EB9

Question 1

what is lineage coalescence and what can it be used for

Answer 1

a model of divergence and polymorphism, it can be used to estimate population parameters, effective popualtion size and histroy of populations.

Question 2

what do inconsistencies between gene regions of sexuals suggest

Answer 2

recombination

Question 3

in any 2 diploid ind. what is the chance that the copies of genes will share a common ancestor in the previous generation (coalesce)

Answer 3

1/2N

*smaller population higher chance related.

Question 4

what is rate of coalescence effected by

Answer 4

the same factors that affect drift

**therefore in a smaller popualtion higher change they are related

Question 5

what is the SNM assumptions

Answer 5

sequences sampled randomly from an ideal population; constant in size, random mating, no selection
*simple null

Question 6

assuming the neutral model what is the expected no. of differences between any 2 homologous sequences equal to

Answer 6

the time (no. of generations) they have been seperated from their most recent CA X the mutation rate

Question 7

what is the average no. of differences between any two random sequences equal to

Answer 7

4Neu

Question 8

what kind of distribution does the probability that any two individuals share a CA T generations ago follow and why

Answer 8

geometric

as probability decreases with no. of generations.

Question 9

what is the average pairwise differences between random sequences equal to and what can this be used to estimate

Answer 9

pi

can be used to estimate theta - the theoretical parameter

Question 10

what does the amount of diversity in a population measured by pi depend on

Answer 10

the population size and rate of mutation.

Question 11

what happens to diversity if population size or mutation rate is doubled

Answer 11

diversity doubles

Question 12

what happens to diversity if population size is doubled but mutation rate is halved

Answer 12

remain the same

Question 13

what can estimates of neutral diversity (theta) be used to estimate

Answer 13

the population size in various groups of organisms

Question 14

How can you obtain estimates of population size

Answer 14

sample bits of DNA and count no. of pairwise differences

Question 15

what effect does increasing genome size have on diversity

Answer 15

larger organisms have larger genomes, more genes and lower diversity

Question 16

What are the diversity patterns between human chromosomes and why

Answer 16

1. pi seems similar for all chromosomes apart from C21 X and Y
2. diversity is proportional to population size, and in humans 2X adn 1Y so could expect diversity of Y to be 25% that of autosome and X 75%
3. observed diversity is lower 61% X and 20% Y so must be other causes: selection
   * *chromosome 21 low diversity probably also due to selection

Question 17

what are the diversity patterns within human chromosome 6

Answer 17

pi measured along blocks of 200kb for chromosome 6
pi widely varaible even though no difference in population size.
some high peaks of diversity particularly at MHC genes (subject to balancing selection)

Question 18

what are the census Ne and effective Ne

Answer 18

census: count
effective: estimated from an ideal population which behaves similarly to our observed

Question 19

what is Nc and Ne when population is ideal

Answer 19

Nc ~ Ne

Question 20

when may large populations behave genetically like small

Answer 20

when only a fraction of individuals contribute to the reproductive pool, or of there has been a bottle neck in their recent past.

Question 21

what do estimates of pi tend to do for census size

Answer 21

underestimate

Question 22

How does census population differ from effective in E.coli gut bacteria and why

Answer 22

Each gut contains only a few predominant clones that reproduce asexually and are occassionally replaced by new clones.
Ne of E. coli population may be closer to no. of mammalians hosts rather than no. of individual bacteria.
more diversity between guts than within

Question 23

Why do only a relatively small no. of genes need to be sampled for coalescence

Answer 23

as however large initial no. of genes, a typical genealogy will just have two lineages for half of its history, so little info will be added by doing more as they would all be part of the same ancestral lineage.

Question 24

what is time to coalescence

Answer 24

4Ne (assuming SNM)

Question 25

what do exponentially growing populations show

Answer 25

faster coalescence the further back you go as coalescence is faster in smaller populations.

Question 26

what do genealogies of HIV from 200 UK individuals show

Answer 26

most of the terminal branches ending in individuals are very long showing exponential growth.