DNA is the genetic material. The instructions for making and “operating” an organism are written in DNA. DNA is divided

1. Basic genetics terminology DNA is the genetic material. The instructions for making and “operating” an organism are written in DNA. DNA is divided into sections called genes.

2. What a gene does • Each gene codes for a single protein. The gene specifies the sequence of amino acids that should be joined together to make a protein. • Together the genes determine the characteristics of an organism.

3. Alleles and genes • Alleles are different versions of a gene. • If a single gene codes for flower color, white and blue flowers would be coded for by 2 different alleles.

4. Number of copies of genes • You possess two copies of each gene in your body*. • One copy is inherited from each parent. • For a given gene you may have two different alleles or two copies of the same allele. (* excluding genes on sex chromosomes in males).

5. Homozygous vs heterozygous • A homozygous individual has two copies of a particular allele. (AA) • A heterozygous individual has two different alleles. (Aa)

6. Genotype and phenotype • An organism’s genes (its genotype) play a large role in determining its physical appearance (its phenotype). • But remember an organism’s phenotype is also affected by the environment.

7. The relationship between genes and evolution • We express evolutionary ideas in terms of genes because genes are the only thing that are passed from one generation to the next.

8. Process of Natural Selection • In the process of natural selection, genes that help organisms to survive and reproduce become more common. • Genes that help less or are harmful gradually are eliminated from the population.

9. Process of Natural Selection • Individuals that are the best adapted to their environments (the best camouflaged, best at finding food, etc.) will generally be more successful at breeding than less well adapted individuals. • As a result, their genes (which make them well adapted) will be commoner in the next generation than the genes of less well adapted individuals.

10. Chapter 23. The Evolution of Populations • Remember individual organisms do not evolve. Individuals are selected, but it is populations that evolve. • Because evolution occurs when gene pools change from one generation to the next, understanding evolution require us to understand population genetics.

11. Some terminology • Population: All the members of one species living in single area. • Gene pool: the collection of genes in a population. It includes all the alleles of all genes in the population.

12. Some terminology • If all individuals in a population all have the same allele for a particular gene that allele is said to be fixed in the population. • If there are 2 or more alleles for a given gene in the population then individuals may be either homozygous or heterozygous (i.e. have two copies of one allele or have two different alleles)

13. Detecting evolution in nature • Evolution is defined as changes in the structure of gene pools from one generation to the next. • How can we tell if the gene pool changes from one generation to the next? • We can make use of a simple calculation called the Hardy-Weinberg Equilibrium

14. Hardy-Weinberg Equilibrium • Before discussing Hardy-Weinberg need to review some basic facts about Mendelian Inheritance. • In Mendelian Inheritance alleles are shuffled each generation into new bodies in a way similar to which cards are shuffled into hands in different rounds of a card game. • The process of Mendelian Inheritance preserves genetic diversity from one generation to the next. A recessive allele may not be visible because it is hidden by the presence of a dominant allele, but it is still present.

15. Hardy-Weinberg Equilibrium • The shuffling process occurs because an individual has two copies of any given gene (one inherited from father and one from mother), but can put only one or the other copy into a particular sperm or egg. E.g. for an individual who is heterozygous Aa 50% of sperm will contain A and 50% will contain a.

16. Hardy-Weinberg Equilibrium • Individuals alleles thus go through a process where they are sorted into gametes (sperm or egg) which combine to form a zygote which will one day again sort alleles into gametes. • See Chapter 14 to review Mendelian Inheritance

18. Hardy-Weinberg Equilibrium • Consider a population of 100 individuals. This population will contain 200 copies of any given gene because each individual has two copies. • Gene we are interested in has two alleles A and a.

19. Hardy-Weinberg Equilibrium • If 80% of the alleles in the gene pool are A and 20% are a, we can predict the genotypes in the next generation. • Basic probability: To determine the probability of two independent events both occurring, you should multiply the probabilities of the individual events together.

20. Hardy-Weinberg Equilibrium • Probability of an AA individual is 0.8*0.8 = 0.64 • Probability of an aa individual is 0.2*0.2 = 0.04 • Probability of an Aa individuals is 0.2*0.8 = 0.16, but there are two ways to produce an Aa individual so 0.16*2= 0.32. • Note these probabilities sum to 1.

22. Hardy-Weinberg Equilibrium • General formula for Hardy-Weinberg is p2 + 2pq + q2 = 1, where p is frequency of allele 1 and q is frequency of allele 2. p + q = 1.

23. Hardy-Weinberg Equilibrium • Hardy-Weinberg equilibrium can be used to estimate allele frequencies from information about phenotypes and genotypes.

24. Hardy-Weinberg Equilibrium • E.g. approx 1 in 10,000 babies are born with phenylketonuria (PKU) (causes retardation if diet is not kept free of amino acid phenylalanine). • Disease due to individual being homozygous for a recessive allele k. i.e., the babies’ genotype is kk.

25. Hardy-Weinberg Equilibrium • What is frequency of k allele in population? • q2 = frequency of PKU in population = 0.0001. • q = square root of q2 or 0.01. Frequency of allele k • Therefore p the frequency of the K allele = 1 - 0.01 = 0.99 • Frequency of carriers (heterozygotes) in population is 2pq = 2*0.99*0.01 = 0.0198 or almost 2% of population. Much greater than frequency of PKU.

26. Working with the H-W equation • You need to be able to work with the Hardy-Weinberg equation. • For example, if 9 of 100 individuals in a population suffer from a homozygous recessive disorder can you calculate the frequency of the disease-causing allele? Can you calculate how many heterozygotes are in the population?

