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DAY 2 Lecture 3

DAY 2 Lecture 3. III. Alterations of Hardy-Weinberg proportions. Taenia solium. Nasonia vitripenis. Rh - Rh -. Rh + Rh -. 1. Heterozygote deficits. Endogamy. Underdominance. Wahlund effect. Homogamy. Technical causes. Null alleles Short allele dominance Allelic dropout Stuttering.

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DAY 2 Lecture 3

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  1. DAY 2 Lecture 3

  2. III. Alterations of Hardy-Weinberg proportions

  3. Taenia solium Nasonia vitripenis Rh-Rh- Rh+Rh- 1. Heterozygote deficits Endogamy Underdominance Wahlund effect Homogamy Technical causes Null alleles Short allele dominance Allelic dropout Stuttering

  4. Selfing AA Aa aa Dt Ht Rt s: selfing 1-s: panmixia Large population size, N Mutation rate u=0 Migration rate m=0

  5. Selfing AA Aa aa Dt Ht Rt

  6. Selfing AA Aa aa Dt Ht Rt At equilibrium, Ht=Ht+1=Heq

  7. Selfing AA Aa aa Dt Ht Rt At equilibrium, Ht=Ht+1=Heq

  8. Selfing AA Aa aa Dt Ht Rt At equilibrium, Ht=Ht+1=Heq

  9. Selfing AA Aa aa Dt Ht Rt At equilibrium, Ht=Ht+1=Heq Wright's generalized formulation

  10. 0.5 Autofécondation 100% ou homogamie codominante 0.4 Croisements frère/soeur 100 % Homogamie 100% (p=0.5) 0.3 H Homogamie 100% (p=0.25) 0.2 Homogamie 100% (p=0.75) 0.1 0 0 10 20 30 40 50 t Endogametic reproductive systems 100% selfing or codominant homogamy 100% full sib mating For the loci in concern homogamy homogamy dominant homogamy

  11. Wahlund effect

  12. Wahlund effect

  13. Wahlund effect Chesser and Nei'sFST >0 Wright's FST

  14. Wahlund effect

  15. Underdominance Panmixia, large population of size N, no mutation or migration, fecundity f (>1) 2 alleles, A and a in frequencies pt and1-pt at generation t Mean fitness

  16. Underdominance 2 alleles, A and a in frequencies pt and1-pt at generation t

  17. Underdominance 2 alleles, A and a in frequencies pt and1-pt at generation t Equilibrium is reached when allelic frequencies stop moving i.e. when Δp=pt+1- pt=0 <=> <=>

  18. <=> Underdominance 2 alleles, A and a in frequencies pt and1-pt at generation t Equilibrium when frequencies stop moving i.e. when Δp=pt+1- pt=0 s≤1 <=>

  19. <=> <=> peq=0, A removed peq=1, A fixed peq=1/2, unstable polymorphic equilibrium Underdominance 2 alleles, A and a in frequencies pt and1-pt at generation t Equilibrium when frequencies stop moving i.e. when Δp=pt+1- pt=0

  20. Underdominance 2 alleles, A and a in frequencies pt and1-pt at generation t Equilibrium when frequencies stop moving i.e. when Δp=pt+1- pt=0 =A2*(1-A2)*(2*A2-1)

  21. Technical causes of heterozygote deficits Null alleles Alloenzymes Normal enzyme functional Precipitation with coloration salts Mutation in the active site Non-functionnal enzyme No precipitation Heterozygotes Heterozygotes

  22. CTCTCTCT CTCTCTCT AGAGAGAG AGAGAGAG CTCTCTCTCT CTCTCTCTCT CTCTCTCTCT CTCTCTCTCT AGAGAGAGAG AGAGAGAGAG AGAGAGAGAG AGAGAGAGAG Technical causes of heterozygote deficits Nul alleles Microsatellites Primer1 Normal heterozygous profile Primer2 Primer1 Primer2 Primer1 Heterozygous profile perceived has homozygous Primer2 Primer1 Primer2 Mutation Primer1 Null homozygous profile perceived as missing data Primer2 Primer1 Primer2

  23. Technical causes of heterozygote deficits Competition for Taq polymerase: Allelic dropout A random phenomenon (first arrived to Taq, first served) in general due to small DNA quantities and/or weak affinity of all primers (primers defined on another species/population)

  24. Technical causes of heterozygote deficits Competition for Taq polymerase: short allele dominance Heterozygote deficits Allele size A random but essentially determinist phenomenon (short alleles are more easily amplified) in general due to small DNA quantities and/or to a weak affinity of all primers (primers defined on another species/population), Here, heterozygote deficits decrease with allele size

  25. CTCTCTCTCT AGAGAGAGAG CTCTCTCTCT AGAGAGAGAG Technical causes of heterozygote deficits Stuttering Error made by Taq polymerase: addition of a motive during PCR Primer1 Primer2 Primer1 Primer2 Here, heterozygote deficits are more frequent for alleles close in size

