Genetic Evidence

Australia: The Land Where Time Began

Genetic Evidence

The only differences found is that the Aboriginal People are unique in lacking blood groups A₂ and B. The genetics of all humans is so similar that it has proven difficult to find any genetic distinction between the Australian Aboriginal People and other groups. There was also no genetic connection to the Veddoid peoples of India and Sri Lanka, and the Ainu of Japan, groups which have been suggested in the past to be related to the Australian Aboriginal People.

Mitochondrial DNA shows a 3-way split between humans about 200 000 years ago into Africans, Caucasians and Australian-Oriental lineages. The problem with the mitochondrial DNA method is that it is not precise enough to detect changes over shorter periods.

The genetic evidence that found that Mungo Man (LM 3 or WLH 3) was not related to modern Australian Aboriginal People does not agree with the cultural evidence, such as burial practices evident in the Lake Mungo burial. see Continuity and Antiquity

Gregory J Adcock et al. at the Research School of Pacific and Asian Studies and John Curtin School of Medical Research, Australian National University, Canberra, extracted mitochondrial DNA from the bones of the skeleton known as Lake Mungo 3 and compared it to that of ancient and modern Aboriginal People, the results indicated that this lineage probably diverged before the most recent common ancestorof contemporary human mitochondrial genomes. So this individual was probably not in the direct line of descent of the Aboriginal People, or any other living people, belonging to a side branch that probably diverged from the line leading to other human groups. These findings have been disputed on several grounds, methodology, interpretation and the possibility that the sample was contaminated. (Colgan, 2001; Cooper et al., 2001; Groves, 2001; Trueman, 2001; but cf Adcock et al., 2001b,c). (Habgood & Franklin, 2008). If the results prove to be correct, it would indicate that the most divergent mtDNA would be from Australia, rather than Africa. (Habgood & Franklin, 2008).

2011 study Science, 23 September 2011: 1770

The genome of an Australian Aboriginal man who had donated a lock of his hair early in the 20th century has been used in a DNA study. As the man lived in the remote southwest of Western Australia 100 years ago, before European settlement had reached anywhere near his area the chances of him having any genes contributed from any population, such as from the white settlers or Asian contacts to the north, other than the Aboriginal people were deemed to be virtually nil. According to the authors⁴ the ancestral Aboriginal people, modern humans, left Africa 24,000 years before the migration out of Africa of the modern humans that were ancestral to Europeans and Asians. The authors⁴ suggest the study supports the view that at about 64,000-70,000 years ago the ancestral Aboriginal People branched from other modern humans who gave rise to the Asian and European populations, arriving in Australia via Asia about 50,000 years ago.

The authors⁴ suggest that as the ancestral Aboriginal populations moved through Asia towards Australia groups of them stayed at various places along the way. Then about 25,000 years later the migrating populations of Asians mixed with these Aboriginal populations, thus explaining the similarities, the authors⁴ describe the Asians as becoming Aboriginal-like, genetically speaking. Willerslev says the ancestral Aboriginal People were the part of an African population that 'went exploring' 25,000-24,000 years before the the rest of the modern humans. He suggests the second wave of migrants stayed a while in either Africa or possibly the Middle East, though he also says that it still has to be determined if the actual split of the original population occurred in Africa or at some place outside Africa.

An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia⁵

The authors⁵ based their study on a lock of hair that was donated by an Aboriginal man early in the 20th century in southern Western Australia. Analysis of the hair detected no evidence of having an admixture of European genes and contamination levels of less than 0.5 % have been estimated for the genetic material. The results indicate that Australian Aboriginals descended from a dispersal of humans into eastern Asia from Africa, possibly somewhere between 62,000 and 75,000 years ago, predating the dispersal that gave rise to the modern Asians, that occurred about 25,000-38,000 years ago. There is also evidence of genetic mixing between the populations of the 2 dispersals prior to the divergence from the modern Asian line of the native Americans. The hypothesis that the present-day Aboriginal Australians are the decedents of the earliest humans to arrive in Australia, and probably represent one of the oldest continuous populations outside of Africa, is said by the authors⁵ to be supported by this study.

