EE Lecture 5: Phenotype and Genotype

Question 1

what is a haplotype

Answer 1

an association of different alleles on a chromosome - likely to be inherited together

Question 2

what is a haplogroup

Answer 2

closely related haplotypes (non identical sequences)

Question 3

what is a closely related set of non identical sequences called

Answer 3

a haplogroup

Question 4

what is an assoiation of different alleles on a chromosome likely to be inherited together called

Answer 4

haplotype

Question 5

how can you confirm a haplogroup

Answer 5

by doing a single nucleotide polymorphism SNP test

Question 6

what are the most commonly studied haplogroups in humans

Answer 6

Y-DNA

mtDNA

Question 7

how do Y-DNA and mtDNA change

Answer 7

NOT RECOMBINATION

only change by a chance mutation at each generation with no intermixture between parents’ genetic material

Question 8

what is linkage equilibrium a property of

Answer 8

haplotypes not genotypes

Question 9

what is linkage equilibrium

Answer 9

when 2 genes/traits/loci are inherited completely independently in each generation

Question 10

what is the term for when 2 genes/traits/loci are inherited completely independently in each gen

Answer 10

linkage eqbm

Question 11

what is the term for populations where combos of alleles/genotypes can be found in expected proportions

Answer 11

they are in linkage eqbm

Question 12

at what level of linkage diseqbm does linkage eqbm occur

Answer 12

linkage eqbm occurs when linkage diseqbm = 0

Question 13

what is linkage diseqbm (wrt. polymorphism)

Answer 13

it is the correlation ebtween polymorphisms

Question 14

what is linkage diseqbm influenced by

Answer 14

genetic linkage
selection
rate of recombination
rate of mutation
genetic drift
non random mating
popn structure eg. pop bottleneck

Question 15

what is the mutation drift eqbm

Answer 15

rate of mutation is balanced by rate of genetic flow

Question 16

what is the amount of genetic variation a function of

Answer 16

Ne and mu

Question 17

what does the mutation drift eqbm suggest about alleles

Answer 17

theyre uncorrelated due to recombination

Question 18

what is the null hypothesis used when testing for selection

Answer 18

that alleles are uncorrelated due to recombination

Question 19

what does selective sweep allow for

Answer 19

rapid adaptation

Question 20

what is selective sweep

Answer 20

the reduction or elimination of variation among the nucleotides in neighbouring DNA of a mutation, as a result of recent and strong positive natural selection

Question 21

when can selective sweep occur

Answer 21

can occur when a new mtation occurs that increases the fitness of the carrier

Question 22

what is selective sweep measured through

Answer 22

linkage disequilibrium eg. whether a given haplotype is overpresentted in a pop

Question 23

what does strong linkage diseqbm indicate

Answer 23

recent selective sweep (due to recombination)

Question 24

what does natural selection cause

Answer 24

loss of genetic diversity around the selected site
incresed LD around the selected site
an excess of the most common allele
deficiencyu of intermediate frequency alleles
LD decays with time since selection began

Question 25

how does natural selection affect LD (linkage diseqbm)

Answer 25

increased LD around the selected site | LD decays with time since selection began

Question 26

broadly describe what trait development is a result of

Answer 26

trait development = enviro and genotype = phenotype

Question 27

how many years ago did selection begin

Answer 27

5000 yrs ago

Question 28

how is trait variation apportioned

Answer 28

Vp=Ve+Vg

Question 29

what does Vp = ?

Answer 29

VP=Ve +Vg

Question 30

what does Vp stand for

Answer 30

phenotypic variation in the pop

Question 31

what does Ve stand for

Answer 31

environmental variance

Question 32

what does Vg stand for

Answer 32

genetic variation

Question 33

what is apportionment for quantitative traits

Answer 33

Va=Vg | Va=additive genetic variance, depends on magnitude of effects of alleles and allele frequency

Question 34

what is symbol for additive genetic variance

Answer 34

Va

Question 35

what does additive genetic variance depend on

Answer 35

magnitude of effect of alleles and allele frequency

Question 36

what is Va for a single locus with 2 allele

Answer 36

Va = 2pqa^2

Question 37

what does 2pqa^2 equal

Answer 37

Va for a single lous with two alleles

Question 38

what is Va for multiple loci

Answer 38

Va=2∑piqiai^2

Question 39

what is a

Answer 39

the additive effect of an allele

Question 40

what does 2∑piqiai^2 equal

Answer 40

Va for multiple loci

Question 41

when inheritance is purely additive, where does the heterozygote lie

Answer 41

at mid point between homozygotes

Question 42

what does the phenotypic variation between each genotype represent

Answer 42

environmental variance Ve

Question 43

define heritability in terms of variation

Answer 43

the proportion of variation that is explained by genetics

Question 44

what is the proportion of variation that is explained by genetics

Answer 44

heritability

Question 45

how can heritability be estimated

Answer 45

as the correlation etween the mean of the parents and offspring

Question 46

what is the result of low correlation between the mean of the parents and offspring on heritability

Answer 46

low correlation = low heritability

Question 47

give equation for heritability

Answer 47

h^2 = Va/Vp

Question 48

what does Va/Vp equal

Answer 48

h^2 (heritability)

Question 49

what does R stand for

Answer 49

response to selection

Question 50

what is Response to selection

Answer 50

difference in means between parents and offspring

Question 51

what is S -what does it stand for

Answer 51

selection differential | difference in means between pops and the selected parents

Question 52

what is the difference in means between parents and offspring called

Answer 52

response to selection R

Question 53

what is the difference in means between pops and the selected parents

Answer 53

selection differential S

Question 54

with axis of midparent on X and offspring mean on Y, which axis does S correlate to

Answer 54

difference in X axis = S

Question 55

with axis of midparent on X and offspring mean on Y, which axis does R correlate to

Answer 55

difference in Y axis = R

Question 56

when correlation between parental and F1 phenotypes is high, what does this suggest about heritability

Answer 56

heritability is high

Question 57

what size is R when heritability is lower

Answer 57

R is small

Question 58

when heritability is high and the selection differential is high, what value is R

Answer 58

R is large

Question 59

give an example of human niche construction and covergent evoln

Answer 59

the evoln of lactase persistance in humans

Question 60

what is niche construction

Answer 60

the process by which orgs construct important components of their local enviro in ways that introduce novcl selection pressures

Question 61

discuss the evoln of lactase persistance

Answer 61

humans usually stop producing lactase after adolescence most adults are lactose intolerant there have been 5 lactase persistance mutations around the world LP trait frequency is found in c.35% of adults but variance in continents

Question 62

when do humans usually stop producing lactase

Answer 62

after adolescence

Question 63

how many lactase persistance mutations have there been

Answer 63

5 c.Europe = 7500YA 3 in sub saharan Africa 7000YA at least one in Middle East and N.Africa 8-10kYA

Question 64

when and were the lactase persistance mutations around the world

Answer 64

c. Europe 7500YA 3 in sub Saharan Africa 7000YA one in Middle East and North Africa 8-10KYA

Question 65

what is % LP trait frequency

Answer 65

35%

Question 66

what are the advantages of being LP lactose persistant

Answer 66

milk good source protein/fat | strong selective pressures could have just been episodic eg. drought