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Sunday, March 29, 2015

Gene-centered view of evolution


From Wikipedia, the free encyclopedia

The gene-centered view of evolution, gene selection theory, or selfish gene theory holds that adaptive evolution occurs through the differential survival of competing genes, increasing the frequency of those alleles whose phenotypic effects successfully promote their own propagation, with gene defined as "not just one single physical bit of DNA [but] all replicas of a particular bit of DNA distributed throughout the world".[1] The proponents of this viewpoint argue that, since heritable information is passed from generation to generation almost exclusively by genetic material, natural selection and evolution are best considered from the perspective of genes.

This is in contrast to the organism-centered viewpoint adopted historically by biologists. Proponents of the gene-centered viewpoint argue that it permits understanding of diverse phenomena such as altruism and intragenomic conflict that are otherwise difficult to explain from an organism-focused perspective.

The gene-centered view of evolution is a synthesis of the theory of evolution by natural selection, the particulate inheritance theory, and the non-transmission of acquired characters. It states that those alleles whose phenotypic effects successfully promote their own propagation will be favorably selected relative to their competitor alleles within the population. This process produces adaptations for the benefit of alleles that promote the reproductive success of the organism, or of other organisms containing the same allele (kin altruism and green-beard effects), or even its own propagation relative to the other genes within the same organism (intragenomic conflict).

Overview

The gene-centered view of evolution is a different way of looking at the basis of evolutionary development. It turns the whole solution of evolution inside-out for the purpose of examination. What this new perspective reveals is a more easily understood model for the evolution of social characteristics such as selfishness and altruism that much of the study of evolution, caught up in the survival of the individual organisms, or, alternatively, groups of organisms, overlooks.

Acquired characteristics are not genetically inherited

Discoveries in science such as the formulation of the central dogma of molecular biology made it clear that the inheritance of acquired characteristics (such as wealth) was not a genetic process and identified genes as lasting entities that survive through many generations. Maynard Smith summarized the issue:


The rejection of the inheritance of acquired characters, combined with the classical mathematical evolutionary biology developed by Ronald Fisher,[3] J. B. S. Haldane, and Sewall Wright, paved the way to the formulation of the selfish-gene theory.[clarification needed] For cases where environment can influence heredity, see epigenetics.[clarification needed]

The gene as the unit of selection

The view of the gene as the unit of selection was developed mainly in the works of W. D. Hamilton,[4][5][6] Colin Pittendrigh[7] and George C. Williams.[8] It was later popularized by Richard Dawkins in his books The Selfish Gene (1976)[9] and The Extended Phenotype (1982).[10]

According to Williams' 1966 book Adaptation and Natural Selection,


Williams argued that "[t]he natural selection of phenotypes cannot in itself produce cumulative change, because phenotypes are extremely temporary manifestations." Each phenotype is the unique product of the interaction between genome and environment. It does not matter how fit and fertile a phenotype is, it will eventually be destroyed and will never be duplicated.

Since 1954, it has been known that DNA is the main physical substrate to genetic information, and it is capable of high-fidelity replication through many generations. So, a particular sequence of DNA can have a high permanence and a low rate of endogenous change.

In normal sexual reproduction, an entire genome is the unique combination of father's and mother's chromosomes produced at the moment of fertilization. It is generally destroyed with its organism, because "meiosis and recombination destroy genotypes as surely as death."[8] Only half of it is transmitted to each descendant due to independent segregation.

The gene as an informational entity persists for an evolutionarily significant span of time through a lineage of many physical copies.

In his book River out of Eden, Dawkins coins the phrase God's utility function to explain his view on genes as units of selection. He uses this phrase as a synonym of the "meaning of life" or the "purpose of life". By rephrasing the word purpose in terms of what economists call a utility function, meaning "that which is maximized", Dawkins attempts to reverse-engineer the purpose in the mind of the Divine Engineer of Nature, or the Utility Function of God. Finally, Dawkins argues that it is a mistake to assume that an ecosystem or a species as a whole exists for a purpose. He writes that it is incorrect to suppose that individual organisms lead a meaningful life either; in nature, only genes have a utility function – to perpetuate their own existence with indifference to great sufferings inflicted upon the organisms they build, exploit and discard.

Organisms as vehicles

Genes are not naked in the world. They are usually packed together inside a genome, which is itself contained inside an organism. Genes group together into genomes because "genetic replication makes use of energy and substrates that are supplied by the metabolic economy in much greater quantities than would be possible without a genetic division of labour."[11] They build vehicles to promote their mutual interests of jumping into the next generation of vehicles. As Dawkins puts it, organisms are the "survival machines" of genes.[9]

The phenotypic effect of a particular gene is contingent on its environment, including the fellow genes constituting with it the total genome. A gene never has a fixed effect, so how is it possible to speak of a gene for long legs? It is because of the phenotypic differences between alleles. One may say that one allele, all other things being equal or varying within certain limits, causes greater legs than its alternative. This difference enables the scrutiny of natural selection.