The authors⁵ point out the contentiousness of the genetics of the Australian Aboriginal people, though they say that with regard to the evolution of modern humans it is very important. All populations at the present that are non-African are believed to have arisen from a single dispersal of moderns from Africa, and subsequently were affected by the serial founder effect. It has been hypothesised, based on this, that a single early migration populated eastern Asia rather than multiple dispersals. This is the "single-dispersal model" that predicts that the Australian Aboriginal population diversified from within the Asian cluster. It has been shown by recent whole-genome studies that about 17,000-43,000 BP a split occurred between the Europeans and Asians. Some of the earliest anatomical evidence of modern humans outside Africa has been found in greater Australia, Australia plus Melanesia, including New Guinea, that date to about 50,000 BP, population continuity within Australia is not compatible with a divergence of the Aboriginal Australasians from within the Asian cluster. Based on the archaeological and fossil evidence it has been suggested that the occupation of greater Australia took place by an early population expansion, possibly dispersing independently from Africa, before the expansion of population that resulted in the majority of Eurasians of the present. The descendants of the earlier migration were assimilated or replaced by the populations that dispersed later, as suggested by the 'multiple-dispersion model', the Australian Aboriginal population being one of the few exceptions.

The authors⁵ used 6 g of the hair mentioned above of an Aboriginal man from the southern part of Western Australia to extract DNA for sequencing, which displayed a high degree of fragmentation, the base pair lengths averaging 69 pairs. They sequenced the genome to an overall depth of 6.4x; the approximately 60 % of the genomic regions covered was sequenced to average depth of 11x (the theoretical maximum being about 85%). Misincorporation levels of cytosine-thymine, typical of ancient DNA, were low (maximum of 3 % of all cytosines) being restricted to a region at each terminus that was 5-nucleotides long. They therefore trimmed the read termini to improve the single-nucleotide polymorphism (SNP) call quality.

Mapping and genotyping the genome identified 2,782,401 SNPs, 449,115 of which were considered to be of high confidence, a false positive rate of less than 2.4 %, and were used for further analysis. 28,395 of these (6.3%) not being reported previously. The authors⁵ estimated that, based on the X-chromosome heterozygosity, levels of contamination from being handled by people of European descent were less than 0.5 %, which agrees with other studies (Rasmussen et al., 2010; Gilbert et al, 2008) that found that pretreatment can decontaminate ancient human hair. There was no evidence of recent European admixture or contamination that could be detected at the level of the genotype. An average depth of sequencing achieved was 338x for the mitochondrial genome of this Australian Aboriginal man. It was found to belong to a subclade of haplogroup O (hg O) that was new, termed by the authors⁵ O1a. The 4 major lineage groups specific to Australia include haplogroup O, being reported from a number of parts of the Northern Territory (15-16%) (Hudjashov et al., 2007; Ingman, M, & Gyllensten, 2003; van Holst Pellekaan et al., 2006). His Y-chromosome was assigned to KM526* macro haplogroup, from high confidence SNPs. The unresolved K-M526* lineages are more common, more than 5%, only among the contemporary populations of Australasia, though the majority of East and West Eurasian Y-chromosomes are accounted for by the O and P branches of the K-M526 haplogroup (Hudjashov et al., 2007; Karafet, T.M., et al., 2010). Among contemporary Australian Aboriginals both uni-parental markers fall within the known pattern (Hudjashov et al., 2007), adding to the evidence that the genomic sequence has not been contaminated.

The high-confidence SNPs were compared with Illumina SNP chip data, taken from 1220 individuals from 79 populations. These included individuals from the Kusunda from Nepal and the Aeta from the Philippines. These 2 groups have been suggested to be relict populations from the dispersal across eastern Asia that has been postulated (Lahr, M., 1996; Whitehouse, T. et al., 2004). Genetic differentiation among Africans, Asians, and populations from greater Australia has been illustrated by the results of principal components analysis (PCA). It has been found that the Australian genome clusters with samples from the highlands of Papua New Guinea (PNG), leading to the conclusion that it is therefore positioned roughly between South and East Asians. The Munda speakers from India and the Aeta from the Philippines have been found to be the closest population to Australian Aboriginals, with the exception of the Papuans from Bougainville. The authors⁵ used 542 individuals from 43 populations in Asia and Greater Australia, including 25 additional populations from India that all fell on the Eurasian axis, including those of Greater Andamese and Onge from the Andaman Islands to confirm this pattern (Reich, D. et al., 2009). The lack of European contamination or recent admixture in the sequence of the genome was confirmed by the PCA and admixture results.

