Mechanisms of Evolution

Biological Evolution

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Scientific theories of evolution seek to explain the mechanisms of the observable fact of biological evolution. Scientists observing biological evolution first sought to explain observed morphological changes over time – phenotypic evidence of changes in body structure found in the fossil record. Since the advent of modern molecular genetics, biological evolution has come to be understood as a change in genotype – a genetic alteration in the intergenerational frequency of alleles in populations.

However, morphologic changes may reflect alterations in the regulation of genetic expression without a major alteration in genotype – witness the considerable differences that selective breeding has wrought in size and configuration within one canine species. Similarly, the paramount importance of gene regulation probably explains much of the morphological difference between humans and chimps – two species who share 98% of their DNA. Recently, researchers have demonstrated that gene regulation has enabled rapid phenotypic speciation in sticklebacks. Along the same lines of modification of genetic expression, alternative splicing enables a single gene to give rise to multiple versions of a protein.

mutation → allele → pre-mRNA → constitutive pre-mRNA splicing and/or epigenetic alternative splicing → proteins → intergenerational fate of allele

There are two basic types of mechanism involved in biological evolution. First are the genetic sources of alteration of a gene within the genotype of an individual. Second are those statistical mechanisms that determine the fate of an altered allele. These are the mechanisms that increase or decrease frequency of an allele (a form of a gene at a locus) within a population.

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Beyond Darwin and Neo-Darwinism

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Charles Darwin accurately predicted that his theories would evoke skepticism from scientists and ridicule from the religious. Happily, scientists came to accept his ideas, and his breakthrough insights have proved highly influential. Unhappily, those biblical literalists who insist that "Genesis" is an accurate description of life's origins, continue to unjustly vilify Darwin's theories.

Summary of Darwin's observations and his Theory of Evolution by Natural Selection:

1. Most animals have such high fertility rates that their population size would increase exponentially if all individuals were to reproduce.
2. Yet, except for seasonal fluctuations, populations remain relatively stable in size.
3. Because environmental resources are limited, individuals compete for resources, limiting survival and reproduction.
4. Individual characteristics vary within populations and those members of a population that are better adapted for survival in the face of competition are more likely to pass their characteristics on to the next generation.

5. Thus, species gradually accumulate inherited adaptations that best suit them for their environment, passing these on to progeny. Speciation involves gradually accumulated differentiation of characteristics.

Darwin was not aware of the existence of DNA, nor of the mechanisms that alter genotype. Darwin focussed on the inheritance of adaptive individual characteristics that had ensured reproductive success, and the resultant slow accumulation of adaptive phenotypic change. Darwin did not say that all species are gradually evolving (cf. quote.)

Subsequent evolutionary theorists first disputed Darwin's concept of gradual evolution. Gould and Eldredge introduced the concept "phyletic gradualism " which they discredited through the concept of punctuated equilibria. The Theory of Punctuated Equilibria was proposed in order to explain patchiness in the fossil record and the the localized adaptive radiation of species observed following extinction events. This stage of thinking about evolutionary mechanisms has been termed "Neo Darwinism".

Modern advances in molecular genetics, coupled with studies of population genetics have led to the "Modern Synthesis" of understanding concerning mechanisms of evolution. Current understanding incorporates knowledge of genetic drift, gene flow, mutation, recombination, and natural selection mechanisms.

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Creationists and defenders of "intelligent design" theory commonly attack a "strawman" depiction of Darwinism or Neo-Darwinism as representing current thinking in their attempt to discredit evolutionary science. It is important for any person wishing to defend evolution-as-fact and modern evolutionary theories to attain a thorough understanding of modern evolutionary theory as well as fallacious creationist arguments.

Punctuated equilibria

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Examination of the fossil record (aside from natural incompleteness) reveals a patchiness not predicted by “phyletic gradualism”, as described by Eldredge and Gould. Species with widespread distribution exhibit relatively stable morphology, while new species with different morphologies arise relatively abruptly.

Features of the Theory of Punctuated Equilibria:
1. Interpretation of paleontology ought to be based on the study of living or recently living organisms (neontology).
2. Large, widespread species usually change slowly, if at all, during their time of residence.
3. Sampling of the fossil record will reveal a pattern of stasis in most species, and the abrupt appearance of newly derived species is a consequence of ecological succession and dispersion.
4. Most speciation proceeds independently from a single ancestral line (cladogenesis) rather than by in toto replacement by a morphogenetically distinct population (anagenesis).
5. Adaptive change in lineages occurs mostly during periods of speciation (during cladogenesis).
6. Trends in adaptation occur mostly through the mechanism of species selection.
7. Daughter species usually develop during a time that is short in comparison to the residence time of the species (across limited strata).
8. Most speciation results from isolation of a small, reproductively isolated, geographically peripheral sub-population (parapatric or peripatric speciation, or allopatric speciation of peripheral isolates). That is, daughter species usually develop in a geographically limited region.

A passage in Darwin’s Origin of Species indicates that Darwin viewed the cumulative changes that lead to speciation as acting slowly. However, Darwin indicates that “free intercrossing” retards speciation, which he describes as intermittent and affecting, “only a very few of the inhabitants of the same region at the same time.” [see Charles Darwin, Origin of Species 1st Edition 1859, p.153]

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Therefore, it might reasonably be suggested that Eldredge and Gould described “phyletic gradualism” for the purpose of contrast with their own theory of punctuated equilibrium. (adapted from here.)

The modern synthesis

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The Modern Synthesis of Evolution combines understanding of Population Genetics and Molecular Genetics : genetic drift, gene flow, mutation, recombination, and natural selection mechanisms. See also overview of basic mechanisms of evolution.

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"The major tenets of the evolutionary synthesis, then, were that populations contain genetic variation that arises by random (ie. not adaptively directed) mutation and recombination; that populations evolve by changes in gene frequency brought about by random genetic drift, gene flow, and especially natural selection; that most adaptive genetic variants have individually slight phenotypic effects so that phenotypic changes are gradual (although some alleles with discrete effects may be advantageous, as in certain color polymorphisms); that diversification comes about by speciation, which normally entails the gradual evolution of reproductive isolation among populations; and that these processes, continued for sufficiently long, give rise to changes of such great magnitude as to warrant the designation of higher taxonomic levels (genera, families, and so forth)."- Futuyma, D.J. in Evolutionary Biology, Sinauer Associates, 1986; p.12

Basic mechanisms of evolution

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There are two basic types of mechanism involved in biological evolution. First are the genetic sources of alleles – altered genes at a locus – within the genotype of an individual. Regulatory mechanisms determine genetic expression, and hence the manifestation of genotype as phenotype. Selection acts upon phenotypes. So, second are those statistical, population-level mechanisms that determine the fate of an altered allele. Collectively, these are the mechanisms that alter biological variation by increasing or decreasing the frequency of alleles between generations.

Overall,
Regulatory mechanisms that affect phenotype:
Constitutive gene regulation,
Alternative splicing,
Epigenetic mechanisms.

Mechanisms that add alleles:
Horizontal Gene Transfer,
Endosymbiotic Gene Transfer,
Mutation,
Recombination,
Gene flow,
Natural selection.

Mechanisms that remove alleles:
Natural selection,
Genetic drift,
Bottleneck,
Founder effect.

Table Mechanisms of Biological Evolution : Gene Regulation in E.coli :

Genetic mutations are of interest to molecular geneticists because they cause disease and because they are the basic currency of biological evolution. Mutations that affect regulatory sequences are of particular significance to evolution because of their widespread phenotypic influence: '“pleiotropic” genes - those with multiple on-switches that enable the expression of a single gene in different tissues or at different stages of development. . . this pleiotropy gives evolution an artistic freedom to play with the regulatory elements in specific regions without making mutations that would affect the gene throughout the body. . . More generally, these kinds of molecular studies are enabling new advances in understanding the machinery of evolution. “These techniques are enabling dramatic progress in understanding the deep mechanics of evolution in more and more detail,” he said. “Researchers are now finding the actual `smoking guns' of evolution by documenting specific evolutionary changes at the DNA level. “And studies of phenomena such as fruitfly wing spots show how evolution is not some one-off process. It repeats itself over and over. They show that there is more than one way to tinker with the same gene, and by extension, to independently evolve the same trait,” Carroll said. ”' [HHMI news] [Abstract below]

Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila.
The gain, loss or modification of morphological traits is generally associated with changes in gene regulation during development. However, the molecular bases underlying these evolutionary changes have remained elusive. Here we identify one of the molecular mechanisms that contributes to the evolutionary gain of a male-specific wing pigmentation spot in Drosophila biarmipes, a species closely related to Drosophila melanogaster. We show that the evolution of this spot involved modifications of an ancestral cis-regulatory element of the yellow pigmentation gene. This element has gained multiple binding sites for transcription factors that are deeply conserved components of the regulatory landscape controlling wing development, including the selector protein Engrailed. The evolutionary stability of components of regulatory landscapes, which can be co-opted by chance mutations in cis-regulatory elements, might explain the repeated evolution of similar morphological patterns, such as wing pigmentation patterns in flies.
Gompel N, Prud'homme B, Wittkopp PJ, Kassner VA, Carroll SB. Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila. Nature. 2005 Feb 3;433(7025):481-7. Comment in: Nature. 2005 Feb 3;433(7025):466-7.

Evolutionary developmental biology: how and why to spot fly wings. [Nature. 2005] PMID: 15690019
Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. [Nature. 2006] PMID: 16625197
Evolution of yellow gene regulation and pigmentation in Drosophila. [Curr Biol. 2002] PMID: 12372246
Direct regulation of knot gene expression by Ultrabithorax and the evolution of cis-regulatory elements in Drosophila. [Development. 2005] PMID: 15753212
Regulation of body pigmentation by the Abdominal-B Hox protein and its gain and loss in Drosophila evolution. [Cell. 2006] PMID: 16814723
See all Related Articles...

Creationists direct their attacks upon evolution at point mutations (SNPs) that affect coding for proteins, and in so doing they divert attention (either knowingly or out of ignorance*) toward mutations that are more likely to cause disease than to effect evolutionary changes.

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* in the case of science-educated, professional (paid) proponents of creationism (idists & fodis), the explanation for this fallacious attack is probably a deliberate (fallacious) straw man argument, while the average internet debator (proid) appears to be ignorant of biological sciences and to be parroting the misinformation that abounds in creationist books and on creationist websites.

Speciation

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A variety of speciation situations are postulated:

Allopatric speciation occurs when a geographical barrier sub-divides a parent species, resulting in geographic and reproductive isolation such that the descendent species can no longer interbreed upon removal of the barrier.

Anagenesis differs from cladogenesis in that one species progressively transforms into a replacement species when sufficient gene mutations fix in the descendant population. At this point, the ancestral species has become extinct. This mechanism is distinct from the increase in numbers of species generated by cladogenetic branching events.

Cladogenesis is the mechanism of speciation in which one or more lineages (clades) arise from an ancestral line. Such speciation events increase the variety of plants or animals through branching of the phylogenetic tree. Cladogenesis is differentiated from anagenesis, which is the in toto replacement of one species by an anatomically distinct species.

Peripatry (paripatry) is a subset of allopatry in which an isolated group has a smaller population than the parent group. Ernst Mayr introduced the term. Peripatric speciation occurs when the smaller sub-group of a species enters a novel niche within the range of the parent species, becoming geographically and reproductively isolated. Peripatric speciation (paripatric) is distinguished from allopatric speciation by the smaller size of the isolate group, and from sympatric speciation, which involves no barrier to breeding.

