Friday, January 14, 2011

On Neanderthals, Denisovans, and other archaics

Andaman Islanders. Related peoples once inhabited the coastal regions of southern, southeastern, and eastern Asia.

The past year brought two major advances: the long awaited sequencing of the Neanderthal genome and the genetic sequencing of an another archaic human, the Denisovans of East Asia, whose existence had previously been unsuspected.

The bottom line comes down to four points:

Before the East African ‘big bang’ gave rise to modern humans some 80,000 to 60,000 years ago, there had been at least four groups of archaic humans:

a) Skhul-Qafzeh hominins
- were almost modern anatomically
- were derived from a demic expansion that spread over most of Africa and the Middle East about 110,000 years ago
- evolved directly into modern humans through the rapid expansion of an East African subgroup

b) Neanderthals
- differed much more anatomically from modern humans
- were behaviorally similar to Skhul-Qafzeh hominins
- probably had body fur and other cold adaptations
- were derived from an earlier expansion out of Africa 250,000 - 400,000 years ago
- inhabited Europe, the Middle East (during glacial maxima), Central Asia, and Siberia as far east as Lake Baikal

c) Hobbits
- were small and possibly a form of Homo erectus
- inhabited at least a portion of southeast Asia
- may have been a regional variant of the Denisovans

d) Denisovans (Homo altaiensis?)
- were another archaic population distinct from modern humans
- inhabited Asia from Lake Baikal eastward (
see earlier post)

These archaic humans have left significant genetic admixture in all modern human populations. The admixture is about 1 to 4% in Eurasians (from Neanderthals), 8% in Melanesians (from Neanderthals and Denisovans), and 13% in sub-Saharan Africans (from Skhul-Qafzeh-like hominins).

This admixture might have accelerated human evolution by providing modern humans with useful alleles. To date, no such alleles have been found. The admixture seems to be confined to genes of low adaptive value.

Although Denisovans inhabited East Asia, they left no admixture in present-day East Asians. Yet their admixture is discernible in present-day Melanesians. It seems that the first modern humans to replace Denisovans were not ancestral East Asians but rather ancestral Melanesians. This is consistent with archeological and ethnographic evidence that the coastal regions of southern, southeastern, and eastern Asia were initially settled by people related to the indigenous populations of Melanesia, Papua-New Guinea, and Australia. After the last ice age, they were gradually replaced by populations originating in northern Eurasia (see earlier post). Today, they survive in relic groups like the Veddas of Sri Lanka, the Andaman Islanders, the Semang of the Malayan peninsula, and the Aeta of the Philippines.

References

Green, R.E., J. Krause, A.W. Briggs, T. Maricic, U. Stenzel, M. Kircher, et al. (2010). A draft sequence of the Neandertal genome, Science, 328, 710-722.
http://www.sciencemag.org/cgi/reprint/328/5979/710.pdf

Reich, D., R.E. Green, M. Kircher, J. Krause, N. Patterson, E.Y. Durand, et al. (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia." Nature, 468, 1053-1060.

Watson, E., P. Forster, M. Richards, and H-J. Bandelt. (1997). Mitochondrial footprints of human expansions in Africa, American Journal of Human Genetics, 61, 691-704.

19 comments:

Tod said...

It sounds like Skhul-Qafzeh hominins were an awful lot more like modern humans than Denisovans.

Sub-Saharan Africans and Melanesians have been able to adapt to garden agriculture and flourish after contact with the outside world in a way many aboriginal people have not.

Iain said...

Hobbits?

Thanks - I learn something interesting every time I read this blog.

RS said...

An interesting question is why proto-Melanesians crossed with the very distant Denisovans, whereas proto-Asians didn't cross with the much less distant Melanesians.

Anonymous said...

Tod,

They were anatomically modern, but their cultural production was scarcely different from that of the Neanderthals.

Iain,

I know. It sounds funny, but "Hobbit" seems to be the most common name.

RS,

Proto-East-Asians did cross with Melanesian-like populations, particulary on the eastern islands of Indonesia, but also in parts of mainland southeast Asia.

B.K. Fix said...

Today, they survive in relic groups like the Veddas of Sri Lanka, the Andaman Islanders, the Semang of the Malayan peninsula, and the Aeta of the Philippines.

These groups look Australo-Melanesiany, but as far as I know the genetic evidence hasn't supported a link. The Aeta are similar to other Filipinos, the Vedda are similar to other South Asians, etc.

Peter Frost said...

B.K. Fix,

You're correct for the Aeta (who are highly intermixed with surrounding Filipino groups). The Andaman Islanders show a much stronger genetic affinity with sub-Saharan Africans than with neighboring South Asians. The genetic evidence portrays Veddas as outliers.

In any case, I wouldn't expect a close genetic affinity with present-day Melanesians because these "indigenous South Asians" settled the coastal regions of southern, southeast, and eastern Asia some 50,000 years ago. They resemble each other physically because they have stayed put in the same ecological zone and have maintained a similar lifestyle. Hence the selection pressurs have remained the same.

gcochran said...

"being genetically twice as distant from modern humans"


Nope.

Peter Frost said...

"... the date of the most recent common mtDNA ancestor shared by the Denisova hominin, Neanderthals and modern humans is approximately one million years ago ... or twice as deep as the most recent common mtDNA ancestor of modern humans and Neanderthals. ... the fact that the divergence of the Denisova hominin mtDNA is about twice as old as the divergence of Neanderthal and modern human mtDNAs is robust to most assumptions"

Krause et al. (2010) The complete mitochondrial DNA genome of an unknown hominin from southern Siberia, Nature

gcochran said...

