EB23

Question 1

What is diversity in humans like

Answer 1

for a relatively young species (200,000 years) a lot of diversity can be observed within humans, however compared to other species its quite low

Question 2

what is one of the main reasons for diversity in terms of phenotypes of humans

Answer 2

we are globally distributed which sets us apart from other primate species.

• humans can be found in variety of habitats
  1. high altitude (tibet)
  2. arid - ME
  3. rainforest - pigmys kongho
  4. cold - siberia, alaska
  5. island populations: melanesians and polynesians: scottish

Question 3

what is a a haplotype`

Answer 3

specific patterns of NSP more likely to be inherited together, variation across mulitple sites

Question 4

what is a haplogroup

Answer 4

group of closely related haplotypes, patterns of haplotypes and haplogroups give us insights over what happens in the course of evolution.

Question 5

what is the liklihood a new allele will reach fixation

Answer 5

1/2Ne

Question 6

what is linkage equilibrium

Answer 6

no association between alleles even after recombination when they are adjacent on a chromosome
*when in equilibrium there should be no correlation between varients, however in reality there is always some degree of linkage

Question 7

what is LD

Answer 7

the correlation between polymorphisms, if one polymorphism is present can predict likelihood of presence of linked allele

Question 8

what is a selective sweep

Answer 8

when a new advantageous alelle enters a population and is selected for, all linked variation will increase in frequency intially as recombination takesa while to break up the linkage.
*reduction or elimination of variation amongst nts in the neughbouring DNA of a beneficial mutation, tend to increase LD.

Question 9

what happens if all variation is lost in a selective sweep

Answer 9

recombination can not be seen as there is no variation to record such events. `

Question 10

what is an incomplete selective sweep

Answer 10

excess of most common allele but not full takeover

Question 11

what can natural selection be recognised by

Answer 11

1. loss of genetic diversity around the selected site.
2. increased LD around the selected site
3. an excess of the most common allele
4. deficiency of intermediate frequencys of alleles
5. LD decays with time since selection began

Question 12

what is lactase persistance

Answer 12

most humans cant digest milk as adults, however around 8000 years ago cattle domestication and pastoralism occured, correlated with lactase persistence.
LCT enzyme expression stops around weaning in all mammals except humans.

Question 13

what can frequency of lactase persistance be correlated with

Answer 13

pastoral populations

Question 14

what is lactase and how is it broken down

Answer 14

lactase is a dissacharide (gluc/galac)

to digest must cleave bonds between sugars via LCT enzyme

Question 15

Describe lactase persistance evolution in humans

Answer 15

strong south north cline in persistance in europe, the more north the more persistance
ability to digest milk has happened atleast 5X independantly in humans, LD patterns can be seen around these variants.

Question 16

what causes lactase persistance

Answer 16

mutation in promoter region of LCT MCM6 prevents expression being turned off.
SNPs in intron 13 and 9

Question 17

How has global popualtion structure been inferred, what did this show

Answer 17

from 650,000 SNPs tying genetics to geography.
7 major ancestry components in humans identified
1. africa, 2. Mid east, 3. europe, 4. C.S asia, 5. E.asia, 6. Oceania 7. America

Question 18

What do regions of the genome which differ between populations and have Fst>0.65 (alelle frequency difference) show

Answer 18

local adaptation

Question 19

what did proportion of SNPS with Fst>0.65 show

Answer 19

proportion of SNPs with high Fst increases in those that are most functional, effecting gene expression or protein sequence *5’UTR or non synonymous mutations.
* this shows selection

Question 20

how was skin colour variation investigated

Answer 20

Fst was calculated around loci involved in natural variation in pigmentation and plotted the maximum pairwise Fst between georgraphic regions in a 100kb window surrounding the SNP.

Question 21

what is skin colour variation around the world the result of

Answer 21

lots of different genes, specific populations have selected for different variants.
* if there is a selective advantage for lighter skin further from the equator, varaint with light skin would be selected for.
Which variants and in which genes in a population is a matter of chance so get variable patterns of population differentiation.

Question 22

What is an example of a highly differentiated gene

* how does this gene change around the world

Answer 22

EDAR
associated with multiple phenotypes.
1. a specific variant is completely fixed in E. asian populations (almost 100% will have a variant on both chromosomes), whereas the rest of the world will have the other variant at near fixation. *native americans who descend from East asians also have this variant.
2. rest of the world, almost 100% will have the other variant on both chromosomes.

Question 23

What are the three hair variations and their morphologies under the microscope

Answer 23

1. Asians: thick round cuticle hair: leads to straight hair
2. Caucasians: thinner oval shaped cuticle: leads to wavier hair
3. African: much thinner and flatter cuticle: tightly coiled thin hair

Question 24

What type of hair is the EDAR variant associated with in east asian populations

Answer 24

very thick straight hair

Question 25

what does the LD around EDAR suggest

Answer 25

lots of LD so suggests recent selection within the last 10 20 thousand years

Question 26

what did modelling EDAR in mice show

Answer 26

Cloned human variant into mice and observed associated phenotype
no. of cells served as a proxy for hair shaft thickness
EDAR: asian homo had asian phenotype thick hair cuticle
EDAR homo for other = thinner hair

Question 27

what effect was EDAR shown to have on breast tissue

Answer 27

east asian woman tend to have smaller breasts

cloned mouse model with asian EDAR (homo) had reduced size of mammary fat pad.

Question 28

how was EDAR shown to be associated with sweat glands

Answer 28

increased density and no. of eccrine sweat glands in mice with east asian variant.
looked at humans and found east asian ind. who have this variant do have higher density of sweat glands than people without.

Question 29

how was EDAR shown to be asssociated with mouse eyelid glands

Answer 29

small eyelids associated with east asian phenotype

found no correlation with EDAR vaiant and eyelids

Question 30

what are the three hypothesis for selection for EDAR variant in asians

Answer 30

1. changes in hair, teeth and breasts were passengers in thermoregulation.
2. a series of selection on different traits at different times made the variant so common
3. sexual selection: thick hair and small breasts are visible sexual signals which if preferred by men could quickly become more ocmmon