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SC435 Genetics Seminar • Welcome to our LAST SEMINAR • We will continue our population genetics and variation • The seminar will begin at 9:00PM ET Unit 8 • Discussion board • Unit 9 Quiz • Final Project Unit Readings Chapter 14 Chapter 15 3 Molecular evolution • • • • • • Accumulation of sequence differences through time is the basis of molecular systematics, which analyses them in order to infer evolutionary relationships A gene tree is a diagram of the inferred ancestral history of a group of sequences A gene tree is only an estimate of the true pattern of evolutionary relations Neighbor joining = one of the way to estimate a gene tree Bootstrapping = a common technique for assessing the reliability of a node in a gene tree Taxon = the source of each sequence Fig. 14.1 Molecular evolution • A gene tree does not necessarily coincide with a species tree: The sorting of polymorphic alleles in the different lineages Recombination within gene make it possible for different parts of the same gene to have different evolutionary histories Population Genetics • Population genetics = application of genetic principles to entire populations of organisms • Population = group of organisms of the same species living in the same geographical area • Subpopulation = any of the breeding groups within a population among which migration is restricted • Local population = subpopulation within which most individuals find their mates 7 Population Genetics • Gene pool = the complete set of genetic information in all individuals within a population • Genotype frequency = proportion of individuals in a population with a specific genotype • Genotype frequencies may differ from one population to another • Allele frequency = proportion of any specific allele in a population • Allele frequencies are estimated from genotype frequencies 8 Mating Systems • Random mating means that mating pairs are formed independently of genotype • Random mating of individuals is equivalent of the random union of gametes • Assortative mating = nonrandom selection of mating partners; it is positive when like phenotypes mate more frequently than would be expected by chance and is negative when reverse occurs • Inbreeding = mating between relatives Hardy–Weinberg Principle • When gametes containing either of two alleles, A or a, unite at random to form the next generation, the genotype frequencies among the zygotes are given by the ratio p2 : 2pq : q2 this constitutes the Hardy–Weinberg (HW) Principle p = frequency of a dominant allele A q = frequency of a recessive allele a p + q =1 10 Fig. 14.10 Hardy–Weinberg Principle • One important implication of the HW Principle is that allelic frequencies will remain constant over time if the following conditions are met: • The population is sufficiently large • Mating is random • Allelic frequencies are the same in males and females • Selection does not occur = all genotypes have equal in viability and fertility • Mutation and migration are absent 12 Hardy–Weinberg Principle • Another important implication is that for a rare allele, there are many more heterozygotes than there are homozygotes for the rare allele Fig. 14.12 13 DNA Typing • The use of polymorphisms in DNA to link suspects with samples of human material is called DNA typing • Highly polymorphic sequences are used in DNA typing • Polymorphic alleles may differ in frequency among subpopulations = population substructure • DNA exclusions are definitive 14 Allelic Variation • Allelic variation may result from differences in the number of units repeated in tandem = simple tandem repeat (STR) • STRs can be used to map DNA since they generate fragments of different sizes which can be detected by various methods • Most people are heterozygous for SSR alleles 15 Fig. 14.17 Inbreeding • • • Inbreeding means mating between relatives Inbreeding results in an excess of homozygotes compared with random mating In most species, inbreeding is harmful due to rare recessive alleles that wouldn’t otherwise become homozygous Fig. 14.9 17 Fig. 14.23 Evolution • Evolution refers to changes in the gene pool of a population or in the allele frequencies present in a population • Evolution is possible because genetic variation exists in populations • Four processes account for most of the evolutionary changes 18 Evolution 1. Mutation = the origin of new genetic capabilities in populations = the ultimate source of genetic variation 2. Migration = the movement of organisms among subpopulations 3. Natural selection = the process of evolutionary adaptation = genotypes best suited to survive and reproduce in a particular environment give rise to a disproportionate share of the offspring 4. Random genetic drift = the random, undirected changes in allele frequencies, especially in small populations 19 Natural Selection • Natural selection is the driving force of adaptive evolution and is a consequence of the hereditary differences among organisms and their ability to survive and reproduce in the prevailing environment • Adaptation = progressive genetic improvement in populations due to natural selection 20 Natural Selection In its modern formulation, the concept of natural selection rests on three premises: More organisms are produced than can survive and reproduce Organisms differ in their ability to survive and reproduce, and some of these differences are due to genotype The genotypes that promote survival are favored and contribute disproportionately to the offspring of the next generation 21 Fitness • Fitness is the relative ability of genotypes to survive and reproduce • Relative fitness measures the comparative contribution of each parental genotype to the pool of offspring genotypes in each generation • Selection coefficient refers to selective disadvantage of a disfavored genotype 22 Selection in Diploids • Frequency of favored dominant allele changes slowly if allele is common • Frequency of favored recessive allele changes slowly if the allele is rare • Rare alleles are found most frequently in heterozygotes • When