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> Researchers have access to only a few Neanderthal genomes, and most of those have been sequenced at a low resolution. This has made it hard to identify mutati

> Researchers have access to only a few Neanderthal genomes, and most of those have been sequenced at a low resolution. This has made it hard to identify mutations that evolved after their lineage split from that of humans some 500,000–750,000 years ago. But in the past few years, Pääbo and his team have generated three high-quality Neanderthal genomes from DNA found in caves in Croatia and Russia. Can anyone with domain knowledge chime in on this? Is the sample set of genomes enough to suggest these mutations were prevalent in the neanderthal population? And even so, might they have had a completely different effect on neanderthal physiology?

bencollier49 6y ago
I wonder how neanderthal genetics varied from locality to locality. Presumably those in Russia were somewhat different to those in e.g. Gibralter.
- dahfizz 6y ago
  My understanding is that Neanderthals didn't occupy that large of a region. There are ancient human ancestors all over the globe but actual Homo neanderthalensis did not leave modern day Europe. It is actually thought that this could have contributed to their decline. Compare with modern day humans who explored the whole globe: some ancient dude even paddled his way to Australia! It's hard for a species that widespread to go extinct.
  - dalbasal 6y ago
    Homo Neanderthalis has been found in europe, the middle east, the altai mountains, armenia and other places. The were widespread, and interbred with sapiens, denisovans and probably other types. There is even renewed interest in finding American and/or Australian neanderthals and denisovans... As the known range has grown, those seem more plausible.
- dalbasal 6y ago
  Probably a lot. First, neanderthals were closely related to Denisovans. In Denisova cave itself, both neanderthals & denisovans were found and even a first generation hybrid. So.. you could call it a denisovan-neanderthal complex with various subpopulations over time and geography. The altai neanderthals have been suggested as a subspecies/type... so there are differences there. In europe and the middle east, there's a decent phenotypical distinction between early and late (classical) neanderthals. The earlier type was less distinctively neanderthal... kind of more sapien looking. Later populations developed that distinctively bony face. ..Sapiens too, probably. We descend mostly from a small population of sapiens, but that doesn't mean other populations didn't exist. They just don't have descendants. For example, modern europeans have a relatively homogenous, low level of neanderthal DNA. At different points of history, certain populations could have ben 25% neanderthal... and genetically distinct from other groups. This is all normal mammalian population dynamics. Modern Sapiens are the unusual ones. We went through a genetic bottleneck and lost a lot of diversity.
searine 6y ago
>Can anyone with domain knowledge chime in on this? Due to the age of the genomes, C's deaminate and are recorded erroneously as T's. The solution is usually to throw out those sites from the sequencing results (which account for a large fraction of the genome in the garbage). By sequencing many different neanderthal individuals you can start to reconstruct some of those lost parts of the genome. https://en.wikipedia.org/wiki/Ancient_DNA#Problems_and_errors https://en.wikipedia.org/wiki/Ancient_DNA#Problems_and_error... >Is the sample set of genomes enough to suggest these mutations were prevalent in the neanderthal population? We aren't really at population scale genomics of neanderthals yet. We are still trying to piece together a truely high-quality reference genome (of one individual). Once that is complete, the next step is a population of about 100. Based on the human genome, the chimpanzee genome, the neanderthal genome and the ancestrally reconstructed most recent common ancestor at each of the nodes in between, we can estimate allele frequencies within the different populations.

bencollier49 6y ago

I wonder how neanderthal genetics varied from locality to locality. Presumably those in Russia were somewhat different to those in e.g. Gibralter.

dahfizz 6y ago
My understanding is that Neanderthals didn't occupy that large of a region. There are ancient human ancestors all over the globe but actual Homo neanderthalensis did not leave modern day Europe. It is actually thought that this could have contributed to their decline. Compare with modern day humans who explored the whole globe: some ancient dude even paddled his way to Australia! It's hard for a species that widespread to go extinct.
- dalbasal 6y ago
  Homo Neanderthalis has been found in europe, the middle east, the altai mountains, armenia and other places. The were widespread, and interbred with sapiens, denisovans and probably other types. There is even renewed interest in finding American and/or Australian neanderthals and denisovans... As the known range has grown, those seem more plausible.
dalbasal 6y ago
Probably a lot. First, neanderthals were closely related to Denisovans. In Denisova cave itself, both neanderthals & denisovans were found and even a first generation hybrid. So.. you could call it a denisovan-neanderthal complex with various subpopulations over time and geography. The altai neanderthals have been suggested as a subspecies/type... so there are differences there. In europe and the middle east, there's a decent phenotypical distinction between early and late (classical) neanderthals. The earlier type was less distinctively neanderthal... kind of more sapien looking. Later populations developed that distinctively bony face. ..Sapiens too, probably. We descend mostly from a small population of sapiens, but that doesn't mean other populations didn't exist. They just don't have descendants. For example, modern europeans have a relatively homogenous, low level of neanderthal DNA. At different points of history, certain populations could have ben 25% neanderthal... and genetically distinct from other groups. This is all normal mammalian population dynamics. Modern Sapiens are the unusual ones. We went through a genetic bottleneck and lost a lot of diversity.

searine 6y ago

>Can anyone with domain knowledge chime in on this? Due to the age of the genomes, C's deaminate and are recorded erroneously as T's. The solution is usually to throw out those sites from the sequencing results (which account for a large fraction of the genome in the garbage). By sequencing many different neanderthal individuals you can start to reconstruct some of those lost parts of the genome. https://en.wikipedia.org/wiki/Ancient_DNA#Problems_and_errors https://en.wikipedia.org/wiki/Ancient_DNA#Problems_and_error... >Is the sample set of genomes enough to suggest these mutations were prevalent in the neanderthal population? We aren't really at population scale genomics of neanderthals yet. We are still trying to piece together a truely high-quality reference genome (of one individual). Once that is complete, the next step is a population of about 100. Based on the human genome, the chimpanzee genome, the neanderthal genome and the ancestrally reconstructed most recent common ancestor at each of the nodes in between, we can estimate allele frequencies within the different populations.