"A gene can have multiple phenotypic effects, each of which may be of positive, negative or neutral value. It is the net selective value of a gene's phenotypic effect that determines the fate of the gene."[12] For instance, a gene can cause its bearer to have greater reproductive success at a young age, but also cause a greater likelihood of death at a later age. If the benefit outweighs the harm, averaged out over the individuals and environments in which the gene happens to occur, then phenotypes containing the gene will generally be positively selected and thus the abundance of that gene in the population will increase.

Even so, it becomes necessary to model the genes in combination with their vehicle as well as in combination with the vehicle's environment.

Selfish-gene theory

The selfish-gene theory of natural selection can be restated as follows:[12]


The result is that "the prevalent genes in a sexual population must be those that, as a mean condition, through a large number of genotypes in a large number of situations, have had the most favourable phenotypic effects for their own replication."[13] In other words, we expect selfish genes ("selfish" meaning that it promotes its own survival without necessarily promoting the survival of the organism, group or even species). This theory implies that adaptations are the phenotypic effects of genes to maximize their representation in future generations. An adaptation is maintained by selection if it promotes genetic survival directly, or else some subordinate goal that ultimately contributes to successful reproduction.

Individual altruism and genetic egoism

The gene is a unit of hereditary information that exists in many physical copies in the world, and which particular physical copy will be replicated and originate new copies does not matter from the gene's point of view.[14] A selfish gene could be favored by selection by producing altruism among organisms containing it. The idea is summarized as follows:
If a gene copy confers a benefit B on another vehicle at cost C to its own vehicle, its costly action is strategically beneficial if pB > C, where p is the probability that a copy of the gene is present in the vehicle that benefits. Actions with substantial costs therefore require significant values of p. Two kinds of factors ensure high values of p: relatedness (kinship) and recognition (green beards).
—Haig,[11] 1997, p. 288
A gene in a somatic cell of an individual may forego replication to promote the transmission of its copies in the germ line cells. It ensures the high value of p = 1 due to their constant contact and their common origin from the zygote.

The kin selection theory predicts that a gene may promote the recognition of kinship by historical continuity: a mammalian mother learns to identify her own offspring in the act of giving birth; a male preferentially directs resources to the offspring of mothers with whom he has copulated; the other chicks in a nest are siblings; and so on. The expected altruism between kin is calibrated by the value of p, also known as the coefficient of relatedness. For instance, an individual has a p = 1/2 in relation to his brother, and p = 1/8 to his cousin, so we would expect, ceteris paribus, greater altruism among brothers than among cousins. In this vein, geneticist J. B. S. Haldane famously joked, "Would I lay down my life to save my brother? No, but I would to save two brothers or eight cousins."[15] However, examining the human propensity for altruism, kin selection theory seems incapable of explaining cross-familiar, cross-racial and even cross-species acts of kindness.

Green-beard effect

Green-beard effects gained their name from a thought-experiment of Richard Dawkins,[9] who considered the possibility of a gene that caused its possessors to develop a green beard and to be nice to other green-bearded individuals. Since then, "green-beard effect" has come to refer to forms of genetic self-recognition in which a gene in one individual might direct benefits to other individuals that possess the gene. Such genes are essentially especially selfish, benefiting themselves regardless of the fates of their vehicles.

All kinds of altruism

Kindness

On the other hand, a single trait, group reciprocal kindness, is capable of explaining the vast majority of altruism that is generally accepted as "good" by modern societies. Imagine a green-bearding behavioral trait whose recognition does not depend on the recognition of some external feature such as beard color, but relies on recognition of the behavior itself. Imagine now that the behavior is altruistic. The success of such a trait in sufficiently intelligent and undeceived organisms is implicit. Moreover, the existence of such a trait predicts a tendency for kindness to unrelated organisms that are apparently kind, even if the organisms are of a completely different species. Moreover, the gene need not be exactly the same, so long as the effect is similar. Multiple versions of the gene—or even meme—would have virtually the same effect in a sort of symbiotic green-bearding cycle of altruism.

Deceit

Whenever recognition plays a role in evolution, so does deception. Just like the harmless lizard that has evolved a pattern that mimics its poisonous cousin and therefore tricks predators, the selfish creature may pretend to be kind by "growing a green beard" (whatever that green beard may be). Thus green-bearding and the selfish-gene theory also give rise to an explanation for the evolution of lies and deceit, characteristics that do not benefit the population as a whole.