You could at least bother to read the Denisovan paper in Nature:

"The Denisova genome diverged from the reference human genome
11.7%(CI: 11.4–12.0%) of the way back along the lineage to the human–chimpanzee ancestor. For the Vindija Neanderthal, the divergence is 12.2% (CI: 11.9–12.5%). Thus, whereas the divergence of the Denisova
mtDNA to present-day human mtDNAs is about twice as deep as that of
Neanderthal mtDNA, the average divergence of the Denisova nuclear
genome from present-day humans is similar to that of Neanderthals."

Relying on one locus (mtDNA) when there is published data on tens of thousands of loci is just silly.

Tod said...

G.Cochran, you (and others) were right all along about humans having archaic ancestry, I would not be surprised if you were right about this issue too.

However as I understand it you are suggesting that some of the most adaptive (successful) alleles in modern humans originated in archaics.

This may be naive, but why do Australian Aborigines, the humans with the most obvious archaic traits (presumably stemming from a massive introgression of archaic alleles) seem to have made less evolutionary advances than the rest of humanity? Aborigines seem to have stagnated after they recieved all these archaic alleles.

Peter Frost said...

Greg,

You're right and I stand corrected. I had read about the discrepancy between the mtDNA dating and the nuclear DNA dating(in a summary article, not in the original paper). I assumed that the mtDNA estimate was the better one because nuclear DNA is more sensitive to natural selection. Having fully read the paper, I'm still not convinced by the two possible explanations that it gives, but no one else seems to find such a discrepancy unusual.

Insightful said...

I love this post, Peter. Very insightful!..

Anonymous said...

So do you guys have any insights on how neanderthal could have affect how us Europeans might think or behave? Is there currently any speculation?

Anonymous said...

"The Andaman Islanders show a much stronger genetic affinity with sub-Saharan Africans than with neighboring South Asians"


Wikipedia:

Genetic analysis indicates that male Onges and Jarawas almost exclusively belong to Haplotype D, which is also found in Tibet and Japan, but is rare on the Indian mainland and elsewhere in Asia.[30] However, this is a subclade of the D haplogroup which has not been seen outside of the Andamans, which marks the insularity of these tribes.[31] The only other group that is known to predominantly belong to haplogroup D are the Ainu aboriginal people of Japan.[32] Male Great Andamanese, unlike the Onge and the Jarawa, have a mixed presence of Y-chromosome haplogroups O, L, K and P, which places them between mainland Indian and Asian populations.[31]

The mtDNA distribution, which indicates maternal descent, describes all the Onge and a heavy majority of the Great Andamanese as belonging to haplogroup M, found ubiquitously in India, where it represents 60% of all maternal lineages.[31][33]

Anonymous said...

So do you guys have any insights on how neanderthal could have affect how us Europeans might think or behave? Is there currently any speculation?

It will vary depending on the allelic frequencies. In France the alleles are so that they prefer wine, while for most of the other European populations or populations of European descent, the preferred drink is beer. Soccer is also more preferred over continental Europe, while American football is preferred in the US, with Britain and rugby as an intermediate genetic condition.

It's not just "Europeans", though, but all Eurasians and Oceanians that have neanderthal admixture, so we must think of African versus non-African characteristics of thought and behavior, not European versus non-European. The Indian's taste for Indian food, for example, might be a sign of a different neanderthal allele than that encountered in Italians or in the French. Whereas the African appreciation for chicken is unparalleled in the rest of the World, showing their lack of Neanderthal admixture.

Anonymous said...

@ Anonymous of the 15th of August.

I am so sorry that you have obviously missed out on the evolution of intelligence! Are you serious about that unscientific bullshit you wrote down? Or were you mere joking. I hope for you the latter.....

At awe with these stupid remarks!

BunBun4life said...

I saw that show on Hobbits, and they proved very clearly to me that the remains were Australopithecus Afarensis the same as LUCY our alleged missing link in Africa. Whats wrong? Not ready to admit all races and humans on earth didn't evolve from black africans in the shortest time span imaginable and then populated an entire planet in an incredibly short time span? Yeah because it didn't happen that way.

That documentary on 'the hobbits' also showed the find of SEVERAL Australopithecus skulls & almost completely full skeletons found in GEORGIA and were at least 2 million years old, that also proves that our common NON HUMAN ancestor was already out of Africa MILLIONS of years ago, which makes a hell of a lot more sense.

Inuits in Alaska have not changed in 10,000 years, they have not lightened or turned blonde or blue eyed or into a different race.

Because things like that take MILLIONS of years.

Even the monkeys in Asia have epicanthal FOLDS, and you think some blacks just walked over there and turned chinese ? BULL SHIT

Anonymous said...

Thought the fossils from Ethiopia of Homo Sapiens (IDATU?) were 200,000 years old.

Is there any chance that some homo sapiens evolved outside of Africa? and that they interbred with some line of modern homo sapiens sapiens?

Randi Ridnour said...

You said having stated that there were a number archaic forms present, that they left significant genetic admixture in all modern Human populations. Of course this is not true of the Sub-Saharan Africans whom don't appear to have any of the archaic genetic admixture. What say you?