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VI. Mutation A. Overview B. Changes in Ploidy - These are the most dramatic changes, adding a whole SET of chromosomes 1. Mechanism #1: Complete failure of Meiosis 2. Mechanism #2: Failure of Mitosis in Gamete-producing Tissue 2n 1) Consider a bud cell in the flower bud of a plant. 2n 1) Consider a bud cell in the flower bud of a plant. 4n 2) It replicates it’s DNA but fails to divide... Now it is a tetraploid bud cell. 2n 1) Consider a bud cell in the flower bud of a plant. 3) A tetraploid flower develops from this tetraploid cell; eventually producing 2n SPERM and 2n EGG 4n 2) It replicates it’s DNA but fails to divide... Now it is a tetraploid bud cell. 2n 1) Consider a bud cell in the flower bud of a plant. 4n 2) It replicates it’s DNA but fails to divide... Now it is a tetraploid bud cell. 3) A tetraploid flower develops from this tetraploid cell; eventually producing 2n SPERM and 2n EGG 4) If it is self-compatible, it can mate with itself, producing 4n zygotes that develop into a new 4n species. Why is it a new species? How do we define ‘species’? “A group of organisms that reproduce with one another and are reproductively isolated from other such groups” (E. Mayr – ‘biological species concept’) How do we define ‘species’? Here, the tetraploid population is even reproductively isolated from its own parent species…So speciation can be an instantaneous genetic event… 2n 4n 4n 1n 2n 2n 3n Zygote 1n 2n Gametes Triploid is a dead-end… so species are separate Zygote Gametes VI. Mutation A. Overview B. Changes in Ploidy - These are the most dramatic changes, adding a whole SET of chromosomes 1. Mechanism #1: Complete failure of Meiosis 2. Mechanism #2: Complete failure of Mitosis 3. The Frequency of Polyploidy For reasons we just saw, we might expect polyploidy to occur more frequently in hermaphroditic species, because the chances of ‘jumping’ the triploidy barrier to reproductive tetraploidy are more likely. Over 50% of all flowering plants are polyploid species; many having arisen by this duplication of chromosome number within a lineage. VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘aneuploidy’ (changes in chromosome number) 1. Mechanism: Non-disjunction (failure of a homologous pair or sister chromatids to separate) VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘aneuploidy’ (changes in chromosome number) 1. Mechanism: Non-disjunction (failure of a homologous pair or sister chromatids to separate) 2. Human Examples a. trisomies Trisomy 21 – “Downs’ Syndrome” VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘aneuploidy’ (changes in chromosome number) 1. Mechanism: Non-disjunction (failure of a homologous pair or sister chromatids to separate) 2. Human Examples a. trisomies Trisomy 21 – “Downs’ Syndrome” Trisomy 18 – Edward’s Syndrome Trisomy 13 – Patau Syndrome Some survive to birth Trisomy 9 Trisomy 8 Trisomy 22 Trisomy 16 – most common – 1% of pregnancies – always aborted VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘aneuploidy’ (changes in chromosome number) 1. Mechanism: Non-disjunction (failure of a homologous pair or sister chromatids to separate) Extreme effects listed below; 2. Human Examples most show a phenotype within a. trisomies the typical range for XY males 47, XXY – “Klinefelter’s Syndrome” VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘aneuploidy’ (changes in chromosome number) 1. Mechanism: Non-disjunction (failure of a homologous pair or sister chromatids to separate) 2. Human Examples a. trisomies 47, XXX – “Triple-X Syndrome” No dramatic effects on the phenotype; may be taller. In XX females, one X shuts down anyway, in each cell (Barr body). In triple-X females, 2 X’s shut down. VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘aneuploidy’ (changes in chromosome number) 1. Mechanism: Non-disjunction (failure of a homologous pair or sister chromatids to separate) 2. Human Examples a. trisomies 47, XYY – “Super-Y Syndrome” Often taller, with scarring acne, but within the phenotypic range for XY males VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘aneuploidy’ (changes in chromosome number) 1. Mechanism: Non-disjunction (failure of a homologous pair or sister chromatids to separate) 2. Human Examples b. monosomies 45, XO– “Turner’s Syndrome” (the only human monosomy to survive to birth) VI. Mutation A. B. C. D. Overview Changes in Ploidy Changes in ‘Aneuploidy’ (changes in chromosome number) Change in Gene Number/Arrangement VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘Aneuploidy’ (changes in chromosome number) D. Change in Gene Number/Arrangement 1. Mechanism #1: Unequal Crossing-Over a. process: If homologs line up askew: A B a b VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘Aneuploidy’ (changes in chromosome number) D. Change in Gene Number/Arrangement 1. Mechanism #1: Unequal Crossing-Over a. process: If homologs line up askew And a cross-over occurs A B a b VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘Aneuploidy’ (changes in chromosome number) D. Change in Gene Number/Arrangement 1. Mechanism #1: Unequal Crossing-Over a. process: If homologs line up askew And a cross-over occurs