Sympatry involves no geographical separation of sub-populations of individuals. Sympatric speciation events occur most often in plants by the mechanism of polyploidy in which the number of chromosomes is doubled or tripled. John Maynard Smith proposed a model called disruptive speciation, in which homozygotes might have greater fitness than heterozygotes under some environmental conditions.

Genetic drift

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Only a small fraction of all possible gene combinations that could be produced by a population will be transmitted to the next generation. Natural selection involves transmission of gene combinations that derived from parental genotypes that have proven favorable to survival and to reproductive success.

However, random transmission (genetic drift) of alleles between generation is also an important factor in generating differences between parental and descendent gene pools. Random factors include the chance survival and meeting of parents (bottlenecks and the founder effect), the chance assortment of alleles at meiosis, and the chance survival of zygotes, seeds, or hatchlings.

Genetic drift is more important in small populations, because random effects are swamped by statistical averaging in large population. However, even large populations comprise numerous small interbreeding groups (demes). Evolution operates on demes.

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Gene flow

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Gene flow refers to the movement of genes from the gene pool of one population into that of another. The rate of entry of non-native genes into the population is measured as the proportion of the alleles at a locus in a generation that originated externally. Gene flow can be referred to as the genetically successful stray rate into a population. Gene flow increases biodiversity and acts against speciation pressures by rendering two populations more similar to each other.

The exchange of genetic material is brought about by movement of individual animals, gametes, or spores. Genes can flow both within and between species (horizontal gene transfer, antigenic shift, reassortment).

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Mutation

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Genetic mutations involve structural, usually transmissible change in DNA or RNA within a cell or organism. Somatic mutations affect the cells of an organism, yet are not trasmitted to the next generation unless they affect the germline, those cells, such as ova and sperm that are committed to reproduction.

Sources of variation:
¨ alternative exons ¨ Alu elements ¨ alternative splicing ¨ alternative 3' splicing ¨ alternative 5' splicing ¨ cassette exons ~ Conserved & Consensus ~ Deletion ~ Duplication ¨ epigenetic mechanisms ~ Epistasis ¨ ESE ¨ ESS ¨ exon skipping ¨ gene regulation and biological evolution ¨ genetic variation ~ Insertion ¨ intron retention ¨ ISE ¨ ISS ¨ ¨~ Inversion ~ Meiosis
~ mispairing ~ Non-disjunction ~ Recombination ~ Substitution ~ Translocation
~ Horizontal Gene Transfer ~ Conjugation ~ Transduction ~ Transformation

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Damage to DNA can be caused by mutations such as replication errors or incorporation of mismatched nucleotides (substitution errors – transitions and transversions). DNA can suffer single or double-strand breaks (left). DNA damage can result from unintentional and intentional environmental mutagens such as oxygen radicals, hydroxyl radicals, ionizing or ultraviolet radiation, toxins, alkylating agents, and chemotherapy agents, particularly anti-cancer drugs. Cells have evolved mechanisms for repair of DNA, and all organisms, prokaryotic and eukaryotic, utilize at least three enzymatic excision-repair mechanisms: base excision repair, mismatch repair, and nucleotide excision repair.

Transmissible mutations affect the germline or result from errors during replication and cell division. Gene mutations have small-scale effects on sequences of nucleic acids, while chromosomal mutations involve larger-scale disruption of genetic material. Sequence mutations result from nucleotide alterations, insertions, deletions, or re-arrangements of gene segments, while, on a larger scale, chromosomes are altered during replication and cell division by deletion, duplication, inversion, recombination, translocation, transposition, and non-disjunction.

Depending upon their effects upon an organism within a particular environment, mutations may be neutral, beneficial, or deleterious. The commonest mutations affect single nucleotides (point mutations or SNPs). Because the genetic code is redundant, many single nucleotide substitutions are neutral. Insertion of mobile genetic elements, transposons and retrotransposons, increases genetic variability. The human genome, for example, includes approximately 500,000 Alu elements located within introns, and 25,000 of those could become new exons, coding for polypeptide sequences, by undergoing a single-point mutation.

As a result of alternative splicing, mutations that alter a splice site or a nearby regulatory sequence can have subtle effects by shifting the ratio of the resulting proteins without entirely eliminating any form. Alternative splicing also generates new polypeptide combinations from already existing code. Recently, researchers have demonstrated that modification of regulation of a single gene has enabled rapid phenotypic speciation in sticklebacks.

HHMI 30 New Mutations per Lifetime : Videos - external - Artificial Life an excerpt from the PBS series Nova Science Now - A Mutation Story on the reciprocal relationship between malaria and the sickle-cell trait - Double Immunity plague and HIV - Why Animals Mate Non-randomly: Tale of the Peacock concerning non-random mating - Sweaty T-Shirts and Human Mate Choice on pheromones - Is Love in Our DNA - poll on how we choose our mates -

External : Transposons part 1, transposons part 2 : Barbara McClintock and mobile genetic elements :

Natural selection

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“Can it, then, be thought improbable, seeing that variations useful to man have undoubtedly occurred, that other variations useful in some way to each being in the great and complex battle of life, should sometimes occur in the course of thousands of generations? If such do occur, can we doubt (remembering that many more individuals are born than can possibly survive) that individuals having any advantage, however slight, over others, would have the best chance of surviving and of procreating their kind? On the other hand, we may feel sure that any variation in the least degree injurious would be rigidly destroyed. This preservation of favourable variations and the rejection of injurious variations, I call Natural Selection. Variations neither useful nor injurious would not be affected by natural selection, and would be left a fluctuating element, as perhaps we see in the species called polymorphic.” Darwin, "Origin of Species", Ch. 4
Darwin recognized that selection is the most important mechanism acting upon variability to bring about long-term, intergenerational change. Individual organisms that are better adapted to an environment are more likely to survive and reproduce. The modern synthesis of evolutionary theory combines an understanding of the genetic mechanisms (genotype and regulation of expression) that determine phenotype, and population genetics explains the fate of genetic variability (alleles) within populations of organisms.

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Horizontal Gene Transfer

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Three mechanisms of horizontal (lateral) gene transfer are recognized: direct bacterial conjugation, bacteriophage mediated transduction between bacteria, and bacterial transformation by uptake of DNA fragments.

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This unit will EVOLVE further by the mechanisms of research and typing.

Conjugation

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Conjugation enables bacteria to exchange genetic material because of tube-like connections called pili.

Conjugation is often likened to a form of sexual reproduction or mating, though it is merely a process by which donor bacteria deliver genetic material to recipient bacteria, utilizing tube-like connections called pili.

Bacteria often contain small circular, double-stranded DNA molecules that are termed plasmids. Bacterial plasmids are not connected to the main bacterial chromosomes and replicate independently. The donor bacterium contains conjugative or mobilizable genetic elements, usually a conjugative plasmid or episome plasmid that can integrate itself into the bacterial chromosome by genetic recombination. One such conjugative plasmid is called the F-plasmid. This is an episome about 100 thousand base-pairs in length, which carries its own origin of replication, called oriV. Most conjugative plasmids have systems ensuring that the recipient cell does not already contain a similar element, ensuring that there is only one copy of the F-plasmid in the F-positive bacterium. diagram of conjugation events diagram of molecular events

One cell contains an F-plasmid (pink), distinct from the prokaryotic genomer (blue). The cell with an F-plasmid also possesses pili, which make contact with the F-negative cell, which does not have pili (top right diagram).

The middle diagram indicates passage of genetic material through a pilum from the F+ bacterium to a F- bacterium. This mechanism is under debate. (Compare with a 27,000 x magnification tem image tem conjugation E. coli)

Transfer through the pili (above right) may not be a strictly accurate depiction of the actual transfer mechanism. The mechanism utilizes proteins coded by the tra or trb loci, and these may open a channel between the bacteria (bottom diagram). In this case, the pili are probably utilized to anchor and draw together the donor and recipient bacteria (top diagram). (Compare with conjugation in alga Conjugation of Spirogyra and a protist Conjugation of Paramecium.)

Once conjugation has been initiated by a mating signal, a complex of proteins called the relaxosome opens up one plasmid DNA strand at the origin of transfer, or oriT. The relaxosome system of the F-plasmid system comprises proteins TraI, TraY, TraM, and a protein that functions as the integrated host factor, IHF. The transferred strand – the T-strand – is unwound from the duplex before transfer into the recipient bacterium in a 5'-terminus to 3'-terminus direction. The remaining strand is replicated. Replication in concert with conjugation is termed conjugative replication, and is similar to the rolling circle replication of lambda phage. Replication may also occur independent of conjugative action – this is vegetative replication, beginning at the oriV.

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Transduction

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In transduction, a viral bacteriophage acts as a vector, transmitting fragments of DNA that it has acquired while infecting one bacterium to another bacterium that it subsequently attacks.

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This unit will EVOLVE further by the mechanisms of research and typing.

Transformation

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Bacteria possess mechanisms for uptake of proteins and plasmids (DNA fragments) from their environment. The DNA fragments are incorporated into the bacterial genome of competent bacteria, transforming the DNA of those bacteria.

In transformation, naked DNA from the donor is taken up by the recipient. The ability to adsorb, fragment, up-take, and recombine foreign DNA (as ssDNA) is termed competence. Natural competence involves a genetically programmed physiological state achieved by some strains of gram-negative (H. influenzae, N. gonorrhoeae) and gram-positive (S. pneumoniae, B. subtilis) bacteria. Artificial competence may be induced in some strains of bacteria (E. coli) through techniques utilizing CaCl2 and temperature manipulation.

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This unit will EVOLVE further by the mechanisms of research and typing.

Non-disjunction

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Non-disjunction arises when chromosomes fail to move to opposite poles of the mitotic spindle during mitosis or meiosis. As a result, one daughter cell will possess an extra chromosome (trisomy in diploid organisms), while the other daughter cell has only one chromosome (monosomy in diploid organisms).

This mutation is a cause of fetal loss as well as several genetic syndromes, such as trisomy 21 (Down Syndrome).

Molecular Genetics

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Molecular genetics is the study of molecules and mechanisms involved in genetic inheritance. Archival information molecules are long polymers of deoxyribonucleic acid (DNA) comprising bases in specific sequence. The bases adenine (A), thymine (T), cytosine (C), and guanine (G), function as codon triplets – sequences of three bases that code for specific amino acids or for translation initiation (start codons) or termination (stop codons). Uracil is substituted for thymine in RNA.

The segments of DNA that contain protein-coding instructions are called genes, and these gene sequences comprise a portion of the total genome of a cell. The genome includes both the genes (coding-sequences, domains) and the non-coding sequences – both exons, which include open reading frames, and introns.

Because the 64 possible combinations of GATC code for only the 20 amino acids commonly found in proteins, the code is 'degenerate' (redundant) with more than one triplet combination coding for each amino acid. (This code reduncancy provides hereditary stability by reducing mutation mistakes.) The double helix of DNA comprises paired nucleotide strands with bases hydrogen bonded to complementary bases in the adjacent chain. Adenine pairs with thymine or uracil (A-TU), and cytosine pairs with guanine (CG).

