Population Genomics Flashcards
define heritability
Degree to which genetic variation accounts for phenotypic variation seen in a population
what does snpedia show
heritability data for different phenotypes. used monovular twins for this data
what is a qualitative trait
similar meaning to phenotype
dichotomous - affected/not affected
categoric
whats is a quantitative trait
measurable phenotype, eg fruit size.
cumulative actions of multiple alleles.
continuous distribution of alleles.
example of a qualitative trait
PKU - phenylalanine hydroxylase - characterised by intellectual disability, microcephaly, seizures, eczema.
define genetic drift
change in allele frequency in a popualtion due to random sampling of organisms.
Time change of allele frequency
when allele frequency reaches 100% it is…
fixation
what is the founder effect?
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.
what is a bottleneck
reduction in size of population due to environmental events or human activities
what is nucleotide diversity?
Degree of polymorphism within a population
average number of nucleotide differences per site between 2 DNA sequences
denoted by π
define a selective sweep
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.
what is 23 and me?
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.
what is genomic selection
Select particular individuals to archive better phenotype (performance).
GWAS
genome wide association studies
GWAS
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.
define gene pool
collection of all genes in all individuals in a population
how do you calculate allele frequency in a gene pool?
percentage of each allele
what does population genomica concern?
changes in allele frequencies
define gene
molecular unit of heredity
encodes functional protein
define gene
define allele
molecular unit of heredity
encodes functional protein
one of a number alternative forms of the same locus
point mutation
one NT replaced by another
what are inversion and translocation mutations?
inversion - reverses direction of part of chromosome
translocation - part of one chr attaches to another
domestication
process by which plants or animals are genetically modified over time by humans to more desirable traits
what is gene introgression
..
gives gene flow from one population to another. eg by mating 2 species
why is backcrossing useful?
backcross hybrid to one of the parents to make it more genetically similar to parent
what was detected in studies of rice domestication?
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.
what is overdominance?
Heterozygote advantage
Heterozygous individuals have a higher fitness than homozygous individual
example of overdominance
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
Assumptions of hardy weinberg
Organisms are diploid Generations are non-overlapping Population size is infinitely large There is no migration No mutation No natural selection Mating is random
describe hardy weinberg equilibrium
allele freq do not change between generations
basic formulas in hardy weinberg
p+q=1 ->alleles
p^2 + 2pq +q^2 = 1 ->genotype
what is a haplotype?
multiloci genotype
what is genetic recombination
combinations of alleles at different loci become shuffled in offspring.
what is genetic linkage?
Tendency of alleles that are close together to be inherited together.
what is linkage equilibrium
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
linkage disequilibrium constant
D = PABPab - PAbPaB
if haplotypes are in equilibrium, =0
What is a haplotype block?
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
whats a haplogroup
a group of similar haplotypes which share a common ancestor
what can arise from mutation and gene flow?
new alleles
