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Everyone probably has wondered at some time what makes Aboriginal Australians different from other people, where they came from and how old their ethnic type is. Well, wonder no more. Following up on the previous post, "Australian Aboriginal DNA Gets Attention," this post will summarize the groundbreaking article in Science magazine, M. Rasmussen et al., "An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia" (Science 334, 7 Oct. 2011, 94-98).

First the abstract:

We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.

Above:  Aboriginal Men about 1900 from the Coranderrk Community. La Trobe Picture Collection.

This study of Aboriginals will be cited as a landmark case in genetics because the authors took especial care to disarm any criticism concerning possible admixture and contamination, achieved a stupendous rate of success in sequencing DNA sites and used smart comparators to verify their model of what makes Aboriginals different, including Neanderthals, Denisovans, Andamanese, Filipinos, Indians, Papua New Guineans and Melanesians. Fifty-eight co-authors are listed, with Morten Rasmussen of the Feinstein Institute for Medical Research, Manhasset, New York, named as the first lead author.

First sentence:

The genetic history of Aboriginal Australians is contentious but highly important for understanding the evolution of modern humans.

Some mysteries pointed out about Aboriginal Australian DNA by the authors include:

--The Aboriginal population contains a lot of diversity, including specimens of most of the world's haplogroups, male and female

--Related populations suggested are hunger-gatherers from Nepal and the Philippines, Great Andamanese and Onge from the Andaman Islands, Highland Papua New Guineans and certain peoples from India

--It was previously unclear whether Aboriginals resulted from a single dispersal out of Africa or multiple-dispersal model

--The role of hybridization with other archaic peoples was also not clear.

The authors confirm that "before European contact occurred, Aboriginal Australian and PNG Highlands ancestors had been genetically isolated from other populations (except possibly each other) since at least 15,000 to 30,000 years B.P." Also, "our results favor the multiple-dispersal model in which the ancestors of Aboriginal Australian and related populations split from the Eurasian population before Asian and Europeans split from each other" (97). "We find that the European and Asian populations split from each other only 25,000 to 38,000 years B.P., in agreement with previous estimates."

The new study finds that Aboriginals have an amount of admixture with Neanderthals and Denisovans comparable to Europeans and Asians, although they have more Denisovan DNA than other people. "This admixture may have occurred in Melanesia or, alternative, in Eurasia during the early migration wave" (97).

In sum, the Aboriginals are part of the same first-out-of-Africa branch of the human tree as Europeans and Asians, their ancestors splitting 62,000 to 75,000 years ago from Africans, and leaving relic related populations in the Highlands of Papua New Guinea and the Philippines. A second expansion wave through India, Indo-China and Southeast Asia replaced the original stock, while the Aboriginals became stranded and isolated in Australia about 50,000 years ago. 

"This means that Aboriginal Australians likely have one of the oldest continuous population histories outside sub-Saharan Africa today" (98).

Properly positioning Australian Aboriginals in the expansion of humans out of Africa opens the way to connecting the dots for all the other prehistoric peoples. The migration map presented by Rasmussen et al should be carefully studied for clues about the origins of Asians and Native Americans, to begin with.



Reconstruction of early spread of modern humans outside Africa. Note admixture between early dispersal (red) and second dispersal (black), as well as presence of archaic Denisovans in Asia. Science magazine.

According to a professor of immunology and microbiology at Stanford University, humans were able to survive, spread and expand their populations once they left Africa because of immunities to disease they acquired from Neanderthals and Denisovans, who had lived in Europe and Asia already for hundreds of thousands of years.

A review of the new research appears in the online science magazine Discover under the date of June 20, 2011. The professor's name is Peter Parham.

