I have a very specific question concerning modern human/neanderthal studies. As long as I understand, neanderthal trace in human genome is due to some recombinant loci. That means, neanderthal clonal genes (Y-chromosome, mt-DNA) were completely washed out from the modern human populations due to gene drift, but some recombinant loci still remain in the gene pool. Moreover, they exist in literally any non-African human person.
Discovering presence of neanderthal alleles in the sapiens genome became possible after scientists sequenced neanderthal genome. Thus, the location of the neanderthal alleles in Eurasian genomes is known and, perhaps, even available. That means, primers can be easily designed for these fragments and the "neanderthal" fragments should be relatively easy to sequence for any modern human.
That means, by sequencing these fragments for humans from the different parts of Eurasia one can reconstruct the underlining Neanderthal phylogeny, i.e. one can compare the neanderthals from West Europe, Caucasus, Central and East Asia, whose differences may well be much deeper in time than the differences between respective modern human lineages, which are thought to diverge 100 TY or similar. Should the existing differences between modern human populations be completely attributed to the divergence that started 100,000 TY? Or, perhaps, they at least partly root into the time of divergence among neanderthal geographic populations?
It sounds too simple, that means, most likely is something wrong and stupid in this logic, or evolutionary anthropologists already working on this. Or?
Would appreciate much for the comment.
See various papers about Neanderthal DNA by the research group of Svante Pääbo:
https://www.researchgate.net/search.Search.html?query=p%C3%A4%C3%A4bo+neandert*
I will read them and look for an answer on the specific question if it does exist. Thank you.
Concerning your specific question: The problem might be to recover a large enough sample of fossil neanderthal DNA (not only a single genome but many specimens from different regions, different time slices) to discuss questions of intraspecific variation.
But see the study of Sankararaman + colleagues (2012): At least some similarity between non-African H. sapiens and H. neanderthalensis can be attributed to interbreeding (in Europe or Asia) between these two in the Late Pleistocene after the divergence of African and non-African H. sapiens.
Article The Date of Interbreeding between Neandertals and Modern Humans
"The problem might be to recover a large enough sample of fossil neanderthal DNA (not only a single genome but many specimens from different regions, different time slices) to discuss questions of intraspecific variation."
- there is exactly what I mean. Obviously, the sample of fossil neanderthal DNA is insufficient for reconstructing phylogeography. On the other hand, fragments of neanderthal DNA are incorporated in modern human genome. The question is whether it is possible to extract these fragments from modern human DNA and use them for reconstructing phylogeography.
On the paper of Sankararaman et al.: " the last gene flow from Neandertals (or their relatives) into Europeans likely occurred 37,000-86,000 years before the present (BP), and most likely 47,000-65,000 years ago", thus, it is possible to extract DNA incorporated into human genome 47,000-65,000 years ago and sequence it?
There is a very nice paper by L Excoffier who modelised the admixture between Neandertal and Sapiens. One of the results is to show that we expect different parts of Neandertal genome to have been retained up to now in each non-african individuals. So it would be very difficult to find different homologous Neandertal fragments and do population genetics with them. Else your idea would be very nice. You should also look to a paper by Labuda's team on the X chromosome (Dystrophin gene), I do not remember all the details, but he was able to clearly identify some Nenadertal "fragments".
Best regards
Evolution purged many Neanderthal genes from human genome
https://www.researchgate.net/post/Reconstructing_neanderthal_evolution_using_modern_human_DNA
Neanderthal DNA contributes to human gene expression:
https://www.sciencedaily.com/releases/2017/02/170223124316.htm
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