Population Genomics

Question 1

define heritability

Answer 1

Degree to which genetic variation accounts for phenotypic variation seen in a population

Question 2

what does snpedia show

Answer 2

heritability data for different phenotypes. used monovular twins for this data

Question 3

what is a qualitative trait

Answer 3

similar meaning to phenotype
dichotomous - affected/not affected
categoric

Question 4

whats is a quantitative trait

Answer 4

measurable phenotype, eg fruit size.
cumulative actions of multiple alleles.
continuous distribution of alleles.

Question 5

example of a qualitative trait

Answer 5

PKU - phenylalanine hydroxylase - characterised by intellectual disability, microcephaly, seizures, eczema.

Question 6

define genetic drift

Answer 6

change in allele frequency in a popualtion due to random sampling of organisms.
Time change of allele frequency

Question 7

when allele frequency reaches 100% it is…

Answer 7

fixation

Question 8

what is the founder effect?

Answer 8

loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population. As a result of the loss of genetic variation, the new population may be distinctively different, both in genotype and phenotype.

Question 9

what is a bottleneck

Answer 9

reduction in size of population due to environmental events or human activities

Question 10

what is nucleotide diversity?

Answer 10

Degree of polymorphism within a population
average number of nucleotide differences per site between 2 DNA sequences
denoted by π

Question 11

define a selective sweep

Answer 11

Selective Sweep : Reduction of diversity among the nucleotides in neighboring DNA of a mutation as the result of the recent fixation of a beneficial allele due to strong selection.

Question 12

what is 23 and me?

Answer 12

A privately held personal genomics and biotechnology company based in Mountain View, California.
Genomic prediction. Sequence DNA and the make reports of predicted traits, disease risks, carrier status.

Question 13

what is genomic selection

Answer 13

Select particular individuals to archive better phenotype (performance).

Question 14

GWAS

Answer 14

genome wide association studies

Question 15

GWAS

Answer 15

genome wide association studies
see association between phenotype and genotype do stat test on allele freq at each locus.
To see if any variants are associated with the trait.

Question 16

define gene pool

Answer 16

collection of all genes in all individuals in a population

Question 17

how do you calculate allele frequency in a gene pool?

Answer 17

percentage of each allele

Question 18

what does population genomica concern?

Answer 18

changes in allele frequencies

Question 19

define gene

Answer 19

molecular unit of heredity

encodes functional protein

Question 20

define gene

define allele

Answer 20

molecular unit of heredity
encodes functional protein

one of a number alternative forms of the same locus

Question 21

point mutation

Answer 21

one NT replaced by another

Question 22

what are inversion and translocation mutations?

Answer 22

inversion - reverses direction of part of chromosome

translocation - part of one chr attaches to another

Question 23

domestication

Answer 23

process by which plants or animals are genetically modified over time by humans to more desirable traits

Question 24

what is gene introgression

Answer 24

..

gives gene flow from one population to another. eg by mating 2 species

Question 25

why is backcrossing useful?

Answer 25

backcross hybrid to one of the parents to make it more genetically similar to parent

Question 26

what was detected in studies of rice domestication?

Answer 26

geographically mapped rice genome variation
studied genome of 1500 rice accessions.
data base OrzyaGenome contains SNP information
detected selective sweep regions and reconstructed large scale phylogeny of these regions.

Question 27

what is overdominance?

Answer 27

Heterozygote advantage

Heterozygous individuals have a higher fitness than homozygous individual

Question 28

example of overdominance

Answer 28

aa = abnormal B hemoglobin sickle cell anaemia - low fitness
AA - normal B hemo, vulnerable to malaria.. middle fitness
Aa = resistant to malaria and no sickle cell disease - high fitness

Question 29

Assumptions of hardy weinberg

Answer 29

Organisms are diploid
Generations are non-overlapping
Population size is infinitely large
There is no migration
No mutation
No natural selection
Mating is random

Question 30

describe hardy weinberg equilibrium

Answer 30

allele freq do not change between generations

Question 31

basic formulas in hardy weinberg

Answer 31

p+q=1 ->alleles

p^2 + 2pq +q^2 = 1 ->genotype

Question 32

what is a haplotype?

Answer 32

multiloci genotype

Question 33

what is genetic recombination

Answer 33

combinations of alleles at different loci become shuffled in offspring.

Question 34

what is genetic linkage?

Answer 34

Tendency of alleles that are close together to be inherited together.

Question 35

what is linkage equilibrium

Answer 35

haplotype frequencies in a population have the same value that they would have if the genes at each locus were combined at random. equal chance of inheriting any combination

linkage disequilibrium = genes are linked and more likely to be inherited in certain combinations

Question 36

linkage disequilibrium constant

Answer 36

D = PABPab - PAbPaB

if haplotypes are in equilibrium, =0

Question 37

What is a haplotype block?

Answer 37

haplotypes occur in ‘blocks’ with stong linkage disequilibrium across a chromosome.
if one allele in a block is known irs easy to predict the rest of the bock

Question 38

whats a haplogroup

Answer 38

a group of similar haplotypes which share a common ancestor

Question 39

what can arise from mutation and gene flow?

Answer 39

new alleles