Genome sequences of extinct hominins Flashcards

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1
Q

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

A

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

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2
Q

what are process which result in highly fragmented DNA

A

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

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3
Q

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

A

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

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4
Q

give an example of the process that results in miscoding lesion

A

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

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5
Q

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

A

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

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6
Q

why is hish sequence overage needed

A

to distinguish miscoding lesions from genuine SNP

norm want x50

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7
Q

what is a miscoding lesion

A

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

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8
Q

how can modern contamination be reduced

A

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

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9
Q

what revealed from seq analysis of N from Denisova caves

A
38kya
DNA from 3 inds mtDNA suggets highly related
52% coverage
70% DNA frag aligned to human genome
long runs homozygosity - inbreed suggest
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10
Q

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

A
HS and (N+D) = 553-589kya
N and D =38kya
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11
Q

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

A

Mezaamaiskayathan more than Altai

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12
Q

what is the first fossil of denisovans found

A
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
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13
Q

what region of genome has strong N to D gene flow

A

human leukocyte antigen

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14
Q

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

A

arent direct descendents of H.erectus

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

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15
Q

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

A
at least 3 migr oofa
first H.erectus
then N/D ancestor
the H,sap 
= although argued still too simple probs more waves
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16
Q

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

A

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

17
Q

what % of genome in present day eurasians inherited from N

A

1.5-2.1

18
Q

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

A

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

19
Q

what important about the Pester cu Oase fossil

A

shows not an isolated event occured repeatedly

20
Q

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

A

4-6%
3-6%
0.3%

21
Q

what other interesting baout D and admix

A

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

- importance of modelling

22
Q

what examples of benefits of admixture

A

toll like recpetors
EPAS1 and altitude
skin colour

23
Q

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

A

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

24
Q

what evidence is there for benefits of admixture in tibetans

A

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