Population Genetics (1).pptx

Fundamentals of Population Genetics Key terminology • Population genetics-Study of genetic variation in populations and how it changes over time. • Population- A group of individuals who share a common set of genes, live in the same geographic area, and actually or potentially interbreed. • Gene p...

Fundamentals of Population Genetics Key terminology • Population genetics-Study of genetic variation in populations and how it changes over time. • Population- A group of individuals who share a common set of genes, live in the same geographic area, and actually or potentially interbreed. • Gene pool- Alleles shared by individuals in a population. Questions population geneticist try to answer • How much genetic variation is present in a population? • Are genotypes randomly distributed in time and space or is there a distribution pattern? (What does this look like in humans?) • What processes affect the composition of a population’s gene pool? • Do these processes produce genetic divergence among populations? * Remember that populations are dynamic! The Hardy-Weinberg law • Hardy Weinberg law explains what happens to alleles and genotypes in an “ideal” population, meaning one that is infinitely large, is not subject to any evolutionary forces such as mutation, migration or selection and in which mates are randomly selected. Under these conditions the Hardy-Weinberg law makes two predictions 1) The frequencies of alleles in the gene pool do not change over time. 2) If a locus may be occupied by either of two alleles, A or a, then after one generation of random mating, the frequencies of the resulting genotypes AA, Aa, and aa in population can be represented by p2 + 2pq + q2= 1 p= frequency of allele A and q= frequency of allele a Hardy-Weinberg (continued) • Hardy-Weinberg model uses Mendelian principles of segregation and simple probability to explain relationship between allele and genotype frequencies. Example- Assume in a population A=0.7 and a=0.3. Allele frequency is p + q =1. Do not confuse with genotype 2 frequency (p2 + 2pq + q = 1). Egg Egg fr(A)=0 .7 fr (AA)= 0.7 fr(A)=0 X 0.7= 0.49 fr(a)=0 .3 Fr (Aa)= 0.7 X 0.3= 0.21 .7 Sperm Fr (Aa)= 0.7 fr(a)=0 X 0.3= 0.21 .3 Fr (aa)= 0.3 X 0.3= 0.09 fr(A)=p fr (AA)= p2 fr(a)=q Fr (Aa)= pq fr(A)=p Sperm Fr (Aa)= pq fr(a)=q Fr (aa)= q2 Hardy-Weinberg examples (two alleles) • What is the genotypic frequency of a population with two alleles at the same loci one dominant and one recessive if the allele frequency for the recessive allele is 0.15? • What are the allele frequencies of A and a in a population that has a homozygous recessive genotypic frequency of 0.16? Additionally, what is the genotypic frequencies for individuals who are homozygous dominant and heterozygous? Hardy-Weinberg more than two alleles. • Can you think of locus with more than two alleles in humans? • Blood type ABO is example of locus with more than two alleles. How many possible genotypes exist for the blood phenotypes. Allele frequency p + q + (AA, r= 1 BB,OO, AB, AO,BO) •6 different combinations Genotype Frequency (p + q+ r)2 =p2 + q2 + r2 + 2pq + 2pr + 2qr = 1 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4089147/#:~:text=Hardy%2DWeinberg%20model%20for%20ABO%20blood%20group.&text=Hardy%2DWeinberg%20equation%20for%20ABO, Hardy-Weinberg example (three alleles) • For a population blood type frequencies are A=0.53, B=0.13, O=0.26 and AB=0.08. What is the frequency for the A allele in type A individuals? Focus on two alleles at a time. r2 = 0.26 r= 0.51 AA=p2 AO=2pr p2 + 2pr+ r2 = 0.26 +0.53 (p + r) 2= 0.79 p + r= √0.79 =0.89 p= 0.89-r p= 0.89-0.51 p= 0.38 What does q equal? Frequencies of X-Linked traits • Remember homogametic sex has (XX) and heterogametic sex has (XY). • Allele frequency for X linked trait is equal to the probability a male will have the trait. • Example colorblindness: 8% of human males are colorblind. q= colorblind allele, p= normal color allele. What percentage of females are colorblind and what percentage are carriers? p2 + 2pq + q2= 1 Natural Selection drives allele frequency