Crux of the matter, according to Royal Society report

• Parham began by taking a close look at a family of genes called  human leukocyte antigens (HLAs), which play a central role in our body’s immune responses. We are able to react to a wide array of diseases because our HLA genes are highly variable, each containing dozens of  alleles (forms of genes).
• Our ancestors in Africa, however, would have had a small number of HLA alleles because they likely traveled in small bands and had little contact with other groups. Moreover, their HLAs would have only protected them against African diseases.
• When Parham compared the HLAs of modern humans with those of Neanderthals and Denisovans, he noticed some overlaps. In particular, he found that HLA-C*0702, an allele common in Europeans and Asians but nonexistent in Africans, was also present in the Neanderthal genome. Similarly, HLA-A*11, which is found in modern Asians but not in Africans, popped up in Denisovan DNA.
• Overall, about 50 percent of HLA Class I alleles in Europeans seemed to come from Neanderthals, 70 to 80 percent in East Asians from Denisovans, and 90 to 95 percent in Papuans from Denisovans, Parham said at a recent Royal Society meeting.

DNA Consultants introduced its Neanderthal Index, a measure of affinity with archaic populations of Europe and the Middle East, one year ago this month.

Dr. Donald Yates says he is planning a visit to Vindija cave near Varazdin in Croatia this month to see firsthand the world's most important site for the discovery of Neanderthal bones and lifeways, dating to about 30,000 years ago.

Human history changed drastically with the 1974 Neanderthal discoveries at Vindija Cave. Photo Tomislav Kranjcic.

Analysis of ancient nuclear DNA, recovered from 40,000-year-old remains in the Denisova Cave, Siberia, hints at the multifaceted interaction of human populations following their migration out of Africa.

The new discipline of palaeogenetics is delivering increasing dividends, the latest news coming from Reich, Pääbo and colleagues on page 1053 of this issue. The authors' analysis of nuclear DNA of a human-like finger bone, found in Denisova Cave in southern Siberia, points towards a complex model of migration and colonization after anatomically modern humans moved out of Africa some 50,000–60,000 years ago.

Ever since 1925, when Raymond Dart's report of the first Australopithecus skull in southern Africa upended Victorian views of human origins, there has been debate over whether our species arose only once and spread throughout the world, replacing all extant species of Homo, or whether our ancestors interbred with the other populations and subspecies. The most extreme version of the 'candelabra' model of human origins — according to which human species arose multiple times independently of our Homo ergaster ancestors — has been largely discounted.

But it has been difficult to assess more nuanced models, such as the possibility of genetic exchange with some archaic populations, including Neanderthals, and now perhaps ancient Siberians. Until recently, genetic data and interpretation of the fossil record seemed to favour a complete-replacement model, in which all human species trace all of their genetic ancestry to a single origin in one or more African populations of moderate size some 200,000 years ago2, 3, 4, 5. However, the Denisovan nuclear genome sequence, along with that of Homo neanderthalensis published by some of the same authors6, suggest that the out-of-Africa population history of Homo sapiens is probably much more intertwined than previously thought, with more intertwining in some parts of the world than others.

Read more and follow discussion at Nature.

Triangles and circles respectively represent sampling locations of Neanderthal remains and of present-day human genomes. The blue arrows indicate generally accepted major migrations of anatomically modern humans, following their departure from Africa 50,000–60,000 years ago. At this time, there were two primary archaic species in Eurasia, Neanderthals and Homo erectus; Reich, Pääbo and co-workerssuggest that a third group was also present, represented by the ancient Denisovan genome. From ancient DNA, they identify additional putative events involving two episodes of limited gene flow: first, genetic admixture from Neanderthals to modern humans, shortly after the exit from Africa; second, subsequent admixture with the archaic population exemplified by the nuclear DNA extracted from the Denisova finger bone. This second event seems to affect only the ancestors of present-day Melanesians, who are thought to have colonized Papua New Guinea some 45,000 years ago. African populations, both past and present, are genetically highly diverse, as indicated by the multiple labels.

See also "New Hominin Probably Explains Distinctiveness of Melanesians"

Nature 468: 1053-60.

Published online

22 December 2010

Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population ‘Denisovans’ and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.