Population Genetics (Learning Objectives)

Transcription

1 Population Genetics (Learning Objectives) Define the terms population, species, allelic and genotypic frequencies, gene pool, and fixed allele, genetic drift, bottle-neck effect, founder effect. Explain the difference between microevolution and macroevolution. Review how genotypic and allelic frequencies are calculated. Given the appropriate information about a population you should be able to calculate the genotypic and allelic frequencies of homozygous dominant, recessive, or heterozygous individuals (following the example discussed in class). Visit this website to learn the factors that lead to changes in genotypic and allelic frequencies between generations: OSU.swf What is the Hardy-Weinberg Equilibrium and what are its conditions. What are the factors that lead to microevolution? What is the source of new alleles within any population?

2 Definitions Gene pool = The collection of all alleles in the members of the population Population genetics = The study of the genetics of a population and how the allele frequencies vary with time Gene Flow = Movement of alleles between populations when people migrate and mate

3 Changes allelic frequencies in populations

4 Populations not individuals are the units of evolution - If all members of a population are homozygous for the same allele, that allele is said to be fixed

5 Allele Frequencies Allele frequency = # of particular allele Total # of alleles in the population Count both chromosomes of each individual Allele frequencies affect the frequencies of the three genotypes

6 Evolution Microevolution small changes due to changing allelic frequencies within a population from generation to generation Macroevolution large changes in allelic frequencies over 100 s and 1000 s of generations leading to the formation of new species

7 Calculating the allelic frequencies from the genotypic frequencies What is the allelic frequency (of R and r) in this population?

8 Genotypic frequency RR= 320/500 = 0.64 Rr = 160/500= 0.32 rr = 20/500 = 0.04

9 What is the allelic frequency in a population of 500 flowers? How many total alleles are there? 500 X 2 = 1000 Frequency of R allele in population RR + Rr = 320 X = = /1000 = 0.8 =80% Frequency of r allele = = 0.2 =20% or rr +Rr = 20 X = /1000 = 0.2

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11 - Meiosis and random fertilization do not change the allele and genotype frequencies between generations - The shuffling of alleles that accompanies sexual reproduction does not alter the genetic makeup of the population

12 The Hardy-Weinberg theorem describes the gene pool of a non-evolving population Hardy Weinberg animation utorials/flash/life4e_15-6-osu.swf

13 Hardy-Weinberg Equation p = allele frequency of one allele q = allele frequency of a second allele p + q = 1 p 2 + 2pq + q 2 = 1 All of the allele frequencies together equals 1 All of the genotype frequencies together equals 1 p 2 and q 2 2pq Frequencies for each homozygote Frequency for heterozygotes

14 Populations at Hardy-Weinberg equilibrium must satisfy five conditions. (1) Very large population size. In small populations, chance fluctuations in the gene pool, genetic drift, can cause genotype frequencies to change over time. (2) No migrations. Gene flow, the transfer of alleles due to the movement of individuals or gametes into or out of our target population can change the proportions of alleles. (3) No net mutations. If one allele can mutate into another, the gene pool will be altered.

15 (4) Random mating. If individuals pick mates with certain genotypes, then the mixing of gametes will not be random and the Hardy-Weinberg equilibrium does not occur. (5) No natural selection. If there is differential survival or mating success among genotypes, then the frequencies of alleles in the next variation will deviate from the frequencies predicted by the Hardy- Weinberg equation. Evolution results when any of these five conditions are not met - when a population experiences deviations from the stability predicted by the Hardy-Weinberg theory.