During cellular reproduction, strands of archival DNA are copied or replicated. Transcription is the first step in gene expression – DNA instructions are converted into mRNA codons, rRNAs, miRNAs, and tRNAs. Coding instructions of nucleotide sequences in archival DNA, which have been transcribed and processed into mRNAs are translated into polypeptides and proteins at cytoplasmic ribosomes. Translation is the ultimate step in gene expression, in which archival genetic instructions are converted into specified sequences of amino acids in peptides, polypeptides, and proteins.

In prokaryotic cells – without a nuclear membrane – translation into polypeptides and proteins may begin prior to termination of transcription. The molecular genetics of eukaryotic cells is more complicated than that of prokaryotes. Various molecules of ribonucleic acid (RNA) participate in the transcription of the DNA code into processed mRNA in a series of RNA processing stages including capping, polyadenylation, and pre-mRNA splicing.Following pre-mRNA processing, RNAs undergo extranuclear transfer. Mature RNAs may undergo post-transcriptional modulation (via miRNAs) before translation of the archival DNA instructions into specific sequences of amino acids in the polypeptides and proteins that participate in cellular function and structure. Transfer RNAs (tRNA) deliver specific amino acids to the cytoplasmic ribosomes along the rough endoplasmic reticulum. Ribosomal RNAs participate in assembly of polypeptides and proteins at ribosomes. Here RNAs serve as ribozymes – non-protein enzymes.

A number of processes are involved in control of cellular function through the maintenance of accuracy of genetic inheritance – damage to DNA is repaired, and faulty RNA is destroyed.

DNA damage may result from replication errors, incorporation of mismatched nucleotides (substitution errors – transitions and transversions), oxygen radicals, hydroxyl radicals, ionizing or ultraviolet radiation, toxins, alkylating agents, and chemotherapy agents. A number of vital mechanisms repair DNA damage to bases (including C to T, C to U, and T U mismatch) and to strands, including double strand breaks. All organisms, prokaryotic and eukaryotic, utilize at least three enzymatic excision-repair mechanisms for damaged bases: base excision repair, mismatch repair, and nucleotide excision repair.

Given the importance of mRNA as an information-carrying molecule, faulty pre-mRNAs and mRNAs must be eliminated – they are destroyed by nonsense-mediated decay or nonstop decay:
1. A pre-mRNA made from a mutant gene usually has an exon junction complex (EJC) in the wrong position. This error activates nonsense-mediated decay (NMD) and destroys the pre-mRNA before it can be used to make flawed proteins. There are at least two kinds of NMD: one requires the protein UPF2 and the other does not.
2. Nonstop decay is mRNA turnover mechanism that has none of the properties of normal mRNA turnover or of NMD. A multi-enzyme complex called the exosome is important for nonstop decay. The exosome is the site for binding of a specific adapter protein called Ski7p. Nonstop decay shares none of the enzymes required for nonsense-mediated decay.

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Important features of the genome and proteome

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Important features of the genome and proteome:
1) Segments of nucleic acid that code for a useful sequence can be re-used, and need not arise de novo for each protein in an organism’s proteome.
2) The original genetic code probably employed 2 not 3 bases to code for each amino acid, and there were probably less than 20 constituent amino acids in primordial proteomes.
3) Many codons – the 2 or 3 base coding sequences – overlap with one another. That is, several sequences may code for a single amino acid within the polypeptide. This redundancy feature protects the proteome from random point mutations in the genome. For example, these are the triplet codons for arginine: CGU CGC CGA CGG AGA AGG
4) The function of proteins depends upon their tertiary and quaternary (3D) structure, and not on the primary (amino acid sequence) structure.
5) Homologous proteins, those that perform similar functions in different organisms, share sequences that are evolutionarily invariant, or conserved. Other amino acids may be substituted into the sequences whose sole function is to connect the important sequences without altering the 3D configuration or function of a protein.
6) Many small RNAs are important as enzymes and in epigenetic regulation – these RNAs are coded for by segments of DNA that do not code for proteins. Translation of RNA to protein is orchestrated by RNA and proteins.
7) Because the sequences of bases in RNA and one strand of DNA are complementary, the sequences of bases in RNA are equivalent to those in the other strand of DNA (with RNA's U switched to DNA's T). This means that RNA could have provided the template for encoding of its own sequences, thus eliminating any need for re-invention of a DNA code from which to transcribe RNAs.
8) The enormous number of different sequences of bases in the hypothetical 26 base RNA strand in the example demonstrates the possible ‘experiments’ that could be performed in a primordial soup mix. Remember that the example merely examined permutations and combinations for a 26 base nucleic acid polymer.

Conserved & Consensus

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In general, a consensus sequence is that idealized sequence in which each position represents the base/amino acid most often found when many sequences are compared. A genetic consensus sequence is a sequence of nucleotides that is common to different genes or genomes. There may be some variations but such sequences show considerable similarity. So, a consensus sequence is the prototype sequence that most others approach.

Consensus sequences are evolutionarily conserved motifs that are disclosed by multiple sequence alignments when species are compared by software algorithms for pattern recognition. Such bioinformatic analyses reveal which sequences are conserved (unchanged) over evolutionary time. Conserved sequences are often regulatory sequences that control biosynthesis or they are signal sequences that regulate maturation or direct molecules to specific intracellular sites. Evolutionary distance can be estimated by the amount of divergence of variable residues and evolutionary relatedness by the conservation of such sites.

For example, the highly conserved, consensus sequence for the 5' donor splice site is (for RNA): (A or C)AG/GUAAGU. That is, most exons end with AG and introns begin with GU (GT for DNA, image). The highly conserved, consensus sequence for the 3' acceptor splice site is (for RNA): (C/U)greater than 10N(C/U)AG/G, where most introns end in AG after a long stretch of pyrimidines. The branch site within introns (area of lariat formation close to the acceptor site during splicing) has the consensus sequence UAUAAC (image). In most cases, U can be replaced by C and A can be replaced by G. However, the penultimate (bold) A residue is fully conserved (invariant).

Left: diagram of highly conserved, consensus (DNA) sequences for 5' donor splice site, branch site, and 3' acceptor splice site (click to enlarge).

Right: diagram of percentage occurrence of (RNA) nucleotides at 5' donor splice site, branch site, and 3' acceptor splice site (click to enlarge).

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Deletion

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The deletion mutation eliminates one or more nucleotides from a DNA sequence, and may produce a non-functional protein. If the number of deleted bases is not a multiple of 3, then the deletion will cause frameshift, with potentially serious consequences.

Deletion and insertion mutations often occur in repetitive sequences, such as deletion of "AT" from the sequence "ATAT" in the CFTR gene. Such mutations are most often caused by a "replication slippage", where the new strand mispairs with the template strand at repetitive sequences. Slippage can cause mispairing of several repeats. Forward slippage results in deletion mutations, while backward slippage results in insertions.

Replication slippage is mainly responsible for microsatellite polymorphisms, which are also called short tandem repeats (STR). In microsatellites, the repeat unit comprises only 1 to 6 bp and the whole repetitive region spans less than 150 bp, while minisatellites range from 1 to 20 kb, and satellites span from 100 kb to more than 1 Mb.

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External : Tandem repeats and morphological variation

Duplication

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Duplication of a segment of the arm of a chromosome is similar to insertion of sequences at the level of genes. Duplications have played an important role in the evolution of the genomes of many species.

Duplication results from unequal recombination (crossing-over) when homologous chromosomes are mis-aligned during meiosis. The frequency of duplication events depends upon the number of shared repetitive elements on the homologous chromosomes. The recombination products of duplication events include duplication at the site of exchange combined with a reciprocal deletion. Thus, duplication events produce an increase of some genetic material. Once established in a genome, functional gene duplicates persist by a variety of mechanisms.

In 1970, Susumu Ohno proposed that several rounds of genome duplication (polyploidy) occurred during vertebrate evolution (see Skrabanek and Wolfe, 1998). Ohno hypothesized that “natural selection merely modified, while redundancy created”, that is, while mutation merely provides material for possible selection, duplication creates. Ohno further hypothesized that evolutionary leaps such as the emergence of new body plans would require major events, as drastic as whole-genome duplication.[r] Study of evolutionary divergence rates in duplicated genes, and their comparison with their non-duplicated counterparts have demonstrated that "Ohno's model is correct in 95% of cases of accelerated divergence: one gene copy preserved the ancestral function, while the other copy was free to diverge. The new functions included gene silencing, anti-viral defense mechanisms, and new signaling pathways. Moreover, as a group, the ancestral and derived function genes show distinct patterns in expression, localization, and generality of function."[s]

Comparison of the tetraodon and human genomes has revealed a signature of duplicate mapping. Studying the gene correspondence between human genes and their orthologs in fish chromosomes, a team of researchers demonstrated that the human genome was doubly covered by interleaved stretches of homology to pairs of fish chromosomes, revealing that the signature of whole-genome duplication exists in the fish genome, pointing to an event common to zebrafish, fugu, and pufferfish. These results illustrate that the signatures of evolutionary change were in fact applicable across kingdoms, exhibiting basic principles of evolutionary mechanisms.[s] Comparative maps of mammalian genomes show that large chunks of chromosome are conserved between species. For example, about 200 conserved chromosomal regions (synteny) are known between mouse and human.[s]

The flowering plants, angiosperms have a marked tendency to undergo chromosomal duplication ('polyploidization') and subsequent gene loss ('diploidization').[s]

Genome sequencing suggests that the genome of yeast duplicated (became polyploid) at some point during its evolutionary past. Genome duplication in an ancestor of Saccharomyces cerevisiae occurred relatively recently, following its divergence from many other fungi such as Kluyveromyces lactis. It has been suggested that duplicated chromosomal regions in yeast are remnants of a whole-genome duplication (tetraploidy) that occurred 10^8 years ago [s]. Subsequently, many of the duplicated genes were deleted and the chromosomes were rearranged by reciprical translocation. See Yeast Gene Duplications website for details of the duplicated chromosomal regions.

Modeling gene and genome duplications in eukaryotes. modified:
Recent analysis of complete eukaryotic genome sequences has revealed that gene duplication has been rampant. Moreover, next to a continuous mode of gene duplication, in many eukaryotic organisms the complete genome has been duplicated in their evolutionary past. Such large-scale gene duplication events have been associated with important evolutionary transitions or major leaps in development and adaptive radiations of species. Here, we present an evolutionary model that simulates the duplication dynamics of genes, considering genome-wide duplication events and a continuous mode of gene duplication. Modeling the evolution of the different functional categories of genes assesses the importance of different duplication events for gene families involved in specific functions or processes. By applying our model to the Arabidopsis genome, for which there is compelling evidence for three whole-genome duplications, we show that gene loss is strikingly different for large-scale and small-scale duplication events and highly biased toward certain functional classes. We provide evidence that some categories of genes were almost exclusively expanded through large-scale gene duplication events. In particular, we show that the three whole-genome duplications in Arabidopsis have been directly responsible for >90% of the increase in transcription factors, signal transducers, and developmental genes in the last 350 million years. Our evolutionary model is widely applicable and can be used to evaluate different assumptions regarding small- or large-scale gene duplication events in eukaryotic genomes.
Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y. Modeling gene and genome duplications in eukaryotes. (Free Full Text Article) Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5454-9. Epub 2005 Mar 30.

Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity.
Controversy surrounds the apparent rising maximums of morphological complexity during eukaryotic evolution, with organisms increasing the number and nestedness of developmental areas as evidenced by morphological elaborations reflecting area boundaries. No "predictable drive" to increase this sort of complexity has been reported. Recent genetic data and theory in the general area of gene dosage effects has engendered a robust "gene balance hypothesis," with a theoretical base that makes specific predictions as to gene content changes following different types of gene duplication. Genomic data from both chordate and angiosperm genomes fit these predictions: Each type of duplication provides a one-way injection of a biased set of genes into the gene pool. Tetraploidies and balanced segments inject bias for those genes whose products are the subunits of the most complex biological machines or cascades, like transcription factors (TFs) and proteasome core proteins. Most duplicate genes are removed after tetraploidy. Genic balance is maintained by not removing those genes that are dose-sensitive, which tends to leave duplicate "functional modules" as the indirect products (spandrels) of purifying selection. Functional modules are the likely precursors of coadapted gene complexes, a unit of natural selection. The result is a predictable drive mechanism where "drive" is used rigorously, as in "meiotic drive." Rising morphological gain is expected given a supply of duplicate functional modules. All flowering plants have survived at least three large-scale duplications/diploidizations over the last 300 million years (Myr). An equivalent period of tetraploidy and body plan evolution may have ended for animals 500 million years ago (Mya). We argue that "balanced gene drive" is a sufficient explanation for the trend that the maximums of morphological complexity have gone up, and not down, in both plant and animal eukaryotic lineages.
Freeling M, Thomas BC. Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res. 2006 Jul;16(7):805-14.

Modeling gene and genome duplications in eukaryotes. [Proc Natl Acad Sci U S A. 2005] PMID: 15800040
Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. [Genome Res. 2006] PMID: 16760422
Widespread genome duplications throughout the history of flowering plants. [Genome Res. 2006] PMID: 16702410
New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. [Genome Res. 2003] PMID: 12799346
Extensive genomic duplication during early chordate evolution. [Nat Genet. 2002] PMID: 12032567

Extensive genomic duplication during early chordate evolution.
Opinions on the hypothesis that ancient genome duplications contributed to the vertebrate genome range from strong skepticism to strong credence. Previous studies concentrated on small numbers of gene families or chromosomal regions that might not have been representative of the whole genome, or used subjective methods to identify paralogous genes and regions. Here we report a systematic and objective analysis of the draft human genome sequence to identify paralogous chromosomal regions (paralogons) formed during chordate evolution and to estimate the ages of duplicate genes. We found that the human genome contains many more paralogons than would be expected by chance. Molecular clock analysis of all protein families in humans that have orthologs in the fly and nematode indicated that a burst of gene duplication activity took place in the period 350 650 Myr ago and that many of the duplicate genes formed at this time are located within paralogons. Our results support the contention that many of the gene families in vertebrates were formed or expanded by large-scale DNA duplications in an early chordate. Considering the incompleteness of the sequence data and the antiquity of the event, the results are compatible with at least one round of polyploidy.
McLysaght A, Hokamp K, Wolfe KH. Extensive genomic duplication during early chordate evolution. Nat Genet. 2002 Jun;31(2):200-4. Epub 2002 May 28. Comment in: Nat Genet. 2002 Jun;31(2):128-9.

Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. [Mol Biol Evol. 2004] PMID: 15014147
New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. [Genome Res. 2003] PMID: 12799346
Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution. [Mol Biol Evol. 1998] PMID: 9729879
Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution. [J Exp Zoolog B Mol Dev Evol. 2003] PMID: 14508816
Phylogenetic analysis of T-Box genes demonstrates the importance of amphioxus for understanding evolution of the vertebrate genome. [Genetics. 2000] PMID: 11063699

Timing and mechanism of ancient vertebrate genome duplications -- the adventure of a hypothesis.
Complete genome doubling has long-term consequences for the genome structure and the subsequent evolution of an organism. It has been suggested that two genome duplications occurred at the origin of vertebrates (known as the 2R hypothesis). However, there has been considerable debate as to whether these were two successive duplications, or whether a single duplication occurred, followed by large-scale segmental duplications. In this article, we review and compare the evidence for the 2R duplications from vertebrate genomes with similar data from other more recent polyploids.
Panopoulou G, Poustka AJ. Timing and mechanism of ancient vertebrate genome duplications -- the adventure of a hypothesis. Trends Genet. 2005 Oct;21(10):559-67

Evolution and diversity of fish genomes. [Curr Opin Genet Dev. 2003] PMID: 14638319
Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates. [Proc Natl Acad Sci U S A. 2004] PMID: 14757817
Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. [Mol Biol Evol. 2004] PMID: 15014147
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. [Nature. 2004] PMID: 15496914

Turning the clock back on ancient genome duplication. [Curr Opin Genet Dev. 2003] PMID: 14638327
Were vertebrates octoploid? [Philos Trans R Soc Lond B Biol Sci. 2002] PMID: 12028790
Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference. [Mol Biol Evol. 2004] PMID: 14694077
Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution. [J Exp Zoolog B Mol Dev Evol. 2003] PMID: 14508816
Analysis of lamprey and hagfish genes reveals a complex history of gene duplications during early vertebrate evolution. [Mol Biol Evol. 2002] PMID: 12200472

Tables Mechanisms of Biological Evolution : Gene Regulation in E.coli :

Exaptation

2007-11-20T01:56:00.000-12:00

The function of traits can shift under the influence of evolutionary selection, such that a trait serving one function evolves to serve another function. This process, which is commonly observed in both anatomy and behavior, was termed exaptation by Gould and Vrba.

1) A character, previously shaped by natural selection for a particular function (an adaptation), is coopted for a new use—cooptation, or
2) A character whose origin cannot be ascribed to the direct action of natural selection (a nonaptation), is coopted for a current use—cooptation.

Such shifts in the function of a trait are referred to as exaptation, cooption, or preadaptation. Feathers provide the classic example of exaptation – having initially evolved for temperature regulation, feathers later evolved for their function in flight. Human hands result from a long sequence of exaptations – fins in fish; forelimbs in transitional forms such as Tiktaalik, Acanthostega, or Ichthyostega; forelimbs in tetrapods; structures for grasping of tree branches in arboreal primates; tool-grasping structures in hominids and humans. The proteins that form the bacterial flagellum are derived from proteins that served other functions in smaller assemblages.

Interest in exaptation results from its relationship to both the process and product of evolution: to the process that creates complex traits and to the product that may be imperfectly designed.

Gould, Stephen Jay, and Elizabeth S. Vrba (1982), "Exaptation - a missing term in the science of form," Paleobiology 8 (1): 4-15.

Frameshift

2007-11-19T06:56:00.000-12:00

Frameshift mutations, or framing errors arise when a number other than a multiple of 3 of nucleotides are inserted into or deleted from a DNA sequence. Because a codon comprises a nucleotide triplet, indels other than multiples of 3 will cause a shift of the reading frame.

Missense mutations code for different amino acids, which may or may not alter the activity of a protein; and, nonsense mutations code for a stop codon, or premature termination codon (PTC+) which alters the code to that for a truncated protein. Nonsense mutations elicit nonsense-mediated mRNA decay (NMD).

Substitution mutations involve the replacement of one or more nucleotides with an equal number of different nucleotides – most substitutions involve a change in only one nucleotide (point mutations, single nucleotide polymorphisms). Because an equal number of nucleotides are substituted, frameshift is not a problem.

Deletions or insertions of short regions can occur by strand slippage, and deletions or insertions of longer regions can occur via homologous recombination. Deletion and insertion mutations often occur in repetitive sequences, such as deletion of "AT" from the sequence "ATAT" in the CFTR gene. Such mutations are most often caused by a "replication slippage", where the new strand mispairs with the template strand at repetitive sequences. Slippage can cause mispairing of several repeats. Forward slippage results in deletion mutations, while backward slippage results in insertions.

Replication slippage is mainly responsible for microsatellite polymorphisms, which are also called short tandem repeats (STR). In microsatellites, the repeat unit comprises only 1 to 6 bp and the whole repetitive region spans less than 150 bp, while minisatellites range from 1 to 20 kb, and satellites span from 100 kb to more than 1 Mb.

Mobile elements called insertion sequences exist in nature. These sequences encode only the information necessary for their insertion into DNA. Depending upon the particular insertion sequence, they can insert at specific regions or at random.

If the number of inserted bases is not a multiple of 3, insertion will cause frameshift, with serious consequences. A number of diseases are caused by insertions without frameshift - Huntington's chorea, Myotonic Dystrophy, Fragile X site A, Fragile X site E, Fragile X site F, Kennedy disease, SCA1, DRPLA.

External : Tandem repeats and morphological variation

Insertion

2007-11-16T10:04:00.000-12:00

Mutations develop from both insertion and loss of segments of DNA. Deletions or insertions of short regions can occur by strand slippage, and deletions or insertions of longer regions can occur via homologous recombination.

Diagram of insertion of a segment of chromosome a into chromosome b, resulting in shortened chromosome a' and lengthened chromosome b' (click to enlarge image).

If the number of inserted bases is not a multiple of 3, insertion will cause frameshift, with serious consequences. A number of diseases are caused by insertions without frameshift - Huntington's chorea, Myotonic Dystrophy, Fragile X site A, Fragile X site E, Fragile X site F, Kennedy disease, SCA1, DRPLA.

Proteins gradually evolve by the accumulation of mutations.

Mobile elements called insertion sequences exist in nature. These sequences encode only the information necessary for their insertion into DNA. Depending upon the particular insertion sequence, they can insert at specific regions or at random.

Tables Mechanisms of Biological Evolution Gene Regulation in E.coli :

It has been known since the beginning of the twentieth century that unstable or variable gene loci occur in plants. Breakage-fusion (reunion)-bridges are formed during anaphase whenever two chromosomes fuse at their ends, generating a fusion product with two centromers. If these two fused chromosomes are subsequently carried to different poles than the regular chromosomes, a chromosomal fraction results. During the subsequent S-phase, the chromatid with a fused-fraction at its terminus will replicate, leading again to a fusion of the homologous chromatids. Consequently a chromosome comprising one chromatid with two centromeres will occur in the subsequent mitosis, rather than a chromosome from two chromatids and one centromere. Consequently, a second fraction occurs during anaphase when the second round of the cycle starts.

B. McClintock recognized (between ‘47 and ‘51) that the chromosomal fraction is restricted to certain sections of the chromosome, which she termed Ds (dissociation). The Ds segment is a mutator gene, which behaves like a pseudoallele that can be located at different gene loci. This mutator gene can insert itself into other genes, rendering them inactive. Thus, it is a control element that changes its location within the chromosome, causing mutations wherever it inserts. Such mutator genes are also called "jumping genes".

A further set of elements, the Ac (activation) elements, support the chromosomal fraction or a translocation of a Ds element. An Ac element can be regarded as a multiple allele, and it may occur different sites in all chromosomes. A number of gene loci are known to be influenced by the Ds-Ac-system or other control elements. Detection of the spm-system (suppressor-mutator) and the elucidation of its function established that the control elements not only act as switches (a yes/ no decision) but that they also modulate the degree of gene expression.

Insertion elements and transposons were first detected in bacterial DNA during the late sixties. This discovery explained the connection between transposons and the chromosome fraction control elements.

