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Chapter 18 Population Genetics.docx

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Social Science
SOSC 1140
Cameron Johnston

Chapter 17: Population Genetics A measure of the commonness of an allele in a population; the Allele frequency proportion of all alleles of that gene in the population that are of this specific type Breeding of successive generations by the deliberate human selection of Artificial selection certain phenotypes or genotypes as the parents of each generation Darwinian fitness The relative probability of survival and reproduction for a genotype Endogamy Mating between individuals within a group or subgroup, rather than at random in a population Enforced outbreeding Deliberate avoidance of mating between relatives Equilibrium An array of genotypic or phenotypic frequencies in a population that distribution remains constant over time Fixed allele An allele for which all members of the population under study are homozygous, and so no other alleles for this locus exist in the population A random difference from the parental population in the frequency of a Founder effect genotype in a new colony that results from a small number of founders Frequency-dependent Fitness differences whose intensity changes with the relative frequency fitness of genotypes in the population Frequency- Fitness that does not depend on interactions with other members of the independent fitness same species The change in the frequency of an allele in a population resulting from Genetic drift chance differences in the actual numbers of offspring of different genotypes produced by different individual members The proportion in a population of individual members of a particular Genotype frequency genotype Haplotype A genetic class described by a sequence of DNA or of genes that are together on the same physical chromosome The stable frequency distribution of genotypes A/A, A/a, and a/a, in the proportions of p , 2pq, and q , respectively (where p and q are Hardy-Weinberg equilibrium frequencies of the alleles A and a), that is a consequence of random mating in the absence of mutation, migration, natural selection, or random drift A measure of the genetic variation in a population; with respect to one Heterozygosity locus, states as frequency of heterozygotes for that locus Homozygosity by Homozygosity that results from the inheritance of two copies of one gene descent that was present in an ancestor Inbreeding Mating between relatives Inbreeding coefficient The probability of homozygosity that results because the zygote obtains copies of the same ancestral gene Deviation in the frequency of haplotypes in a population from the Linkage disequilibrium frequency expected if the alleles at different loci are associated at random Distribution of haplotype frequencies in a population such that the Linkage equilibrium frequencies are the arithmetic products of the frequencies of the alleles at the different loci in the haplotype Mean fitness The mean of the fitness of all individual members of a population The number of mutation events per gene copy in a population, per unit of Mutation rate time (e.g. per cell generation) The differential rate of reproduction of different types in a population as a Natural selection result of different physiological, anatomical, or behavioural characteristics of the types Negative assortative Preferential mating between phenotypically unlike partners mating Negative inbreeding Preferential mating between individuals who are unrelated A phenotypic relation in which the phenotypic expression of the Overdominance heterozygote is greater than that of either homozygote The occurrence in a population 9or among opulations) of several Polymorphism phenotypic forms associated with alleles of one gene or homologs of one chromosome A group of individuals that mate with one another to produce the next Population generation The study of the frequencies of different genotypes in populations and Population genetics the changes in those frequencies that result from patterns of mating, natural selection, mutation, migration, and random chance Positive assortative A situation in which like phenotypes mate more commonly than expected mating by chance Changes in allele frequency that result because the genes appearing in Random genetic drift offspring are not perfectly representative sampling of the parental genes Random mating Mating between individuals in which the choice of a partner is not influenced by the genotypes (with respect to specific genes under study) The production of different average numbers of offspring by different Selection genotypes in a population as a result of the different phenotypic properties of those genotypes Single Nucleotide A nucleotide-pair difference at a given location in the genomes of two or polymorphism more naturally occurring individuals A phenotypic