Genome sequences of extinct hominins

Question 1

what are some of the problems in the study of ancient DNA

Answer 1

not always presereved - depends on conditions
DNA mol highly fragemented
contaminatinom
miscoding lesions

Question 2

what are process which result in highly fragmented DNA

Answer 2

heat induced hydrolysis of B-N glycosidic bonds- removes bases the structure then left unstable

Question 3

how does the strucute left by heat induced hydrolysis of B-N glycosidic bonds then become highly fragmented

Answer 3

hydrolysis of double strand DNA - results in gaps which when denature in PCR results in lots of sgl strand fragments

Question 4

give an example of the process that results in miscoding lesion

Answer 4

deamination of cytosine to uracil
- amino groupp replace with oxygen , in pcr turns C to T
v common in ancient DNA

Question 5

what is the problem with deamination of cytosine to uracil in ancient DNA

Answer 5

v common
v difficult to interpret
some studies remove uracil residues using enz

Question 6

why is hish sequence overage needed

Answer 6

to distinguish miscoding lesions from genuine SNP

norm want x50

Question 7

what is a miscoding lesion

Answer 7

change in nucleotide occuring during degradation that alters th eseq that is read after PCR

Question 8

how can modern contamination be reduced

Answer 8

wear gloves
most of th econtamination on outside so scrae off
work done under high contaniment

Question 9

what revealed from seq analysis of N from Denisova caves

Answer 9

38kya
DNA from 3 inds mtDNA suggets highly related
52% coverage
70% DNA frag aligned to human genome
long runs homozygosity - inbreed suggest

Question 10

what does comparison of the N D HS genomes suggest about divergence

Answer 10

HS and (N+D) = 553-589kya
N and D =38kya

Question 11

what pop of N are non afr HS more close rel to

Answer 11

Mezaamaiskayathan more than Altai

Question 12

what is the first fossil of denisovans found

Answer 12

75kya
fingerbone and two teeth 
from altai mountains siberia 
mtDNA rev a unknown hominin
but nuclear DNA suggest sister group of N
genome 30 coverage 
teeth sim to australopithecus
low gen div

Question 13

what region of genome has strong N to D gene flow

Answer 13

human leukocyte antigen

Question 14

what has genome seq of N and D revealed about oofa hypo

Answer 14

arent direct descendents of H.erectus

discredit the prev model of two migr oofa first by erectus then sap

Question 15

what is the current model for oofa suggested by D and N

Answer 15

at least 3 migr oofa
first H.erectus
then N/D ancestor
the H,sap 
= although argued still too simple probs more waves

Question 16

what did comparisons of N and mod human afr and non afr show

Answer 16

degree of divergence between N and mod eu less than N and mod afr = smalle inbreeding

Question 17

what % of genome in present day eurasians inherited from N

Answer 17

1.5-2.1

Question 18

name the diff fossils which show ev of the admixture between N and H sah.

Answer 18

hs fossils
Ust-ishim, siberia= dated 43-47kya = inbreeding with N 65-50kya
Kostenki,russia - 39-36kya = ibreed with N 54kya
Pestera cu oase,romaina - 37-42kya = inbreed 42-38kya, had 6-9% N ancestry therefore N within the last 4-6 gen

Question 19

what important about the Pester cu Oase fossil

Answer 19

shows not an isolated event occured repeatedly

Question 20

what % of D derived genome in papuans / ocenia /asiatoday

Answer 20

4-6%
3-6%
0.3%

Question 21

what other interesting baout D and admix

Answer 21

evidence of admix in D from unknown hominin = 0.5-0.8%

- importance of modelling

Question 22

what examples of benefits of admixture

Answer 22

toll like recpetors
EPAS1 and altitude
skin colour

Question 23

what evidence is there that toll like receptors from admixture and why pot adv

Answer 23

cluster of three rec (TLR6-TLR1-TLR10)
part of innante immune syst
cthe cluster show haplotypes transferred to mod humans
haplotypeV11 in mod humans id to D
haplotype IV in mod humans id to N
archais like variatns more active - inc act to pathogens =ev of interbreed help h.sap

Question 24

what evidence is there for benefits of admixture in tibetans

Answer 24

EPAS1 gene
TF control expr of genes that help in anoix conditions - altitude
diff halpotype models show that tibetans haplo closer to D than any other mod human - only 9 diff between tibettand and D