Lab 16: Population Genetics and Evolution (MK Fall 2024) PDF

Lab 16: Population Genetics: Hardy-Weinberg Theorem Fall 2024: 11.1, 11.2 Key working definitions Population: A group of organisms of the same species that occur in the same area and can interbreed (share a gene pool) to form fertile offspring. Gene pool: the sum of all the allel...

Lab 16: Population Genetics: Hardy-Weinberg Theorem Fall 2024: 11.1, 11.2 Key working definitions Population: A group of organisms of the same species that occur in the same area and can interbreed (share a gene pool) to form fertile offspring. Gene pool: the sum of all the alleles at all the gene loci of all the individuals in a population. Species: Group of organisms that can interbreed with each other and produce fertile offspring. Evolution: The change in populations over time (populations evolve, individuals do not) (at least 2 generations to observe Evolution) Eastern Same grey Eastern grey species. squirrel, squirrel Sciurus S.carolinensis carolinensi Different (Georgia) s (Maine) populations. How does evolution happen? (Darwin/Wallace) Natural selection: Gene variation causes variability in traits. Some individuals in a population have inherited traits that allow them to produce more surviving offspring than individuals without those traits. The population gradually includes more individuals with advantageous characteristics. Acts directly on phenotypes and indirectly on genotypes. In order to quantify how advantageous one individual’s traits are compared to another, we use the term fitness. Fitness: The number of surviving offspring an individual produces for the next generation (relative measure). Selection favors phenotypes with the greatest fitness. Darwin vs Lamarck Lamarck: individuals accumulate changes during their lifetime that are advantageous, and they pass these traits on to their offspring. Differs from Darwin’s theory that individuals are born with either advantageous or disadvantageous traits. Both say: if the traits are advantageous they are passed on. Population genetics: the study of genes in populations Fuses evolutionary biology with genetics of populations to investigate how evolutionary change arises due to natural selection and other factors. Why don’t dominant alleles drive out recessive alleles in a population? In 1908 Hardy and Weinberg investigated this by studying allele frequencies in a gene pool, and came up with the following Hardy-Weinberg principle: ○ If certain conditions are met, the frequency of alleles in a population remain constant from generation to generation (regardless of what the starting frequencies are) ○ If this principle is met (allelic frequencies do not change), the genotypes are said to be in Hardy-Weinberg equilibrium (HWE), meaning that there is no evolution occurring. Conditions required for HWE 1. The population is infinitely large, to avoid the potential effects of genetic drift- change in the frequencies of alleles due to chance. 2. Mating is random (in respect to the traits/alleles being studied). 3. There are no new mutations at the gene locus to change allelic frequencies. 4. There is no immigration or emigration: no individuals are moving in or out of the population (no gene flow). 5. There is no selection: all genotypes have equivalent reproductive success. These are the five main agents of evolutionary change: drift, non-random mating, mutation, gene flow, and selection. If one or more of these HWE assumptions are not met, then the population is said to be evolving. Conditions required for HWE 1 2 3 5 4 1. Genetic Drift Frequencies of alleles may change by chance alone. Particularly important in small populations. Founder effect: few individuals found a new population (small allelic pool) Bottleneck effect: drastic reduction in population (and therefore gene pool size) 1. Genetic drift: founder effect The founder effect occurs when a few individuals become isolated from a larger population Allele frequencies in the small founder population can be different from those in the larger parent population 1. Genetic drift: bottleneck effect A sudden reduction in population size due to a change in the environment. Resulting gene pool may no longer be reflective of original population’s gene pool. If population remains small, it may be further affected by genetic drift. 