I Thessalonians 5:21 21 Prove [test] all things; hold fast that which is good.

1. I Thessalonians 5:21 21Prove [test] all things; hold fast that which is good.

2. Evolution OfPopulations Timothy G. Standish, Ph. D.

3. Macro and Micro Evolution • Macro evolution is the evolution of higher taxonomic groups (formation of a new genus, family etc.) • Micro evolution - Change in allele frequency within a species or population of a species • Micro evolution is population genetics • Population genetics has been observed and this is what is being talked about when scientists say that evolution has been observed • Macro evolution has not been observed in any definitive way

4. Speciation, Yes.Natural Selection, ??? • After The Origin of Species was published in 1859, the scientific community quickly accepted that speciation occurred • Remember that speciation was not an entirely new idea, it had been proposed by Lamark and Franz Unger (Mendel’s mentor) among others • The mechanism for speciation proposed by Darwin, natural selection, was not as quickly accepted

5. Other Ideas About Speciation From Huxley’s book • Many believed that new species resulted from hybridization between old species (not necessarily untrue) • Orthogenesis (ortho = straight genesis = beginning) - The idea that evolution was progressing along a predictable path toward some ideal. Really a throw back to Lamarkism • 1920s After the rediscovery of Mendel's work, the idea that evolution occurred in rapid leaps due to mutations radically altering phenotype was popular

6. The Modern Synthesis • Darwin recognized that variation existed in populations and suggested natural selection as a mechanism for choosing some variants over others resulting in survival of the fittest and gradual changes in populations of organisms. • Without a mechanism for generation of new variation, populations would be selected into a corner where only one variation would survive and new species could never arise. • The Modern Synthesis combines the mechanism of DNA mutations generating variation with natural selection of individuals in populations to produce new species.

7. Where Speciation Occurs • Real acceptance of natural selection came after it was realized that evolution occurs on the level of populations not individuals • Individuals that have more success at reproducing than others are selected over others in a population • If one type of individual is chosen (selected) over another type, it will change the make up of the population by passing its genes on to more members of the next generation • Individuals are selected, populations evolve

8. What is a Population? • A group of individuals of the same species in the same geographical area: • Human population of Berrien Springs • Chicken population of Hong Kong • Human population of the United States • What is a species? • A group of populations that have the potential to interbreed in nature • We’ll come back to this question

9. Population Genetics • Is mathematics • One definition: • Algebraic description of population's genetic makeup including allelic frequencies and genotypic frequencies • Emphasizes - Genetic variation within populations (on which selection can occur) • Recognizes - The importance of quantitative traits

10. History • 1908 - G. H. Hardy, an English mathematician and W. Weinberg, a German physician, simultaneously discovered an equation that relates allelic and genotypic frequencies in populations that meet certain requirements commonly found in real populations. • 1920s - Developed very rapidly due to work by R. A. Fisher, J. B. S. Haldane, and S. Wright.

11. History Cont. • 1960+ Has become a major area of genetics due to: • Computers - Allowing rapid computation on large data sets • Electrophoresis - Allows the rapid gathering of large amounts of empirical data • Newer techniques that allow the analysis of relationships among species

12. The Hardy-Weinberg Theorem • The corner stone of population genetics • “The frequency of alleles in a population will remain constant over time if certain conditions are met” • Infinite (or at least very large) population size • Isolation from other populations - No migration • No net mutations • Random mating • No natural selection

13. The EquationThat Says it all • If we look at one gene in a population with 2 alleles, A and a, and we let: • p = f(A) q = f(a) -> f(A) + f(a) = p + q = 1 and • p = 1 - q and q = 1 - p • Probability of getting an individual with a given genotype can be calculated on the basis of the probability of getting parents with given genotypes: (p + q)(p + q) = 1 x 1 = 1 • (p + q)2 = 1 2 • p2 + 2pq + q2 = 1

14. p2 + 2pq + q2 = 1 • This equation allows us to predict genotypic frequencies on the basis of allelic frequencies and allelic frequencies on the basis of genotypic frequencies • f(AA) = f(A) x f(A) = p2 • f(aa) = f(a) x f(a) = q2 • f(Aa) =2 [f(A) x f(a)] = 2pq