The search for a common ancestry between Australian Aboriginals and other groups involved use of the D test on the SNP chip data and genomes. The results indicated that between the Australian Aboriginals and Asians, that included Japanese, Cambodian, Han and Dai, there was a significantly larger proportion of shared derived alleles than between the Australian Aboriginals and Europeans, in this case French. The French were found to share a significantly larger proportion of derived alleles with the Asians than the French shared with Australian Aboriginals. It was not possible to discriminate between the 2 models of origin, though the results of this study do rule out the simple models in which the populations were isolated completely since divergence. Consistent evidence of gene flow between populations of greater Australia (Australian Aboriginals/PNG highlanders) and Asian Ancestors following the split of the latter from the Native Americans under various models is not provided by the results of this study, and the authors⁵ suggest that some degree of gene flow may have occurred between the inhabitants of Bougainville and some Asian ancestors after that time. They also suggest that prior to European contact Australian Aboriginals and PNG Highlands ancestors had been isolated genetically from other populations, though possibly not from each other, since at least 15,000-30,000 BP (Goebel, T. et al., 2008).

The authors⁵ sequenced 3 Han Chinese genomes to an average depth of 23-24x and used a test that compared the patterns of similarity between these of the Australian Aboriginals to individuals of African or European descent to determine which of the human dispersal models best fits the data. The D_4P test they used, closely related to the D test (Green, R.E. et al., 2010; Reich, D. et al., 2010), though it is much more robust to errors and is capable of detecting subtle demographic signals in the data that large amounts of secondary gene flow may mask.

The single dispersal model predicts an equal number of sites that support group 1[(YRI, ASN), (CEU,ABR)] and group 2[(YRI,ABR), CEU,ASN)], using the sites in which the Australian Aboriginals differ from the Han Chinese, that represent eastern Asia (ASN), and comparing the ABR and the ASN with the European sample (CEU) at the Centre d'Etude du Polymorphisme Humain (CEPH) and the Yoruba that represent Africa (YRI). The multi-dispersal model predicts more group 2. The results of the study indicated that there was an excess of sites, 51.4%, that was statistically significant, where the Yoruba and Australian genomes were grouped together, group 2, relative to the Yoruba and East Asian genomes together (group 1, 48.6%, P < 0.001), which is consistent with a basal divergence of Australian Aboriginals relative to East Asians and Europeans. The authors⁵ suggest there is another possible explanation of their findings according to which modern European and East Asian populations appear to be more similar to each other as a result of gene flow between the 2 groups, which generates an excess of sites showing group 2, even with the single dispersal model. They suggest that it is indicated by simulations under such a model that the amount of gene glow between Europeans and East Asians (Gutenkunst, R.N. et al., 2009) is not capable of generating the excess sites showing group 2 unless all 3 groups, Australian Aboriginals, East Asians and Europeans all split from each other at about the same time, and there was subsequently no migration between the Australian Aboriginals and the East Asians. As the Australian Aboriginals have been found to be genetically closer to the East Asians than to Europeans, such a model would be inconsistent with the results of the D test, PCA and discriminant analysis of principal components (DAPC). According to the findings of this study a model in which Australian Aboriginals derive directly from populations of ancestral Asians, that is proposed by the single dispersal model, is incompatible with the genomic data, the results favouring the multiple dispersal model which suggests the ancestral Australian Aboriginals, as well as related populations, split from the Asian population prior to the split between the Asian and European populations.

The authors⁵ developed a population genetic method for estimating demographic parameters from diploid whole-genome data, in order to estimate the divergence times. Estimates of rates of migration and divergence times between population pairs are found by using patterns of allele frequencies and linkage disequilibrium. They estimated that 62,000-75,000 BP, based on this method, that the Australasian Aboriginal People split from the ancestral Eurasian population, an estimate that is consistent with mtDNA-based coalescence estimates of 45,000-75,000 BP of the founder lineages that were non-African (Hudjashov et al., 2007; Endicott, P. et al., 2009; Soares, P. et al., 2009). According to the authors⁵ they also found that European and Asian populations separated as late as 38,000-25,000 BP, which agrees with previous estimates (Gutenkunst, R.N. et al., 2009; Keinan, A. et al., 2007). The divergence of all 3 populations is similar to the representative African sequence. The excess of sites observed showing group 2, discussed above, is predicted by the estimated split time of the Aboriginal Australasians from the ancestral Eurasian populations that resulted from this study. A block bootstrap approach was used to obtain confidence intervals and test hypotheses. Longer divergence time between East Asians and Australian Aboriginals than between East Asians and Europeans were always obtained in 100 bootstrap samples, indicating that the null hypothesis of the null hypothesis of a trichotomy in the population phylogeny can be discarded with statistical significance of about P<0.01. The authors⁵ took into account changes in population sizes, and the effect of gene flow following divergence between different populations, though their models remain relatively simple, and the models they considered are a small subset of all the human demography models that are possible. They made no attempt to model directly the combined effect of demography and selection, and they suggest the true human diversification history is likely to be more complex than the simple demography models they considered in this study.

