Population Genetics

1. Population Genetics Dr.SoumitraChakravarty

2. Natural Selection • Natural selection is one of the basic mechanisms of evolution, along with mutation, migration, and genetic drift. • Darwin's grand idea of evolution by natural selection is relatively simple but often misunderstood. http://evolution.berkeley.edu/evolibrary/article/evo_25

3. To find out how it works, imagine a population of beetles: • There is variation in traits.For example, some beetles are green and some are brown. http://evolution.berkeley.edu/evolibrary/article/evo_25

4. Natural Selection 2. There is differential reproduction.Since the environment can't support unlimited population growth, not all individuals get to reproduce to their full potential. In this example, green beetles tend to get eaten by birds and survive to reproduce less often than brown beetles do. http://evolution.berkeley.edu/evolibrary/article/evo_25

5. Natural Selection • 3. There is heredity.The surviving brown beetles have brown baby beetles because this trait has a genetic basis. http://evolution.berkeley.edu/evolibrary/article/evo_25

6. Natural Selection • 4. End result:The more advantageous trait, brown coloration, which allows the beetle to have more offspring, becomes more common in the population. If this process continues, eventually, all individuals in the population will be brown. http://evolution.berkeley.edu/evolibrary/article/evo_25

7. Survival of the fittest !FITNESS • Biologists use the word fitness to describe how good a particular genotype is at leaving offspring in the • next generation relative to how good other genotypes are at it. • So if brown beetles consistently leave more offspring than green beetles because of their color, • you'd say that the brown beetles had a higher fitness. http://evolution.berkeley.edu/evolibrary/article/evo_25

8. Fitness is a relative thing! • A genotype's fitness depends on the environment in which the organism lives. The fittest genotype during an ice age, for example, is probably not the fittest genotype once the ice age is over. • Fitness is a handy concept because it lumps everything that matters to natural selection (survival, mate-finding, reproduction) into one idea. The fittest individual is not necessarily the strongest, fastest, or biggest. A genotype's fitness includes its ability to survive, find a mate, produce offspring — and ultimately leave its genes in the next generation. http://evolution.berkeley.edu/evolibrary/article/evo_25

9. Fitness • caring for your offspring producing thousands of young — many of whom won't survive (above right), and sporting fancy feathers that attract females (left) are a burden to the health and survival of the parent. • These strategies do, however, increase fitness because they help the parents get more of their offspring into the next generation.

10. Sexual Selection • Sexual selection is a "special case" of natural selection. Sexual selection acts on an organism's ability to obtain (often by any means necessary!) or successfully copulate with a mate. Selection makes many organisms go to extreme lengths for sex: • peacocks maintain elaborate tails • elephant seals fight over territories • fruit flies perform dances • Going to even more extreme lengths, the male redback spider literally flings itself into the jaws of death in order to mate successful

11. Importance of sexual selection

12. Artificial selection • people (instead of nature) select which organisms get to reproduce

13. Adaptation • An adaptation is a feature that is common in a population because it provides some improved function • The creosote bush is a desert-dwelling plant that produces toxins that prevent other plants from growing nearby, thus reducing competition for nutrients and water. • Color changing in cameleon.

14. katydids

15. Natural Selection ! This doesn’t work this way !!

16. Gene flow • Gene flow — also called migration — is any movement of genes from one population to another. Gene flow includes lots of different kinds of events, such as pollen being blown to a new destination or people moving to new cities or countries. • If genes are carried to a population where those genes previously did not exist, gene flow can be a very important source of genetic variation

17. Genetic drift • Genetic drift — along with natural selection, mutation, and migration — is one of the basic mechanisms of evolution. • In each generation, some individuals may, just by chance, leave behind a few more descendents (and genes, of course!) than other individuals. The genes of the next generation will be the genes of the "lucky" individuals, not necessarily the healthier or "better" individuals. That, in a nutshell, is genetic drift. It happens to ALL populations — there's no avoiding the vagaries of chance.