27. Working with the H-W equation • p2 + 2pq + q2 = 1. The terms in the equation represent the frequencies of individual genotypes. [A genotype is possessed by an individual organism so there are two alleles present in each case.] • P and q are allele frequencies. Allelefrequencies are estimates of how common alleles are in the whole population. • It is vital that you understand the difference between allele and genotye frequencies.

28. Working with the H-W equation • 9 of 100 (frequency = 0.09) of individuals are homozygous for the recessive allele. What term in the H-W equation is that equal to?

29. Working with the H-W equation • It’s q2. • If q2 = 0.09, what’s q? Get square root of q2, which is 0.3, which is the frequency of the allele a. • If q=0.3 then p=0.7. Now plug p and q into equation to calculate frequencies of other genotypes.

30. Working with the H-W equation • p2 = (0.7)(0.7) = 0.49 -- frequency of AA • 2pq = 2 (0.3)(0.7) = 0.42 – frequency of Aa. • To calculate the actual number of heterozygotes simply multiply 0.42 by the population size = (0.42)(100) = 42.

31. Other examples of working with HW equilibrium: is a population in HW equilibrium? • In a population there are 100 birds with the following genotypes: • 44 AA • 32 Aa • 24 aa • How would you demonstrate that this population is not in Hardy Weinberg equilibrium

32. Three steps • Step 1: Calculate the allele frequencies. • Step 2: Calculate expected numbers of each genotype (i.e. figure out how many homozygotes and heterozygotes you would expect.) • Step 3: Compare your expected and observed data.

33. Step 1 allele frequencies • Step 1. How many “A” alleles are there in total? • 44 AA individuals = 88 “A” alleles (because each individual has two copies of the “A” allele) • 32 Aa individuals = 32 “A” alleles (each individual one A allele) • Total “A” alleles is 88+32 =120.

34. Step 1 allele frequencies • Total number of “a” alleles is similarly calculated as 2*24 + 32 = 80 • What are allele frequencies? • Total number of alleles in population is 120 + 80 = 200 (or you could calculate it by multiplying the number of individuals in the population by two 100*2 =200)

35. Step 1 allele frequencies • Allele frequencies are: • A = 120/200= 0.6. Let p = 0.6 • a = 80/200 = 0.4. Let q = 0.4

36. Step 2 Calculate expected number of each genotype • Use the Hardy_Weinberg equation p2 + 2pq + q2 = 1 to calculate what expected genotypes we should have given these observed frequencies of “A” and “a” • Expected frequency of AA = p2 = 0.6 * 0.6 = 0.36 • Expected frequency of aa = q2 = 0.4*0 .4 =0.16 • Expected frequency of Aa = 2pq = 2*.6*.4 = 0.48

37. Step 2 Calculate expected number of each genotype • Convert genotype frequencies to actual numbers by multiplying by population size of 100 • AA = 0.36*100 = 36 • aa = 0.16*100 = 16 • Aa = 0.48*100 = 48

38. Step 3 Compare Observed and Expected values Observed population is: 44 AA 32 Aa 24 aa Expected population is: 36AA 48Aa 16aa These numbers are not the same so the population is not in Hardy-Weinberg equilibrium. An assumption of the Hardy Weinberg equilibrium is being violated. What are those assumptions?

39. Hardy-Weinberg Equilibrium • Remember that the Hardy-Weinberg equation tells us what we would expect to find if alleles are simply randomly assorted into gametes and gametes come together randomly to produce new genotypes. • If a population is found to depart significantly from H-W equilibrium this is strong evidence that evolution is taking place, i.e., the gene pool of the population is changing.

40. Hardy-Weinberg Equilibrium • Five Conditions under which Hardy-Weinberg equilibrium holds: • No gene flow – no migration. • Random mating – no inbreeding. • Nomutations. • Large population size – reduces effects of chance events • No natural selection.

41. Gene flow • Movement of individuals between populations can alter gene frequencies in both populations. • Frequent migration may cause populations’ gene pools to become more similar to each other.

42. Non-random mating • Mating preferentially with others that are phenotypically similar to you [in extreme cases inbreeding (mating with relatives)] can prevent random mixing of genes • Homozygotes are common in inbred populations.

43. Inbreeding in California Sea Otters • Because inbreeding produces an excess of homozygotes in a population, deviations from Hardy-Weinberg expectations can be used to detect such inbreeding in wild populations.

44. Inbreeding in California Sea Otters • Sea otters, once abundant along the west coast of the U.S., were almost wiped out by fur hunters in the 18th and 19th centuries. photo: www.turtletrack.org

45. Inbreeding in California Sea Otters • California population reached a low of 50 individuals (now over 1,500). As a result of this bottleneck, the population has less genetic diversity than it once had.

46. Inbreeding in California Sea Otters • Population is still at a low density and Lidicker and McCollum (1997) investigated whether this resulted in inbreeding. • They determined genotypes of 33 otters for PAP locus, which has two alleles S (slow) and F (fast)

47. Inbreeding in California Sea Otters • The genotypes of the 33 otters were: • SS 16 • SF 7 • FF 10 • This gives approximate allele frequencies of S= 0.6 and F = 0.4

48. Inbreeding in California Sea Otters • If otter population in H-W equilibrium, genotype frequencies should be • SS = 0.6* 0.6 = 0.36 • SF =2*0.6*0.4 = 0.48 • FF = 0.4*0.4 = 0.16 • However actual frequencies were: • SS= 0.485, SF= 0.212, FF =0.303

49. Inbreeding in California Sea Otters • There are more homozygotes and fewer heterozygotes than expected for a random mating population. • Having considered alternative explanations for deficit of heterozygotes, Lidicker and McCollum (1997) concluded that sea otter populations show evidence of inbreedng.

50. Mutation • Mutation adds new genes, but generally so slowly that H-W equilibrium not affected. • However, mutation and sexual recombination ultimately responsible for the variation that natural selection depends on.