Ancient DNA Examples

Question 1

Neanderthal mtDNA

Answer 1

Right humerus 30-100KYA
PCR
Sequence not in human range of variation avg 24.6 nucleotide differences
Estimated divergence of mtDNA of MH and NT = 550-690KYA (4x age of modern mtDNA divergence) = didn’t contribute to our mtDNA

Question 2

FOXP2

Answer 2

Importance in speech

SNP same in MH and NT

Question 3

MC1R

Answer 3

Pigment gene

Red hair allele in NT not seen in MH

Question 4

NT mtDNA with NGS

Answer 4

6 complete mtDNAs
High diversity between NTs and MHs
Low diversity in NTs = small population

Question 5

NT Genome Project

Answer 5

3 bones from 3 individuals 38-44KYA
Low coverage
Compared to chimp, changes are common to MH and NT
Divergence time 270-440KYA
AA changes present in MH but ancestral in NTs = targets of selection in homosapiens

Question 6

NTs contribute to modern genome?

Answer 6

Differences between NT and MH:

NTs closer to non-Africans than Africans = admixture outside of Africa, interbreeding and contributed to Eurasian genome

Question 7

Denisovan tooth and distal phalanx of 5th digit

Answer 7

V different 30-48KYA
mtDNA no match to NT or MH = new species, x2 more differences between DN and MH than NT and MH = more distantly related
Excess sharing of DNA with Papuans and Melanesians (5% of genome) - interbreeding

Question 8

HLA I

Answer 8

Vital immune system component
HLA-B*73 allele comes from admixture with DN in W Asia - introgressed into modern Eurasians and Oceanians
>50% alleles from Modern Eurasian come from admixture and later introduced into Africans

Question 9

EPAS1

Answer 9

Important gene in adaptation to altitude
Tibetan haplotype closely related to DN haplotype than any other
Freq of haplotype correlated with altitude in Himalayan pop - positive selection, one gene from admixture driven to high freq

Question 10

Toe bone in DN cave

Answer 10

High homozygosity - offspring of first cousins?
Evidence of admixture (17% DN genome from NTs/4% from unknown hominin)
Further mtDNA from others in same cave = up to 80 differences between them = equivalent to MH diversity

Question 11

Mum and Dad NT and DN

Answer 11

NT and DN separated >390KYA
Bone fragment 50% autosomes of both
NT mtDNA
Mixing of late Pleistocene hominin groups common - why they so distinct?

Question 12

Oldest Genome

Answer 12

Theoretical limit ~1MYA
Oldest hominin specimen 400KYA
Oldest is from horse bone 560-780KYA

Question 13

Romanvos

Answer 13

Family 7 killed alongside servants and doctors
Grave of 9 found - 4 males, 2 females, 3 female children
DNA fingerprinting - 1 male father?, 1 female mother?, children related?
MtDNA = mother and children

Question 14

Richard III

Answer 14

MtDNA - 2 descendants matched each other and Richard
Y - 4 descendants matched each other but not Richard (false paternities)
Autosomal SNPs = blue eyes, blond hair

Question 15

Necropolis in Mongolia

Answer 15

Autosomal STRs show closely related individuals buried together
Y STRs and mtDNA showed shared patrilines and matrilines

Question 16

Greenland Paleo-Eskimo

Answer 16

NGS 4000YA permafrost hair - impenetrable to exogenous DNA
High depth
Evidence of migration from Siberia into New World 5.5KYA
Brown eyes, dry ear wax, blood type A+, prone to baldness

Question 17

Oetzi

Answer 17

Europes oldest mummy 3300BC
MtDNA = European subtype not seen before
Last meal = ibex meat
Whole genome sequenced = Lymes Disease, Infertile, Brown eyes

Question 18

Lactase persistence

Answer 18

High freq in current European pop, single SNP C>T in promoter region upstream of lactase gene, associated with rise of dairying
Neolithic samples 7KYA = ancestral allele, 5-4KYA = 27% dairy allele

Question 19

Chicken domestication

Answer 19

Started in China 5KYA

Arrived in South America and spread

Question 20

Gained horses

Answer 20

Easier to ride - Viking migration
Single mutation in DMRT3 gene
2 horses in England have it 850-900AD
More frequent in Iceland 9-11th C (V migration)

Question 21

Yersinia pestis (Plague)

Answer 21

Find what strain responsible for what plague
How it spread
Mutations
Original sequence

Question 22

Paget’s disease

Answer 22

2nd most common metabolic bone disorder (abnormal remodelling and structure)
Men > Women - highest prevalence in UK pop of British descent
Genetic and environmental (been on the decrease)
Mutation in SQSTM1 gene in 1/2 familial cases
Norton Priory:
- 6 skeletons 15th C, characteristics of Paget’s
- Did not find the alteration in SQSTM1 gene
- Was more serious Paget’s, possibly another gene involved