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: http://zoology.okstate.edu/zoo_lrc/biol1114/tutorials/flash/life4e_15-6- 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?
Definitions A population is a localized group of interbreeding individuals in a given geographic area A species is a group of populations who interbreed and produce fertile offspring
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 alleles vary with time Gene Flow = Movement of alleles between populations when people migrate and mate
Changes allelic frequencies in populations
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
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
Phenotype Frequencies Frequency of a trait varies in different populations. Example: PKU an autosomal recessive trait Table 14.1
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
Calculating the allelic frequencies from the genotypic frequencies What is the allelic frequency (of R and r) in this population?
Genotypic frequency RR= 320/500 = 0.64 Rr = 160/500= 0.32 rr = 20/500 = 0.04
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 2 + 160= 640+160= 800 800/1000 = 0.8 =80% Frequency of r allele = 1-0.8 = 0.2 =20% or rr +Rr = 20 X 2+ 160= 200 200/1000 = 0.2
- 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
The Hardy-Weinberg theorem describes the gene pool of a non-evolving population Hardy Weinberg animation http://zoology.okstate.edu/zoo_lrc/biol1114/t utorials/flash/life4e_15-6-osu.swf practice questions http://nhscience.lonestar.edu/biol/hwe.html
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
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.
(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.
Genetic Drift changes allelic frequencies in populations
The bottleneck effect The founder effect
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
Source of the Hardy-Weinberg Equation Figure 14.3 Figure 14.3
Figure 14.4 Solving a Problem
Figure 14.4 Solving a Problem
Calculating the Carrier Frequency of an Autosomal Recessive Figure 14.5 Figure 14.3
Calculating the Carrier Frequency of an Autosomal Recessive Table 14.3
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
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 0.0001. - The frequency of the recessive allele (q) is the square root of 0.0001 = 0.01. - The frequency of the dominant allele (p) is p = 1 - q or 1-0.01 = 0.99. The frequency of carriers (heterozygous individuals) is 2pq = 2 x 0.99 x 0.01 = 0.0198 or about 2%. About 2% of the U.S. population carries the PKU allele.
Question What is the chance or probability that two unrelated white Caucasian US individuals will have an affected child?
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
Calculating the Risk with Calculating the Risk with X-linked Traits X-linked Traits Figure 14.6 30
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 31
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) 32
DNA Repeats 33
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 http://highered.mheducation.com/sites/dl/free/007283512 5/126997/animation40.html http://science.howstuffworks.com/dna-profiling.htm
DNA Profiling Techniques RFLPs- Restriction Fragment length polymorphisms (limited utility) PCR- Amplification of select genomic regions spanning stretches of STRs
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 36
Comparing DNA Repeats Comparing DNA Repeats Figure 14.7 37
Practical Applications of DNA Fingerprinting Paternity and Maternity Personal Identification/ Criminal Identification and Forensics
Practical Applications of DNA Fingerprinting Forensic Biotechnology Whodunit? by Jenny Shaw, Vanessa Petty, Theresa Brown, and Sarah Mathiason
Practical Applications of DNA Fingerprinting
Jeffreys used his technique to demonstrate that Dolly was truly a clone of the 6- year old ewe that donated her nucleus Figure 14.9 41
Box Figure 14.1 42
DNA Profiling Technical Steps Blood sample is collected from suspect White blood cells release DNA Restriction enzymes cut DNA Electrophoresis aligns fragments by size Pattern of DNA fragments transferred to a nylon sheet 43
DNA Profiling Technical Steps Exposed to radioactive probes Probes bind to DNA Sheet placed against X ray film Pattern of bands constitutes DNA profile Identify individuals 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 45
CODIS Figure 14.10 Probability that any two individuals have same thirteen markers is 1 in 250 trillion 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 47
To Solve A Crime Figure 14.12 48
Figure 14.12 49
Using DNA Profiling to Identify Victims Recent examples of large-scale disasters World Trade Center attack (2001) Indian Ocean Tsunami (2004) Hurricane Katrina (2005) 50
Challenges to DNA Profiling 51
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 52