The Evolution Gene (The Evolution Gene Series Book 1)

In addition, Jiang et al. These results suggest a huge potential for protein diversity plant genomes. Besides these extensive studies in Drosophila , mammals, and plants, there have been many valuable investigations of chimeric genes and retrogenes in Caenorhabditis elegans 65 , fish 24 , 48 , silkworm , and chicken Inexpensive whole genome analysis has also made possible the identification of genes at the very earliest stages of their evolution, before fixation. Abundant copy number variation CNV has been detected in Drosophila 39 , 41 , , humans 46 , mouse 53 , and C.

Dopman and Hartl 39 , Emerson et al. The recent sequencing of 43 genomes in two D. The large number of new genes segregating in populations is just now beginning to be appreciated and investigated further. An active area of research will be to perform functional and statistical analyses of these new genes to understand their earliest stages of evolution. In all, these studies have shown that new gene origination rates can differ between taxa, yet are appreciable in all groups studied.

These results further strengthen the conclusion that new gene origination is a general evolutionary process. With the large number of new genes identified in various organisms, researchers were able to investigate statistical patterns of new gene characteristics to explore the mechanistic and evolutionary forces that impact the formation, origination, and evolution of new genes. Surprisingly, these authors found a significant excess of autosomal retrogenes derived from X-linked parental genes XA , and a significant deficiency of retrogenes formed in the opposite direction AX or between autosomes AA.

These two observations clearly reveal a striking pattern of new gene origination in flies: These results hold in the 12 sequenced species of Drosophila 98 , and in Anopheles gambiae 4 , Gene traffic appears to be general in Drosophila for different mechanisms of new gene formation, as Vibranovski et al. Moreover, the neo-X chromosome, an autosomal chromosome arm that fused to the ancestral X chromosome in the Drosophila genus evolution, also shows the same excess of gene traffic 86 , Retrogene traffic in Drosophila A; 10 , and humans B; The size of arrow indicates the intensity of gene movement between chromosomes, and the percentages show quantitatively the excess of movement over the null expectation random origination and insertion.

The functions of the retrogenes are indicated. Relative to Drosophila , human and mouse revealed similar yet distinct patterns of gene traffic The mouse genome shows a very similar pattern. Several microarray-based studies of male-biased genes and their chromosome locations by Ranz et al. In Drosophila , Zhang et al. In general, models to explain gene traffic, and experimental evaluation of those models, show that natural selection is a major force governing gene traffic, but that mutational processes likely also play a role Meiotic sex chromosome inactivation MSCI in the male germline 10 , 42 , , , dosage compensation in the heterogametic sex 2 , , sexual antagonism between male- and female-beneficial genes 21 , , and meiotic drive , have all been implicated in driving gene traffic.

The relative role of each of these forces has been hotly debated. Conversely, genes expressed in the mitotic phases of spermatogenesis are randomly distributed throughout the genome. Other studies suggest reduced expression throughout spermatogenesis, including in the spermatogonia, which also discredits dosage compensation models 97 ; however, see A clear-cut single cell transcriptome is needed to clarify these issues. Besides the MSCI model, other non-germline-based models, e. Early studies revealed a connection between the expression and the ages of new genes. Almost all retrogenes in Drosophila appear to have testis expression 33 , and to have maintained testis-biased or testis-specific expression independent of age Whether or not the testis is the starting point for new genes, a general survey of the expression patterns for new genes that originated within vertebrates revealed strong positive correlation with the age in both transcription intensity and spatial expression It is possible that this testis-biased pattern of retrogene expression is due to our inability to detect genes expressed at low levels in different tissues, but this issue should be resolved soon with advances in next-generation sequencing.

Evolutionary forces such as natural selection and genetic drift operate on both facets of new gene evolution: The two phases of new gene evolution, fixation and acquisition of a beneficial role, may overlap. In this section we will discuss theoretical models developed to describe how new genes arise and acquire novel functions, as well as discuss general approaches to studying new genes and the selective forces that act on them.

Muller was among the first to recognize the potential importance of duplicate genes in evolution. He proposed a simple model whereby new duplicate genes could acquire novel, beneficial functions distinct from those of the original copies. But Ohno also predicted that duplicate genes are most often inactivated and become pseudogenes. This classic model assumes that the new gene is functional upon duplication and that the new gene subsequently acquires mutations that provide a novel beneficial function.

