EB9 Flashcards
(26 cards)
what is lineage coalescence and what can it be used for
a model of divergence and polymorphism, it can be used to estimate population parameters, effective popualtion size and histroy of populations.
what do inconsistencies between gene regions of sexuals suggest
recombination
in any 2 diploid ind. what is the chance that the copies of genes will share a common ancestor in the previous generation (coalesce)
1/2N
*smaller population higher chance related.
what is rate of coalescence effected by
the same factors that affect drift
**therefore in a smaller popualtion higher change they are related
what is the SNM assumptions
sequences sampled randomly from an ideal population; constant in size, random mating, no selection
*simple null
assuming the neutral model what is the expected no. of differences between any 2 homologous sequences equal to
the time (no. of generations) they have been seperated from their most recent CA X the mutation rate
what is the average no. of differences between any two random sequences equal to
4Neu
what kind of distribution does the probability that any two individuals share a CA T generations ago follow and why
geometric
as probability decreases with no. of generations.
what is the average pairwise differences between random sequences equal to and what can this be used to estimate
pi
can be used to estimate theta - the theoretical parameter
what does the amount of diversity in a population measured by pi depend on
the population size and rate of mutation.
what happens to diversity if population size or mutation rate is doubled
diversity doubles
what happens to diversity if population size is doubled but mutation rate is halved
remain the same
what can estimates of neutral diversity (theta) be used to estimate
the population size in various groups of organisms
How can you obtain estimates of population size
sample bits of DNA and count no. of pairwise differences
what effect does increasing genome size have on diversity
larger organisms have larger genomes, more genes and lower diversity
What are the diversity patterns between human chromosomes and why
- pi seems similar for all chromosomes apart from C21 X and Y
- 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%
- observed diversity is lower 61% X and 20% Y so must be other causes: selection
* *chromosome 21 low diversity probably also due to selection
what are the diversity patterns within human chromosome 6
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)
what are the census Ne and effective Ne
census: count
effective: estimated from an ideal population which behaves similarly to our observed
what is Nc and Ne when population is ideal
Nc ~ Ne
when may large populations behave genetically like small
when only a fraction of individuals contribute to the reproductive pool, or of there has been a bottle neck in their recent past.
what do estimates of pi tend to do for census size
underestimate
How does census population differ from effective in E.coli gut bacteria and why
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
Why do only a relatively small no. of genes need to be sampled for coalescence
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.
what is time to coalescence
4Ne (assuming SNM)
