Here are the numbers I’ve found so far for Neanderthal and Denisovan DNA in different populations:
Sriram Sankararaman et al, in The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans, 2016, report:
Native Americans: 1.37%
Central Asia: 1.4%
East Asia: 1.39%
Oceana (Melanesians): 1.54%
South Asia: 1.19%
(I have seen it claimed that the high Neanderthal percents for Oceanan populations (that is, Melanesians and their relatives,) could be a result of Denisovan DNA being incompletely distinguished from Neanderthal.)
Prufer et al, [pdf] 2017, report somewhat higher values:
East Asians: 2.3–2.6%
While Lohse and Frantz estimate an even higher rate of between 3.4–7.3% for Europeans and East Asians. (They found 5.9% in their Chinese sample and 5.3% in their European.)
I found an older paper by Prufer et al with estimates for three Hispanic populations, but doesn’t clarify if they have Native American ancestry:
|Population||Individuals||Neandertal ancestry (%)|
|Europeans||CEU–Euros from Utah||85||1.17±0.08||0.21±0.17|
|East Asians||CHB–Han Chinese Beijing||97||1.40±0.08||0.30±0.21|
|CHS–Han Chinese South||100||1.37±0.08||0.27±0.21|
|Americans||CLM: Colombians from Medellin||60||1.14±0.12||0.22±0.16|
|MXL: Mexicans from LA||66||1.22±0.09||0.21±0.15|
|PUR: Puerto Ricans||55||1.05±0.12||0.20±0.15|
|Africans||LWK: Luhya in Webuye, Kenya||97||0.08±0.02||0.04±0.07|
|ASW: African Americans South West US||61||0.34±0.22||0.07±0.11|
Since the paper is older, all of its estimates are lower than current estimates, because we now have more Neanderthal DNA to compare against. However, you can still see the general trend.
The difference between “autosomes” and “X” highlighted here is that (IIRC) autosomes includes all chromosomes except the XY pair, and X is the X from that pair. They’re breaking them up this way because the X chromosome tends to have very little Neanderthal on it (and the Y even less), probably because Neanderthal DNA on these particular chromosomes was selected against.
Neanderthal DNA appears to have been selected for in areas that control hair and skin–people who had just left Africa were adapted to the African environment, and Neanderthal hair and skin traits helped them survive in colder, darker winters. We also see a lot of Neanderthal DNA influencing inflammation/immune response–these may have helped people fend off new diseases. But we see almost no Neanderthal (or Denisovan) DNA in areas of the genome that code for sperm, eggs, testes, ovaries, etc. These parts of people were probably already finely tuned to work together, didn’t need to change with the environment, and changing anything probably just made them less efficient–so Neanderthal (and Denisovan) DNA on the X and Y chromosomes has been purged from the Homo Sapiens gene pool.
North African Populations Carry Signature of Admixture with Neanderthals reports its data relative to the European average (which I believe is the CEU pop, 1.17%, so I’ll do the math for you to figure how much Neanderthal they have.)
Algeria 44.57% = 0.52% Neanderthal
Tunisia 100.16% = 1.172 N
Tunisia 138.13% = 1.6% N (This is an interesting population that has been highly endogamous and thus better reflects historical populations in the area.)
Egypt 58.45% = 0.68% N
Libya 56.36% = 0.66% N
Morroco North 69.17% = 0.81% N
Morocco South 17.90% = 0.21% N
Saharawi 50.90% = 0.6% N
Canary Island* 101.44% = 1.187% N
China Beijing 193.43% = 2.26 % N
China 195.41% = 2.29% N
Texas Indu Gupti 84.37% =0.987% N
Andalusia*118.66% = 1.39% N
Tuscan 94.90% = 1.11% N
Basque BASC 129.48% = 1.51% N
Galicia* GAL 115.86% = 1.36% N
Yoruba YRI 0.00% = 0% N
Luyha LWK −14.89% = N
The authors note that they are not sure how the Luyha received a negative score–perhaps the presence of admixed DNA from yet another species is interfering with the results.
According to Wikipedia:
Denisovan DNA is most commonly found in Melanesians, Papulans, Aboriginal Australians and Aboriginal Filipinos, who all have similar amounts around 4-6%, indicating that they probably were all one group when their ancestors met the Denisovans. However, the similar-looking but historically quite isolated Onge people have no Denisovan–so they split off before the event.
In Papuans, Neanderthal DNA tends to be expressed in brain tissue, Denisovan in bones and other tissues.
Asians have a small amount of Denisovan DNA; Tibetans have a particular gene that lets them absorb oxygen effectively at high altitudes that they got from the Denisovans.
The Mende People of Sierra Leon may derive 13% of their DNA from an as-yet unknown hominin species (ancient DNA and bones do not preserve well in parts of Africa, so finding remains and identifying the species may be difficult.)
The Yoruba derive 8 or 9% of their DNA from the same hominin.
Masai have a small fraction of Neanderthal–since they are 30% non-African, probably about 0.35% of their genome–but you can read the paper yourself.
Biaka Pygmies and Bushmen (San): 2% from an unknown archaic.
With more testing, better and more comprehensive numbers are sure to turn up.