The novel function is then preserved in the genome by natural selection. However, strictly duplicate genes are redundant, and beneficial mutations are extremely rare. How do new duplicate genes remain in the population long enough to accumulate a beneficial, selected mutation s?

BACKGROUND AND HISTORICAL OVERVIEW

This problem led to the development of models that predict selective preservation of both copies at all stages of their evolution: The AR model proposes that gene duplication itself is favored, e. Thus, AR posits that novel functions are acquired post-duplication. IAD and EAC, in contrast, propose that ancestral loci develop novel beneficial secondary functions before duplication 8 , Under IAD, repeated gene duplication is favored to increase the dosage of the novel secondary function. Different duplicates are then free to optimize the ancestral or function, and only the two best copies are retained in the genome.

The increase in the number of duplicate genes under the AR and IAD models also provides additional targets for beneficial mutations, thus increasing the probability and speed of functional improvement. EAC predicts that the bifunctional ancestral gene is subject to selection before gene duplication, adaptive conflict between the ancestral and new function constrains improvement of the selected function s before duplication, and that adaptive changes and functional improvement occur in the daughter genes after duplication. For additional information on duplicate gene evolution, see Conant and Wolfe 32 , who suggest that preservation of new genes stems from the co-option of existing functions to serve new purposes, and Walsh , for detailed mathematical descriptions of the models and relative probabilities of neofunctionalization and pseudogenization.

Examples of EAC 35 , IAD , and AR 47 have been published, and each model has specific predictions for what we should observe if a new gene originated by each process However, none of these models can be used as a statistical framework for rigorously testing the roles of evolutionary forces in new gene origination. Classic molecular population genetic tests based on nucleotide substitution patterns and allele frequency spectra do provide this framework and have been used extensively to detect selection on new genes.

In addition, Thornton introduced a coalescent-based model that can be used to test for selection on copy number variation CNV. Each of these 5 models classic, AR, IAD, EAC, and statistical models predicts that new genes should experience strong natural selection after they are formed. We will now discuss some of the evidence indicating that this often appears to be the case. The first study to identify signatures of selection on a new gene journeying to fixation was performed by Llopart et al. Selection has also been detected on CNV in D.

Similarly, Schrider et al. Overall, these studies show that natural selection can play a key role in driving new genes to fixation.

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In addition, they highlight the use of classic population genetic tests in determining whether selection acts on new genes during their journeys to fixation. Positive Darwinian selection acting on new genes in Drosophila. A Positive selection for the fixation of new retrogenes in Drosophila and humans The numerator and denominator show the numbers of retrogenes that originate on the autosomes and the X, respectively. B The jingwei gene The ratios over the branches are the numbers of nonsynonymous changes over the numbers of synonymous changes, while the ratios in the triangles are the ratios of divergence between the species to polymorphisms.

In addition to studies of the evolutionary forces governing the fixation of new genes, many studies have investigated the effects of selection and drift on new gene sequences. Long and Langley 81 showed that the new chimeric gene jingwei in D. Similarly, Nurminsky et al. This fusion protein underwent rapid structural renovations, including the conversion of a Cdic intron into an exon and and AnnX exon and Cdic intron into a testis-specific promoter. Low levels of sequence polymorphism, preservation of coding potential, and the absence of Sdic in other closely related species suggests that Sdic was rapidly swept to fixation.

These first discoveries sparked searches for general evolutionary patterns in new genes. Jones and Begun 63 searched for common patterns in the evolution of three Adh -derived chimeric genes in different lineages of Drosophila. All three new genes quickly accumulated a large number of amino acid replacement substitutions in the Adh- derived region shortly after they arose, several at identical amino acid sites. Strikingly, Jones and Begun 63 and Shih and Begun showed that different Adh -derived fusion genes often accumulate mutations at the same sites, regardless of which other gene they have fused to Figure 5C.

