# Genomics week 6

version from 2017-11-27 17:50

## Section 1

What is HWE In a large random mating population, allele and genotype frequencies do not change from one generation to the next after 1st generation
What are the assumptions for HWE -Random mating -Infinite population size -No mutation or selection -No migration
What is the basic formula for prediction of future generation (p+q)2 = p2+2pq+q2
How to compare genetic difference between populations; Categorical data/simple solution Compare the genotype and allele frequencies using descriptive methods! e.g. Population A (45%) allele frequency is higher by 10% than population B (35%).
How to compare genetic difference between populations; statistical comparisons -Using R x C contingency chi-square method (Multi-dimensional chi-square). -Organise the data into columns and rows and workout the totals for the table. -Work out the expected numbers from observed data and work out the chi-square for the Whole table. -Expected Numbers for a particular cell can be worked out as following. -Expected Number = (Row Total * Column Total) /Grand Total. -Work out Expected Number for each cell and then using the formula . X2 = Total (observed –expected)2 / expected
what do RT, CT and GT Row total, column total, grand total,
How to work out degrees of freedom (Numbers of columns - 1) * (No of rows - 1)
What are the main factors affecting allele frequencies and HWE-Gene flow/Migration -Genetic Drift and Founder effect -Non-Random mating/Inbreeding -Selection -Mutation

## Section 2

What is gene flow?The interchange of alleles between populations -> change in allele frequencies
What does exogamy mean?-Most animals do not mate with close kin! -Humans have marriage rules, specifying who one can marry and where one must/can live: +e.g. cross-cousin vs. parallel vs. no cousins; +patrilocal, +Matrilocal
What does endogamy mean?1. ANTHROPOLOGY; the custom of marrying only within the limits of a local community, clan, or tribe. 2. BIOLOGY; the fusion of reproductive cells from related individuals; inbreeding; self-pollination.
What is the effect of migration on allele frequencies. If there is a migration from 1 into 2 as well as from 2 into 1, the population will eventually become one population. They will reach an equilibrium; q=(q1 + q2)/2. i.e. q at equilibrium will be the average of all the q’s
Effects of migration on HWE and allele frequencieslook at slide 11, Pooling of migrants from different populations leads to statistically significant deviation from HWE.
main reason to move away from HWEGenetic drift, migration, selection and gene flow

## Section 3

What is random genetic drift -Due to small population size; deviations in allele frequencies simply due to chance, sometimes called “Sampling error". -The smaller the population, the more noticeable the effects of drift. -Changes are totally random!!!!!! -If a population is small enough, the effects of drift may swamp the other forces, even selection. example pg 13.
What is fixation is the change in a gene pool from a situation where there exists at least two variants of a particular gene (allele) to a situation where only one of the alleles remains.
Loss is random (accidental)
What does the loss of an allele causereduction of variation in the population (within)
What happens if the experiment (pg 14) is repeated?increase in variation between populations
Which alleles/populations are more susceptible to lossthose in low frequency and small populations.
What is the founder effect The establishment of a new population by a few founders who carry only a small proportion of the total genetic variation in the parental population. Results in the loss of alleles, the reduction of variation and the increase in rare alleles. Founder effect can often be traced to an historical event.
What is the bottleneck effect -when individuals found a population, they carry with them a sample of the genetic variation of their population. -consider: a population founded by two individuals can have at most four alleles per locus!
What does PAM stand for Positive assortative mating
definition of PAM individuals tend to mate only with others of like genotype (type of non random mating) example; inbreeding.
What does PAM cause Net increase in homozygotes; decrease in heterozygotes
What is the inbreeding coefficient a simple calculation to work out the level of inbreeding at a locus.
What does inbreeding cause -increases recessive genes and diseases. -Coefficient can be positive or negative! Positive  Inbreeding. Negative  Out breeding or Gene flow (migration)!
Where does inbreeding still occur Endogamous populations tend to marry within their own religion/cultural /social system. Many examples from different parts of the world.