To test for admixture in the genome sequence of Australian Aboriginals with archaic humans [Neanderthals and Denisovans] they used 2 approaches (Green, R.E. et al., 2010; Reich, D. et al., 2010). They investigated whether high-confidence Neanderthal admixture segments that had previously been identified in Europeans and Asians (Green, R.E. et al., 2010) were also present in Australian Aboriginals. They found that in Australian Aboriginals the proportion of such segments are very similar to proportions previously observed in the sequences of Europeans and Asians. They used the D test to look for evidence of admixture of Denisovans within the genome of Australian Aboriginals, in which the test involves the proportion of alleles that are shared between an out-group sequence (Denisovan) and 2 in-group sequences. The result of this test indicated that compared to other Europeans and Africans, including Andaman Islanders, there was a relative increase in sharing of alleles between the genomes of Denisovans and Australian Aboriginals, though slightly less than the sharing of alleles that were observed for Papuans. The D test proved to be very sensitive to errors in the ingroup sequences, and when both ingroup and outgroup ancient DNA sequences are involved in comparisons shared errors are of particular concern. The latter result is consistent with the hypothesis of an increased degree of admixture between the Denisovans or related groups and the ancestral groups of the Melanesians of the present (Reich, D. et al., 2010), though it is not certain if these results have been influenced by these errors. The authors⁵ suggest any such admixture may have occurred during the early wave of migration, in either Melanesia or Eurasia.

It is not clear the degree to which a single individual is generally representative of the Australian Aboriginals' evolutionary history

Conclusion

According to the authors⁵ it is unclear to what degree this individual is representative of Australian Aboriginal evolutionary history more generally. They conclude that the ancestors of this Aboriginal man, and possibly all Aboriginals, are of similar distance from Africans as are other Eurasians, and that at about 62,000-75,000 BP the Aboriginal ancestors split from the gene pool that gave rise to all other populations of modern humans. The authors⁵ say their study supports the model of human evolution according to which the modern Australian Aboriginal people descended from an early wave of expansion into Asia about 62,000-75,000 BP. Their data also supports the substantial population admixing and replacement of populations of the first wave by the 2nd expansion wave, predicted by this model, though a few populations are descendants of the early dispersal, such as those in Australia and the highlands of Papua New Guinea and Aeta. According to the authors⁵ this is compatible with data from mtDNA that indicate they derived from the same few founder haplogroups shared by all populations outside Africa, though all haplogroups observed in Australia are unique to this area. The data also support the the suggestion that modern Aboriginal Australians have descended from the first humans that entered Australia at least about 50,000 BP. Aboriginal Australians are indicated by this to probably have one of the oldest population histories, that is continuous, outside sub-Saharan Africa of the present.

See Deep Sea Fishing-oldest evidence

Sources & Further reading

Josephine Flood, Archaeology of the Dreamtime, J. B. Publishing
Phillip J. Habgood & Natilie R. Franklin, The revolution that didn't arrive: A review of Pleistocene Sahul, Journal of Human Evolution, 55, 2008
de Lange, Catherine, Dec 211/Jan 2112. Cosmos.
Willerslev, Eske & Nielson, Rasmus, 2011, Science Magazine Podcast, Science, 23 September 2011.
Rasmussen, Morten, Xiaosen Guo, Yong Wang, Kirk E. Lohmueller, Simon Rasmussen, Anders Albrechtsen, Line Skotte, et al. "An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia." Science 334, no. 6052 (October 7, 2011 2011): 94-98.
Gibbons, Ann. "Aboriginal Genome Shows Two-Wave Settlement of Asia." Science 333, no. 6050 (September 23, 2011 2011): 1689-91.