EE Lecture 5: Phenotype and Genotype Flashcards
what is a haplotype
an association of different alleles on a chromosome - likely to be inherited together
what is a haplogroup
closely related haplotypes (non identical sequences)
what is a closely related set of non identical sequences called
a haplogroup
what is an assoiation of different alleles on a chromosome likely to be inherited together called
haplotype
how can you confirm a haplogroup
by doing a single nucleotide polymorphism SNP test
what are the most commonly studied haplogroups in humans
Y-DNA
mtDNA
how do Y-DNA and mtDNA change
NOT RECOMBINATION
only change by a chance mutation at each generation with no intermixture between parents’ genetic material
what is linkage equilibrium a property of
haplotypes not genotypes
what is linkage equilibrium
when 2 genes/traits/loci are inherited completely independently in each generation
what is the term for when 2 genes/traits/loci are inherited completely independently in each gen
linkage eqbm
what is the term for populations where combos of alleles/genotypes can be found in expected proportions
they are in linkage eqbm
at what level of linkage diseqbm does linkage eqbm occur
linkage eqbm occurs when linkage diseqbm = 0
what is linkage diseqbm (wrt. polymorphism)
it is the correlation ebtween polymorphisms
what is linkage diseqbm influenced by
genetic linkage selection rate of recombination rate of mutation genetic drift non random mating popn structure eg. pop bottleneck
what is the mutation drift eqbm
rate of mutation is balanced by rate of genetic flow
what is the amount of genetic variation a function of
Ne and mu
what does the mutation drift eqbm suggest about alleles
theyre uncorrelated due to recombination
what is the null hypothesis used when testing for selection
that alleles are uncorrelated due to recombination
what does selective sweep allow for
rapid adaptation
what is selective sweep
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
when can selective sweep occur
can occur when a new mtation occurs that increases the fitness of the carrier
what is selective sweep measured through
linkage disequilibrium eg. whether a given haplotype is overpresentted in a pop
what does strong linkage diseqbm indicate
recent selective sweep (due to recombination)
what does natural selection cause
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
how does natural selection affect LD (linkage diseqbm)
increased LD around the selected site
LD decays with time since selection began
broadly describe what trait development is a result of
trait development = enviro and genotype = phenotype
how many years ago did selection begin
5000 yrs ago
how is trait variation apportioned
Vp=Ve+Vg
what does Vp = ?
VP=Ve +Vg
what does Vp stand for
phenotypic variation in the pop
what does Ve stand for
environmental variance
what does Vg stand for
genetic variation
what is apportionment for quantitative traits
Va=Vg
Va=additive genetic variance, depends on magnitude of effects of alleles and allele frequency
what is symbol for additive genetic variance
Va
what does additive genetic variance depend on
magnitude of effect of alleles and allele frequency
what is Va for a single locus with 2 allele
Va = 2pqa^2
what does 2pqa^2 equal
Va for a single lous with two alleles
what is Va for multiple loci
Va=2∑piqiai^2
what is a
the additive effect of an allele
what does 2∑piqiai^2 equal
Va for multiple loci
when inheritance is purely additive, where does the heterozygote lie
at mid point between homozygotes
what does the phenotypic variation between each genotype represent
environmental variance Ve
define heritability in terms of variation
the proportion of variation that is explained by genetics
what is the proportion of variation that is explained by genetics
heritability
how can heritability be estimated
as the correlation etween the mean of the parents and offspring
what is the result of low correlation between the mean of the parents and offspring on heritability
low correlation = low heritability
give equation for heritability
h^2 = Va/Vp
what does Va/Vp equal
h^2 (heritability)
what does R stand for
response to selection
what is Response to selection
difference in means between parents and offspring
what is S -what does it stand for
selection differential
difference in means between pops and the selected parents
what is the difference in means between parents and offspring called
response to selection R
what is the difference in means between pops and the selected parents
selection differential S
with axis of midparent on X and offspring mean on Y, which axis does S correlate to
difference in X axis = S
with axis of midparent on X and offspring mean on Y, which axis does R correlate to
difference in Y axis = R
when correlation between parental and F1 phenotypes is high, what does this suggest about heritability
heritability is high
what size is R when heritability is lower
R is small
when heritability is high and the selection differential is high, what value is R
R is large
give an example of human niche construction and covergent evoln
the evoln of lactase persistance in humans
what is niche construction
the process by which orgs construct important components of their local enviro in ways that introduce novcl selection pressures
discuss the evoln of lactase persistance
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
when do humans usually stop producing lactase
after adolescence
how many lactase persistance mutations have there been
5
c.Europe = 7500YA
3 in sub saharan Africa 7000YA
at least one in Middle East and N.Africa 8-10kYA
when and were the lactase persistance mutations around the world
c. Europe 7500YA
3 in sub Saharan Africa 7000YA
one in Middle East and North Africa 8-10KYA
what is % LP trait frequency
35%
what are the advantages of being LP lactose persistant
milk good source protein/fat
strong selective pressures could have just been episodic eg. drought