Intragenomic conflict

As genes are capable of producing individual altruism, they are capable of producing conflict among genes inside the genome of one individual. This phenomenon is called intragenomic conflict and arises when one gene promotes its own replication in detriment to other genes in the genome. The classic example is segregation distorter genes that cheat during meiosis or gametogenesis and end up in more than half of the functional gametes. These genes persist even resulting in reduced fertility. Egbert Leigh compared the genome to "a parliament of genes: each acts in its own self-interest, but if its acts hurt the others, they will combine together to suppress it" to explain the relative low occurrence of intragenomic conflict.[16]

Price equation

The Price equation (also known as Price's equation) is a covariance equation that is a mathematical description of evolution and natural selection. The Price equation was derived by George R. Price, working in London to rederive W. D. Hamilton's work on kin selection.

Main figures in selection debate

Besides Richard Dawkins and George C. Williams, other biologists and philosophers have expanded and refined the selfish-gene theory, such as John Maynard Smith, George R. Price, Robert Trivers, David Haig, Helena Cronin, David Hull, Philip Kitcher, and Daniel C. Dennett.

Individuals opposing this gene-centric view include Ernst Mayr, Stephen Jay Gould, David Sloan Wilson, and philosopher Elliott Sober.

Proponents of multilevel selection (MLS) include E. O. Wilson, David Sloan Wilson, Elliott Sober, Richard E. Michod,[17] and Samir Okasha.[17]

Criticisms

Prominent opponents of this gene-centric view of evolution include evolutionary biologist Ernst Mayr, paleontologist Stephen Jay Gould, biologist and anthropologist David Sloan Wilson, and philosopher Elliott Sober.
Writing in the New York Review of Books, Gould has characterized the gene-centered perspective as confusing book-keeping with causality. Gould views selection as working on many levels, and has called attention to a hierarchical perspective of selection. Gould also called the claims of Selfish Gene "strict adaptationism", "ultra-Darwinism", and "Darwinian fundamentalism", describing them as excessively "reductionist". He saw the theory as leading to a simplistic "algorithmic" theory of evolution, or even to the re-introduction of a teleological principle.[18] Mayr went so far as to say "Dawkins' basic theory of the gene being the object of evolution is totally non-Darwinian."[19]

Gould also addressed the issue of selfish genes in his essay "Caring groups and selfish genes".[20] Gould acknowledged that Dawkins was not imputing conscious action to genes, but simply using a shorthand metaphor commonly found in evolutionary writings. To Gould, the fatal flaw was that "no matter how much power Dawkins wishes to assign to genes, there is one thing that he cannot give them – direct visibility to natural selection."[20] Rather, the unit of selection is the phenotype, not the genotype, because it is phenotypes that interact with the environment at the natural-selection interface. So, in Kim Sterelny's summation of Gould's view, "gene differences do not cause evolutionary changes in populations, they register those changes."[21] Richard Dawkins replied to this criticism in a later book, The Extended Phenotype, that Gould confused particulate genetics with particulate embryology, stating that genes do "blend", as far as their effects on developing phenotypes are concerned, but that they do not blend as they replicate and recombine down the generations.[10]

Since Gould's death in 2002, Niles Eldredge has continued with counter-arguments to gene-centered natural selection.[22] Eldredge notes that in Dawkins' book A Devil's Chaplain, which was published just before Eldredge's book, "Richard Dawkins comments on what he sees as the main difference between his position and that of the late Stephen Jay Gould. He concludes that it is his own vision that genes play a causal role in evolution," while Gould (and Eldredge) "sees genes as passive recorders of what worked better than what".[23]

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Modern evolutionary synthesis


From Wikipedia, the free encyclopedia

The modern evolutionary synthesis is a 20th-century synthesis of ideas from several fields of biology which provides a widely accepted account of evolution. It is also referred to as the new synthesis, the modern synthesis, the evolutionary synthesis, millennium synthesis or the neo-Darwinian synthesis.

The synthesis, produced between 1936 and 1947, reflects the consensus about how evolution proceeds.[1] The previous development of nineteenth century evolutionary ideas by Charles Darwin, Gregor Mendel and others and the population genetics, between 1918 and 1932, was a stimulus, as it showed that Mendelian genetics was consistent with natural selection and gradual evolution. The synthesis is still, to a large extent, the current paradigm in evolutionary biology.[2]

The modern synthesis solved difficulties and confusions caused by the specialisation and poor communication between biologists in the early years of the 20th century. At its heart was the question of whether Mendelian genetics could be reconciled with gradual evolution by means of natural selection. A second issue was whether the broad-scale changes (macroevolution) seen by palaeontologists could be explained by changes seen in local populations (microevolution).

The synthesis included evidence from biologists, trained in genetics, who studied populations in the field and in the laboratory. These studies were crucial to evolutionary theory. The synthesis drew together ideas from several branches of biology which had become separated, particularly genetics, cytology, systematics, botany, morphology, ecology and paleontology.