change • Natural Selection- A non-random difference among individuals of different genotypes in survival or reproduction rate or both. • Scenario: Assume that in a population you have 100 individuals. The frequency of A=0.5 and a=0.5. After one mating you would expect 25 AA, 50 Aa, 25aa. Now suppose individuals with different genotypes have different survival rate, all 25 AA survive, 45 Aa (90%) survive, 20 aa (80%) survive. When the survivors reproduce each contributes two gametes. What are the frequencies of the two alleles in the surviving population? Videos to watch for Tuesday discussion • https://www.youtube.com/watch?v=lIRXDDG6yB8 • https://www.youtube.com/watch?v=YkI3zkQ4WBo&t=25 9s Natural Selection classifications - Three classifications 1) Directional 2) Stabilizing 3) Disruptive Directional Selection • Genotypes conferring one or the other phenotypic extremes becomes selected for or against, often as a result of changes to the environment. Stabilizing Selection • Favors the intermediate phenotypes, both extremes are selected against. • Well characterized example is birth weight in humans. Disruptive (Diversifying) Selection • The selection against intermediates and for both intermediate extremes. • Well characterized example oysters. Migration and Gene Flow can alter allele frequencies • Migration occurs when individuals move between populations. Changes in allele frequency can be predicted. • Example-Imagine species in which a given locus has two alleles, A and a. There are two populations of this species one on an island and one on the mainland. Pi’ = (1-m)Pi + m(Pm) Pm= A on mainland Pi= A on island Pi’= A on the island in the next generation m= Migrants from main island Migration Example problem • Example (continued)- Assume the Pi= 0.4 and Pm= 0.6 and that 10 percent of the parents of the next generation are migrants from the mainland (m=0.1). What is the frequency of the A allele on the island in the next generation (Pi’)? Pi’ = (1-m)Pi + m(Pm) Pm= A on mainland Pi= A on island Pi’= A on the island in the next generation m= Migrants from main island Pi’ = (1 – 0.1)(0.4) + (0.1 X 0.6) = 0.36 + 0.06 = 0.42 Example or migration allele frequency change in humans (Parra study) Genetic Drift causes random changes in allele frequencies • Genetic Drift is defined as significant random fluctuations in allele frequencies through chance deviation. • Genetic Drift can arise due to founder effect or genetic bottleneck. Founder effect example in humans • Founder effect in the Navajo tribe (OCA2) oculocutaneous albinism trait. • Several genes result in albinism, OCA2 is specific to Navajo tribe not found in closely related apache tribe. Yi et al. 200 Bottleneck Effect examples • Over the past several decades cheetah populations have been decimated due to climate change, hunting by humans and habitat destruction. Low genetic variability in cheetahs today (90% homozygosity in genome). • Scientist suggest that Koloas have recently undergone a bottleneck. Bottleneck in humans • In humans historically plagues, genocides and natural disasters cause bottleneck. Nonrandom mating changes genotype but not allele frequency • Assortative mating within populations are non-random occurrences. • Positive assortment- Individuals mate with others with similar genotypes. • Negative assortment- Individuals mate with others with dissimilar genotypes. Coefficient of inbreeding (F) • Inbreeding increases homozygosity and subsequently loss of heterozygosity. • It can be predicted with the following equation below. • Inbreeding can lead to inbreeding depression. F= H(e) – H(o) H(e) H(e)=expected heterozygosity H(o)=observe heterozygosity When F=1 then all individuals are homozygous (alleles are derived from same common ancestor) When F=0 no individual has two alleles derived from a common ancestral copy) Extreme inbreeding example • Artificial selection (selective breeding)- occurs when specific desired traits are selected for during mating. • Are there any pros or cons to artificial selection? • Are the any moral issues with the concept of artificial selection?