L20 Archaic Genome

Ancient DNA sequencing (1980)

1984- 150-year-old museum quagga, sequenced from dried muscle 229 from dried muscle

1985- s400 year old mummy

Amplified and cloned multiple DNA fragments

Antediluvian DNA

Plant and animal remains inside amber, ancient fossils

Many of the studies are not replicable

DNA is likely to be from contamination

Ancient DNA sequencing- hype (1990s)

Reports of the sequencing of very old DNAs

Many of the studies are not replicable

The DNA is likely to be from contamination

Damaged DNA

DNA decay after cell death

Hydrolysis (break DNA strand > short fragment)

Alkylation (DNA crosslinks> prevent amplification)

Oxidation and hydrolysis (DNA mutation> C to U deamination is a main source of sequencing errors)

The older the DNA, the lower the quality

DNA preservation

Theoretical DNA preservation - 1 million years

Best preservation condition: permafrost

Contamination

Environmental DNA: bacteria /plant

Excess non-sample DNA

Reduce sequence throughput

Modern DNA is less damaged and amplified better than ancient DNA

Reduce sequence throughput

Wrong information

Solutions to contamination

Extract DNA from bone

Clean lab

Bioinformatic solution

New methods for library construction

Linker ligation enrich fragmented single strand DNA

Human RNA probes to capture hominoid DNA

Questions that can be addressed about other homo species

time for separation, demographic history of archaic homo species, gene flow between modern/archaic homo species

Admixture appears to be quite common in human history

Both archaic genomes had gene flow into modern humans, also evidence of archaic gene flow into africans. some of the introgeression has functional implications

Adaptive archaic introversion

Archaic and modern human admixed. advantageous alleles in archaic genomes retained in modern human