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
Table Mechanisms of Biological Evolution : Gene Regulation in E.coli :
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 :
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
Table Mechanisms of Biological Evolution : Gene Regulation in E.coli :
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 :
Labels: deletion, germline, insertion, inversion, mutation, non-disjunction, recombination, translocation, transposition
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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.