  26. Lecture 4

  27. III. Alterations of Hardy-Weinberg proportions (continued)

  28. Falciform anemia and Plasmodium falciparum Ixodes ricinus Schistosoma mansoni III. Alterations of Hardy-Weinberg proportions 2. Heterozygous excesses Overdominance Heterogamy MHC or HLA Clover Clonality Candida albicans Trypanosoma brucei Dioecious small populations Sex-biased dispersal Heterosis Technical causes Echo bands Duplicated loci

  29. Overdominance Panmixia in a large sized population of size N, no mutation or migration, with fecundity f (>1) 2 alleles, A and a in frequencies pt and1-pt at generation t

  30. Overdominance 2 alleles, A and a in frequencies pt and1-pt at generation t

  31. Overdominance 2 alleles, A and a in frequencies pt and1-pt at generation t Equilibrium when Δp=pt+1- pt=0 s≤1

  32. peq=0, A eliminated peq=1, A fixed peq=1/2, stable polymorphic equilibrium Overdominance 2 alleles, A and a in frequencies pt and1-pt at generation t

  33. Overdominance 2 alleles, A and a in frequencies pt and1-pt at generation t s<1 =A2*(1-A2)*(1-2*A2)

  34. Overdominance Geneticload

  35. Heterogamy BC AB AC ACt BCt ABt Clover Then equilibrium is reached when ABeq=ACeq=BCeq=1/3

  36. Allele D? Heterogamy AB AC BC ACt BCt ABt

  37. Clonality No mutation or migration, large population, no selection, a proportion c of zygotes invested in clonal reproduction and 1-c in panmixia AA Aa aa Dt Ht Rt At equilibrium Ht=Ht+1=Heq and then: Convergence to HW but strong linkage disequilibrium is expected

  38. Clonality +Drift +Mutation AA Aa aa Dt Ht Rt Aa Heq~1

  39. IV.Wright's F-statistiques

  40. 1. Wright's Island model

  41. 2.Inside individuals relative to the sub-population they belong to: FIS AA Aa aa Do Ho Ro H: probability of drawing two different alleles, from one individual in a sub-population (HI) from two individuals from the same sub-population (HS), from two individuals from two different sub-populations (HT) Chesser and Nei

  42. 3.Inside sub-populations relative to the total population: FST H: probability of drawing two different alleles, from one individual from one sub-population (HI) from two individuals from the same sub-population (HS), from two individuals from two different sub-populations (HT) Wright, for an infinite Island model and two alelles Chesser and Nei Wright's F are also variance ratios

  43. 4.Inside individuals relative to the total population: FIT H: probability of drawing two different alleles, from one individual from one sub-population (HI) from two individuals from the same sub-population (HS), from two individuals from two different sub-populations (HT) Chesser and Nei

  44. 5.Definitions according to heterozygosity Chesser & Nei (1-FIT)=(1-FIS)(1-FST) FIS: Heterozygote deficit resulting from a deviation from the panmictic model between individuals in sub-populations FST: Heterozygote deficit resulting from a deviations of the panmictic model between populations (subdivision) FIT: Global heterozygote deficit that results from the two previous ones FIS=-1 (one heterozygote class) FIS=0 (local panmixia) FIS=1 (only homozygous individuals) FIS<0 => heterozygote excess (e.g. clonality) FIS>0 => homozygous excess (e.g. selfing) FST=0 => no variation between sub-populations (e.g. free migration) FST>0 => genetic differentiation between sub-populations FST=1 => each sub-population fixed for one or the other available allele (absence of migration) FIT<0 => heterozygote excess (e.g. clonality) FIT=0 => global panmixia or clonality + Wahlund effect FIT>0 => homozygous excess (e.g. selfing and/or Wahlund))

  45. 6.Definitions according to inbreeding FIS: Inbreeding of individuals relative to inbreeding of sub-populations FST: Inbreeding of sub-populations relative to total inbreeding FIT: Inbreeding of individuals relative to total inbreeding Q=1-H: probability of drawing two identical alleles, from one individual QI, from two different individuals from the same sub-population QS and from two different sub-populations from the total population QT Weir Rousset These formulations are more consistent with the initial meaning of these indices (1-FIT)=(1-FIS)(1-FST)

  46. FST FIT FIS F IS l 7.Summing up

  47. 7.Summing up FIS: Inbreeding of individuals relative to inbreeding of sub-populations FST: Inbreeding of sub-populations relative to total inbreeding FIT: Inbreeding of individuals relative to total inbreeding FIS=-1 (one heterozygote class) FIS=0 (local panmixia) FIS=1 (only homozygous individuals) FIS<0 => heterozygote excess (e.g. clonality) FIS>0 => homozygous excess (e.g. selfing) FST=0 => no variation between sub-populations (e.g. free migration) FST>0 => genetic differentiation between sub-populations FST=1 => each sub-population fixed for one or the other available allele (absence of migration) FIT<0 => heterozygote excess (e.g. clonality) FIT=0 => global panmixia or clonality + Wahlund effect FIT>0 => homozygous excess (e.g. selfing and/or Wahlund))

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