Table Mechanisms of Biological Evolution : Gene Regulation in E.coli :

External : Transposons part 1, transposons part 2 : Barbara McClintock and mobile genetic elements :

Inversion

2007-11-16T10:03:00.000-12:00

Meiosis

2007-11-12T19:16:00.000-12:00

Meiosis produces germ cells, or gametes with half (haploid) the number of chromosomes of a diploid cell.

First cell division: meiosis I: single diploid parent cell successively passes through:
1. prophase 1
2. metaphase 1
3. anaphase 1
4. telophase 1 & prophase 2

Second cell division: meiosis II:
5. metaphase 2
6. anaphase 2
7. telophase 2,
producing 4 haploid daughter cells.

Recombination provides a mechanism for genetic variability and is a mechanism of biological evolution. Recombination between homologous chromosomes in meiosis I involves the formation and repair of double strand breaks (DSBs), and meiosis I employs the same enzymes as does DSB repair. Many biologists consider the main function of sexual reproduction is to provide this mechanism for maintaining the integrity of the genome.

Tables Mechanisms of Biological Evolution Gene Regulation in E.coli :

mispairing

2007-11-12T15:05:00.000-12:00

Mispairing refers to the presence of at least one nucleotide in one strand of a DNA molecule, which is not the complement of the nucleotide at the corresponding locus in the other strand.

Slipped strand mispairing occurs during DNA replication. Regions of DNA that are capable of assuming hairpin-like secondary structures are particularly prone to this error because displacement of the strands disrupts alignment of bases. Mispairing results in the repeated replication of the same stretch of DNA, and provides an explanation for satellite DNA.

Deletion and insertion mutations, indels, often occur in repetitive sequences. For example, deletion of "AT" from the sequence "ATAT" in the CFTR gene. Such mutations are most often caused by a "replication slippage", where the new strand mispairs with the template strand at repetitive sequences.

Tandem repeat sequences are particularly prone to high mutation rates because of mispairing and replication slippage. Slippage can cause mispairing of several repeats. Forward slippage results in deletion mutations, while backward slippage results in insertions. Replication slippage results in mispairing not because the nucleotides are altered, but because the number of repeats may vary between one strand and the other. Such repeats are retained in sections of the genome that can tolerate variability.

Replication slippage is mainly responsible for microsatellite polymorphisms, which are also called short tandem repeats (STR) or simple sequence repeats (SSR). In microsatellites, the repeat unit comprises only 1 to 6 bp and the whole repetitive region spans less than 150 bp, while minisatellites range from 1 to 20 kb, and satellites span from 100 kb to more than 1 Mb. SSRs occur throughout the genome, while tandem repeats occur in telomeres and centromeres. The nucleotide sequence of repeats is fairly well conserved across a species, but variation in the length of the repeat is common, as in VNTRs, or variable number tandem repeats.

Once an alteration (such as a point-mutation) occurs within a tandem repeat, the cell's replication machinery is able align the two DNA strands and the alteration will be replicated and inherited. Subsequent deletion of the alignment-promoting alteration would restore slippage. Thus, purity of repetition indicates a lengthy history of deletion and expansion. Strands of repeated sequences can code for polypeptides with repeated amino acids, and the ratio of such poly-amino-acid chains can regulate transcription factors. Polyglutamine can increase the rate of transcription, while polyalanine reduces it. Polyadenylation is a stage of RNA processing in which the 3’ end of the pre-mRNA is cleaved before a stretch of adenosines are added to the end of the molecule.

Animation of slipped strand DNA mispairing DNA Animation :
Table Mechanisms of Biological Evolution : Gene Regulation in E.coli :

External : Tandem repeats and morphological variation

Recombination

2007-11-07T19:46:00.000-12:00

Recombination occurs during meiosis and involves a shuffling of genes, resulting in genetic variation.

Table Mechanisms of Biological Evolution : Gene Regulation in E.coli :

Substitution

2007-11-06T03:51:00.000-12:00

Substitution mutations involve the replacement of one or more nucleotides with an equal number of different nucleotides – most substitutions involve a change in only one nucleotide (point mutations, single nucleotide polymorphisms).

Transition mutations involve the substitution of a pyrimidine nucleotide for a pyrimidine, or a purine nucleotide for a purine. Transversion mutations involve switching between a pyrimidine nucleotide and a purine.

Substitution mutations generate silent, missense, or nonsense mutations depending upon the consequences of the substitutions. Silent mutations code for the same amino acid in the protein; missense for different amino acids, which may or may not alter the activity of a protein; and, nonsense for a stop codon, which alters the code to that for a truncated protein. Accordingly, substitution mutations can be neutral, beneficial, or deleterious.

Missense point mutations can transform the Ras proto-oncogene into the Ras oncogene. Mutations of Ras proto-oncogenes are common → H-RAS, N-RAS, and K-RAS oncogenes. Inappropriate activation of the Ras gene plays a key role in signal transduction, proliferation, and malignant transformation. Mutagenic mutation alters the Ras protein so that the GTPase reaction can no longer be stimulated by GAP, increasing the half life of active Ras-GTP mutants and ensuring that this molecular switch remains 'on'. Unchecked proliferation occurs because mutations that prevent GTP hydrolysis favor constitutive activation as RAS-GTP. The commonest neoplastic mutations are at the 12 (G to T transversion, Gly→Val) → GAP insensitive, and the 61 positions → stabilizing against GTP hydrolysis.
Table Mechanisms of Biological Evolution : Gene Regulation in E.coli :

Translocation

2007-11-05T06:56:00.000-12:00

Translocation involves the exchange of sections of genetic material between non-homologous chromosomes.

In balanced translocations, the total complement of a cell's genetic material is normal, with material merely located on non-homologous chromosomes. In unbalanced translocations, which are associated with disease, cells contain an increased or reduced complement of genetic material. Translocations are also classified as Robertsonian (resulting from fusion of acrocentric chromosomes) or reciprocal (resulting from exchange of segments of chromosomal arms).

Table Mechanisms of Biological Evolution : Gene Regulation in E.coli :

Population Genetics and Formulae

2007-10-31T23:59:00.000-12:00

Evolution is expected to occur when selection acts on a trait that has a heritable basis of phenotypic variation. Quantitative genetic models allow an evolutionary trajectory to be predicted from the strength of selection and the amount of genetic variance, usually expressed as the heritability, h2 [1]. However, while simple theoretical models assume a constant environment, environmental heterogeneity has long been recognised as an important factor influencing the evolutionary dynamics of fitness-related traits in the wild [2]. Specifically, selection can vary considerably from year to year within a population [3,4], and it is increasingly recognised that environmental conditions also influence the heritability on which any response to selection depends [5,6]. Although these observations generate an expectation of an environment-driven coupling of the magnitude of selection and heritability, to our knowledge, no prior study has combined estimates of trait heritability with estimates of the strength of selection across a range of environmental conditions in order to fully assess the evolutionary implications of environmental heterogeneity.
A. J. Wilson, J. M. Pemberton, J. G. Pilkington, D. W. Coltman, D. V. Mifsud, T. H. Clutton-Brock, L. E. B. Kruuk. Environmental Coupling of Selection and Heritability Limits Evolution . PLoS Biology Volume 4 Issue 7 JULY 2006

Table Mechanisms of Biological Evolution : Gene Regulation in E.coli :

Mendel's Laws

2007-10-30T23:58:00.000-12:00

Mendel's First Law - the law of segregation:
During gamete formation each member of the allelic pair separates from the other member to form the genetic constitution of the gamete.

Right: punnet square showing combinations of alleles for a diploid organism with one or another variant of a single allele, 'A' or 'a' from each parent:
Statistically, hyrid offspring will possess
1 AA : 2 Aa or aA : 1 aa

If 'A' is dominant and 'a' is recessive, then statistically 1/4 of the offspring will have both dominant combinations (AA), 1/2 of the offspring will display the dominant trait yet carry the recessive trait by possessing one dominant and one recessive combination (Aa or aA), and 1/4 of offspring will have two recessive genes (aa)

Mendel's Second Law - the law of independent assortment:
During gamete formation the segregation of the alleles of one allelic pair is independent of the segregation of the alleles of another allelic pair.

Combinations of alleles for a diploid organism with one or another of two alleles from each parent produces the 9:3:3:1 ratio for the two dihybrids.
Offspring:
9/16 with both dominant traits:
A_B_ = AABB, AABb, AaBb, AaBB, AAbB, AAbB, aABb, AabB, aAbB
3/16 with dominant trait 'A' and recessive trait 'b': A_bb = AAbb, Aabb, aAbb
3/16 with dominant trait 'B' and recessive trait 'a': aaB_ = aaBb, aabB, aaBB
1/16 with both recessive traits ab: aabb

Tables Mechanisms of Biological Evolution : Gene Regulation in E.coli :

Epistasis

2007-10-30T23:50:00.000-12:00

Epistasis is defined as the influence of the genotype at one locus on the effect of a mutation at another locus. Thus, epistasis is the interaction between two or more genes to control a single phenotype.

Crossing dihybrids produces a modified Mendelian ratio – a 9:3:3:1 ratio for two dihybrids, in accordance with Mendel's second law, the law of independent assortment.

Epistasis plays a crucial role in a variety of evolutionary phenomena such as speciation, population bottle necks, and the evolution of genetic architecture – the evolution of dominance, canalization, and genetic correlations.

Tables Mechanisms of Biological Evolution : Gene Regulation in E.coli :
Algorithms of Evolution: * epistasis * multilinear epistatic model

Bottleneck

2007-10-23T10:04:00.000-12:00

A bottleneck occurs when a disaster has killed individuals by chance and not on the basis of their adaptation. This randomly eliminates gene combinations, leaving a non-representative sampling of the parent gene pool. A bottleneck is a mechanism of genetic drift.

Tables Mechanisms of Biological Evolution : Gene Regulation in E.coli :

Founder effect

2007-10-19T09:03:00.000-12:00

The founder effect is a mechanism of genetic drift that operates when a small sub-group of a population, containing a random and non-representative sampling of genes, is reproductively isolated from the parent population.

Tables Mechanisms of Biological Evolution : Gene Regulation in E.coli :

Persistence of functional gene duplicates

2007-10-17T20:03:00.000-12:00

Fitting In: Newly Evolved Genes Adopt A Variety Of Strategies To Remain In The Gene Pool: modified: "To determine the basis for the persistence of functional gene duplicates in the genome, three scientists at the Institute of Molecular Systems Biology at the Swiss Federal Institute of Technology in Zürich have collaborated on the largest systematic analysis of duplicated gene function to date. Using an integrative combination of computational and experimental approaches, they classified duplicate pairs of genes involved in yeast metabolism into four functional categories: (1) back-up, where a duplicate gene copy has acquired the ability to compensate in the absence of the other copy, (2) subfunctionalization, where a duplicate copy has evolved a completely new, non-overlapping function, (3) regulation, where the differential regulation of duplicates fine-tunes pathway usage, and (4) gene dosage, where the increased expression provided by the duplicate gene copy augments production of the corresponding protein.Their results, which appear in the October issue of the journal Genome Research, indicate that no single role prevails but that all four of the mechanisms play a substantial role in maintaining duplicate genes in the genome."

Tables Mechanisms of Biological Evolution : Gene Regulation in E.coli : Cold Spring Harbor Laboratory :

Phyletic gradualism

2007-09-09T16:01:00.000-12:00

As described by Eldredge and Gould, the essential features of phyletic gradualism are:
1. New species arise by the transformation of an ancestral population into its modified descendants.
2. The morphological transformation is even and slow.
3. The transformation involves large numbers of organisms, usually the entire ancestral population.
4. The transformation occurs over all or a large part of the ancestral species' geographic range.

