Genome sequences of extinct hominins Flashcards Preview

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Flashcards in Genome sequences of extinct hominins Deck (24):
1

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

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

2

what are process which result in highly fragmented DNA

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

3

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

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

4

give an example of the process that results in miscoding lesion

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

5

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

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

6

why is hish sequence overage needed

to distinguish miscoding lesions from genuine SNP
norm want x50

7

what is a miscoding lesion

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

8

how can modern contamination be reduced

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

9

what revealed from seq analysis of N from Denisova caves

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

10

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

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

11

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

Mezaamaiskayathan more than Altai

12

what is the first fossil of denisovans found

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

13

what region of genome has strong N to D gene flow

human leukocyte antigen

14

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

arent direct descendents of H.erectus
discredit the prev model of two migr oofa first by erectus then sap

15

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

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

16

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

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

17

what % of genome in present day eurasians inherited from N

1.5-2.1

18

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

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

what important about the Pester cu Oase fossil

shows not an isolated event occured repeatedly

20

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

4-6%
3-6%
0.3%

21

what other interesting baout D and admix

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

22

what examples of benefits of admixture

toll like recpetors
EPAS1 and altitude
skin colour

23

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

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

what evidence is there for benefits of admixture in tibetans

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