Lecture 5 Population Genetics I PDF

Lecture 5 Population Genetics I Monterey Aquarium GEGE2001/2901 Lecturer: Nate Lo [email protected]  Lecture 5: Population Genetics I Learning outcomes Understand genes, alleles, dominance, po...

Lecture 5 Population Genetics I Monterey Aquarium GEGE2001/2901 Lecturer: Nate Lo [email protected]  Lecture 5: Population Genetics I Learning outcomes Understand genes, alleles, dominance, populations in a pop gen context Calculating allele and genotype frequencies for genes with 2 and 3 alleles, and sex linked loci Define assumptions of Hardy-Weinberg Equilibrium Notes: Lecture material for all 4 population genetics lectures is derived primarily from Meneely et al (Genetics: Genes, Genomes and Evolution), with a few examples from Klug et al (Essentials of Genetics). These are available in library but I will make relevant pages available in Canvas - you only need to learn the material I present You are strongly recommended to attend or watch the lectures as the slides themselves won’t always contain all the information you need to know  Genes Can be Understood in Different Ways A mutation e.g. AàC gives rise to new allele (e.g. that causes curly hair) Male gametes C c Female gametes C CC Cc c Cc cc 1. As a way traits 2. As DNA 3. As the structure are passed on of a population summarizes neo-darwinian Evolution is simply changes in allele synthesis – melding of ideas frequencies over multiple generations of Darwin, Mendel, Fisher… We are short term vehicles Population genetics examines this process for our genes! the cosmopolitan white shark Whatabstract Graphical do we mean by ‘population’? Authors Isabel Wag Martina E. Catherine Correspo p, q p, q leslie.r.nob c.s.jones@ N = 5500 galice.g.ho Ne < 500 p, q In brief Wagner et Wagner et al 2024 distinct all In population genetics, we are concerned with the Indo-Pacifi effective population (Ne): number of individuals withinshark whic a larger population capable of reproduction years ago, biogeogra conservati  Allele (or Haplotype) Frequencies Allele: one of two or more versions of DNA sequence (a single base or segment of bases) at a given genomic location Haplotype: set of DNA variants along a single chromosome that are inherited together, because they are close to each other, and recombination is rare We can count or compute the frequency of each allele or haplotype in a population (using DNA sequencing)  Allele and Genotype Frequencies If gametes unite at random, Note: The “2” genotype arises since Aa frequencies will and aA are the same genotype be the product of the allele ~20,000 protein coding genes, frequencies Most traits controlled by many genes; each with 10-20 alleles we study single gene, 2 allele case Example: Rhesus D in pregnancy Male gametes D d Female gametes D DD Dd Rh+ Rh+ d Dd dd Rh+ Rh- FOAMed  Example: Rhesus D in pregnancy Question: Population 1 has 36% Rh- individuals, and population 2 has 1% Rh- individuals. What are the frequencies of D and d in each population? With males from what population should a Rh- female mate to reduce risk to her second baby? Calculating frequencies for multiple alleles: ABO Chegg Calculating frequencies for multiple alleles: ABO Notes: - IA and IB are codominant, but both dominant to i - thus IAIA and IAi have same phenotype, as do IBIB and IBi Allele frequencies: p+q+r=1 Genotype frequencies: lumenlearning (p + q + r)2 = p2 + q2 + r2 + 2pq + 2pr + 2qr = 1 Calculating frequencies for multiple alleles: ABO Question: if blood-type frequencies are A = 0.504, B = 0.175, O = 0.185, what are allele IA , IB and i frequencies?  Calculating frequencies for sex-linked loci The genotype frequencies (p2, 2pq, q2) we considered earlier are for loci located on autosomal chromosomes What about for sex chromosomes (e.g. females XX; males XY)? Consider an X-chromosome gene with two alleles A and a: Gender Genotype Frequency Males: the two genotypes Male A p have same frequencies as a q gene frequencies! Female AA q2 Females: as for autosomal Aa 2pq case aa q2  Sex-linked loci: example Colour blindness in humans is caused by a recessive X-linked gene. If frequency of colourblind females in a population is 1%, what is the expected % of colourblind males?  Lecture 5: Population Genetics I Learning outcomes Understand genes, alleles, dominance, populations in a pop gen context Calculating allele and genotype frequencies for genes with 2 and 3 alleles, and sex linked loci Define assumptions of Hardy-Weinberg Equilibrium  When do allele + genotype frequencies in a population stay the same? These result in Mutation, migration, drift, and a population at selection cause evolution equilibrium (change in allele freqs over time)