lecture 13/14 - sae 2

Question 1

describe directional selection favoring A allele

Answer 1

Dominant = selection acts more quickly
recessive = rarer, more visible as it becomes more prominent

Question 2

describe balancing selection

Answer 2

not directional
end up somewhere in middle = intermediate freq of a and b
both alleles maintained

Question 3

describe selection viewed from genomic perspective - directional selection favouring allele A

Answer 3

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

Question 4

what can selective sweeps do

Answer 4

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

Question 5

describe selective sweep graph

Answer 5

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

Question 6

describe lactase allele variant

Answer 6

allele variations which affect lactase
Lactase allele variant that causes lactase to persist through life

Question 7

describe complex trait genetics

Answer 7

trait coded for by many genes - influenced by environmental conditions
no discreet variation

Question 8

describe simple trait vs complex traits (quantitative)

Answer 8

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”

Question 9

why is qualitative genetic variation important

Answer 9

Important for understanding the evolution of common diseases, crop improvement, and the rate of evolutionary change
for diseases, agriculture and response to climate change

Question 10

name 2 types of complex traits

Answer 10

body size - height
running speed - finishing time in a marathon

Question 11

what is variance

Answer 11

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

Question 12

describe threshold traits

Answer 12

“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

Question 13

what is phenotypic variance of a trait

Answer 13

How much is due to differences in the environment
that individuals experience and how much is due to genetic differences among individuals

Question 14

describe multifactorial model for complex trait variation

Answer 14

Variances add up
both contribute to phenotype
Environmental and genetic

Question 15

describe length of flower plant ex

Answer 15

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)

Question 16

describe tobacco corolla length phenotypic variance (Vx)- gen

Answer 16

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

Question 17

what is heritability

Answer 17

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

Question 18

what can be use to infer the presence and effects of genes that influence genetic variance

Answer 18

molecular markeres = QTL and GWAS

Question 19

describe GWAS

Answer 19

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

Question 20

what can we use to detect genes that influence complex diseases

Answer 20

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

Question 21

what is a manhattan plot

Answer 21

looks like manhattan skyline
each dot = a SNP at a position on chromosome
Summarizes GWAS
above line = low that is just a coincidence

Question 22

describe heritability and twin studies

Answer 22

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

Question 23

describe broad sense heritability for humans

Answer 23

characteristic of trait but also of population sample and environment analysis conducted in
Depends on specific sample
not fixed values associated with traits

Question 24

does environment always matter

Answer 24

phenotype values should line up with a correlation of 1 but ALWAYS some environment effects
Environment influences expression of traits

Question 25

describe twin studies - effect on heritability

Answer 25

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)

Question 26

when is it hard to apply heritability constant

Answer 26

to diff environments and diff pop samples
especially if sample size small

Question 27

describe principles of QTL analysis

Answer 27

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)

Question 28

describe QTL mapping of hairless gene of plants

Answer 28

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

Question 29

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

Answer 29

GWASSSSS

Question 30

describe recombination over one gen vs many gens

Answer 30

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

Question 31

describe tobacco corolla length phenotypic variance (Vx)- specific

Answer 31

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

Question 32

define QTL mapping

Answer 32

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)