In addition, each of the 4 Adh -derived fusion genes exhibits strong signals of accelerated amino acid substitution using classic population genetic statistical tests e. Some of these observations have recently been borne out by genome-wide studies. And using molecular population genetic tests, Chen et al. In addition, this signal of selection diminishes as genes grow older. Altogether these studies indicate that there are general patterns to new gene evolution: In addition to analyses of new gene frequencies and nucleotide changes, many groups have investigated the evolutionary forces acting on new genes by analyzing new gene functions, genomic locations, or expression patterns.

This complementary approach has revealed several fundamental patterns of new gene origination. These proteins independently evolved in the different orders, yet they consist of nearly identical tripeptide repeats. These tripeptide repeats were generated de novo by amplification of short nucleotide sequences. These studies showed that similar environmental pressures may favor the generation of genes with similar functions. In addition, as we showed in the previous section, testis-biased genes are under-represented on the D.

This larger target for retrogene integration allows a higher proportion of these retrogenes to acquire testis-biased expression. These general observations of the location of sex-biased genes, and their general movement off of the X chromosome, indicate that differences in expression alone can dictate where in the genome new genes originate. Together, these results show that studies of general patterns of extant gene locations, structures, and expressions can be informative of new gene origination and evolution.

Studying the roles of new genes in phenotypic evolution recently became feasible with the advent of sophisticated genetic tools, molecular techniques and significant progress in related areas of important phenotypes in biology. Young genes are often assumed to be dispensable because important functions are thought to require a long evolutionary time to be developed and optimized However, studies in the last decade have found numerous young genes with important, and sometimes essential, functions at the molecular, cellular, and individual level New genes can generate new biochemical pathways and products if they are enzymes or become enzymes.

In Arabidopsis , Weng et al. New genes can also be quickly integrated into existing gene networks. Integration appears to be driven by natural selection. Several new genes have become new hubs. But in a short evolutionary time 4—6 MYs Zeus acquired new binding sites through which it activates or represses hundreds of downstream genes involved in reproduction.

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This observation indicates that gene expression networks can be rapidly and globally reshaped in evolution by new genes. New genes integrated into and reshaped gene networks.

New Gene Evolution: Little Did We Know

The orange box highlights a module composed of two new genes involved in the pathway to form and process actin. DID4 green box interacts with 13 new genes within a few steps. B New genes form hubs in protein-protein interaction networks Consequently, it evolved into a new DNA binding motif that evolved hundreds of new gene links to rewire the gene networks that control reproduction Surprisingly, new genes can quickly acquire essential roles in development. Silencing expression of these young genes causes development failure in early to late pupa, and in some cases earlier Figure6A and 6B.

Furthermore, tissue-specific knockdown of these young genes can cause morphological defects in adult flies. Silencing new genes can also have a critical effect on reproduction, even when the individual can complete development. The duplicate gene nsr novel spermatogenesis regulator exists only in the four species of the D. Similarly, silencing Zeus , a gene in the same group of Drosophila , causes sterility by disrupting testis and sperm development The essential effects of new genes on development.

A Development was terminated at the final stage of development when three different genes were knocked down using RNA interference RNAi. B YLL1 originated in the common ancestor of the D. Some of the new brain genes have significant effects on the behavior. For example, Xcbp1 and Desr influence foraging behaviors 28 and sphinx influences courtship behaviors The incorporation of new genes into the brain is not specific to Drosophila. A high proportion of hominoid-specific and human-specific genes are expressed in the prefrontal cortex and temporal lobe, the newest brain structures, in early fetal development.

New genes impact sexual dimorphism by participating in the genetic systems that control sexual reproduction and sex determination As the aforementioned patterns of new gene origination show, the vast majority of new genes are sex-biased, especially male-biased, expressed and their origination processes show directional copying between the sex chromosomes and autosomes e. A number of new genes have been identified with various phenotypic effects ranging from the testicular descent in theria RLN3 ; , testis size in mouse noncoding RNA gene, Poldi ; 57 , sperm-competition in D.

What specific roles can new genes play, and what characteristics of new genes enable them to become essential components of these processes so quickly? New genes now appear to be potent drivers of phenotypic evolution and the genetic control of important biological processes, and show that organismal development and organ development have evolved species-specific and lineage-specific components. Understanding the evolution and modification of these components through the incorporation of new genes is a crucial area of further research.

