First Neanderthal fossils
Discovered in a quarry in the Neander Valley in Germany in 1856
Initially thought to be from a bear, realised it was then a hominin!
Dated at about 40KYA
Other sites include:
Old Man of La Chapelle-aux-Saints (France) – 50KYA
Kebara (Israel) – 60KYA
Shanidar (Iraq) – 60KYA
Vindija (Croatia) – 40KYA
Mezmaiskaya (Russia)- 70KYA
El Sidron (Spain) – 43KYA
All dated at a similar time
Ancient DNA – fantasy or reality
How DNA sequences have been extracted from a termite fossil in Amber- broke amber and extracted ribosomal DNA- achieved it- turned out to be contamination and wasn’t actually termite DNA
Svante Pääbo – Neanderthal Man
1985 – Published paper in Nature describing how he sequenced DNA from a 7000 year-old mummy.
Later turned out to be contamination, but set his career down aDNA path. Nobel Prize in 2022
How ancient?
- DNA is constantly being damaged and repaired
- When an organism dies, DNA gets degraded, especially in the presence of water but also radiation
- Sometimes DNA can bind to minerals on teeth or bone- best chance of it to last
- Next-generation sequencing produces short reads, so DNA can be less intact
How to choose the right sample
- Pääbo’s lab began to develop robust protocols for working with ancient DNA
- Much of this was done in the 1990s on non-hominins
- 1991 – published paper on DNA from 5000 year old ‘iceman’
The first Neanderthal mtDNA sequence
- Mitochondrial DNA was sequenced from bone from the 1856 specimen
- Rigorous tests for contamination etc.
- Sequence was different from modern humans
- Divergence estimated at 550 – 690 KYA (much older than common ancestor of modern human sequences)
Additional Neanderthal mtDNA sequences
Humans and neanderthals under going extreme genetic bottlenecks.
Mitochondrial DNA can be limited in what it tells us- only inherited from the mother
Problem – so far, only mtDNA
- Mitochondrial DNA has many copies per cell
- Working with nuclear DNA was going to be much harder
- MtDNA is only a tiny fraction of the genome – it may not be representative, and it certainly cannot tell us about which genes make us human
Towards a whole genome (2006)
Sequencing was performed using 454 technology (an early next-gen sequencing method)
254,000 reads of 100-200bp were obtained
15,000 were good matches to primate sequences
(remainder was bacterial, etc)
Aligned the reads to the human genome
0.04% of the genome is covered
Reads match the X & Y chromosomes
The fossil was male
Data indicate a common ancestor about 500KYA
Data suggest ancestral population size was small
Top sample- did it twice - not much human contamination - top least contaminated (Found in croatia)
How was the neanderthal genome made
started with 3 bones (different specimens but from the same cave) from Vindija Cave, Croatia
3 libraries per bone made for 454 sequencing
Used to identify libraries with highest % hominin DNA- least bacteria
- 95-99% of DNA from non-primates (mostly bacterial)
DNA was cut with enzymes that preferentially digest bacterial DNA
- Performed Illumina Sequencing – 5.3 Gbp of Neanderthal DNA obtained
- All three samples were females (including the 2006 ‘male’ one!)
- Bioinformatic analysis suggests <1% of reads are contaminated human DNA
Divergence time between humans and Neanderthals
About 12.7% of differences between humans and chimps arose after the human-Neanderthal split
Therefore humans and Neanderthals diverged about:
0.127 x 6.5 MYA = ~825KYA
Rather technical figure, which accounts for biased error rates towards specific bases
Features unique to humans, rationale
If Chimpanzees and Neanderthals have one allele, and humans have another allele, then the human allele is probably derived, after the human – Neanderthal split
These could be mutations that make us what we are.
10.5 Million differences between humans and chimps
Neanderthal nucleotide known for about 3.2 million of them
Humans and Neanderthals same for about 87% (i.e. difference arose before the split)
Only 78 substitutions found that change an amino-acid and are fixed in humans
Selective sweeps just after the split
- THADA – associated with Type II diabetes
- DYRK1A – may cause cognitive impairment in Down’s Syndrome patients
- NRG3 – may cause schizophrenia
- CADPS2 – associated with autism
- RUNX2 – associated with dysplasia and morphological traits where humans differ from Neanderthals
ABBA-BABA
Developed a test known as the ABBA-BABA test- detects admixture of interbreeding
Positive values of D, mean the Neanderthal matches human 1 more than human 2
Two European Americans (CEU), two East Asians, (ASN) and 4 West Africans (YRI)
Positive values mean Neanderthal is closer to first human (European/Asian) than second human (African)
Admixture (conclusions)
- Estimated that 1-4% of non-African genomes are Neanderthal in origin
- The authors suggest that scenario 3, admixture between Neanderthals and an ancestor of non-Africans is the most likely.
- Scenario 4 (no admixture) is plausible
- Most of have some neatherndal genes in our genome.
Distinguishing admixture and popn structure
- Estimated that 1-4% of non-African genomes are Neanderthal in origin
- The authors suggest that scenario 3, admixture between Neanderthals and an ancestor of non-Africans is the most likely.
- Scenario 4 (no admixture) is plausible
- Most of have some neatherndal genes in our genome.
Selection on Neanderthal-derived genes
- Used data from the 1000 Genomes Project to identify Neanderthal-derived alleles
- If Neanderthal-derived alleles are over-represented, then they have been under positive selection
- If Neanderthal-derived alleles are under-represented, then they have been under purifying (negative) selection
- Neanderthal ancestry is less at functionally more important regions – consistent with purifying selection
- Neanderthal ancestry is lower on the X than on the autosomes – consistent with sex-linkage of genes involved in male hybrid sterility
- Neanderthal-derived alleles associated with keratin filaments are at high frequencies in Europeans – a possible role of Neanderthal genes in adaptation to non-African environments (see Lecture 13)