16 Genetic Drift changes allelic frequencies in populations

17 The bottleneck effect The founder effect

18 Caused by four factors: 1. Non-Random mating Microevolution 2. Genetic drift due to sampling/ bottleneck & founder effects, geographic & cultural separation 3. Migration- of fertile individuals 4. Mutation- in germline cells transmitted in gamete 5. Natural selection- accumulates and maintains favorable genotypes in a population

19 Phenotype Frequencies Frequency of a trait varies in different populations. Example: PKU an autosomal recessive trait Table 14.1

20 Calculation of % PKU carriers from screening About 1 in 10,000 babies in US are born with PKU - The frequency of homozygous recessive individuals = q 2 = 1 in 10,000 or The frequency of the recessive allele (q) is the square root of = The frequency of the dominant allele (p) is p = 1 - q or = The frequency of carriers (heterozygous individuals) is 2pq = 2 x 0.99 x 0.01 = or about 2%. About 2% of the U.S. population carries the PKU allele.

21 Source of the Hardy-Weinberg Equation Figure 14.3 Figure 14.3

22 Figure 14.4 Solving a Problem

23 Figure 14.4 Solving a Problem

24 Calculating the Carrier Frequency of an Autosomal Recessive Figure 14.5 Figure 14.3

25 Calculating the Carrier Frequency of an Autosomal Recessive Table 14.3

26 Calculating the Carrier Frequency Figure 14.3 of an Autosomal Recessive What is the probability that two unrelated Caucasians will have an affected child? Probability that both are carriers = 1/23 x 1/23 = 1/529 Probability that their child has CF = 1/4 Therefore, probability = 1/529 x 1/4 = 1/2,116

27 Calculating the Risk with X-linked Traits For females, the standard Hardy-Weinberg equation applies p 2 + 2pq + q 2 = 1 However, in males the allele frequency is the phenotypic frequency p + q = 1 Allelic frequency determined from the incidence in new born males

28 Calculating the Risk with Calculating the Risk with X-linked Traits X-linked Traits Figure

29 Hardy-Weinberg Equilibrium Rare for protein-encoding genes that affect the phenotype Applies to portions of the genome that do not affect phenotype Includes repeated DNA segments Not subject to natural selection 29

30 DNA and Genomic Technological applications DNA Technology and its tools (DNA modification Enzymes and plasmids, DNA Gel Electrophoresis, PCR) DNA Finger Printing/Profiling, The FBI's Combined DNA Index System (CODIS) Production of recombinant proteins and transgenic organisms Gene Editing Gene-specific replacement using homologous recombination Gene specific cutting- CRISPR-Cas9 Animal Reproductive cloning by nuclear transplantation and therapeutic production of organs and tissues

31 DNA technology to produce genetically modified organisms and recombinant proteins

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33 Genetic and Genomic Technologies Genetic Variability and DNA Technologies Single nucleotide polymorphisms (SNPs) Short Tandem Repeats (STRs) Biotechnology tools for DNA Profiling or fingerprinting Restriction Fragment length polymorphism Restriction enzymes DNA Gel Electrophoresis Polymerase Chain Reaction (PCR)

34 DNA Repeats Short repeated segments are distributed all over the genome Repeat numbers can be considered alleles and used to classify individuals Types Variable number of tandem repeats (VNTRs) Short tandem repeats (STRs) 34

35 DNA Repeats 35

36 DNA Profiling Developed in the 1980s by British geneticist Sir Alec Jeffreys Also called DNA fingerprinting Identifies individuals Used in forensics, agriculture, paternity testing, and historical investigations 5/126997/animation40.html

37 DNA Profiling Techniques RFLPs- Restriction Fragment length polymorphisms (limited utility) PCR- Amplification of select genomic regions spanning stretches of STRs

38 Box Figure

39 Practical Applications of DNA Fingerprinting Paternity and Maternity Personal Identification/ Criminal Identification and Forensics

40 Practical Applications of DNA Fingerprinting Forensic Biotechnology Whodunit? by Jenny Shaw, Vanessa Petty, Theresa Brown, and Sarah Mathiason

41 Practical Applications of DNA Fingerprinting

42 DNA Profiling Technique that detects differences in repeat copy number (current) Calculates the probability that certain combinations can occur in two sources of DNA by chance DNA evidence is more often valuable in excluding a suspect Should be considered along with other types of evidence 42