Julian Huxley invented the term, when he produced his book, Evolution: The Modern Synthesis (1942). Other major figures in the modern synthesis include R. A. Fisher, Theodosius Dobzhansky, J. B. S. Haldane, Sewall Wright, E. B. Ford, Ernst Mayr, Bernhard Rensch, Sergei Chetverikov, George Gaylord Simpson, and G. Ledyard Stebbins.

Summary of the modern synthesis

The modern synthesis bridged the gap between the work of experimental geneticists and naturalists, and paleontologists. It states that:[3][4][5]
  1. All evolutionary phenomena can be explained in a way consistent with known genetic mechanisms and the observational evidence of naturalists.
  2. Evolution is gradual: small genetic changes regulated by natural selection accumulate over long periods. Discontinuities amongst species (or other taxa) are explained as originating gradually through geographical separation and extinction. This theory contrasts with the saltation theory of Bateson (1894).[6]
  3. Natural selection is by far the main mechanism of change; even slight advantages are important when continued. The object of selection is the phenotype in its surrounding environment.
  4. The role of genetic drift is equivocal. Though strongly supported initially by Dobzhansky, it was downgraded later as results from ecological genetics were obtained.
  5. Thinking in terms of populations, rather than individuals, is primary: the genetic diversity existing in natural populations is a key factor in evolution. The strength of natural selection in the wild is greater than previously expected; the effect of ecological factors such as niche occupation and the significance of barriers to gene flow are all important.
  6. In palaeontology, the ability to explain historical observations by extrapolation from microevolution to macroevolution is proposed. Historical contingency means explanations at different levels may exist. Gradualism does not mean constant rate of change.
The idea that speciation occurs after populations are reproductively isolated has been much debated. In plants, polyploidy must be included in any view of speciation. Formulations such as 'evolution consists primarily of changes in the frequencies of alleles between one generation and another' were proposed rather later. The traditional view is that developmental biology ('evo-devo') played little part in the synthesis,[7] but an account of Gavin de Beer's work by Stephen J. Gould suggests he may be an exception.[8]

Developments leading up to the synthesis

1859–1899

Charles Darwin's On the Origin of Species was successful in convincing most biologists that evolution had occurred, but was less successful in convincing them that natural selection was its primary mechanism. In the 19th and early 20th centuries, variations of Lamarckism, orthogenesis ('progressive' evolution), and saltationism (evolution by jumps) were discussed as alternatives.[9] Also, Darwin did not offer a precise explanation of how new species arise. As part of the disagreement about whether natural selection alone was sufficient to explain speciation, George Romanes coined the term neo-Darwinism to refer to the version of evolution advocated by Alfred Russel Wallace and August Weismann with its heavy dependence on natural selection.[10] Weismann and Wallace rejected the Lamarckian idea of inheritance of acquired characteristics, something that Darwin had not ruled out.[11]

Weismann's idea was that the relationship between the hereditary material, which he called the germ plasm (German, Keimplasma), and the rest of the body (the soma) was a one-way relationship: the germ-plasm formed the body, but the body did not influence the germ-plasm, except indirectly in its participation in a population subject to natural selection. Weismann was translated into English, and though he was influential, it took many years for the full significance of his work to be appreciated.[12] Later, after the completion of the modern synthesis, the term neo-Darwinism came to be associated with its core concept: evolution, driven by natural selection acting on variation produced by genetic mutation, and genetic recombination (chromosomal crossovers).[10]

1900–1915

Gregor Mendel's work was re-discovered by Hugo de Vries and Carl Correns in 1900. News of this reached William Bateson in England, who reported on the paper during a presentation to the Royal Horticultural Society in May 1900.[13] It showed that the contributions of each parent retained their integrity rather than blending with the contribution of the other parent. This reinforced a division of thought, which was already present in the 1890s.[14] The two schools were:
  • Saltationism (large mutations or jumps), favored by early Mendelians who viewed hard inheritance as incompatible with natural selection[15]
  • Biometric school: led by Karl Pearson and Walter Weldon, argued vigorously against it, saying that empirical evidence indicated that variation was continuous in most organisms, not discrete as Mendelism predicted.
The relevance of Mendelism to evolution was unclear and hotly debated, especially by Bateson, who opposed the biometric ideas of his former teacher Weldon. Many scientists believed the two theories substantially contradicted each other.[16] This debate between the biometricians and the Mendelians continued for some 20 years and was only solved by the development of population genetics.

