Lecture Notes in Population Genetics - …

1 Lecture NotesinPopulation GeneticsKent E. HolsingerDepartment of Ecology & Evolutionary Biology, U-3043 University of ConnecticutStorrs, CT 06269-3043c 2001-2015 Kent E. HolsingerCreative Commons LicenseThese Notes are licensed under the Creative Commons Attribution License. To view a copy of thislicense, visit or send a letter to Creative Commons,559 Nathan Abbott Way, Stanford, California 94305, The genetic structure of populations11 genetic transmission in populations32 The Hardy-Weinberg Principle and estimating allele frequencies73 Inbreeding and self-fertilization214 Testing Hardy-Weinberg315 Analyzing the genetic structure of populations396 Analyzing the genetic structure of populations.

2 A Bayesian approach537 Analyzing the genetic structure of populations: individual assignment618 Two-locus Population genetics67II The Genetics of natural selection759 The Genetics of Natural Selection7710 Estimating viability8911 Selection at one locus with many alleles, fertility selection, and sexualselection95iiiIII genetic drift10312 genetic Drift10513 Mutation, Migration, and genetic Drift11914 Selection and genetic drift12515 The Coalescent129IV Quantitative genetics13516 Introduction to quantitative genetics13717 Resemblance among relatives14718 Evolution of quantitative traits15719 Selection on multiple characters16520 Association mapping.

3 The background from two-locus genetics173V Molecular evolution18321 Introduction to molecular Population genetics18522 Patterns of nucleotide and amino acid substitution199VI Phylogeography21723 AMOVA and Statistical phylogeography21924 Population genomics24125 genetic structure of human populations in Great Britain253ivPrefaceAcknowledgmentsI ve used various versions of these Notes in my graduate course on Population since 2001. Some of them date back even earlier thanthat. Several generations of students and teaching assistants have found errors and helpedme to find better ways of explaining arcane concepts.

4 In addition, the following people havefound various errors and helped me to correct CadyNora MitchellRachel PrunierUzay SezenRobynn ShannonJennifer SteinbachsKathryn TheissYufeng WuI am indebted to everyone who has found errors or suggested better ways of explainingconcepts, but don t blame them for any errors that are left. Those are all IThe genetic structure of populations1 Chapter 1 genetic transmission in populationsMendel s rules describe how genetic transmission happens between parents and a monohybrid cross:A1A2 A1A2 14A1A112A1A214A2A2 Population Genetics describes how genetic transmission happens between apopulationofparents and a Population of offspring.

5 Consider the following data from theEst-3 locus ofZoarces viviparus:1 Genotype of offspringMaternal genotypeA1A1A1A2A2A2A1A1305516A1A2459136 0877A2A28771541 This table describes, empirically, the relationship between the genotypes of mothers and thegenotypes of their offspring. We can also make some inferences about the genotypes of thefathers in this Population , even though we didn t see 305 out of 821 male gametes that fertilized eggs fromA1A1mothers carried theA1allele (37%).2. 877 out of 2418 male gametes that fertilized eggs fromA2A2mothers carried theA1allele (36%).

6 1from [10]3 QuestionHow many of the 2,696 male gametes that fertilized eggs fromA1A2motherscarried theA1allele?RecallWe don t know the paternal genotypes or we wouldn t be asking this question. There is no way to tell which of the 1360A1A2offspring receivedA1from theirmother and which from their father. Regardless of what the genotype of the father is, half of the offspring of a het-erozygous mother will be Heterozygous offspring of heterozygous mothers contain no information aboutthe frequency ofA1among fathers, so we don t bother to include them in many of the 1336 homozygous progeny of heterozygous mothers receivedanA1allele from their father?

7 Answer459 out of 1336 (34%)New questionHow many of the offspring where the paternal contribution can be identifiedreceived anA1allele from their father?Answer(305 + 459 + 877) out of (305 + 459 + 877 + 516 + 877 + 1541) or 1641 out of4575 (36%)An algebraic formulation of the problemThe above calculations tell us what s happening for this particular data set, but those of youwho know me know that there has to be a little math coming to describe the situation moregenerally. Here it is:Genotype NumberSexA1A1F11femaleA1A2F12femaleA2A2F 22femaleA1A1M11maleA1A2M12maleA2A2M22mal e2 Assuming we re looking at data from a locus that has only two alleles.

8 If there were four alleles at alocus, for example,allof the offspring might be +F122F11+2F12+2F22qf=2F22+F122F11+2F12+2 F22pm=2M11+M122M11+2M12+2M22qm=2M22+M122 M11+2M12+2M22,wherepfis the frequency ofA1in mothers andpmis the frequency ofA1in every individual in the Population must have one father and one mother, thefrequency ofA1among offspring is the same in both sexes, namelyp=12(pf+pm),assuming that all matings have the same average fecundity and that the locus we re studyingis : Why do those assumptions matter?

9 Answer: Ifpf=pm, then the allele frequency among offspring is equal to the allelefrequency in their parents, , the allele frequency doesn t change from one generation tothe next. This might be considered the First Law of Population Genetics : If no forces act tochange allele frequencies between zygote formation and breeding, allele frequencies will force lawsThis is an example of what philosophers call azero force law. Zero force laws play a veryimportant role in scientific theories, because we can t begin to understand what a force doesuntil we understand what would happen in the absence of any forces.

10 Consider Newton sfamous dictum:An object in motion tends to remain in motion in a straight line. An object atrest tends to remain at (as you may remember from introductory physics)5F=ma .3qf= 1 pfandqm= 1 pmas that there are enough offspring produced that we can ignore genetic drift. Have you noticed that Ihave a fondness for footnotes? You ll see a lot more before the semester is through, and you ll soon discoverthat most of my weak attempts at humor are buried in t worry if you re not good at physics.