It is apparent that we have just a glimpse of the emerging world of new genes, and that they play crucial roles in rapidly the evolving genetic systems governing biological diversity. Questions about new gene evolution have opened many doors for both our understanding of existing diversity and for new research. For example, most studies examined new genes generated from a few mechanisms, e.

In addition, even those new genes which are easiest to identify are seriously biased against, and biological studies tend to neglect them Continued efforts will be invaluable for understanding the abundance of new genes, the mechanisms which have been neglected so far, and even new gene evolution in non-model organisms. An outstanding challenge is to understand the roles of new genes in the evolution and biology of phenotypes, and the studies we have highlighted have left important, unresolved questions to be answered.

For example, what evolutionary forces drive gene traffic? How do new genes evolve essential developmental functions, and how quickly? How are important structures, such as the human brain, able to incorporate new gene functions, and how do new genes contribute to novel cognitive function? Future studies of more, diverse phenotypes will help shed light onto the general patterns and modes of new gene evolution and the influence of new genes on evolving systems.

In addition, understanding how phenotypes rapidly evolve will require a deep understanding underlying local and global gene networks. This will be a tremendous challenge, ranging from the experimental deciphering and graphic description of the gene networks to a valid comparative analysis of the ancestral and derived networks shaped by new genes, and eventually the causal relationship of the altered networks with the evolution of phenotypes.

We thank all members in the M. Papazian for their supports to new gene studies throughout the past fifteen years when we explored this new and exciting area. The process by which a mutation spreads to all individuals in a population. A group of taxa which shares a common ancestor.

Behaviour, Development and Evolution

Genes which are thought to have lost their ability to code for a full-length protein. X chromosome inactivation during spermatogenesis favors relocation of genes involved in spermatogenesis to autosomes. The process by which a new gene acquires a novel function. Given the right circumstances, and enough time, evolution leads to the emergence of new species.

Scientists have struggled to find a precise and all-inclusive definition of species. Ernst Mayr defined a species as a population or group of populations whose members have the potential to interbreed naturally with one another to produce viable, fertile offspring. The members of a species cannot produce viable, fertile offspring with members of other species. Speciation is the lineage-splitting event that results in two separate species forming from a single common ancestral population.

Allopatric speciation begins when a population becomes geographically separated. For speciation to occur, separation must be substantial, so that genetic exchange between the two populations is completely disrupted. In their separate environments, the genetically isolated groups follow their own unique evolutionary pathways. Each group will accumulate different mutations as well as be subjected to different selective pressures. The accumulated genetic changes may result in separated populations that can no longer interbreed if they are reunited.

If interbreeding is no longer possible, then they will be considered different species. Usually the process of speciation is slow, occurring over very long time spans; thus direct observations within human life-spans are rare. However speciation has been observed in present-day organisms, and past speciation events are recorded in fossils. These fish have complex mating rituals and a variety of colorations; the slight modifications introduced in the new species have changed the mate selection process and the five forms that arose could not be convinced to interbreed.

The theory of evolution is widely accepted among the scientific community, serving to link the diverse specialty areas of biology. The significance of evolutionary theory is summarised by Theodosius Dobzhansky as " nothing in biology makes sense except in the light of evolution. There is much discussion within the scientific community concerning the mechanisms behind the evolutionary process.

For example, the rate at which evolution occurs is still under discussion. In addition, there are conflicting opinions as to which is the primary unit of evolutionary change—the organism or the gene. Darwin and his contemporaries viewed evolution as a slow and gradual process. Evolutionary trees are based on the idea that profound differences in species are the result of many small changes that accumulate over long periods.

Gradualism had its basis in the works of the geologists James Hutton and Charles Lyell. Hutton's view suggests that profound geological change was the cumulative product of a relatively slow continuing operation of processes which can still be seen in operation today, as opposed to catastrophism which promoted the idea that sudden changes had causes which can no longer be seen at work.

A uniformitarian perspective was adopted for biological changes. Such a view can seem to contradict the fossil record, which often shows evidence of new species appearing suddenly, then persisting in that form for long periods. In the s paleontologists Niles Eldredge and Stephen Jay Gould developed a theoretical model that suggests that evolution, although a slow process in human terms, undergoes periods of relatively rapid change ranging between 50, and , years [95] alternating with long periods of relative stability.