15. A 0.5 A 0.1 a 0.5 a 0.9 A 0.1 A 0.5 AA 0.01 AA 0.25 Aa 0.25 Aa 0.09 a 0.5 a 0.9 Aa 0.25 Aa 0.09 aa 0.81 aa 0.25 Does This Equation Fit With Mendelian Genetics? • In the following cross: • Aa x Aa • 0.5 of alleles in gametes will be A • 0.5 of alleles in gametes will be a • Therefore: • f(A) = p = 0.5 • f(a) = q = 0.5 • p2 + 2pq + q2 = 1 • (0.5)2 + 2(0.5)(0.5) + (0.5)2 = 1 • 0.25 + 0.5 + 0.25 = 1 • f(AA) = 0.25, f(Aa) = 0.5, f(aa) = 0.25

16. Problem 1 MN Blood Types in US. Whites • MN blood types are inherited in a codominant fashion, thus heterozygous individuals can easily be detected • In a sample of the U. S. white population, blood types were determined as follows: • M (Genotype MM) = 1,787 • MN (Genotype MN) = 3,039 • N (Genotype NN) = 1,303

17. + + + 2 ( MM ) ( MN ) 2 ( 1 , 787 ) 3 , 039 3 , 574 3 , 039 p = = = = 0 . 54 2 ( Total ) 2 ( 6 , 129 ) 12 , 258 or + ( MM ) 1 / 2 ( MN ) p = Total Problem 1 AMN Blood Types in US. Whites MM 1,787 MN 3,039 NN 1,303 • A) What is the frequency of the M allele? • Answer - As each individual is heterozygous and there are a total of 6,129 in the sample there should be 2(6,129) = 12,258 alleles • 2 M alleles in each MM genotype = 2(1,787) = 3,574 alleles • 1 M allele in each MN genotype = 3,039 alleles • Total M alleles/Total of all alleles = f(M) = p

18. Problem 1 BMN Blood Types in US. Whites MM 1,787 MN 3,039 NN 1,303 • B) What is the frequency of the N allele? • Answer: • As p + q = 1 • q = 1 - p • q = 1 - 0.54 • q = 0.46

19. Problem 1 CMN Blood Types in US. Whites MM 1,787 MN 3,039 NN 1,303 • C) Is this population described by the Hardy-Weinburg formula? • Answer: Predicted genotypic numbers in a population of this size = • f(MM)(Total) = p2 (Total) = (0.54)2(6,129) = 0.292 (6,129) = 1,790 • f(MN) (Total) = 2pq (Total) = 2(0.54)(0.46) (6,129) = 0.498 (6,129) = 3,052 • f(NN) (Total) = q2 (Total) = (0.46)2 (6,129) = 0.212 (6,129) = 1,299 • Quick math check: • p2 + 2pq + q2 = 0.292 + 0.498 + 0.212 = 1.002(Close enough) • 1,790 + 3,052 + 1,299 = 6,151 (off by about 12) • 0.002 x 6,129 ≈ 12 • Do Chi square to decide

20. 2 - 2 d ( Obs . Ex .) å å C2 = = e Ex Obs. Ex. O - E (O-E)2/E MM 1,787 1,790 -3 0.005 MN 3,039 3,052 -13 0.0554 NN 1,303 1,299 4 0.0123 X2 = 0.0727 Problem 1 C Cont.MN Blood Types in US. Whites Chi Square: • Degrees of freedom = N - 1 = 3 - 1 = 2 • 0.99 > p > 0.95 • Yes, the population is probably in a Hardy-Weinburg equilibrium

21. What if p2 + 2pq + q2 = 1 Did not Describe the Population? • Remember that the Hardy-Weinburg theorem is true only if certain conditions are met: • If the Hardy-Weinburg equation does not describe the population, it is probably evolving due to violation of one of these conditions • Infinite (or at least very large) population size • Isolation from other populations - No migration • No net mutations • Random mating • No natural selection

22. Infinite Population Size • This same assumption is made in most descriptive statistics • Small population sizes can lead to sampling error so that the next generation is not an accurate representation of the previous generation • Genetic drift - With each generation each allele has a fixed probability of not being passed on, in small populations this probability is significant • Founder effect - A small number of individuals from a large population populate an area. Only the alleles of the few founders are represented in their descendants, not the entire population from which they came (i. e. the human population of Finland) • Bottle neck effect - A large population is reduced to a very small number then recovers, but only those alleles that made it through the bottle neck are in the recovered population (i. e. cheetahs in Southern Africa)

