's rule

Macroevolution is driven by differences between species in origination and extinction rates. Remarkably, these two factors are generally positively correlated: taxa that have typically high diversification rates have also high extinction rates. This observation has been described first by Steven Stanley, who attributed it to a variety of ecological factors. Yet, a positive correlation of origination and extinction rates is also a prediction of the Red Queen hypothesis, which postulates that evolutionary progress (increase in fitness) of any given species causes a decrease in fitness of other species, ultimately driving to extinction those species that do not adapt rapidly enough. High rates of origination must therefore correlate with high rates of extinction. Stanley's rule, which applies to almost all taxa and geologic ages, is therefore a strong indication for a dominant role of biotic interactions in macroevolution.

Research topics

Subjects studied within macroevolution include:

• Adaptive radiations such as the Cambrian Explosion.
• Changes in biodiversity through time.
• Genome evolution, like horizontal gene transfer, genome fusions in endosymbioses, and adaptive changes in genome size.
• Mass extinctions.
• Estimating diversification rates, including rates of speciation and extinction.
• The debate between punctuated equilibrium and gradualism.
• The role of development in shaping evolution, particularly such topics as heterochrony and phenotypic plasticity.

Red Queen hypothesis

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Red_Queen_hypothesis 

The Red Queen hypothesis, also referred to as Red Queen's, the Red Queen effect, the Red Queen model, Red Queen's race, and Red Queen dynamics, is a hypothesis in evolutionary biology which proposes that species must constantly adapt, evolve, and proliferate in order to survive while pitted against ever-evolving opposing species. The hypothesis was intended to explain the constant (age independent) extinction probability as observed in the paleontological record caused by co-evolution between competing species; however, it has also been suggested that the Red Queen hypothesis explains the advantage of sexual reproduction (as opposed to asexual reproduction) at the level of individuals, and the positive correlation between speciation and extinction rates in most higher taxa.

Origin

“Now, here, you see, it takes all the running you can do, to keep in the same place.“ -Lewis Carroll

Leigh Van Valen proposed the hypothesis as an "explanatory tangent" to explain the "law of extinction" (known as "Van Valen's law"), which states that the probability of extinction does not depend on the lifetime of the species (or higher-rank taxon), instead being constant over millions of years for any given taxon. However, the probability of extinction is strongly related to adaptive zones, because different taxa have different probabilities of extinction. In other words, extinction occurs randomly with respect to age but nonrandomly with respect to ecology. Collectively, these two observations suggest that the effective environment of any homogeneous group of organisms deteriorates at a stochastically constant rate. Van Valen proposed that this is the result of an evolutionary zero-sum game driven by interspecific competition: the evolutionary progress (= increase in fitness) of one species deteriorates the fitness of coexisting species, but because coexisting species evolve as well, no one species gains a long-term increase in fitness, and the overall fitness of the system remains constant. The phenomenon's name is derived from a statement that the Red Queen made to Alice in Lewis Carroll's Through the Looking-Glass in her explanation of the nature of Looking-Glass Land:

Now, here, you see, it takes all the running you can do, to keep in the same place.

Van Valen coined the hypothesis "Red Queen" because under this interpretation, species have to "run" or evolve in order to stay in the same place, or else go extinct.

Examples

Positive correlation between speciation and extinction rates (Stanley's rule)

The "law of extinction": The linear relationship between survival times and the logarithm of the number of genera suggests that the probability of extinction is constant over time. Redrawn from Leigh Van Valen (1973).

Palaeontological data suggest that high speciation rates correlate with high extinction rates in almost all major taxa. This correlation has been attributed to a number of ecological factors, but it may result also from a Red Queen situation, in which each speciation event in a clade deteriorates the fitness of coexisting species in the same clade (provided that there is phylogenetic niche conservatism).

Evolution of sex

Discussions of the evolution of sex was not part of Van Valen's Red Queen hypothesis, which addressed evolution at scales above the species level. The microevolutionary version of the Red Queen hypothesis was proposed by Bell (1982), also citing Lewis Carroll, but not citing Van Valen.

The Red Queen hypothesis is used independently by Hartung and Bell to explain the evolution of sex, by John Jaenike to explain the maintenance of sex and W. D. Hamilton to explain the role of sex in response to parasites. In all cases, sexual reproduction confers species variability and a faster generational response to selection by making offspring genetically unique. Sexual species are able to improve their genotype in changing conditions. Consequently, co-evolutionary interactions, between host and parasite, for example, may select for sexual reproduction in hosts in order to reduce the risk of infection. Oscillations in genotype frequencies are observed between parasites and hosts in an antagonistic coevolutionary way without necessitating changes to the phenotype. In multi-host and multi-parasite coevolution, the Red Queen dynamics could affect what host and parasite types will become dominant or rare. Science writer Matt Ridley popularized the term in connection with sexual selection in his 1993 book The Red Queen, in which he discussed the debate in theoretical biology over the adaptive benefit of sexual reproduction to those species in which it appears. The connection of the Red Queen to this debate arises from the fact that the traditionally accepted Vicar of Bray hypothesis only showed adaptive benefit at the level of the species or group, not at the level of the gene (although the protean "Vicar of Bray" adaptation is very useful to some species that belong to the lower levels of the food chain). By contrast, a Red-Queen-type thesis suggesting that organisms are running cyclic arms races with their parasites can explain the utility of sexual reproduction at the level of the gene by positing that the role of sex is to preserve genes that are currently disadvantageous, but that will become advantageous against the background of a likely future population of parasites.