T. H. Morgan began his career in genetics as a saltationist, and started out trying to demonstrate that mutations could produce new species in fruit flies. However, the experimental work at his lab with Drosophila melanogaster, which helped establish the link between Mendelian genetics and the chromosomal theory of inheritance, demonstrated that rather than creating new species in a single step, mutations increased the genetic variation in the population.[17]

The foundation of population genetics

The first step towards the synthesis was the development of population genetics. R.A. Fisher, J.B.S. Haldane, and Sewall Wright provided critical contributions. In 1918, Fisher produced the paper "The Correlation Between Relatives on the Supposition of Mendelian Inheritance",[18] which showed how the continuous variation measured by the biometricians could be the result of the action of many discrete genetic loci. In this and subsequent papers culminating in his 1930 book The Genetical Theory of Natural Selection, Fisher was able to show how Mendelian genetics was, contrary to the thinking of many early geneticists, completely consistent with the idea of evolution driven by natural selection.[19] During the 1920s, a series of papers by J.B.S. Haldane applied mathematical analysis to real world examples of natural selection such as the evolution of industrial melanism in peppered moths.[19] Haldane established that natural selection could work in the real world at a faster rate than even Fisher had assumed.[20]

Sewall Wright focused on combinations of genes that interacted as complexes, and the effects of inbreeding on small relatively isolated populations, which could exhibit genetic drift. In a 1932 paper he introduced the concept of an adaptive landscape in which phenomena such as cross breeding and genetic drift in small populations could push them away from adaptive peaks, which would in turn allow natural selection to push them towards new adaptive peaks.[19] Wright's model would appeal to field naturalists such as Theodosius Dobzhansky and Ernst Mayr who were becoming aware of the importance of geographical isolation in real world populations.[20] The work of Fisher, Haldane and Wright founded the discipline of population genetics. This is the precursor of the modern synthesis, which is an even broader coalition of ideas.[19][20][21] One limitation of the modern synthesis version of population genetics is that it treats one gene locus at a time, neglecting genetic linkage and resulting linkage disequilibrium between loci.

The modern synthesis

Theodosius Dobzhansky, a Ukrainian emigrant, who had been a postdoctoral worker in Morgan's fruit fly lab, was one of the first to apply genetics to natural populations. He worked mostly with Drosophila pseudoobscura. He says pointedly: "Russia has a variety of climates from the Arctic to sub-tropical... Exclusively laboratory workers who neither possess nor wish to have any knowledge of living beings in nature were and are in a minority."[22] Not surprisingly, there were other Russian geneticists with similar ideas, though for some time their work was known to only a few in the West. His 1937 work Genetics and the Origin of Species was a key step in bridging the gap between population geneticists and field naturalists. It presented the conclusions reached by Fisher, Haldane, and especially Wright in their highly mathematical papers in a form that was easily accessible to others. It also emphasized that real world populations had far more genetic variability than the early population geneticists had assumed in their models, and that genetically distinct sub-populations were important. Dobzhansky argued that natural selection worked to maintain genetic diversity as well as driving change. Dobzhansky had been influenced by his exposure in the 1920s to the work of a Russian geneticist named Sergei Chetverikov who had looked at the role of recessive genes in maintaining a reservoir of genetic variability in a population before his work was shut down by the rise of Lysenkoism in the Soviet Union.[19][20]

Edmund Brisco Ford's work complemented that of Dobzhansky. It was as a result of Ford's work, as well as his own, that Dobzhansky changed the emphasis in the third edition of his famous text from drift to selection.[23] Ford was an experimental naturalist who wanted to test natural selection in nature. He virtually invented the field of research known as ecological genetics. His work on natural selection in wild populations of butterflies and moths was the first to show that predictions made by R.A. Fisher were correct. He was the first to describe and define genetic polymorphism, and to predict that human blood group polymorphisms might be maintained in the population by providing some protection against disease.[24]

Ernst Mayr's key contribution to the synthesis was Systematics and the Origin of Species, published in 1942. Mayr emphasized the importance of allopatric speciation, where geographically isolated sub-populations diverge so far that reproductive isolation occurs. He was skeptical of the reality of sympatric speciation believing that geographical isolation was a prerequisite for building up intrinsic (reproductive) isolating mechanisms. Mayr also introduced the biological species concept that defined a species as a group of interbreeding or potentially interbreeding populations that were reproductively isolated from all other populations.[19][20][25] Before he left Germany for the United States in 1930, Mayr had been influenced by the work of German biologist Bernhard Rensch. In the 1920s Rensch, who like Mayr did field work in Indonesia, analyzed the geographic distribution of polytypic species and complexes of closely related species paying particular attention to how variations between different populations correlated with local environmental factors such as differences in climate. In 1947, Rensch published Neuere Probleme der Abstammungslehre: die Transspezifische Evolution (English translation 1959: Evolution above the Species level). This looked at how the same evolutionary mechanisms involved in speciation might be extended to explain the origins of the differences between the higher level taxa. His writings contributed to the rapid acceptance of the synthesis in Germany.[26][27]

