Topic 3

Question 1

Mendels Laws

Answer 1

1. First Law: Random Segregation, alleles at a single locus segregate randomly, offspring have a 50% chance of inheriting each of a parent’s alleles (this is the basis of the HW principle).
2. Second Law: Independent Segregation, Alleles at different loci segregate independently, so that the inheritance of alleles at locus A is independent of the inheritance of alleles at locus B.

Question 2

mendels second law exception

Answer 2

• Mendel’s second law will be true if the loci under consideration are located on different chromosomes, but if they are located close together on the same chromosome, they will not always segregate independently, and can be inherited as a single ‘unit’.
• These loci are said to be Linked, and this will result in, linkage disequilibrium or gametic disequilibrium

Question 3

gametic disequilibrium

Answer 3

• Nonrandom genotypic
  (and hence allelic) associations among loci (also called linkage disequilibrium)

Question 4

gametic and linkage disequilibrium

Answer 4

• The terms gametic disequilibrium and linkage disequilibrium are often used interchangeably.
• However, linkage disequilibrium refers to the specific case where nonrandom genotypic associations among loci are caused by the loci being located close together on the same chromosome.
• Gametic disequilibrium is a broader term, and encompasses linkage disequilibrium, as well as numerous other factors that can cause nonrandom genotypic (and hence allelic) associations among loci, including selection, genetic drift and migration

Question 5

linked loci and mendels second law

Answer 5

• The independent segregation of Linked Loci depends on recombination, which occurs during meiosis, and the fraction of gametes produced that have recombinant genotypes, termed recombinant gametes.
• Recombination breaks down gametic disequilibrium (nonrandom genotypic associations)

Question 6

recombination

Answer 6

• The amount of gametic disequilibrium we have for linked loci will depend on the amount of recombination that occurs during gametogenesis.
• Recombination will eventually break up nonrandom genotypic (and hence allelic) associations among loci. The fraction of recombinant gametes an individual produces is called the recombination fraction, denoted r.
• We will always assume that r is the same in males and females, but this does not have to be the case

Question 7

recombination fraction r

Answer 7

• The value of r can range between 0 and 0.5 and depends on how close together the loci are on the chromosome.
• When r = 0, the loci are so close together that there is never any recombination.
• When r = 0.5, the loci are so far apart that they might as well be on different chromosomes, and there will be no ‘linkage disequilibrium’, but gametic disequilibrium could potentially still be evident for other reasons (e.g., drift, selection, migration).

Question 8

observed gamete frequencies

Answer 8

• We will use g to denote the observed frequency of a gamete such that our observed gamete frequencies are given by gAB, gAb, gaB and gab
• When our observed gamete frequencies are not equal to those expected (see previous slide), we have gametic disequilibrium (or linkage disequilibrium)

Question 9

disequilibrium coefficient D

Answer 9

• D is a parameter that quantifies the amount of gametic disequilibrium. It can take on values ranging from -0.25 to 0.25. If D = 0, we have no gametic disequilibrium
• D is calculated using observed gamete frequencies

Question 10

gametic frequencies and gametic disequilibrium

Answer 10

• Over time, recombination will reduce the value of D, and D will become equal to 0. The observed gamete frequencies will then be equal to their expected frequencies as shown by the
  formulae above

Question 11

double heterozygotes

Answer 11

• Gametes AB and ab are coupling phase gametes
• Gametes Ab and aB are repulsion phase gametes
• Double heterozygotes are individuals that are heterozygous at both loci: e.g., AaBb
• There are two different ways that gametes can unite to form a double heterozygote:
• AB + ab = AaBb = coupling phase double heterozygote
• Ab +aB = AaBb = repulsion phase double heterozygote

Question 12

recombination of double heterozygotes

Answer 12

• AB/ab is a coupling phase double heterozygote (het)
• Ab/aB is a repulsion phase double heterozygote (het)
• Recombination in coupling phase double hets creates Ab and aB gametes- repulsion phase gametes.
• Recombination in repulsion phase double hets creates AB and ab gametes- coupling phase gametes

Question 13

Recombination Changes Gamete Frequencies and reduces D over Time

Answer 13

For example:
g1AB = g0AB + (proportion of AB gametes gained by recombination in repulsion phase hets) – (proportion of AB gametes lost by recombination in coupling phase hets)

Where: g1 is the gamete frequency in the next generation, g0 is the frequency in the starting generation

Question 14

recombination changes gamete frequencies

Answer 14

• The proportions of gametes lost or gained are related to the recombination fraction
• D ranges between -0.25 and 0.25.
• If D is positive, we have an excess of coupling phase gametes.
• These will unite to form an excess of coupling phase double heterozygotes
• But: recombination in coupling phase double hets creates repulsion phase gametes, moving D closer to zero
• If D is negative, we have an excess of repulsion phase gametes.
• These will unite to form an excess of repulsion phase double heterozygotes
• But: recombination in repulsion phase double hets creates coupling phase gametes, moving D closer to zero

Question 15

standardized measure of D

Answer 15

• For any combination of allele frequencies, there is a theoretical maximum and minimum value that D can take
• D’ tells us what proportion of the theoretical
  maximum value of D we have

Question 16

causes of gametic disequilibrium

Answer 16

• Linked Loci on the Same Chromosome
• Asexual Reproduction
• Cryptic Species
• Genetic Drift
• Founder Effects
• Population bottlenecks
• Migration
• Selection

Question 17

what does sex boil down to?

Answer 17

1. Matings between different individuals resulting in new combinations of genes in the offspring
2. Recombination and crossing over in the process of meiosis during gametogenesis creates genetic diversity.
3. Recombination and crossing over in the process of meiosis breaks down gametic disequilibrium, which will also increase genetic diversity

• Together, these factors create genetically diverse offspring and allow the purging of deleterious mutations

Question 18

gametic disequilibrium summary

Answer 18

• Gametic disequilibrium is important in population genetics and can occur because of the proximity of two loci on the same chromosome (linkage disequilibrium), or because of other factors.
• In conjunction with HW disequilibrium, it can provide additional evidence for asexual reproduction, or cryptic species.
• We must always test for gametic disequilibrium when analyzing diploid population genetic data because we want each locus to provide us with an independent assessment of the questions we are addressing, such as the amount of gene flow among populations, the amount of genetic differentiation among populations, or forensic types of analyses