relation in which the phenotypic expression of the Underdominance heterozygote is less than that of either homozygote Variable number A chromosomal locus at which a particular repetitive sequence is present in different numbers in different individuals or in the two different tandem repeat (VNTR) homologs in one diploid individual The probability that a fertilized egg will survive and develop into an adult Viability organism Wild type The genotype or phenotype that is found in nature or in the standard laboratory stock for a given organism Population Genetics • Vieweable asextension of Mendelian genetics o Typically, species split into 2+ populations; hence, many alleles • Founders Fishers, Wright, Haldane: mathematical underpinnings of evolution Questions raised • How much variation? • How do mating patterns affect genetic variation? • What forces influence genetic variation? Mutation, migration, genetic drift (random), natural selection Phenomena investigated [6] • Effect of mating patterns on different genotypes in a population (random, inbreeding, assortative mating) • Migration (mmt of indivs between pop’s) • Mutaton & rate at which it happens • Recombination production of new combinations of characters, reasserts combinations of alleles at different loci • Natural selection changes caused in population composition – different genotypes, different rates of reproduction, & different rates of survival • Random fluctuations because only few offspring…. Hence, genetic drift happens, as life rarely lives up to perfect ratios Observing Variation Population genetics: experimental (describes actual patterns of variation, estimates rates of mating/mutation/recombination/natural selection; random variation in reprod rates); theoretical (makes predictions based on above forces) • Study characters with simple relations to the genotype; ex. Blood Groups (ABO, Rh, MN) • Genotype frequencies observed proportions of genotypes in a population • Allele frequency (p, or q) : frequency of homozygotes + half frequency of heterozygotes ¿of Ms = 180∗2+240 =0.6 • Ex. given 180MM, 240 MN, 80NN; p = freq(M)= totalhaplotypes 500∗2 ; o Similarly, p=freq(M) = freq(MM)+ ½ freq(MN) = 0.36+ ½ (0.48) = 0.6 o q computed as 1-p, or similar to how p is computed above • Polymorphism genetic variation: existence of >1 form of the gene, or >1 phenotype for a character o Wild type the extremely common form of a polymorphism, which most of the population carries • Immunologic Polymorphism encode antigenic specifications (ex. ABO blood types = 3 2 alleles), (ex. HLA system, 2 loci, 5 alleles  5 =25 gametic types, 25 homozygotes possible); heterozygotes n(n-1)/2 of combining different things two at a time Amino Acid Sequence Polymorphism: using gel electrophoresis • Early gels: starch gels; first, study protein variation; then, extended to population genetics, and DNA is electrophoresed today; but proteins do not tell of regulatory sequences (see below) • When one amino acid is substituted for another, if a charged protein substituted an uncharged one, or vice versa, will affect distance travelled on a gel o if two “blobs” show up  heterozygote; ex alcohol dehydrogenase in Asclepias syriaca, or Esterase in t. subulata; glucose phosphate isomerase in AUTOTETRAPLOID (hence showing multiple blobs) T. Subulata • Heterozygosity what average fraction of an individual’s genome is in a heterozygous state (in a population): ~10% in a population  1 in every 10 genes on an individual is heterozygous • The figure on the right was in ppt, but no notes accompany Models [2] of Population Genetic Structure Classical Balance • Morgan, Muller • Dobzhansky, Ford • Lab mutants • Natural populations • High homozygosity • Low homozygosity • Low polymorphism • High polymorphism • Wild type normal genotype • No normal/ideal genotype Electrophoretic Studies Pros [5] Cons [5] • Many loci can be examined • Only protein-coding loci • Usable on any organism • Some variation not identifiable (hidden) • ID heterozygotes (loci co-dominant) • Variation may be non-adaptive • Variation examined close to DNa level • Some: expression tissue/life-stage dependant • Provides marker loci for other studies • May have to sacrifice individual DNA structure & sequence polymorphism  – analyzing DNA  ▯examine variation in genome structure  amongst indivs & between species • Chromosomal polymorphism many species are polymorphic for chromosome number/morphology o Supernumeraries (extra chromsoomes), reciprocal translocations, inversions; • Restriction-site variation inexpensive, rapid way to see overall details of variation; use • restriction enzymes “six-cutter”: every 3096 bp (4 ); “four- 4 cutter”: 4 =256; 0.1-1.0% of heterozygosity per nucleotide site, average =0.4% (D. pseudobscura) based on RFLPs in 17-4; 78 RFLPSm, 53 unique haplotypes  lots of genetic variation
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