George Gaylord Simpson was responsible for showing that the modern synthesis was compatible with paleontology in his book Tempo and Mode in Evolution published in 1944. Simpson's work was crucial because so many paleontologists had disagreed, in some cases vigorously, with the idea that natural selection was the main mechanism of evolution. It showed that the trends of linear progression (in for example the evolution of the horse) that earlier paleontologists had used as support for neo-Lamarckism and orthogenesis did not hold up under careful examination. Instead the fossil record was consistent with the irregular, branching, and non-directional pattern predicted by the modern synthesis.[19][20]

The botanist G. Ledyard Stebbins was another major contributor to the synthesis. His major work, Variation and Evolution in Plants, was published in 1950. It extended the synthesis to encompass botany including the important effects of hybridization and polyploidy in some kinds of plants.[19]

Further advances

The modern evolutionary synthesis continued to be developed and refined after the initial establishment in the 1930s and 1940s. The work of W. D. Hamilton, George C. Williams, John Maynard Smith and others led to the development of a gene-centered view of evolution in the 1960s. The synthesis as it exists now has extended the scope of the Darwinian idea of natural selection to include subsequent scientific discoveries and concepts unknown to Darwin, such as DNA and genetics, which allow rigorous, in many cases mathematical, analyses of phenomena such as kin selection, altruism, and speciation.

In The Selfish Gene, author Richard Dawkins asserts the gene is the only true unit of selection.[28] (Dawkins also attempts to apply evolutionary theory to non-biological entities, such as cultural memes, imagined to be subject to selective forces analogous to those affecting biological entities.)

Others, such as Stephen Jay Gould, reject the notion that genetic entities are subject to anything other than genetic or chemical forces, (as well as the idea evolution acts on "populations" per se), reasserting the centrality of the individual organism as the true unit of selection, whose specific phenotype is directly subject to evolutionary pressures.

In 1972, the notion of gradualism in evolution was challenged by a theory of "punctuated equilibrium" put forward by Gould and Niles Eldredge, proposing evolutionary changes could occur in relatively rapid spurts, when selective pressures were heightened, punctuating long periods of morphological stability, as well-adapted organisms coped successfully in their respective environments.

Discovery in the 1980s of Hox genes and regulators conserved across multiple phyletic divisions began the process of addressing basic theoretical problems relating to gradualism, incremental change, and sources of novelty in evolution. Suddenly, evolutionary theorists could answer the charge that spontaneous random mutations should result overwhelmingly in deleterious changes to a fragile, monolithic genome: Mutations in homeobox regulation could safely—yet dramatically—alter morphology at a high level, without damaging coding for specific organs or tissues.

This, in turn, provided the means to model hypothetical genomic changes expressed in the phenotypes of long-extinct species, like the recently discovered "fish with hands"' Tiktaalik.

As these recent discoveries suggest, the synthesis continues to undergo regular review, drawing on insights offered by both new biotechnologies and new paleontological discoveries.[29] (See also Current research in evolutionary biology).

After the synthesis


The structure of evolutionary biology.
The history and causes of evolution (center) are subject to various subdisciplines of evolutionary biology. The areas of segments give an impression of the contributions of subdisciplines to the literature of evolutionary biology.

There are a number of discoveries in earth sciences and biology which have arisen since the synthesis. Listed here are some of those topics which are relevant to the evolutionary synthesis, and which seem soundly based.

Understanding of Earth history

The Earth is the stage on which the evolutionary play is performed. Darwin studied evolution in the context of Charles Lyell's geology, but our present understanding of Earth history includes some critical advances made during the last half-century.
  • The identification of the first generally accepted fossils of microbial life was made by geologists. These rocks have been dated as about 3.465 billion years ago.[35] Walcott was the first geologist to identify pre-Cambrian fossil bacteria from microscopic examination of thin rock slices. He also thought stromatolites were organic in origin. His ideas were not accepted at the time, but may now be appreciated as great discoveries.[36]
  • Information about paleoclimates is increasingly available, and being used in paleontology. One example: the discovery of massive ice ages in the Proterozoic, following the great reduction of CO2 in the atmosphere. These ice ages were immensely long, and led to a crash in microflora.[37] See also Cryogenian period and Snowball Earth.
Conclusion: Our present knowledge of earth history strongly suggests that large-scale geophysical events influenced macroevolution and megaevolution. These terms refer to evolution above the species level, including such events as mass extinctions, adaptive radiation, and the major transitions in evolution.[41][42]