The above points are sometimes mistakenly ascribed to Darwinian evolutionary theory. However, Darwin’s description of, “very slow, intermittent action of natural selection” [ Ch. 4 ] disagrees with point 2, and another passage in Darwin’s Origin of Species disagrees with points 3 and 4. (adapted from here)

Tables Mechanisms of Biological Evolution : Gene Regulation in E.coli :

Diagrams & Tables: Biological variation

2006-07-30T16:28:00.000-12:00

Diagrams & Tables: Biological variation

STANFORD RESEARCHERS DEVELOP SYSTEM FOR FIELD TESTING MECHANISMS OF EVOLUTION

2006-05-07T06:15:00.000-12:00

STANFORD RESEARCHERS DEVELOP SYSTEM FOR FIELD TESTING MECHANISMS OF EVOLUTION: "Kingsley said they found a number of parallels between traditional laboratory genetics and the traits they examined in the stickleback populations. For example, many of the traits could be traced to major chromosome regions - indicating that evolution can occur through changes of large effect, not just as a series of small changes. Their findings also indicate that genetic control of body regions appears to be modular. "

reference articles

2006-01-31T23:59:00.000-12:00

»» STANFORD RESEARCHERS DEVELOP SYSTEM FOR FIELD TESTING MECHANISMS OF EVOLUTION »» HORIZONTAL GENE TRANSFER, GENOME INNOVATION AND EVOLUTION »» New Evidence For One-way Evolution »» MICROBIOLOGY: ON TYPE IV SECRETION »» Where 'Jumping Genes' Fear To Tread »» New Cellular Evolution Theory Rejects Darwinian Assumptions »» Mobile DNA in obligate intracellular bacteria »» Symbiosis: Teaming up in defence »» Horizontal gene transfer, genome innovation and evolution »» Metabolic maps and functions of the Plasmodium falciparum apicoplast »» Hatena : Search : Endosymbiosis »» Search results : endosymbiosis : Nature »» RE-EVALUATING PROKARYOTIC SPECIES »» STUDYING PLASMID HORIZONTAL TRANSFER IN SITU: A CRITICAL REVIEW »» MECHANISMS OF, AND BARRIERS TO, HORIZONTAL GENE TRANSFER BETWEEN BACTERIA

HORIZONTAL GENE TRANSFER, GENOME INNOVATION AND EVOLUTION

2006-01-31T04:50:00.000-12:00

Nature Reviews Microbiology - Reviews: "To what extent is the tree of life the best representation of the evolutionary history of microorganisms? Recent work has shown that, among sets of prokaryotic genomes in which most homologous genes show extremely low sequence divergence, gene content can vary enormously, implying that those genes that are variably present or absent are frequently horizontally transferred.
Traditionally, successful horizontal gene transfer was assumed to provide a selective advantage to either the host or the gene itself, but could horizontally transferred genes be neutral or nearly neutral? We suggest that for many prokaryotes, the boundaries between species are fuzzy, and therefore the principles of population genetics must be broadened so that they can be applied to higher taxonomic categories.

Summary
Tree-like binary schemes for taxonomic classification have an illustrious history in evolutionary biology, but they do not provide a complete representation of life's history, especially for prokaryotes. Some genes within an organism have tree-like histories that differ from the histories of other genes within the same organism, owing to horizontal gene transfer (HGT). Although all types of genes can be susceptible to horizontal transfer, different types of genes and groups of organisms vary in their propensity for HGT.
Phylogenetic analysis of a concatenation of genes with differing gene histories has the potential to create artifactual histories that reflect neither the history of the organism nor the history of the gene. Methods of phylogenetic reconstruction that do not insist on tree-like phylogenies but explicitly allow for reticulation events promise to yield a more realistic reconstruction of much of life's history.

Phylogenetic reconstruction methodology — and therefore the accurate detection of historical HGT events — can benefit from a better understanding of phylogenetic signal as it relates to rates of change of characters and taxonomic sampling.

The abundance and atypical composition of genes that are transient in prokaryotic genomes such as that of Escherichia coli lead one to wonder whether such genes (and horizontally transferred genes in general) are deleterious, selected for or neutral on transfer. Recent studies seem to indicate extensive gene swapping and few selective sweeps, arguing that many transferred genes might be nearly neutral in selective effect.
Quantitative methods for analysing the frequency and nature of HGT events in microbial communities are needed. Quantitative descriptions yield precise predictions that can be tested statistically, and will help to resolve disputes about the frequency and importance of HGT to microbial evolution by improving clarity of expression, as well as enforcing statistical decision criteria."

J. Peter Gogarten & Jeffrey P. Townsend about the authors HORIZONTAL GENE TRANSFER, GENOME INNOVATION AND EVOLUTION
Nature Reviews Microbiology 3, 679-687 (2005); doi:10.1038/nrmicro1204

New Evidence For One-way Evolution

2006-01-25T11:11:00.000-12:00

UCSD Biologists Find New Evidence For One-way Evolution: "Irreversible loss of complex traits, which result from the combined interaction of several genes, is an old and at times controversial scientific question. While the late evolutionary biologist Stephen Jay Gould popularized the hypothesis of irreversibility, known as Dollo's Law, studies that use current methods to reconstruct the evolution of complex traits often fail to support it. This is because it is often difficult to reconstruct characteristics of extinct ancestors with any certainty."

MICROBIOLOGY: ON TYPE IV SECRETION

2006-01-08T06:25:00.000-12:00

MICROBIOLOGY: ON TYPE IV SECRETION: "Possibly the most familiar example of such an apparatus is the conjugation machinery, a multiprotein complex that facilitates the transfer of genetic material from one bacterial cell to another. In the natural environment, this form of horizontal gene transfer promotes genetic diversity and survival. "

Where 'Jumping Genes' Fear To Tread

2006-01-05T14:15:00.000-12:00

Where 'Jumping Genes' Fear To Tread: "Scientists from the University of Queensland report in the journal Genome Research that large segments of the human genome are conspicuously devoid of ubiquitous mobile DNA elements called transposons. The locations of these regions are highly conserved among mammalian species and are enriched in genes crucial for the regulation of developmental processes.

Transposons, often called "jumping genes," are DNA sequences that have the capacity to move from one chromosomal site to another. More than three million copies of transposons have accumulated in humans throughout the course of evolution and now comprise an estimated 45% of the total DNA content in the human genome.

These mobile genetic elements are scattered throughout the human genome -- separated, on average, by only 500 base pairs. But Dr. John Mattick's laboratory at the University of Queensland, Australia, identified long tracks of genomic segments (greater than 10 kilobases in length) that lack transposable elements. His team identified 860 such sequences in humans, 993 in mice, and 559 in opossums. They named these segments TFRs, or transposon-free regions.

"Strikingly," says Mattick, "many TFRs in the human genome occur in the same position in the mouse and opossum genomes, despite the fact that transposons entered each lineage independently, after each species diverged from a common ancestor. It appears that many TFRs are evolutionarily conserved features that existed prior to -- and have been largely maintained since -- the divergence of eutherian mammals and marsupials approximately 170 million years ago."

The opossum was chosen for inclusion in the analysis because it is a marsupial that has a similar load of transposable elements compared to mice and humans but is evolutionarily distant from the two species. In contrast, the genomes of chicken and fish, which diverged from humans more than 300 million years ago, do not have a significant density of transposons.

Given the strong evolutionary conservation of the TFRs, Mattick's group hypothesized that they are regions of significant biological importance. Upon further characterizing the TFRs, they discovered that many (85%) overlapped at least one annotated gene and that almost all (94%) overlapped at least one known RNA transcript. In addition, the TFRs were enriched in microRNAs, in genes that encode proteins with putative DNA-binding activity, and in genes that are involved in developmental processes. Another striking feature of TFRs was that they are associated with ultra-conserved regions, or genomic segments longer than 200 base pairs with 100% identity between human, mouse, and rat. All of these observations strongly support an important role for TFRs in critical biological processes.

"The majority of the TFRs lie outside of protein-coding sequences, so they presumably represent regions of regulatory information or RNA transcripts that cannot be disrupted. However, it's difficult to explain mechanistically the requirement of 10 or more kilobases of uninterrupted sequence in terms of the current paradigms of transcriptional regulation," explains Mattick. "It appears that TFRs might be the passive signatures of one or more poorly understood mechanisms of gene regulation that operate in higher organisms, suggesting a wider role for noncoding sequences than has hitherto been appreciated." "

External : Transposons part 1, transposons part 2 : Barbara McClintock and mobile genetic elements :

New Cellular Evolution Theory Rejects Darwinian Assumptions

2006-01-05T13:25:00.000-12:00

New Cellular Evolution Theory Rejects Darwinian Assumptions: "Life did not begin with one primordial cell. Instead, there were initially at least three simple types of loosely constructed cellular organizations. They swam in a pool of genes, evolving in a communal way that aided one another in bootstrapping into the three distinct types of cells by sharing their evolutionary inventions. The driving force in evolving cellular life on Earth, says Carl Woese, a microbiologist at the University of Illinois at Urbana-Champaign, has been horizontal gene transfer, in which the acquisition of alien cellular components, including genes and proteins, work to promote the evolution of recipient cellular entities. Woese presents his theory of cellular evolution, which challenges long-held traditions and beliefs of biologists, in the June 18 issue of the Proceedings of the National Academy of Sciences.

Cellular evolution, he argues, began in a communal environment in which the loosely organized cells took shape through extensive horizontal gene transfer. Such a transfer previously had been recognized as having a minor role in evolution, but the arrival of microbial genomics, Woese says, is shedding a more accurate light. Horizontal gene transfer, he argues, has the capacity to rework entire genomes. With simple primitive entities this process can "completely erase an organismal genealogical trace."
His theory challenges the longstanding Darwinian assumption known as the Doctrine of Common Descent – that all life on Earth has descended from one original primordial form. "

Original news release

Mobile DNA in obligate intracellular bacteria

2006-01-05T06:18:00.000-12:00

Search results : endosymbiosis : Nature: "7.Mobile DNA in obligate intracellular bacteria
Seth R. Bordenstein, William S. Reznikoff
SUMMARY: The small genomes of obligate intracellular bacteria are often presumed to be impervious to mobile DNA and the fluid genetic processes that drive diversification
CONTEXT: ...Moran, N. A. & Baumann, P. . Curr. Opin. Microbiol. 3, 270�275 (2000). Buchner, P. Endosymbiosis of Animals with Plant Microorganisms (Interscience Publishers, John Wiley...
Nature Reviews Microbiology 3, 688-699 (01 Sep 2005) Review
Full Text PDF "

Symbiosis: Teaming up in defence

2006-01-05T06:16:00.000-12:00

Search results : endosymbiosis : Nature: "5.Symbiosis: Teaming up in defence
Susan Jones
CONTEXT: ...are renowned for secondary metabolite production, but this is the first example of an endosymbiosis involving a streptomycete. Prior to metamorphosis, larvae spin a cocoon,...
Nature Reviews Microbiology 3, 367-367 (01 May 2005) Highlights
Full Text PDF "