43 Comparing DNA Repeats Comparing DNA Repeats Figure

44 DNA can be obtained from any cell with a nucleus STRs are used when DNA is scarce If DNA is extremely damaged, mitochondrial DNA (mtdna) is often used For forensics, the FBI developed the Combined DNA Index System (CODIS) Uses 13 STRs DNA Sources 44

45 CODIS Probability that any two individuals have same Figure thirteen markers is 1 in 250 trillion DNA Profiling updated 45

46 Population Statistics Used to Interpret DNA Profiles Power of DNA profiling is greatly expanded by tracking repeats in different chromosomes Number of copies of a repeat are assigned probabilities based on their observed frequency in a population Product rule is then used to calculate probability of a certain repeat combination 46

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48 Using DNA Profiling to Identify Victims Recent examples of large-scale disasters World Trade Center attack (2001) Indian Ocean Tsunami (2004) Hurricane Katrina (2005) 48

49 Challenges to DNA Profiling 49

50 Genetic Privacy Today s population genetics presents a powerful way to identify individuals Our genomes can vary in more ways than there are people in the world DNA profiling introduces privacy issues Example: DNA dragnets 50

51 Gene Editing Gene-specific replacement using homologous recombination Gene specific cutting- CRISPR-Cas9

52 Steps: 1. Design primers with lacz linkers 2. PCR amplify D.S. DNA of kanr with lacz linkers from plasmid pkd4 λ Red recombinase* * lacz linkers 3. Induce expression of λ Red in MG1655/pKD46 lacz gene 4. Electroporate MG1655/pKD46 cells with D.S. DNA lacz-frtkanr-frt-lacz 5. Select for successful disruption by growing cells on LB/ Kanamycin IPTG/X-gal plates Gene Disruption by Homologous Recombination/Recombineering

53 Successful λ-red-stimulated Recombineering 1108 bp lacz gene kan R cassette 1500 bp lacz gene Distance between primers Color of colonies (IPTG/X-gal) Uninterrupted 1108 Blue Number of recombinant/ electroporation Kan R -interrupted 1500 white 6

54 grna Scaffold Scarless Cas9-assisted Recombineering (λ-redstimulated) Choice and design of Cas-9 target sequence (lacz gene) Plasmids used Circular Polymerase Extension Cloning (CPEC) of the lacz target to make pkdsgrna-lacz plasmid Cas-9- Directed Gene Replacement Steps

55 Cas-9- Directed Gene Replacement Concepts

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57 Successful Cas-9-targeted cutting of lacz gene with designed guides in living cells lacz F4 lacz N20 No expression of Cas-9 (-atc) Expression of Cas-9 (+atc)

58 Animal Cloning Reproductive Organism Therapeutic Tissues & Organs

59 Different types of cell in an organism have the same DNA but they transcribe different genes Nuclei do change as cells differentiate: DNA sequences do not change Chromatin structure does

60 Cloning of a Mammal In 1997 by Ian Wilmut edu/units/cloning/whatiscl oning/

61 Other mammals have been cloned The possibility of cloning humans raises unprecedented ethical issues.

62 Stem Cell Research Stem cells unspecialized cells, continually reproduce can differentiate into specialized cell types. can differentiate into multiple cell types Two types of stem cells 1. Adult stem cells & Cord Blood stem cells 2. Embryonic stem cells

63 Under the right conditions, cultured stem cells derived from either source can differentiate into specialized cells. Omnipotent

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65 Adult stem cells Bone marrow stem cells- different kinds of blood cells Embryonic stem cells immortal Somatic Cell reprogramming (2007) Induced Pluripotent Stem Cells (ipsc) Oct , 11:21 AM EST Induced Pluripotent Stem Cell Technology Used to Generate Hepatocytes from Skin Cells GEN News Highlights

66 Induced Pluripotent Stem Cells (ipsc)

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