18. Homologous Structures: have the same basic function but different structure;

19. Ontogeny recapitulates Phylogeny

20. Vestigial organs are indicative of Evolution

21. Population frequency Allele frequency: proportion of chromosome that contain a specific type of allele in a population • Normal allele (p); • Mutant allele (q); Genotype frequency: proportion of each genotype in a population: • Homozygous normal (p2); • Heterozygous normal (2pq); • Homozygous affected (q2);

22. Allele distribution Allelle1 Allelle2 Genotype 1 (Homozygous ) Genotype 2 (Heterozygous) Genotype 3 (Homozygous )

23. Allele frequency: Example Frequency of allele 1 (P): (44*2 + 38)/200 = 0.63; Frequency of allele 2 (Q): (18*2 + 38)/200 = 0.37;

24. Genotype frequency: Example

25. Hardy Weinberg law • Helps predict the distribution of phenotypes & genotypes in large populations; • If a population is large and individuals mate at random, there should be a constant and predictable relationship between genotype frequencies and allele frequencies; Formula : • P2 + 2PQ + Q2 = 1 • P+Q =1 • We can calculate genotype frequencies from allele frequencies or vice-versa;

26. Assumptions made in Hardy-Weinberg law • No new mutations; • No selections for or against the genotype exists; • No migration is occurring in & out of the population; • Hardy-Weinberg equilibrium involves two alleles, dominant & recessive, for any gene & does not consider multiple alleles or any non-Mendelian influences; Maggie May Does Not Smoke": Mutations Migration Drift Non-random mating Selection

27. Practical Application of Hardy-Weinberg law Disease prevalence(PKU) = 1/10,000 live births

29. Deviations from Hardy-Weinberg law • Mutation(Ex: consanguinity, founder effect); • Natural Selection: (alleles promoting survival are selected by nature; Ex: sickle cell disease & malaria, Hemochromatosis & iron-poor environment, cystic fibrosis & typhoid, glucose-6-phosphate dehydrogenase deficiency and hemolytic anemia & Malaria); • Genetic Drift; • Gene Flow (sickle cell disease in the US);

30. Genetic Drift

31. Founder effect The loss of genetic variation when a new colony is established by a very small number of individuals from a larger population

32. q=0.6

33. Consanguinity • Siblings (II-2 and II-3 OR II-4) share ½ of their genes • First cousins (III-3 AND III-4) share 1/8 of their genes ( ½ x ½ x ½ ) • Second cousins (IV-1 and iv-2 ) share 1/ 32 of their genes ( 1/8 x ½ x ½ )

34. Application of Hardy Weinberg law • Frequency of allele 1 = P • Frequency of allele 2 = Q • Frequency of genotype 1-1 = P2 • Frequency of genotype 1-2 = 2PQ • Frequency of genotype 2-2 = Q2 • Normal allele = P • Abnormal allele =Q • Heterozygous = 2PQ

35. Hardy-Weinberg for AR diseases • Only q2 = affected population • 2pq = heterozygote population • P2 = normal population • Disease prevalence= q2

36. The prevalence of PKU is 1/10000. What is the prevalence of carrier state? • Q2 = 1/10000 • 2pq = ?

37. The prevalence of cystic fibrosis carrier state is 1 in 30 live births. What is the frequency of affected children in this condition? • 2Q = 1/30 • Q2 = ?

38. EXAMPLE 1 • The prevalence of PKU is 1/10000. what is the prevalence of carrier state. • Q2 = 1/10000 • 2pq = ?

39. The prevalence of cystic fibrosis carrier state is 1 in 30 live births. What is the frequency of affected children in this condition? • 2pq = 1/30 • q2 = ?

40. An African American couple with a normal family history wants to know their chance of having a child with sickle cell anemia. The incidence of sickle cell trait is 1 in 8 for African Americans. The risk in this case is • 1/8 • 1/16 • 1/60 • 1/120 • 1/256

41. Hardy-Weinberg for AD diseases • 2pq + q2 = affected population; • but sometimes it is 2pq because q2 is a genetic lethal; • P2 = normal population; • Disease Prevalence = 2pq+q2

42. Hardy-Weinberg for X-linked Recessive • Disease prevalence= q • The statement that 1/10000 males has Hemophilia A, indicates that q= 1/10000; • Prevalence of disease in females= 1/108; • Female have two pairs of the X chr, follows HWrule • Prevalence of female carrier= 2q= 1/5000;