Unequal pieces of DNA will be exchanged… the A locus has been duplicated on the lower chromosome and deleted from the upper chromosome B A a b VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘Aneuploidy’ (changes in chromosome number) D. Change in Gene Number/Arrangement 1. Mechanism #1: Unequal Crossing-Over a. process: b. effects: - can be bad: deletions are usually bad – reveal deleterious recessives additions can be bad – change protein concentration VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘Aneuploidy’ (changes in chromosome number) D. Change in Gene Number/Arrangement 1. Mechanism #1: Unequal Crossing-Over a. process: b. effects: - can be bad: deletions are usually bad – reveal deleterious recessives additions can be bad – change protein concentration - can be good: more of a single protein could be advantageous (r-RNA genes, melanin genes, etc.) VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘Aneuploidy’ (changes in chromosome number) D. Change in Gene Number/Arrangement 1. Mechanism #1: Unequal Crossing-Over a. process: b. effects: - can be bad: deletions are usually bad – reveal deleterious recessives additions can be bad – change protein concentration - can be good: more of a single protein could be advantageous (r-RNA genes, melanin genes, etc.) source of evolutionary novelty (Ohno hypothesis - 1970) where do new genes (new genetic information) come from? Gene A Duplicated A generations Mutation – may even render the protein non-functional But this organism is not selected against, relative to others in the population that lack the duplication, because it still has the original, functional, gene. Gene A Duplicated A generations Mutation – may even render the protein non-functional Mutation – other mutations may render the protein functional in a new way So, now we have a genome that can do all the ‘old stuff’ (with the original gene), but it can now do something NEW. Selection may favor these organisms. If so, then we’d expect many different neighboring genes to have similar sequences. And non-functional pseudogenes (duplicates that had been turned off by mutation). These occur – Gene Families And, if we can measure the rate of mutation in these genes, then we can determine how much time must have elapsed since the duplication event… Gene family trees… VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘Aneuploidy’ (changes in chromosome number) D. Change in Gene Number/Arrangement 1. Mechanism #1: Unequal Crossing-Over 2. Mechanism #2: Translocation Translocation Downs. Transfer of a 21 chromosome to a 14 chromosome Can produce normal, carrier, and Down’s child. VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘Aneuploidy’ (changes in chromosome number) D. Change in Gene Number/Arrangement E. Change in Gene Structure 1. Mechanism #1: Exon Shuffling Crossing over WITHIN a gene, in introns, can recombine exons within a gene, producing new alleles. EXON 1a EXON 2a EXON 3a Allele “a” EXON 1A EXON 2A EXON 3A Allele “A” VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘Aneuploidy’ (changes in chromosome number) D. Change in Gene Number/Arrangement E. Change in Gene Structure 1. Mechanism #1: Exon Shuffling Crossing over WITHIN a gene, in introns, can recombine exons within a gene, producing new alleles. EXON 1a EXON 2a EXON 3a Allele “a” EXON 1A EXON 2A EXON 3A Allele “A” EXON 1A EXON 2a EXON 3a Allele “α” EXON 1a EXON 2A EXON 3A Allele “ά” VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘Aneuploidy’ (changes in chromosome number) D. Change in Gene Number/Arrangement E. Change in Gene Structure 1. Mechanism #1: Exon Shuffling 2. Mechanism #2: Point Mutations a. addition/deletion: “frameshift” mutations Normal Mutant: A inserted …T C C G T A C G T …. …A G G C A U G C A … ARG HIS ALA DNA m-RNA …T C C A G T A C G T …. …A G G U C A U G C A … ARG SER CYS Throws off every 3-base codon from mutation point onward VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘Aneuploidy’ (changes in chromosome number) D. Change in Gene Number/Arrangement E. Change in Gene Structure 1. Mechanism #1: Exon Shuffling 2. Mechanism #2: Point Mutations a. addition/deletion: “frameshift” mutations b. substitution Normal Mutant: A for G … T C C G T A C G T …. …A G G C A U G C A … ARG HIS ALA DNA m-RNA …T C C A T A C G T …. …A G G U A U G C A … ARG TYR ALA At most, only changes one AA (and may not change it…) VI. Mutation A. Overview B. Changes in Ploidy C. Changes in ‘Aneuploidy’ (changes in chromosome number) D. Change in Gene Number/Arrangement E. Change in Gene Structure F. Summary MUTATION: -New Genes: point mutation exon shuffling RECOMBINATION: - New Genes: crossing over -New Genotypes: crossing over independent assortment Causes of Evolutionary Change V A R I A T I O N Sources of Variation Natural Selection Mutation (polyploidy can make new species) Modern Evolutionary Biology I. Population Genetics A. Overview Agents of Change Mutation N.S. Recombination - crossing over - independent assortment VARIATION Sources of Variation mutation Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population G. Hardy and W. Weinberg 1. Definitions - Evolution: a change in the genetic structure of a population - Population: a group of interbreeding organisms that share a common gene pool; spatiotemporally and genetically defined - Gene Pool: sum total of alleles held by individuals in a population - Genetic structure: Gene array and Genotypic array - Gene/Allele Frequency: % of alleles at a locus of a particular type - Gene Array: % of all alleles at a locus: must sum to 1. - Genotypic Frequency: % of individuals with a particular genotype - Genotypic Array: % of all genotypes for loci considered; must = 1. Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population 1. Definitions 2. Basic Computations Individuals AA Aa aa 70 80 50 (200) Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population 1. Definitions 2. Basic Computations AA Aa aa Individuals 70 80 50 (200) Genotypic Array 70/200 = 0.35 80/200 = .40 50/200 = 0.25 =1 Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population 1. Definitions 2. Basic Computations AA Aa aa Individuals 70 80 50 (200) Genotypic Array 70/200 = 0.35 80/200 = .40 50/200 = 0.25 =1 ''A' alleles 140 80 0 220/400 = 0.55 Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population 1. Definitions 2. Basic Computations AA Aa aa Individuals 70 80 50 (200) Genotypic Array 70/200 = 0.35 80/200 = .40 50/200 = 0.25 =1 ''A' alleles 140 80 0 220/400 = 0.55 'a' alleles 0 80 100 180/400 = 0.45 Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population 1. Definitions 2. Basic Computations - Determining the Gene Array from the Genotypic Array a. f(A) = f(AA) + f(Aa)/2 = .35 + .4/2 = .35 + .2 = .55 b. f(a) = f(aa) + f(Aa)/2 = .25 + .4/2 = .25 + .2 = .45 KEY: The Gene Array CAN ALWAYS be computed from the genotypic array; the process just counts alleles instead of genotypes. No assumptions are made when you do this. Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 1. Goal: Describe what the genetic structure of the population would be if there were NO evolutionary change – if the population was in equilibrium. Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 1. Goal: Describe what the genetic structure of the population would be if there were NO evolutionary change – if the population was in equilibrium. For a population’s genetic structure to remain static, the following must be true: - random mating - no selection - no mutation - no migration - the population must be infinitely large Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 2.Example: Initial genotypic freq. Gene freq. Genotypes, F1 Gene Freq's Genotypes, F2 AA Aa aa 0.4 0.4 0.2 1.0 Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 2.Example: Initial genotypic freq. Gene freq. Genotypes, F1 Gene Freq's Genotypes, F2 AA Aa aa 0.4 0.4 0.2 f(A) = p = .4 + .4/2 = 0.6 1.0 f(a) = q = .2 + .4/2 = 0.4 Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 2.Example: Initial genotypic freq. Gene freq. Genotypes, F1 Gene Freq's Genotypes, F2 AA Aa aa 0.4 0.4 0.2 f(A) = p = .4 + .4/2 = 0.6 p2 = .36 2pq = .48 1.0 f(a) = q = .2 + .4/2 = 0.4 q2 = .16 = 1.00 Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 2.Example: Initial genotypic freq. Gene freq. Genotypes, F1 Gene Freq's Genotypes, F2 AA Aa aa 0.4 0.4 0.2 f(A) = p = .4 + .4/2 = 0.6 p2 = .36 2pq = .48 1.0 f(a) = q = .2 + .4/2 = 0.4 q2 = .16 = 1.00 f(A) = p = .36 + .48/2 = 0.6 f(a) = q = .16 + .48/2 = 0.4 p2 = .36 q2 = .16 2pq = .48 = 1.00 After one generation with these conditions, the population equilibrates Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 2.Example 3. Utility: If no populations meets these conditions explicitly, how can it be useful? Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 2.Example 3. Utility: If no populations meets these conditions explicitly, how can it be useful? For comparison, like a “perfectly balanced coin” Initial genotypic freq. Gene freq. HWE expections AA Aa aa 0.5 0.2 0.3 f(A) = p = .5 + .2/2 = 0.6 p2 = .36 2pq = .48 1.0 f(a) = q = .3 + .2/2 = 0.4 q2 = .16 CONCLUSION:The real population is NOT in HWE. = 1.00 Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 3. Utility: - if a population is NOT in HWE, then one of the assumptions must be violated. Sources of Variation Recombination - crossing over VARIATION Mutation Agents of Change - independent assortment So, if NO AGENTS are acting on a population, then it will be in equilibrium and WON'T change. N.S. Drift Migration Mutation Non-random Mating Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model D. Deviations from HWE 1. mutation 1. Consider a population with: f(A) = p = 0.6 f(a) = q = 0.4 2. Suppose 'a' mutates to 'A' at a realistic rate of: μ = 1 x 10-5 3. Well, what fraction of alleles will change? 'a' will decline by: qm = .4 x 0.00001 = 0.000004 'A' will increase by the same amount. f(A) = p1 = 0.600004 f(a1) = q = 0.399996 Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model D. Deviations from HWE 1. mutation 2. migration p2 = 0.7 p1 = 0.2 q2 = 0.3 q1 = 0.8 suppose migrants immigrate at a rate such that the new immigrants represent 10% of the new population Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model D. Deviations from HWE 1. mutation 2. migration p2 = 0.7 p1 = 0.2 q2 = 0.3 q1 = 0.8 M = 10% p(new) = p1(1-m) + p2(m) = 0.2(0.9) + 0.7(0.1) = 0.18 + 0.07 = 0.25