Horizontal gene transfer, genome innovation and evolution

2006-01-05T06:15:00.000-12:00

Search results : endosymbiosis : Nature: "4.Horizontal gene transfer, genome innovation and evolution
J. Peter Gogarten, Jeffrey P. Townsend
SUMMARY: To what extent is the tree of life the best representation of the evolutionary history of microorganisms? Recent work has shown that, among sets
CONTEXT: ...in cellular evolution, that is, the mitochondria and plastids, are the result of endosymbiosis. Throughout the decades, MUTUALISM and RETICULATION have often been...
Nature Reviews Microbiology 3, 679-687 (01 Sep 2005) Review
Full Text PDF "

Metabolic maps and functions of the Plasmodium falciparum apicoplast

2006-01-05T06:14:00.000-12:00

Search results : endosymbiosis : Nature: "3.: Metabolic maps and functions of the Plasmodium falciparum apicoplast
Stuart A. Ralph, Giel G. van Dooren, Ross F. Waller, Michael J. Crawford, Martin J. Fraunholz, Bernardo J. Foth, Christopher J. Tonkin, David S. Roos, Geoffrey I. McFadden
SUMMARY: Discovery of a relict chloroplast (the apicoplast) in malarial parasites presented new opportunities for drug development. The apicoplast — although no longer photosynthetic —
CONTEXT: ...of the malaria parasite's distant photosynthetic ancestry. Plastids are derived from the endosymbiosis of cyanobacteria, and the apicoplast is no exception. Importantly,...
Nature Reviews Microbiology 2, 203-216 (01 Mar 2004) Review
Full Text PDF "

Hatena : Search : Endosymbiosis

2006-01-05T06:12:00.000-12:00

Search results : endosymbiosis : Nature: "2.In brief
CONTEXT: ...I. Science 310, 287 (2005) This study describes the formative stages of a secondary endosymbiosis between a protist, here referred to as Hatena ('enigmatic' in Japanese),...
Nature Reviews Microbiology 3, 911-911 (01 Dec 2005)
Full Text PDF "

Search results : endosymbiosis : Nature

2006-01-05T06:10:00.000-12:00

Search results : endosymbiosis : Nature: "
1. Genome watch: Fitting the niche by genomic adaptation
Nicholas Thomson, Stephen Bentley, Matthew Holden, Julian Parkhill
SUMMARY: Studying microbial genomics has shown that the genomes of bacteria are extremely dynamic in evolutionary terms. Many research groups have linked the adaptation of
CONTEXT: ...the authors to produce a hypothetical minimal set of genes that are necessary to sustain endosymbiosis. Curiously, the genome lacks several genes that are involved in...
Nature Reviews Microbiology 1, 92-93 (01 Nov 2003)
Full Text PDF "

RE-EVALUATING PROKARYOTIC SPECIES

2006-01-05T06:06:00.000-12:00

Nature Reviews Microbiology - Perspectives: "There is no widely accepted concept of species for prokaryotes, and assignment of isolates to species is based on measures of phenotypic or genome similarity. The current methods for defining prokaryotic species are inadequate and incapable of keeping pace with the levels of diversity that are being uncovered in nature. Prokaryotic taxonomy is being influenced by advances in microbial population genetics, ecology and genomics, and by the ease with which sequence data can be obtained. Here, we review the classical approaches to prokaryotic species definition and discuss the current and future impact of multilocus nucleotide-sequence-based approaches to prokaryotic systematics. We also consider the potential, and difficulties, of assigning species status to biologically or ecologically meaningful sequence clusters."

Dirk Gevers, Frederick M. Cohan, Jeffrey G. Lawrence, Brian G. Spratt, Tom Coenye, Edward J. Feil, Erko Stackebrandt, Yves Van de Peer, Peter Vandamme, Fabiano L. Thompson & Jean Swings RE-EVALUATING PROKARYOTIC SPECIES Nature Reviews Microbiology 3, 733-739 (2005); doi:10.1038/nrmicro1236

STUDYING PLASMID HORIZONTAL TRANSFER IN SITU: A CRITICAL REVIEW

2006-01-05T06:04:00.000-12:00

Nature Reviews Microbiology - Reviews: "This review deals with the prospective, experimental documentation of horizontal gene transfer (HGT) and its role in real-time, local adaptation. We have focused on plasmids and their function as an accessory and/or adaptive gene pool. Studies of the extent of HGT in natural environments have identified certain hot spots, and many of these involve biofilms. Biofilms are uniquely suited for HGT, as they sustain high bacterial density and metabolic activity, even in the harshest environments. Single-cell detection of donor, recipient and transconjugant bacteria in various natural environments, combined with individual-based mathematical models, has provided a new platform for HGT studies."

Søren J. Sørensen, Mark Bailey, Lars H. Hansen, Niels Kroer & Stefan Wuertz STUDYING PLASMID HORIZONTAL TRANSFER IN SITU: A CRITICAL REVIEW Nature Reviews Microbiology 3, 700-710 (2005); doi:10.1038/nrmicro1232

MECHANISMS OF, AND BARRIERS TO, HORIZONTAL GENE TRANSFER BETWEEN BACTERIA

2006-01-05T06:03:00.000-12:00

Nature Reviews Microbiology - Reviews: "Bacteria evolve rapidly not only by mutation and rapid multiplication, but also by transfer of DNA, which can result in strains with beneficial mutations from more than one parent. Transformation involves the release of naked DNA followed by uptake and recombination. Homologous recombination and DNA-repair processes normally limit this to DNA from similar bacteria. However, if a gene moves onto a broad-host-range plasmid it might be able to spread without the need for recombination. There are barriers to both these processes but they reduce, rather than prevent, gene acquisition."

Christopher M. Thomas & Kaare M. Nielsen MECHANISMS OF, AND BARRIERS TO, HORIZONTAL GENE TRANSFER BETWEEN BACTERIA Nature Reviews Microbiology 3, 711-721 (2005); doi:10.1038/nrmicro1234

MOBILE GENETIC ELEMENTS: THE AGENTS OF OPEN SOURCE EVOLUTION

2006-01-05T06:00:00.000-12:00

Nature Reviews Microbiology - Reviews: "Horizontal genomics is a new field in prokaryotic biology that is focused on the analysis of DNA sequences in prokaryotic chromosomes that seem to have originated from other prokaryotes or eukaryotes. However, it is equally important to understand the agents that effect DNA movement: plasmids, bacteriophages and transposons. Although these agents occur in all prokaryotes, comprehensive genomics of the prokaryotic mobile gene pool or 'mobilome' lags behind other genomics initiatives owing to challenges that are distinct from cellular chromosomal analysis. Recent work shows promise of improved mobile genetic element (MGE) genomics and consequent opportunities to take advantage � and avoid the dangers � of these 'natural genetic engineers'. This review describes MGEs, their properties that are important in horizontal gene transfer, and current opportunities to advance MGE genomics.

Although MGEs are the main agents of horizontal gene transfer (HGT), relatively few have been sequenced and analysis of their genomic and phylogenetic properties lags behind that of organismal chromosomes. Specifically, the major databases do not curate plasmid and phage nucleic acid or protein sequences. Sequencing MGE genomes presents unique challenges because phages require suitable hosts for propagation and plasmids must be physically separated from each other and from the host chromosomal DNA. The relatively small size of MGEs (5−500 kb) and their varied GC content thwart current automated annotation algorithms."

Laura S. Frost, Raphael Leplae, Anne O. Summers & Ariane Toussaint MOBILE GENETIC ELEMENTS: THE AGENTS OF OPEN SOURCE EVOLUTION Nature Reviews Microbiology 3, 722-732 (2005); doi:10.1038/nrmicro1235

External : Transposons part 1, transposons part 2 : Barbara McClintock and mobile genetic elements :

GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS

2006-01-05T05:58:00.000-12:00

Nature Reviews Microbiology - Reviews: "Horizontal gene transfer is an important mechanism for the evolution of microbial genomes. Pathogenicity islands � mobile genetic elements that contribute to rapid changes in virulence potential � are known to have contributed to genome evolution by horizontal gene transfer in many bacterial pathogens. Increasing evidence indicates that equivalent elements in non-pathogenic species � genomic islands � are important in the evolution of these bacteria, influencing traits such as antibiotic resistance, symbiosis and fitness, and adaptation in general. This review discusses the recent lessons that have been learned from pathogenicity islands in pathogenic microorganisms and how they apply to the role of genomic islands in commensal, symbiotic and environmental bacteria.

Summary
Genomic islands (GEIs) are characterized by their large size (>10 kb), their frequent association with tRNA-encoding genes and a different G+C content compared with the rest of the chromosome. Many genomic islands are flanked by repeat structures and carry fragments of other mobile and accessory genetic elements, such as bacteriophages, plasmids and insertion sequence (IS) elements.

Some GEIs can excise themselves spontaneously from the chromosome and can be transferred to other suitable recipients. GEIs contribute to bacterial genome plasticity and, together with other mobile and accessory genetic elements, to the 'horizontal gene pool' of a given bacterial population.

A hypothetical 'life cycle' of GEIs includes the insertion of mobile genetic elements into the bacterial chromosome. Through rearrangements and consecutive insertion and deletion events, the organization and gene content of the original element becomes modified and can lose the features of mobile elements. Owing to the action of bacteriophage integrases that are encoded on genomic islands, these genetic elements can be deleted from the chromosome and, upon transfer into a suitable host, can be chromosomally inserted by site-specific recombination.

GEIs contribute to fitness and adaptation. GEIs typically provide a gain-of-function to the host bacterium. As GEIs promote the transfer of multi-gene families, entire phenotypes can be changed in a single-step gene-transfer event.

GEIs are expected to have a role in ecological niches where microbial cell numbers and diversity are high and/or in environments that are constantly changing. The GEIs identified so far are relevant in the context of pathogenicity, symbiosis, antibiotic resistance, xenobiotic degradation, and primary and secondary metabolism. It is expected that the functional diversity of GEIs is even greater than is currently known.

As GEIs are widely distributed in pathogenic, non-pathogenic and environmental microorganisms, they represent a paradigm rather than a paradox for microbial evolution, underlining the importance of horizontal gene transfer in this process."

Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jörg Hacker GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038/nrmicro884

FROM PIECES TO PATTERNS: EVOLUTIONARY ENGINEERING IN BACTERIAL PATHOGENS

2006-01-05T05:52:00.000-12:00

Nature Reviews Microbiology - Perspectives: "Evolutionary microbiology is a basic science that is increasingly forming the basis for new developments in public-health microbiology. Medical advances might depend on an understanding of the conditions that are required for the emergence and maintenance of human bacterial pathogens. An understanding of the evolutionary engineering rules that lead to virulence or drug resistance � specifically with bacteria in mind � are therefore important and are examined in this article."

Fernando Baquero FROM PIECES TO PATTERNS: EVOLUTIONARY ENGINEERING IN BACTERIAL Nature Reviews Microbiology 2, 510-518 (2004); doi:10.1038/nrmicro909 PATHOGENS

SMALL CHANGE: KEEPING PACE WITH MICROEVOLUTION

2006-01-05T05:46:00.000-12:00

Nature Reviews Microbiology - Reviews: "Bacterial genomes are increasingly viewed in terms of the integration of accessory and dispensable genetic elements into a conserved genomic core. This duality provides both the evolutionary stability that is required for the maintenance of essential functions and the flexibility that is needed for rapid exploitation of new niches. This review focuses on combining genome sequencing, microarray and multilocus sequence data to explore microevolutionary divergence in single species and genera.