2. Non-random mating & 3. Mutation Assortative mating: when phenotypically similar individuals mate (eg: blue individuals only mate with blue, green with green, etc.) Changes to the genetic code (mutations) may cause a change in phenotype, which may or may not be advantageous. Mutation rates usually very low. 4. Gene flow/Migration Movement of alleles among populations. Alleles can move via migration of fertile individuals or gametes (eg: pollen) between populations. Tends to reduce variation across populations over time. Can decrease or increase Eg: movement of alleles with insecticide resistance increase fitness of a population, fitness of their new insect populations depending on which alleles Eg: movement of alleles adapted to warm weather climates are introduced. will decrease fitness of their new cold-weather populations. 5. Selection a)Disruptive selection: eliminates intermediate types. b)Directional selection: eliminates one extreme from a phenotypic array c)Stabilizing selection: eliminates both extremes from an array of phenotypes. 5. Natural Selection( e.g.) Variation must: 1) exist among individuals/phenotypes, 2) be genetically inherited, and 3) affect differences in survival and number of viable offspring produced (fitness). Natural selection is a process, evolution is the outcome. Eg: adaptive melanism: In the Pinacate region of AZ, areas of black lava rock intermix with areas of beige rocks. The rock pocket mice there have two different melanic forms. 5. Natural Selection (e.g.) Eg: Heterozygote advantage. Heterozygotes will be favored: both alleles maintained instead of removing less successful alleles from a population. Sickle cell anemia: homozygotes exhibit severe symptoms (abnormal blood cells, usually die before reproductive age). Heterozygotes: less susceptible to malaria. 5. Artificial selection (e.g.) Human exerted selection. Examples include: Dog or other domestic animal breeds (pressure exerted by breeders) Agriculture 39 pairs of Chr and 98% identical genomes The Hardy-Weinberg rule: calculating allele frequencies Hardy and Weinberg principles arrived at by analyzing the frequencies (proportions) of alleles in successive generations of a population If all the conditions for Hardy-Weinberg equilibrium are met, you can predict the frequency of alleles in a population: Suppose that a population has 2 alleles at a gene locus: A and a The frequency of alleles is designated as: p for dominant, q for recessive. Because there are only two alleles, and p and q are frequencies, the sum of p and q must always equal 1. Thus, the frequency of alleles in the gene pool is: ○ p + q = 1, ○ Thus, p=1-q, q=1-p ○ eg: if q=.25, p=1-.25=0.75 The Hardy-Weinberg rule: calculating allele frequencies Fertilization in matings is a random process, resulting in the following possible genotypes: AA (homozygous dominant), Aa (heterozygous), and aa (homozygous recessive). In algebraic terms, the Hardy-Weinberg equilibrium is written as an equation: p2 + 2pq + q2 = 1 Where: The frequency of genotype AA in the population is p2 p=0.5 q=0.5 The frequency of genotype aa in the population is q2 p=0.5 p2=.25 pq=.2 The frequency of genotype Aa in the population is 2pq 5 Further Hardy-Weinberg examples More practice (Stepwise work) Hardy-Weinberg practice If observed genotypic frequencies are red pink white significantly different from expected Observed 89 27 4 (calculated using allele frequencies), then evolution is occurring: can evaluate this with Expected a Chi-square test. Deviation Practice problem: You measure allele frequencies for a flower Deviation2 population and get 0.8 red (p), and 0.2 white (q). Next generation, you observe D2/Expected phenotypes of: 89 red (p2), 27 pink (2pq), and 4 white (q2) flowers. Is this population in Chi Squared Hardy-Weinberg equilibrium? Hardy-Weinberg practice Step one? If observed genotypic frequencies are red pink white significantly different from expected Observed 89 27 4 (calculated using allele frequencies), then evolution is occurring: can evaluate this with Find population size: a Chi-square test. Expected Deviation Practice problem: You measure allele frequencies for a flower Deviation2 population and get 0.8 red (p), and 0.2 white (q). Next generation, you observe D2/Expected phenotypes of: 89 red (p2), 27 pink (2pq), and 4 white (q2) flowers. Is this population in Chi Squared Hardy-Weinberg equilibrium? Hardy-Weinberg practice Step one? If observed genotypic frequencies are red pink white significantly different from expected Observed 89 27 4 (calculated using allele frequencies), then Find population size: evolution