Lecture 19 Linkage Finish Linkage: The frequency of recombination is used as a measure of distance between A and B. This is the called the &quot;genetic distance&quot;. The unity of distance are centiMorgans (~100 x # recombinants/ (recombinants + parentals) Locus: a position on a chromosome, typically meant in the context of the a gene. For example, the wrinkled locus of pea. Pl. loci. Recombination frequencies between loci can be measured and used to assemble a map example: W-T = 20, W-Y = 10, Y-T = 30 makes a map: Y_10_W___20___T Alleles and gene function Alleles are different forms of a gene The wild-type allele is defined as the one found most frequently in a natural population Natural population: individuals of the same species in a natural environment. Example: Poppies in a meadow, grasses of a species in a prairie, Red-winged blackbirds around Davis, a human tribe in New Guinea Typically, the wild-type allele has good function. Different alleles arise continuously by mutation. Mutants, individuals in which a gene has changed in structure, arise at a frequency of 1/million - 1/100 millions per gene per generation. Given that most species have 20,000 to 40,000 different genes, the probability of carrying a recently formed mutation is very high for any individuals Mutations arise from multiple types of errors, typically in replication of DNA, and can involve any of the following: deletion: part of or the whole gene sequence is lost. Depending on the size of the deletion function loss can be partial or complete insertion: another DNA is spliced into the gene disrupting its structure. Usually loss of function is complete duplication: the whole gene is duplicated either in tandem or by transposition (copying and splicing into) to a new locus. This increases the expression level of the gene (more protein is made) and that can have no, minor, or <a href="/keyword/deleterious-effects/" >deleterious effects</a> point mutation: the sequence of DNA is changed at one base. The effect of base changes can be multiple and will be covered in a future lecture. In the mean time, however, here is a simple summary: the effects go from complete loss of function to none. In some cases, DNA base changes result in changes in protein sequence (a different amino acid is present at a given position). Summary of mutations: the effects of mutations on the function of a gene go from none (most common) to decreasing or increasing its function and even changing its function. Allele types and polymorphism. There are typically many alleles of a gene in a population. -1- The wild-type allele is most frequent. Some time, two alleles are predominant. Individuals that display different traits of a character are said to be polymorphic (multipleshapes) Polymorphisms can be phenotypic or molecular. For example, individuals that carry different alleles are polymorphic even if the alleles cause no change in function. For example, many mutations are said to be neutral, because they do not affect the phenotype of the affected individual The next common type of mutation is the deleterious one. It causes loss of function, or some type of deleterious change (more function, or function in the wrong organ or tissue). Deleterious mutations impair the affected individual. If the reproductive potential of the affected individual is decreased, there will be fewer of the mutant types in the next generation. The rarest type of mutation is the one that improves a character. This could result, for example, from a better enzyme, or from an enzyme that carries out a different, useful function. The ABO blood type. the I gene encodes a glycosyltransferase, an enzyme that attaches a sugar molecule to the lipid head of the red blood cell membrane Three alleles are common: Ia: attaches the 'A' sugar Ib: attaches the 'B' sugar Io: it does not encode an active enzyme Consider the genotype and the resulting membrane sugar group: genotype enzyme activity sugar IaIa IbIb IoIo IaIb IaIo a b none a+b a A B none AB A IbIo b B Note that both Ia and Ib are dominant over Io. When together, they are co-dominant: each exerts its effect. Another pattern of dominance: semidominance snapdragon: RR -&gt; red , rr -&gt; white, Rr -&gt; pink the heterozygous phenotype is determined by a dosage response: less of the R-encoded enzyme results in less of the red pigment dosage effects are common: cystic fibrosis is caused by loss of function of Cl- channel. Individuals with the recessive alleles build up mucus in the lungs because of impaired ion balance -2- individual heterozygous for this allele appear to be more tolerant to cholera, a diarrhea causing disease, perhaps because a different ion balance alters growth of the pathogen in the intestine Copy number alleles. Some allele undergo tandem duplication. This type of variation is common in all tested organisms Copy number variant alleles have been implicated in multiple diseases and phenotypes, such as mental illness, coat pattern in dogs, HIV resistance, malaria susceptibility Mutations accumulate with time. Sexuality helps a species to get rid of deleterious mutations and to keep good mutations by scrambling the genetic material The formation of mutations allows us to clock the divergence of different organisms. -3-