favored allele is dominant, recessive allele in heterozygotes is not exposed to natural selection 23 Fig. 14.25 Selection in Diploids • Frequency of very common or rare alleles changes very slowly • Selection for or against very rare recessive alleles is inefficient • The largest reservoir of harmful recessive alleles is in the genomes of heterozygous carriers, who are phenotypically normal 25 Selection in Diploids • Selection can be balanced by new mutations • New mutations often generate harmful alleles and prevent their elimination from the population by natural selection • Eventually the population will attain a state of equilibrium in which the new mutations exactly balance the selective elimination 26 Maternal Inheritance • Maternal inheritance refers to the transmission of genes only through the female • In higher animals, mitochondrial DNA (mtDNA) shows maternal inheritance • Mitochondria are maternally inherited because the egg is the major contributor of cytoplasm to the zygote • Some rare genetic disorders are the result of mutations in mtDNA and are transmitted from mother to all offspring • The severity of the disorder depends on the proportions of normal and mutant mitochondria among affected individuals 27 Maternal Inheritance • Recombination does not occur in mitochondrial DNA making it a good genetic marker for human ancestry • Human mtDNA evolves at approximately a constant rate = 1 change per mt lineage every 3800 years • Modern human populations originated in subsaharan Africa ~ 100,000 years ago 28 Multifactorial Traits • Multifactorial traits are determined by multiple genetic and environmental factors acting together • Multifactorial = complex traits = quantitative traits • Most traits that vary in the population, including common human diseases with the genetic component, are complex traits • Genetic architecture of a complex trait = specific effects and combined interactions of all genetic and environmental factors 29 Quantitative Inheritance • Quantitative traits = phenotypes differ in quantity rather than type (such as height) • In a genetically heterogeneous population, genotypes are formed by segregation and recombination • Variation in genotype can be eliminated by studying inbred lines = homozygous for most genes, or F1 progeny of inbred lines = uniformly heterozygous • Complete elimination of environmental variation is impossible 30 Quantitative Inheritance • Continuous traits = continuous gradation from one phenotype to the next (height) • Categorical traits = phenotype is determined by counting (hen’s eggs) • Threshold traits = only two, or a few phenotypic classes, but their inheritance is determined by multiple genes and environment (adult-onset diabetes) 31 Fig. 15.5 32 Phenotypic Variation • Variation of a trait can be separated into genetic and environmental components • Genotypic variance sg2 = variation in phenotype caused by differences in genotype • Environmental variance se2 = variation in phenotype caused by environment • Total variance sp2 = combined effects of genotypic and environmental variance sp2 = sg2 + se2 33 Fig. 15.9 34 Phenotypic Variation • Genotype and environment can interact or they can be associated • Genotype-environment (G-E) interaction = environmental effects on phenotype differ according to genotype • Genotype-by-sex interaction: same genotype produces different phenotype in males and females (distribution of height among women and men) 35 Fig. 15.10 36 Genetic Variation • Genotype-environment (G-E) association = certain genotypes are preferentially associated with certain environments • There is no genotypic variance in a genetically homogeneous population sg2 = 0 • When the number of genes affecting a quantitative trait is not too large, the number, n, of genes contributing to the trait is n = D2/8sg2 D = difference between parental strains 37 Broad-Sense Heritability • Broad-sense heritability (H2) includes all genetic effects combined H2 = sg2 / sp2 = sg2 / sg2 + se2 • Knowledge of heritability is useful in plant and animal breeding because it can be used to predict the magnitude and speed of population improvement 38 Heritability: Twin Studies • Twin studies are often used to assess genetic effects on variation in a trait • Identical twins arise from the splitting of a single fertilized egg = genetically identical • Fraternal twins arise from two fertilized eggs = only half of the genes are identical • Theoretically, the variance between identical twins would be equivalent to se2 , and between fraternal twins - sg2/2 + se2 39 Heritability: Twin Studies Potential sources of error in twin studies of heritability: – Genotype-environment interaction increases the variance in fraternal twins but not identical twins – Frequent sharing of embryonic membranes by identical twins creates similar intrauterine environment – Greater similarity in treatment of identical twins results in decreased environmental variance – Different sexes can occur in fraternal but not identical twins 40 Artificial Selection • Artificial selection =“managed evolution” = the practice of selecting a group of organisms from a population to become the parents of the next generation • h2 is usually the most important in artificial selection • Individual selection = each member of the population to be selected is evaluated according to its individual phenotype • Truncation point = arbitrary level of phenotype that determines which individuals will be used for breeding purposes 41 Artificial Selection There are limits to the improvement that can be achieved by artificial selection: • Selection limit at which successive generations show no further improvement can be reached because natural selection counteracts artificial selection due to indirect harmful effects of selected traits (weight at birth versus viability) • Correlated response = effect of selection for one trait on a non-selected trait (number of eggs and their size) 42 Correlation Between Relatives • Correlation coefficient of a trait between relatives is related to the narrow- or broadsense heritability 43