Symbiotic origin of eukaryotic cell structures

Once symbiosis was discovered in lichen and in plant roots (rhizobia in root nodules) in the 19th century, the idea arose that the process might have occurred more widely, and might be important in evolution. Anton de Bary invented the concept of symbiosis;[43] several Russian biologists promoted the idea;[44] Edmund Beecher Wilson mentioned it in his text The Cell;[45] as did Ivan Emanuel Wallin in his Symbionticism and the origin of species;[46] and there was a brief mention by Julian Huxley in 1930;[47] all in vain because sufficient evidence was lacking. Symbiosis as a major evolutionary force was not discussed at all in the evolutionary synthesis.[48]
The role of symbiosis in cell evolution was revived partly by Joshua Lederberg,[49] and finally brought to light by Lynn Margulis in a series of papers and books.[50][51] Some organelles are recognized as being of microbial origin: mitochondria and chloroplasts definitely, cilia, flagella and centrioles possibly, and perhaps the nuclear membrane and much of the chromosome structure as well. What is now clear is that the evolution of eukaryote cells is either caused by, or at least profoundly influenced by, symbiosis with bacterial and archaean cells in the Proterozoic.

The origin of the eukaryote cell by symbiosis in several stages was not part of the evolutionary synthesis. It is, at least on first sight, an example of megaevolution by big jumps. However, what symbiosis provided was a copious supply of heritable variation from microorganisms, which was fine-tuned over a long period to produce the cell structure we see today. This part of the process is consistent with evolution by natural selection.[52]

Trees of life

The ability to analyse sequence in macromolecules (protein, DNA, RNA) provides evidence of descent, and permits us to work out genealogical trees covering the whole of life, since now there are data on every major group of living organisms. This project, begun in a tentative way in the 1960s, has become a search for the universal tree or the universal ancestor, a phrase of Carl Woese.[53][54] The tree that results has some unusual features, especially in its roots. There are two domains of prokaryotes: bacteria and archaea, both of which contributed genetic material to the eukaryotes, mainly by means of symbiosis. Also, since bacteria can pass genetic material to other bacteria, their relationships look more like a web than a tree. Once eukaryotes were established, their sexual reproduction produced the traditional branching tree-like pattern, the only diagram Darwin put in the Origin. The last universal ancestor (LUA) would be a prokaryotic cell before the split between the bacteria and archaea. LUA is defined as most recent organism from which all organisms now living on Earth descend (some 3.5 to 3.8 billion years ago, in the Archean era).[55]
This technique may be used to clarify relationships within any group of related organisms. It is now a standard procedure, and examples are published regularly. April 2009 sees the publication of a tree covering all the animal phyla, derived from sequences from 150 genes in 77 taxa.[56]

Early attempts to identify relationships between major groups were made in the 19th century by Ernst Haeckel, and by comparative anatomists such as Thomas Henry Huxley and E. Ray Lankester. Enthusiasm waned: it was often difficult to find evidence to adjudicate between different opinions. Perhaps for that reason, the evolutionary synthesis paid surprisingly little attention to this activity. It is certainly a lively field of research today.

Evolutionary developmental biology

What once was called embryology played a modest role in the evolutionary synthesis,[57] mostly about evolution by changes in developmental timing (allometry and heterochrony).[58] Man himself was, according to Bolk, a typical case of evolution by retention of juvenile characteristics (neoteny). He listed many characters where "Man, in his bodily development, is a primate foetus that has become sexually mature."[59] Unfortunately, his interpretation of these ideas was non-Darwinian, but his list of characters is both interesting and convincing.[60]
Evolutionary developmental biology (evo-devo) springs from clear proof that development is closely controlled by special genetic systems, and the hope that comparison of these systems will tell us much about the evolutionary history of different groups.[61][62] In a series of experiments with the fruit-fly Drosophila, Edward B. Lewis was able to identify a complex of genes whose proteins bind to the cis-regulatory regions of target genes. The latter then activate or repress systems of cellular processes that accomplish the final development of the organism.[63][64] Furthermore, the sequence of these control genes show co-linearity: the order of the loci in the chromosome parallels the order in which the loci are expressed along the anterior-posterior axis of the body. Not only that, but this cluster of master control genes programs the development of all higher organisms.[65][66] Each of the genes contains a homeobox, a remarkably conserved DNA sequence. This suggests the complex itself arose by gene duplication.[67][68][69] In his Nobel lecture, Lewis said "Ultimately, comparisons of the [control complexes] throughout the animal kingdom should provide a picture of how the organisms, as well as the [control genes] have evolved."