Their theory is called punctuated equilibrium and explains the fossil record without contradicting Darwin's ideas. A common unit of selection in evolution is the organism. Natural selection occurs when the reproductive success of an individual is improved or reduced by an inherited characteristic, and reproductive success is measured by the number of an individual's surviving offspring.

The organism view has been challenged by a variety of biologists as well as philosophers. Richard Dawkins proposes that much insight can be gained if we look at evolution from the gene's point of view; that is, that natural selection operates as an evolutionary mechanism on genes as well as organisms. Others view selection working on many levels, not just at a single level of organism or gene; for example, Stephen Jay Gould called for a hierarchical perspective on selection.

From Wikipedia, the free encyclopedia. A non-technical explanation of the basic concepts and principles of biological evolution. This article is a non-technical introduction to the subject. For the main encyclopedia article, see Evolution. Introduction to evolution Evidence of evolution Common descent Evidence of common descent.

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History of evolutionary theory. Applications of evolution Biosocial criminology Ecological genetics Evolutionary aesthetics Evolutionary anthropology Evolutionary computation Evolutionary ecology Evolutionary economics Evolutionary epistemology Evolutionary ethics Evolutionary game theory Evolutionary linguistics Evolutionary medicine Evolutionary neuroscience Evolutionary physiology Evolutionary psychology Experimental evolution Phylogenetics Paleontology Selective breeding Speciation experiments Sociobiology Systematics Universal Darwinism.

Evolution as fact and theory Social effects Creation—evolution controversy Objections to evolution Level of support. Modern synthesis 20th century. Evidence of common descent. Convergent evolution and Divergent evolution. Biology portal Evolutionary biology portal Science portal. Abiogenesis Creation—evolution controversy Evidence of common descent Evolution as fact and theory Human timeline Level of support for evolution Misconceptions about evolution Nature timeline. United States Geological Survey. Speculations about the age of the earth and primitive mantle characteristics".

Earth and Planetary Science Letters. William ; Kudryavtsev, Anatoliy B. William June 29, Philosophical Transactions of the Royal Society B. Meet your microbial mom". Retrieved 9 October Early edition, published online before print. Watching, from the Edge of Extinction. Retrieved 30 May The New York Times. The New York Times Company. Retrieved 6 May University of California, Berkeley.

Essential Concepts and Common Misconceptions". Philosophical Transactions of the Royal Society B: Alberts, Bruce , ed. Archived from the original on National Geographic Online extra. A Look at Bogus 'History' in Schoolbooks". Staging criteria and macroscopic skeletal morphogenesis of the head and limbs". Evolution Library Web resource. Implications for Plant Conservation".

Annual Review of Ecology and Systematics. Rus; Fleischer, Robert C. Journal of Evolutionary Biology. The Virtual Fossil Museum. A Note on Textbooks". Miller And Levine Biology. The TalkOrigins Foundation, Inc. University of Hawaii Botany Department. University of California, Santa Cruz. American Association for the Advancement of Science. The Scientific Creative Quarterly. Vancouver and Kelowna, BC: University of British Columbia. National Plant Germplasm System.

Behaviour, Development and Evolution - 8. Genes in Development and Evolution - Open Book Publishers

Life's Big Instruction Book. Smithsonian Contributions to Botany. The American Biology Teacher. National Association of Biology Teachers. National Center for Science Education Blog. National Center for Science Education. Research Triangle Park, NC: Natural History Magazine, Inc. The Society for the Study of Evolution. How shall we name and generalise the unit of Darwinism? National Academy of Sciences. The History of an Idea 3rd completely rev. University of California Press.

From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design 2nd ed. Why Evolution is True. The Age of the Earth: Geological Society Special Publication. Geological Society of London. The Evolution of an Idea. Edited, with foreword and commentary by James D. The Selfish Gene 1st ed. The Evolution and Future of the Human Animal 1st ed. Theoretical Introduction 2nd ed. Farber, Paul Lawrence Finding Order in Nature: The Naturalist Tradition from Linnaeus to E.