Further evidence of the Red Queen hypothesis was observed in allelic effects under sexual selection. The Red Queen hypothesis leads to the understanding that allelic recombination is advantageous for populations that engage in aggressive biotic interactions, such as predator-prey or parasite-host interactions. In cases of parasite-host relations, sexual reproduction can quicken the production of new multi-locus genotypes allowing the host to escape parasites that have adapted to the prior generations of typical hosts. Mutational effects can be represented by models to describe how recombination through sexual reproduction can be advantageous. According to the mutational deterministic hypothesis, if the deleterious mutation rate is high, and if those mutations interact to cause a general decline in organismal fitness, then sexual reproduction provides an advantage over asexually reproducing organisms by allowing populations to eliminate the deleterious mutations not only more rapidly, but also most effectively. Recombination is one of the fundamental means that explain why many organisms have evolved to reproduce sexually.

Sexual organisms must spend resources to find mates. In the case of sexual dimorphism, usually one of the sexes contributes more to the survival of their offspring (usually the mother). In such cases, the only adaptive benefit of having a second sex is the possibility of sexual selection, by which organisms can improve their genotype.

Evidence for this explanation for the evolution of sex is provided by the comparison of the rate of molecular evolution of genes for kinases and immunoglobulins in the immune system with genes coding other proteins. The genes coding for immune system proteins evolve considerably faster.

Further evidence for the Red Queen hypothesis was provided by observing long-term dynamics and parasite coevolution in a mixed sexual and asexual population of snails (Potamopyrgus antipodarum). The number of sexuals, the number of asexuals, and the rates of parasitic infection for both were monitored. It was found that clones that were plentiful at the beginning of the study became more susceptible to parasites over time. As parasite infections increased, the once-plentiful clones dwindled dramatically in number. Some clonal types disappeared entirely. Meanwhile, sexual snail populations remained much more stable over time.

In 2011, researchers used the microscopic roundworm Caenorhabditis elegans as a host and the pathogenic bacterium Serratia marcescens to generate a host–parasite coevolutionary system in a controlled environment, allowing them to conduct more than 70 evolution experiments testing the Red Queen hypothesis. They genetically manipulated the mating system of C. elegans, causing populations to mate either sexually, by self-fertilization, or a mixture of both within the same population. Then they exposed those populations to the S. marcescens parasite. It was found that the self-fertilizing populations of C. elegans were rapidly driven extinct by the coevolving parasites, while sex allowed populations to keep pace with their parasites, a result consistent with the Red Queen hypothesis.

Currently, there is no consensus among biologists on the main selective forces maintaining sex. The competing models to explain the adaptive function of sex have been reviewed by Birdsell and Wills.

Evolution of aging

Predator-prey relationship between rabbits and foxes following the principle of the Red Queen hypothesis. The rabbit evolves increasing its speed to escape the attack of the fox, and the fox evolves increasing its speed to reach the rabbit. This evolution is constant, in case one of the two stops evolving, its extinction will occur.

The Red Queen hypothesis has been also invoked by some authors to explain evolution of aging. The main idea is that aging is favored by natural selection since it allows faster adaptation to changing conditions, especially in order to keep pace with the evolution of pathogens, predators and prey.

Interspecies arms race

• A number of predator/prey couple where the weapon involved is the running speed.

"The rabbit runs faster than the fox, because the rabbit is running for his life while the fox is only running for his dinner." Aesop The predator-prey relationship can also be established in the microbial world, producing the same evolutionary phenomenon that occurs in the case of foxes and rabbits. A recently observed example has as protagonists M.xanthus (predator) and E.coli (prey) in which a parallel evolution of both species can be observed through genomic and phenotypic modifications, producing in future generations a better adaptation of one of the species that is counteracted by the evolution of the other, thus generating an arms race that can only be stopped by the extinction of one of the species.

• The interactions between parasitoid wasps and insect larvae, necessary for the parasitic wasp's life cycle, are also a good illustration of an arms race. Indeed, some evolutionary strategy was found by both partners to respond to the pressure generated by the mutual association of lineages. For example, the parasitoid wasp group, Campoletis sonorensis, is able to fight against the immune system of its hosts, Heliothis virescens (Lepidopteran) with the association of a polydnavirus (PDV) (Campoletis sonorensis PDV). During the oviposition process, the parasitoid transmits the virus (CsPDV) to the insect larva. The CsPDV will alter the physiology, growth and development of the infected insect larvae to the benefit of the parasitoid.

Court jester hypothesis

A competing evolutionary idea is the court jester hypothesis, which indicates that an arms race is not the driving force of evolution on a large scale, but rather it is abiotic factors.

Black Queen hypothesis

The Black Queen hypothesis is a theory of reductive evolution that suggests natural selection can drive organisms to reduce their genome size. In other words, a gene that confers a vital biological function can become dispensable for an individual organism if its community members express that gene in a "leaky" fashion. Like the Red Queen hypothesis, the Black Queen hypothesis is a theory of co-evolution.

Trivia

Van Valen originally submitted his article to the Journal of Theoretical Biology, where it was accepted for publication. However, because "the manner of processing depended on payment of page charges", Van Valen withdrew his manuscript and founded a new Journal called "Evolutionary Theory", in which he published his manuscript as the first paper. The journal "Evolutionary Theory" was produced in Van Valens office on a photocopy machine under the motto "substance over form."

Another noteworthy detail is Van Valen's acknowledgement to the National Science Foundation: "I thank the National Science Foundation for regularly rejecting my (honest) grant applications for work on real organisms, thus forcing me into theoretical work".