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==Variation==
==Variation==
Because an individual's [[phenotype]] results from the interaction of their [[genotype]] with the environment, the variation in phenotypes in a population reflects the variation in these organisms' genotypes. The [[modern evolutionary synthesis]] defines evolution as the change over time in this genetic variation. (Stoltzfus A, Mutationism and the dual causation of evolutionary change, Evol. Dev., v. 8, 2006) The frequency of one particular allele will fluctuate, becoming more or less prevalent relative to other forms of that gene. Evolutionary forces act by driving these changes in allele frequency in one direction or another. Variation disappears when an allele reaches the point of [[fixation (population genetics)|fixation]] when it either disappears from the population or replaces the ancestral allele entirely. (Harwood AJ , Factors affecting levels of genetic diversity in natural populations, Philos. Trans. R. Soc. Lond., B, Biol. Sci. v. 353, 1998 [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9533122]
Because an individual's [[phenotype]] results from the interaction of their [[genotype]] with the environment, the variation in phenotypes in a population reflects the variation in these organisms' genotypes. The [[modern evolutionary synthesis]] defines evolution as the change over time in this genetic variation. (Stoltzfus A, Mutationism and the dual causation of evolutionary change, Evol. Dev., v. 8, 2006) The frequency of one particular allele will fluctuate, becoming more or less prevalent relative to other forms of that gene. Evolutionary forces act by driving these changes in allele frequency in one direction or another. Variation disappears when an allele reaches the point of [[fixation (population genetics)|fixation]] when it either disappears from the population or replaces the ancestral allele entirely. (Harwood AJ , Factors affecting levels of genetic diversity in natural populations, Philos. Trans. R. Soc. Lond., B, Biol. Sci. v. 353, 1998 [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9533122]
===Mutation===
===Mutation===
Genetic variation comes from [[randomness|random]] mutations that occur in the genomes of organisms. Mutations are changes in the DNA sequence of a cell's genome and are caused by [[Radioactive decay|radiation]], [[virus]]es, [[transposon]]s and [[mutagen|mutagenic chemicals]], as well as errors that occur during [[meiosis]] or [[DNA replication]]. (Bertram, The molecular biology of cancer, Mol. Aspects Med., v. 21, 2000) (Aminetzach YT, Macpherson JM, Petrov DA, Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila, Science, v. 309 2005)
Genetic variation comes from [[randomness|random]] mutations that occur in the genomes of organisms. Mutations are changes in the DNA sequence of a cell's genome and are caused by [[Radioactive decay|radiation]], [[virus]]es, [[transposon]]s and [[mutagen|mutagenic chemicals]], as well as errors that occur during [[meiosis]] or [[DNA replication]]. (Bertram, The molecular biology of cancer, Mol. Aspects Med., v. 21, 2000) (Aminetzach YT, Macpherson JM, Petrov DA, Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila, Science, v. 309 2005)
===Recombination===
===Recombination===
In asexual organisms, genes are inherited together, or ''linked'', as they cannot mix with genes in other organisms during reproduction. However, the offspring of [[sex]]ual organisms contain a random mixture of their parents' chromosomes that is produced through [[independent assortment]]. In the related process of [[genetic recombination]], sexual organisms can also exchange DNA between two matching chromosomes. These shuffling processes can allow even alleles that are close together in a strand of DNA to be [[Mendelian inheritance#Mendel.27s law of segregation|inherited independently]]. However, as only about one recombination event occurs per million [[base pair]]s in humans, genes close together on a chromosome may not be shuffled away from each other, and tend to be inherited together. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10677316] This tendency is measured by finding how often two alleles occur together, which is called their [[linkage disequilibrium]]. A set of alleles that is usually inherited in a group is called a [[haplotype]], and this co-inheritance can indicate that the locus is under positive selection. Recombination in sexual organisms helps to remove harmful mutations and retain beneficial mutations. Consequently, when alleles cannot be separated by recombination – such as in mammalian [[Y chromosome]]s, which pass intact from fathers to sons – harmful [[Muller's ratchet|mutations accumulate]].[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11127901] In addition, recombination can produce individuals with new and advantageous gene combinations. These positive effects of recombination are balanced by the fact that this process can cause mutations and separate beneficial combinations of genes. The optimal rate of recombination for a species is therefore a trade-off between conflicting factors.
In asexual organisms, genes are inherited together, or ''linked'', as they cannot mix with genes in other organisms during reproduction. However, the offspring of [[sex]]ual organisms contain a random mixture of their parents' chromosomes that is produced through [[independent assortment]]. In the related process of [[genetic recombination]], sexual organisms can also exchange DNA between two matching chromosomes. These shuffling processes can allow even alleles that are close together in a strand of DNA to be [[Mendelian inheritance#Mendel.27s law of segregation|inherited independently]]. However, as only about one recombination event occurs per million [[base pair]]s in humans, genes close together on a chromosome may not be shuffled away from each other, and tend to be inherited together. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10677316] This tendency is measured by finding how often two alleles occur together, which is called their [[linkage disequilibrium]]. A set of alleles that is usually inherited in a group is called a [[haplotype]], and this co-inheritance can indicate that the locus is under positive selection. Recombination in sexual organisms helps to remove harmful mutations and retain beneficial mutations. Consequently, when alleles cannot be separated by recombination – such as in mammalian [[Y chromosome]]s, which pass intact from fathers to sons – harmful [[Muller's ratchet|mutations accumulate]].[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11127901] In addition, recombination can produce individuals with new and advantageous gene combinations. These positive effects of recombination are balanced by the fact that this process can cause mutations and separate beneficial combinations of genes. The optimal rate of recombination for a species is therefore a trade-off between conflicting factors.