Summary
Bacterial genomes are composed of essential 'core' genes, encoding functions relating to central metabolism and informational processing, and 'accessory' genes that commonly encode supplementary metabolic pathways and virulence factors. 'Foreign' genes in bacterial genomes can be identified by atypical base composition; these might have been imported from quite distant bacterial taxa.

Three main tools for examining the microevolution (evolution within species) of bacteria are complete genome sequencing, microarray analysis (which detects changes in gene content) and multi-locus sequencing of 'core' genes. These three approaches have advantages and disadvantages and are most powerfully used in combination.

Most bacterial populations consist of a limited number of widespread clonal complexes on the basis of sequence variation in a sample of core genes. These clonal complexes are generally robust with respect to gene choice and are meaningful biological units. These clusters might represent adaptations to specific microniches, and be set on independent evolutionary trajectories.

Despite high degrees of clonality, analysis of clonal diversification and phylogenetic approaches examining the relationships between clones both indicate that homologous recombination is an important evolutionary force in many bacterial populations. It is possible that sampling bias leads to an artificially high degree of clonality, but also that the selective origin of clones allows them to withstand the homogenizing effects of recombination.

Given the clonal structure of bacterial populations, comparative genomic analysis is most fruitfully carried out with reference to clonal assignments. Such an approach allows a consideration of likely ecological adaptations between isolates and a broad temporal perspective to microevolutionary studies."

Edward J. Feil SMALL CHANGE: KEEPING PACE WITH MICROEVOLUTION Nature Reviews Microbiology 2, 483-495 (2004); doi:10.1038/nrmicro904

Mechanisms of Atheism

2006-01-04T11:04:00.000-12:00

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mediawatchwatch.org.uk
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Men: Leave Church
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mindcore
MINISTER OF RANTS
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mister jebs blog
Modern Agnostic
Moiz Khan - The godless Liberal
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mushinronsha
My Case Against God
My Dirty Little Secret . . .
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Naturalistic Atheism
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New Humanist Blog
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News From the Front - Fair and Balanced
Nice Marmot
Nicest Girl and Destroyer of Planets
Nick Harding
Nihilist Future
Nirmukta
No Double Standards
No Gods Allowed
No More Fake Gods
No More Hornets
No more Mr. Nice Guy!
Nobody's There...
NoBS Radio Show
NoGodBlog.com
Non Credo Deus
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North Alabama Rant
Not really, Alice.
Notes from an Evil Burnee
Nothing Is Sacred
Null Session
Nullifidian
Nut Watch
N^4
Obscene Desserts
Obsessed with reality
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Of Microbes and Men
Oh The Stupidity!
ohm sweet ohm
oldcola
olio
Oliver Benen
OMG!
on the street and in my head
One Fewer God
onegoodmove
Onwards and Forwards
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Oracle and Atheism
Order of St. Nick
Oriented x4
Our Freedom of Espresso
Outchurched
Oz Atheist's Weblog
P!
PA Nonbelievers
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Persephone's Box
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Phoesune - My DeConversion
phreedom.us
physicshead
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Pinoy Atheist
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Plain Perspectives
Planet Atheism
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Plonka's Blog
Podblack Blog
Polypyloctomy
PONZO
Pooflingers Anonymous
Post Thought
Primordial Blog
Principia Atheologica
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Protium the Heathen
Psycho Dave's Commentary
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PTET - godless culture
PURPOSE OF LIFE
QuarkScrew
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quird
R A V E N M O O N
Radical Atheist
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Raising Kids without Religion
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Ramblings of an Atheist Undergrad
Random Intelligence
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Robert's Thought's
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skepticisme
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Suburban Panic!
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Terminal Atheist
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Yet Another Blog You Call This Culture?
You Made Me Say It
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Zatheist
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Zen of Zero
zenbullets
'Satan Is Real' Atheist Music Blog

Evolution of Atheism

1990-01-01T08:37:00.000-12:00

Gray Matters
Adeistic
Avidity
Eine Kleine Nattermusing
eMusings
eVolition
Galaria
Godspell Follies
MetaThoughts
Mimble Wimble
Naturalism
Neologisms
palimpsest
Sechuam
Sintheist
Tabula Flexuosa
Weltschauung

associated

1990-01-01T01:00:00.003-12:00

Associated science sites • Abiogenesis and Evolution • Algorithms of Evolution • Archea Eubacteria • Cancer • Cell Biology • Complex Systems • Cyanobacteria • Diagrams Tables • Endosymbiosis • Enzymes • Evo Devo • Evolution in Action • Fat • Geology • Glossary • Immunology • Life Chemistry • Medical Science • Mechanisms of Evolution • Molecule • Molecular Biology • Molecular Paths • Neurosciences • Organics • Origin of Life • Paleogeology • Pathways • Photosynthesis • Protein • Receptor • Rocks & Minerals • SET • Signaling • Sleep • Stem & Progenitor Cells • Stromatolites • Taxonomy Phylogeny • Tissue • Virus •

And some philosophy/general interest sites: Avidity : Eine Kleine Nattermusing : eMusings : Galaria : Godspell Follies : Harper's Folly : Mimble Wimble : Sintheist : Tabula Flexuosa :

oo

1990-01-01T01:00:00.002-12:00

• Abiogenesis and Evolution • Algorithms of Evolution • Archea Eubacteria • Cancer • Cell Biology • Complex Systems • Cyanobacteria • Diagrams Tables • Endosymbiosis • Enzymes • Evo Devo • Evolution in Action • Fat • Geology • Galaria • Glossary • Godspell Follies • Harper's Folly • Immunology • Life Chemistry • Medical Science • Mechanisms of Evolution • Mimble Wimble • Molecule • Molecular Biology • Molecular Paths • Organics • Origin of Life • Paleogeology • Pathways • Photosynthesis • Protein • Receptor • Rocks & Minerals • SET • Signaling • Sleep • Stem & Progenitor Cells • Stromatolites • Tabula Flexuosa • Taxonomy Phylogeny • Tissue • Virus •

Glossary

1990-01-01T00:02:00.000-12:00

Allopatric speciation occurs when a geographical barrier sub-divides a parent species, resulting in geographic and reproductive isolation such that the descendent species can no longer interbreed upon removal of the barrier.

Anagenesis differs from cladogenesis in that one species progressively transforms into a replacement species when sufficient gene mutations fix in the descendant population. At this point, the ancestral species has become extinct. This mechanism is distinct from the increase in numbers of species generated by cladogenetic branching events.

Cladogenesis is the mechanism of speciation in which one or more lineages (clades) arise from an ancestral line. Such speciation events increase the variety of plants or animals through branching of the phylogenetic tree. Cladogenesis is differentiated from anagenesis, which is the in toto replacement of one species by an anatomically distinct species.

Monophyletic taxon or clade: an accurate grouping of only (opp. polyphyletic) and all (opp. paraphyletic) descendents of a shared common ancestor. A monopyletic group is genetically homogeneous and reflects evolutionary relationships.

Paraphyletic taxon or clade: a monophyletic group that excludes one or more discrete groups descended from the most recent common ancestral species of the entire group. Other descendent species of the most recent common ancestor have been excluded from the paraphyletic taxon, usually because of morphologic distinctiveness.

Phenetic system: groupings of organisms based on mutual similarity of phenotypic (physical and chemical) characteristics. Phenetic groupings may or may not correlate with evolutionary relationships.

Phylogenetic system: groups organisms based on shared evolutionary heritage. DNA and RNA sequencing techniques are considered to give the most meaningful phylogenies.

Phylogenetic separation into evolutionary relationships (clades), based on comparison of genomes is likely to supplant phenotypical (phenetic) taxonomies of the prokaryotes.

Peripatry (paripatry) is a subset of allopatry in which an isolated group has a smaller population than the parent group. Ernst Mayr introduced the term. Peripatric speciation occurs when the smaller sub-group of a species enters a novel niche within the range of the parent species, becoming geographically and reproductively isolated. Peripatric speciation (paripatric) is distinguished from allopatric speciation by the smaller size of the isolate group, and from sympatric speciation, which involves no barrier to breeding.

Polyphyletic taxon: opposite to monophyletic taxon: A polyphyletic group is mistakenly or improperly erected on the basis of homoplasy — characteristics that have arisen despite not sharing a common ancestor. Homoplasy arises because of convergent evolution, parallelism, evolutionary reversals, horizontal gene transfer, or gene duplications. Polyphyletic taxa are genetically heterogeneous because members do not share a common ancestor.

Neontology is a branch of biology that emphasizes the study of modern biota (living or recent organisms) rather than fossilized organisms (paleontology).

Numerical Taxonomies are a common approach to phenetic taxonomy that employ a number of phenotypic characteristics to generate similarity coefficients that may be mapped in dendrograms. Groupings based on numerical taxonomy may or may not correlate with evolutionary relationships.

Taxonomies aim to group organisms according to shared characteristics against the background of biological diversity.

Sympatry involves no geographical separation of sub-populations of individuals. Sympatric speciation events occur most often in plants by the mechanism of polyploidy in which the number of chromosomes is doubled or tripled. John Maynard Smith proposed a model called disruptive speciation, in which homozygotes might have greater fitness than heterozygotes under some environmental conditions.

Item links

1990-01-01T00:00:00.000-12:00

Items
General Mechanisms »» Biological Evolution »» Beyond Darwin and Neo-Darwinism »» Punctuated equilibria »» The modern synthesis »» Basic mechanisms of evolution »» Speciation »» Genetic drift »» Gene flow »» Mutation »» Natural selection »» Horizontal Gene Transfer »» Conjugation »» Transduction »» Transformation »» Non-disjunction »» Genetic Mechanisms : Molecular Genetics »» Important features of the genome and proteome »» Conserved & Consensus »» cooption »» Deletion »» Duplication »» exaptation »» Frameshift »» Insertion »» Inversion »» Meiosis »» mispairing »» pre-adaptation »» Recombination »» Substitution »» Translocation »» Population Genetics : Population Genetics and Formulae »» Mendel's Laws »» Epistasis »» Bottleneck »» Founder effect »» Persistence of functional gene duplicates »» Phyletic gradualism »» Diagrams & Tables: Biological variation »»

Alphabetic – items may be listed more than once under alternative names:
»»» Basic mechanisms of evolution »» Biological Evolution »» Beyond Darwin and Neo-Darwinism »» Bottleneck »» Conjugation »» Conserved & Consensus »» Deletion »» Duplication »» Epistasis »» formulae »» Founder effect »» Frameshift »» Gene flow »» Genetic drift »» genetics »» genome and proteome »» Horizontal Gene Transfer »» Important features of the genome and proteome »» Insertion »» Inversion »» Meiosis »» Mendel's Laws »» mispairing »» Missense Mutation »» modern synthesis »» Molecular Genetics »» Mutation »» Natural selection »» Non-disjunction »» Nonsense Mutation »» Persistence of functional gene duplicates »» Phyletic gradualism »» point mutation »» Population Genetics and Formulae »» proteome and genome »» Punctuated equilibria »» Recombination »» single nucleotide polymorphism »» SNP »» Speciation »» synthesis »» The modern synthesis »» Transduction »» Transformation »» transition »» Translocation »» transversion »»

»» Diagrams & Tables: Biological variation

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