Johns Hopkins University Press. Evolutionary Biology 3rd ed. Evolutionary Science and Society: Biological Sciences Curriculum Study. More Reflections in Natural History 1st ed. Gould, Stephen Jay Dinosaur in a Haystack: Reflections in Natural History. The Structure of Evolutionary Theory. Belknap Press of Harvard University Press. The Remarkable History of a Scientific Theory. Populations, Species, and Evolution: It may be helpful to forget biology for a moment and think about the spread of a new brand of biscuit in supermarkets.

Consider the spread from the perspective of the recipe. While shoppers select biscuits and eat them, it is the recipe for making desirable biscuits that survives and spreads in the long run. A phrase in the recipe might specify the amount of sugar to be added and makes the difference between a popular and a less popular biscuit. In that sense it is selfish. This novel way of looking at things is unlikely to mislead anyone into believing that what shoppers really do in supermarkets, when they pick a particular brand of biscuit off the shelves, is select a word in the recipe used for making the biscuits.

They select the brand of biscuit they like. The agents of differential survival and differential reproductive success will usually be characteristics of whole individuals including the structures they make, but they might be characteristics of molecules or of symbiotic groups, or the evolvability of taxonomic lineages. The mechanistic language does not translate into the teleological language.

For population geneticists, a genetic difference is identified by means of a biochemical, physiological, structural or behavioural difference between organisms after other potential sources of difference have been excluded by appropriate procedures. In the technically precise language of population geneticists, a genetic allele must be compared with another from which it differs in its consequences. In selfish-gene language, it stands alone as an entity, absolute in its own right.

The perception generated by one meaning of gene does not relate to the same evidence as that generated by the other. They may arise because other conditions that are necessary for the peculiarities of their behaviour are shared. Common odours and preferences for familiar smells might arise from the particular combination of bacteria that breakdown the fats secreted onto the body surface. When the bacteria pass from mother to offspring, so does the source of her special smell.

This is not to downplay the roles of genes. But it emphasises that the nothing-but approach to genes is clearly wrong. Taking a systems approach to the role of genes generates much more fruitful understanding than treating them as providing single causes for development and evolution. Denis Noble argues that living organisms operate at multiple levels of complexity and must therefore be analysed from a multi-scale, relativistic perspective.

Noble explains that all biological processes operate by means of molecular, cellular and organismal networks. The interactive nature of these fundamental processes is at the core of biological relativity and, as such, challenges simplified molecular reductionism. Noble shows that such an integrative view emerges as the necessary consequence of the rigorous application of mathematics to biology. Drawing on his pioneering work in the mathematical physics of biology, he shows that what emerges is a deeply humane picture of the role of the organism in constraining its chemistry, including its genes, to serve the organism as a whole, especially in the interaction with its social environment.

This humanistic, holistic approach challenges the common gene-centred view held by many in modern biology. Ecological Development, Niche Construction, and Adaptation. Oxford University Press, https: An accessible and clear-headed introduction to genetics is given in Griffiths, P. Duke University Press, https: As the title of her book suggests, all factors impinging on the developing organism provide information of a kind.

More recently, epigenetics has become mechanistically defined as the molecular processes by which traits defined by a given profile of gene expression can persist across mitotic cell divisions, but which do not involve changes in the nucleotide sequence of the DNA see Carey, N. The general principles apply at higher levels of organisation and are involved in mediating many aspects of developmental plasticity seen in intact organisms. The processes involved in gene expression and suppression can be transmitted from one generation to the next See Gissis, S.

From Subtle Fluids to Molecular Biology. Further support for the revision of the orthodoxies of evolutionary theory has come from microbiology Shapiro, J. A View from the 21st Century. Upper Saddle River, NJ: Shapiro argues that cells must be viewed as complex systems that control their own growth, reproduction and shape their own evolution over time. You can suggest to your library or institution to subscribe to the program OpenEdition Freemium for books.

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Active Role of Behaviour. Search inside the book. Genes in Development and Evolution p. Ecological Development, Niche Construction, and Ad Zoom in Original jpeg, 20k. Zoom in Original jpeg, 22k. Notes 1 This debate is well-described in Noble, D. List of illustrations Caption The process of making a cake.

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