lecture 13/14 - sae 2 Flashcards
describe directional selection favoring A allele
Dominant = selection acts more quickly
recessive = rarer, more visible as it becomes more prominent
describe balancing selection
not directional
end up somewhere in middle = intermediate freq of a and b
both alleles maintained
describe selection viewed from genomic perspective - directional selection favouring allele A
certain gene favoured through selection = then becomes in many people = selective sweep
things that are far apart in genome recombine more than things closer together
if strongly selected over a few gens = becomes dominant haplotype in population = loses diversity, more and more common, allele can also drag down areas that are around it = becomes dom haplotype
what can selective sweeps do
can reduce diversity in genomic regions, especially those with low rates of recombination—they leave behind a trace of past events that have influenced the genome
describe selective sweep graph
selective nt allelic diversity = dips a lot for specific genetic sweep
very low diversity = reflection of past selective sweep
occupies long chromosomal segment, look at region of genome diversity across populations
describe lactase allele variant
allele variations which affect lactase
Lactase allele variant that causes lactase to persist through life
describe complex trait genetics
trait coded for by many genes - influenced by environmental conditions
no discreet variation
describe simple trait vs complex traits (quantitative)
population variation controlled by one or 2 genes = simple trait
population variation controlled by many, like 100 genes
complex = have bell shaped distribution = tends to run in families like diseases
Distribution of phenotypic states is often “bell-shaped”
why is qualitative genetic variation important
Important for understanding the evolution of common diseases, crop improvement, and the rate of evolutionary change
for diseases, agriculture and response to climate change
name 2 types of complex traits
body size - height
running speed - finishing time in a marathon
what is variance
Measurement of how far each number in a dataset is from the mean and thus from every other number in the set
Spread of pop around a mean
variances are additive = sum of variances from each factor and add up and get variance of total pop
describe threshold traits
“either/or”
genes and environmental factors (environmental and genetic liability)
expressed when threshold of environmental factors or genetic makeup is crossed
threshold traits = cancers, heart diseases
what is phenotypic variance of a trait
How much is due to differences in the environment
that individuals experience and how much is due to genetic differences among individuals
describe multifactorial model for complex trait variation
Variances add up
both contribute to phenotype
Environmental and genetic
describe length of flower plant ex
long vs short parent
more doses of L = longer length
F1 progeny = intermediate corolla, 2 L and 2 S
inbred line = inbreed short corolla with short corolla till completely homozygous = no genetic variability = all have same genotype
phenotype = mix of both = turns into bell curve
more genes = more and more like bell curve
Environment can play a role too
(a continuous distribution)
describe tobacco corolla length phenotypic variance (Vx)- gen
P1 and P2 = diff inbred lines
F1 hybrid - hetero for alleles that differ in P1 and P2
F2 progeny segregate for alleles that differ in P1 and P2
= fluctuations in environmental factors = more variance, segregation leads to more variance
what is heritability
broad sense
bounded by 0 (no genetic variance) and 1 (if only source of variance genetic)
dimensionless
Standardized parameter
comparable across traits/species
Relative contribution of genetic variance
H^2 = Vg/Vx
what can be use to infer the presence and effects of genes that influence genetic variance
molecular markeres = QTL and GWAS
describe GWAS
Association mapping or genome-wide association studies (GWAS)…relies on
population surveys that look for correlation between markers and phenotypic
trait values in samples taken from large populations.
like fishing
large database of disorders
BIOBANK
cost lower compares to before
what can we use to detect genes that influence complex diseases
associations between SNPs and disease to detect genes that influence complex diseases
compare to control group
more red = more of certain gene = more ppl with diabetes
records presence of absence of SNPs
what is a manhattan plot
looks like manhattan skyline
each dot = a SNP at a position on chromosome
Summarizes GWAS
above line = low that is just a coincidence
describe heritability and twin studies
understand how heritable a trait is
identical twins separated at birth - raised in random environments = see effect of environment
height of twin = heritability high like language = expect heritability of 0
if in middle = some genetic and environmental variance
describe broad sense heritability for humans
characteristic of trait but also of population sample and environment analysis conducted in
Depends on specific sample
not fixed values associated with traits
does environment always matter
phenotype values should line up with a correlation of 1 but ALWAYS some environment effects
Environment influences expression of traits
describe twin studies - effect on heritability
before = shared womb so this environment could effect expression of traits
2 foster homes with diff environments = ex wealthiness
Correlation between environments twins were raised in = inflates heritability since assumption = is that not correlated
so since violate assumption that environments not correlated
so if environments correlated = inflate estimate of heritability (if adopted by similar families = similar environmental effects)
when is it hard to apply heritability constant
to diff environments and diff pop samples
especially if sample size small
describe principles of QTL analysis
one way to discover the underlying genes controlling for complex phenotypes…..so is QTL analysis
Co-segregation (co-inheritance) of phenotypes
and marker alleles (usually SNPs)
describe QTL mapping of hairless gene of plants
plant model = both inbred lines
one hairless and one hairy
Visualize where hairless gene = hairless part is associated with tip of chromosome
gene in that position is associated with hairlessness
If you find a SNP that is inherited with a disease condition, the SNP is likely to be closer to the gene that codes for the disease when it was found using GWAS or QTL
GWASSSSS
describe recombination over one gen vs many gens
one gen = big blocks
many gens = many recombinations, mish mash
more tightly linked in GWAS = many gens than single gen in
QTL
GWAS = looking at sum of many gens of recombination vs single gen of QTL recombination
describe tobacco corolla length phenotypic variance (Vx)- specific
parents = envir diff between individuals – Vx = Ve
F1 = envir diff between individuals – Vx=Ve
F2 = envir diff between individuals and genetic diff between individuals Vx= Ve + Vg
define QTL mapping
esembles classical mapping approaches (controlled crosses used)…co-segregation of a marker with a trait’s phenotypic value helps you to locate the region of the genome where a gene with influence on the phenotype resides….there may be many such genes (called quantitative trait loci or QTL’s)
