POPULATION GENETICS

Avjinder Singh Kaler

Introduction

• Population genetics focuses on the frequencies, distribution and origins of genes in populations.

• It combines Darwin’s evolutionary theory with Mendelian genetics and molecular biology

• At population level, genetic can be characterized by allelic and genotypic frequencies

• Forces changing allelic and genotypic frequencies are mutation, natural and artificial selection, population admixture (migration), and random genetic drift.

Allelic Frequency

• Frequency of an allele i in the population = probability that a haplotype (a particular haploid combination of alleles in a defined region of chromosome or genome) carries the allele i

• Allelic frequency in a progeny of a cross between two parents

Cross Comment A1 A2 A3 A4

AB x CD four allele 0.25 0.25 0.25 0.25

AB x CC three allele 0.25 0.25 0.5 0

AB x AB Two allele 0.5 0.5 0 0

AA x AA Fixed 1 0 0 0

Hardy-Weinberg Equilibrium

• Genotypic frequency = simple counting in the population

• For a gene with n alleles = n(n+1)/2 possible genotypes

• The relationship between gene frequency and genotypic frequency for a single gene at population level can be used to infer the genetic status of the gene in the population

• HWE: A population is in equilibrium if the gene and genotypic frequencies are constant from generation to generation

• Two allele model where 𝑝𝐴 𝑎𝑛𝑑 𝑝𝑎 allele, and genotypic frequencies 𝑝𝐴𝐴, 𝑝𝐴𝑎, and 𝑝𝑎𝑎

• 𝑝𝐴𝐴 = 𝑝𝐴2, 𝑝𝐴𝑎 = 2𝑝𝐴 𝑝𝑎 , 𝑝𝑎𝑎 = 𝑝𝑎

2

Hardy-Weinberg Equilibrium

• For multiple allele at a single locus, p1, p2 ..pn used to denote the frequencies of alleles A1, A2, ..An.

• Possible genotypes n(n+1)/2 = A11, A12 A22 …Ann.

• Expected genotypic frequencies =multiplication of allele frequencies= (p1, p2 ..pn) x (p1, p2 ..pn)

• Proportion of heterozygosity in a population = 𝑃𝐻 = 1 − 𝐸𝑝2

• For l loci, there are 1

2𝑙 𝑖=1𝑙 (𝑛𝑖(𝑛𝑖 + 1)) possible genotypes where ni is number of alleles

for locus l.

• If all loci are independent and the population is under hardy Weinberg equilibrium at multiple locus level, then expected frequencies is the simple product of expected frequencies for single locus genotypes.

• When loci are linked and population is in LD, EGF is difficult to calculate.

Change in Gene Frequency

• Migration, Mutation and selection are forces that changes gene frequency from generation to generation