The term deep homology was coined to describe the common origin of genetic regulatory apparatus used to build morphologically and phylogenetically disparate animal features.[70] It applies when a complex genetic regulatory system is inherited from a common ancestor, as it is in the evolution of vertebrate and invertebrate eyes. The phenomenon is implicated in many cases of parallel evolution.[71]

A great deal of evolution may take place by changes in the control of development. This may be relevant to punctuated equilibrium theory, for in development a few changes to the control system could make a significant difference to the adult organism. An example is the giant panda, whose place in the Carnivora was long uncertain.[72] Apparently, the giant panda's evolution required the change of only a few genetic messages (5 or 6 perhaps), yet the phenotypic and lifestyle change from a standard bear is considerable.[73][74] The transition could therefore be effected relatively swiftly.

Fossil discoveries

In the past thirty or so years there have been excavations in parts of the world which had scarcely been investigated before. Also, there is fresh appreciation of fossils discovered in the 19th century, but then denied or deprecated: the classic example is the Ediacaran biota from the immediate pre-Cambrian, after the Cryogenian period. These soft-bodied fossils are the first record of multicellular life. The interpretation of this fauna is still in flux.

Many outstanding discoveries have been made, and some of these have implications for evolutionary theory. The discovery of feathered dinosaurs and early birds from the Lower Cretaceous of Liaoning, N.E. China have convinced most students that birds did evolve from coelurosaurian theropod dinosaurs. Less well known, but perhaps of equal evolutionary significance, are the studies on early insect flight, on stem tetrapods from the Upper Devonian,[75][76] and the early stages of whale evolution.[77]

Recent work has shed light on the evolution of flatfish (pleuronectiformes), such as plaice, sole, turbot and halibut. Flatfish are interesting because they are one of the few vertebrate groups with external asymmetry. Their young are perfectly symmetrical, but the head is remodelled during a metamorphosis, which entails the migration of one eye to the other side, close to the other eye. Some species have both eyes on the left (turbot), some on the right (halibut, sole); all living and fossil flatfish to date show an 'eyed' side and a 'blind' side.[78] The lack of an intermediate condition in living and fossil flatfish species had led to debate about the origin of such a striking adaptation. The case was considered by Lamark,[79] who thought flatfish precursors would have lived in shallow water for a long period, and by Darwin, who predicted a gradual migration of the eye, mirroring the metamorphosis of the living forms. Darwin's long-time critic St. George Mivart thought that the intermediate stages could have no selective value,[80] and in the 6th edition of the Origin, Darwin made a concession to the possibility of acquired traits.[81]
Many years later the geneticist Richard Goldschmidt put the case forward as an example of evolution by saltation, bypassing intermediate forms.[82][83]

A recent examination of two fossil species from the Eocene has provided the first clear picture of flatfish evolution. The discovery of stem flatfish with incomplete orbital migration refutes Goldschmidt's ideas, and demonstrates that "the assembly of the flatfish bodyplan occurred in a gradual, stepwise fashion".[84] There are no grounds for thinking that incomplete orbital migration was maladaptive, because stem forms with this condition ranged over two geological stages, and are found in localities which also yield flatfish with the full cranial asymmetry. The evolution of flatfish falls squarely within the evolutionary synthesis.[78]

Horizontal gene transfer

Horizontal gene transfer (HGT) (or lateral gene transfer) is any process in which an organism gets genetic material from another organism without being the offspring of that organism.

Most thinking in genetics has focused on vertical transfer, but there is a growing awareness that horizontal gene transfer is a significant phenomenon. Amongst single-celled organisms it may be the dominant form of genetic transfer. Artificial horizontal gene transfer is a form of genetic engineering.

Richardson and Palmer (2007) state: "Horizontal gene transfer (HGT) has played a major role in bacterial evolution and is fairly common in certain unicellular eukaryotes. However, the prevalence and importance of HGT in the evolution of multicellular eukaryotes remain unclear."[85]

The bacterial means of HGT are:
  • Transformation, the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material (DNA or RNA).
  • Transduction, the process in which bacterial DNA is moved from one bacterium to another by a bacterial virus (a bacteriophage, or 'phage').
  • Bacterial conjugation, a process in which a bacterial cell transfers genetic material to another cell by cell-to-cell contact.
  • Gene transfer agent (GTA) is a virus-like element which contains random pieces of the host chromosome. They are found in most members of the alphaproteobacteria order Rhodobacterales.[86] They are encoded by the host genome. GTAs transfer DNA so frequently that they may have an important role in evolution.[87]
    A 2010 report found that genes for antibiotic resistance could be transferred by engineering GTAs in the laboratory.[86]
Some examples of HGT in metazoa are now known. Genes in bdelloid rotifers have been found which appear to have originated in bacteria, fungi, and plants. This suggests they arrived by horizontal gene transfer. The capture and use of exogenous (~foreign) genes may represent an important force in bdelloid evolution.[88][89] The team led by Matthew S. Meselson at Harvard University has also shown that, despite the lack of sexual reproduction, bdelloid rotifers do engage in genetic (DNA) transfer within a species or clade. The method used is not known at present.

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