Biological Evolution

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

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.

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Punctuated equilibria

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.)

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The modern synthesis

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

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Basic mechanisms of evolution

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.

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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.

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Speciation

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.

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Genetic drift

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

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

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 :

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Natural selection

“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

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.

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Conjugation

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

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.

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Transformation

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.

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Non-disjunction

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).

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