L5: Archaic Genomes Flashcards
Give the frequencies of three different types of genomic variation between human and chimpanzee genome
> 35 million single nucleotide differences
> 40-45 Mb species specific deletions insertions (90 difference in total)
> 10,000 species specific TE insertions
So how different is our genome from Chimps?
4% of our genome (and not 1%) is different from chimpanzee genome and there is a need for better resolution!
What pattern has been seen in our brains over the past?
Human brain size tripled in the last 2 million years
Who received the 2022 Nobel prize for medicine and why?
Svante Paabo for sequencing ancient mummy and neanderthal DNA
Where were neanderthal remains found?
All over Europe, found remains from these migratory hominids; e.g floods swept through and buried remains. They were mostly found in cold caves where remains were well preserved
What differences are often seen in neanderthal remains ?
Much bogger and thicker skulls
Describe the migratory patterns of early hominids from africa
Homo erectus lived in west africa and migrated north. Homo heiderbergensis migrated to europe and near east around 400k years ago. Neanderthals diverged and stayed in Europe while denisova migrated to central and south east asia. Modern homosapiens migrated later and spread out everywhere. They encountered other hominin species when they migrated out of Africa in their big wave out of Africa; Possibly didn’t even realise realise they were another species
When was neanderthal DNA first extracted?
Neanderthal DNA was extracted from fossilized bones in 2008
How is the current state of the neanderthal genome?
A lot of short reads with very high coverage. We have 5 high ceverage neanderthal genomes with an additional 20 low coverage genomes
Therefore where did different lineages depart from each other?
Neanderthalers + denisova migrated into eurasia 400.000 years ago before splitting around 350k years ago. Modern humans left africa around 70k years ago. Dutch, papuan and chinese populations diverged from each other separately since then.
Other:
The last common ancestor of all was 1 million years ago. Modern humans diverged from Nean/Des around 800k years ago. Denisova and neanderthals diverged around 620k years ago.
How did neanderthals live and what was their mating patterns?
Neanderthals had a relatively small populations size and lived in isolated groups. Inbreeding was frequent
How is inspecting neanderthal genomes helpful?
Comparing the genomes of human and Neanderthals sheds light on human-specific evolutionary changes
How different are human and neanderthal genomes? Where may these differences lie?
Not so many SNS differences; 96 fixed amino acid substitutions in a total of 87 proteins. Slight enrichment of genes expressed in the developing cortex; Relatively more gene expression in the brain compared to other genes
In regards to segmental duplications, 3 regions with fixed copy number variations specific to humans: One of which
is BOLA2, 1 copy in Neanderthal, 2-5 copies in Humans (Highly associated with autism)
In the order of 3000 fixed changes that potentially influence gene expression in present-day humans
What was a consequence of the neanderthal and human encounters
Neanderthals and homo sapiens have exchanged genetic material until ~ 30.000 years ago. On average 2-5% of our DNA is derived from Neanderthals, however distribution is unequal over the world’s population which provided new insights into population migration patterns.
How can you determine how much neanderthal DNA?
Can look at the common ancestor to see whether they had it, then compare genomes with africans, who never came into contact with neanderthals to see if this difference is there.