23. Isolation From Other Populations • If members of another population with different allelic frequencies are migrating in, the population being studied will not be in equilibrium • Example: Two populations of 100 individuals: • 1 p1 = 0.1 q1 = 0.9 AA=1, Aa=18, aa=81 • 2 p2 = 0.9 q2 = 0.1 AA=81, Aa=18, aa=1 • Combined together: p1+2 = 0.5 q1+2 = 0.5 • Predicted genotypic frequency: • f(AA) = p2 = 0.25 or 50/200 (actual 0.41 or 82/200) • f(Aa) = 2pq = 0.50 or 100/200 (actual 0.18 or 36/200) • f(aa) = q2 = 0.25 or 50/200 (actual 0.41 or 82/200)

24. m a n No Net Mutations • In reality, heritable mutations are very rare events. • Remember that most mutations are not a good thing for the organism, so it is in the best interest of all living things to avoid damage to their DNA • Even if mutation was common, an equilibrium would be reached: • Let A and a be alleles for a given gene, mutation from A to a =  and mutation from a to A =  A

25. Hi there sweetie! Random Mating • If mates are chosen on the basis of a genetic trait then that trait or allele will be passed to the next generation at higher frequencies than alternative alleles thus allelic frequencies will change over time, and the population will not be in equilibrium • Sexual Selection - Choosing a mate on the basis of their genotype

26. Natural Selection • Natural selection is thought to be the most common cause of changes in allelic frequencies and thus populations being out of equilibrium • It is important to note that for the effect of natural selection to be detected on the basis of violation of Hardy-Weinburg, selection would have to be fairly stringent at the point in time data was collected • Hardy-Weinburg can be used to compare populations of the same species and may infer that selection has occurred assuming the other factors previously mentioned are not at play

27. Natural Selection p= 0.1 q= 0.9

28. Natural Selection p= 0.1 q= 0.9 If selection (s) is 0.5 against aa and fitness = W=1-s

29. Natural SelectionSecond Generation p= 0.17 q= 0.83 AA=2 Aa =30 aa =68

30. Natural SelectionThird Generation p= 0.25 q= 0.75 AA=3 Aa =46 aa =51

31. Natural SelectionFourth Generation p= 0.34 q= 0.66 AA=3 Aa =62 aa =35

32. Natural SelectionFifth Generation p= 0.42 q= 0.58 AA=4 Aa =75 aa =21

33. Natural SelectionSixth Generation p= 0.46 q= 0.54 AA=5 Aa =83 aa =12

34. Natural SelectionSixth Generation • After 6 generations, the population is not in equilibrium: • p= 0.46 q= 0.54 • p2 + 2pq + q2 = 0.212 + 0.497 + 0.292 =1.001 • Expected genotype numbers: • AA = 21 (Actual =5) • Aa = 50 (Actual = 83) • aa = 29 (Actual = 12) • No need to do a Chi square on this one!

35. 0.9 0.8 0.7 0.6 Frequency 0.5 0.4 0.3 0.2 0.1 0 q 1 2 Alleles 3 p 4 5 6 7 8 9 10 Generations Rate of Change With Selection Even with heavy selection (s=0.5) the rate of change in allele frequency declines rapidly after a few generations

36. 0.9 0.8 0.7 0.6 Frequency 0.9 0.5 0.8 0.4 0.7 0.3 0.6 0.2 Frequency 0.5 0.1 0.4 0 q 0.3 1 2 Alleles 3 p 4 5 0.2 6 7 8 9 10 0.1 Generations 0 q 1 2 Alleles 3 p 4 5 6 7 8 9 10 Generations s = 0.1 Rate of Change With Selection The heavier the selection, the faster the change and the quicker the decline in rate of change. s = 0.9

37. Selection Selection Directional Frequency Frequency Frequency Selection Diversifying Types of Selection Stabilizing Pseudopterix pleiorostrum (many beaked fake bird)

38. When the Data Speaks "For example, researchers have calculated that 'mitochondrial Eve'--the woman whose mtDNA was ancestral to that in all living people--lived 100,000 to 200,000 years ago in Africa. Using the new clock, she would be a mere 6,000 years old. No one thinks that's the case, but at what point should models switch from one mtDNA time zone to the other?” Gibbons, A. 1998. Calibrating the mitochondrial clock. Science 279:28-29

39. The End