is occurring: can evaluate this with Expected 89 + 27 + 4 = 120 a Chi-square test. Deviation Practice problem: You measure allele frequencies for a flower Deviation2 population and get 0.8 red (p), and 0.2 white (q). Next generation, you observe D2/Expected phenotypes of: 89 red (p2), 27 pink (2pq), and 4 white (q2) flowers. Is this population in Chi Squared Hardy-Weinberg equilibrium? Hardy-Weinberg practice Step two? If observed genotypic frequencies are red pink white significantly different from expected Observed 89 27 4 Calculate (calculated expected using genotype allele frequencies), then evolution is occurring: frequencies using cangiven evaluate this with allele Expected a Chi-square test. frequencies: p=0.8 (red), and q=0.2 Deviation Practice problem:(white) You measure allele frequencies for a flower Deviation2 population and get 0.8 red (p), and 0.2 white (q). Next generation, you observe D2/Expected phenotypes of: 89 red (p2), 27 pink (2pq), and 4 white (q2) flowers. Is this population in Chi Squared Hardy-Weinberg equilibrium? Hardy-Weinberg practice Step two? If observed genotypic frequencies are red pink white significantly different from expected Observed 89 27 4 (calculated using allele frequencies), then Expected evolution red: 0.8can is occurring: 2 x evaluate 120 = 76.8 this with Expected 76.8 38.4 4.8 Expected pink:test. a Chi-square 2 x 0.8 x 0.2 x 120 = 38.4 Expected white: 0.22 x 120 = 4.8 Deviation Practice problem: You measure allele frequencies for a flower Deviation2 population and get 0.8 red (p), and 0.2 white (q). Next generation, you observe D2/Expected phenotypes of: 89 red (p2), 27 pink (2pq), and 4 white (q2) flowers. Is this population in Chi Squared Hardy-Weinberg equilibrium? Hardy-Weinberg practice Step 3: If observed genotypic frequencies are red pink white significantly different from expected Observed 89 27 4 (calculated using allele frequencies), then Subtract evolution isexpected occurring:from observed can evaluate this to with Expected 76.8 38.4 4.8 find deviation, a Chi-square then fill out rest of Chi test. Square table Deviation Practice problem: You measure allele frequencies for a flower Deviation2 population and get 0.8 red (p), and 0.2 white (q). Next generation, you observe D2/Expected phenotypes of: 89 red (p2), 27 pink (2pq), and 4 white (q2) flowers. Is this population in Chi Squared Hardy-Weinberg equilibrium? Hardy-Weinberg practice Step 3: If observed genotypic frequencies are red pink white significantly different from expected Observed 89 27 4 (calculated using allele frequencies), then Subtract evolution isexpected occurring:from observed can evaluate this to with Expected 76.8 38.4 4.8 find deviation, a Chi-square then fill out rest of Chi test. Square table Deviation 12.2 -11.4 -0.8 Practice problem: You measure allele frequencies for a flower Deviation2 148.84 129.96 0.64 population and get 0.8 red (p), and 0.2 white (q). Next generation, you observe D2/Expected 1.94 3.38 0.13 phenotypes of: 89 red (p2), 27 pink (2pq), Chi Squared 1.94+3.38+0.13 = 5.45 and 4 white (q2) flowers. Is this population in Hardy-Weinberg equilibrium? Hardy-Weinberg practice How many degrees of freedom do we have? Using p= 0.05, do our results support the hypothesis that this population is evolving (chi-squared value > table threshold), or do we reject the hypothesis of evolutionary change (chi-squared value < table threshold) meaning that this population is in Hardy-Weinberg Equilibrium? Further notes on variation and population capacity All populations have the capacity to increase in numbers, but no population can increase indefinitely. Eventually, individuals of a population will end up competing for resources. All individuals have the same genes that specify the same assortment of traits. Most genes occur in different alleles, that produce different phenotypes: some of which compete better than others. Over time, the alleles that produce the most successful phenotypes will increase in the population, and less successful alleles will become less common. Change leads to increased fitness, and increased adaptation to environment. Outputs Exercise 11.1 (p279-282). Testing Hardy-Weinberg Equilibrium (30min) (collaborative work of 4) Exercise 11.2 (p282-297). Simulation of Evolutionary Change Subgroup Target works (in pairs) 1 Experiment A, B 2 Experiment A, C To do list: Table 11.1-3(p280-281), Table 11.4 (only 3 generations) (p286), Table 11.5 (only 3 generations) (p295)