Australia: The Land Where Time Began

A biography of the Australian continent 

Gene Flow to Australia from India in the Holocene Substantiated by Genome-Wide Data

It is commonly believed that following the initial occupation of Australia the continent remained relatively isolated until European first contact, though the genetic history of the Aboriginal People has not been explored in detail in regards to this issue. Pugach et al. carried out analysis of large-scale genotyping data of aboriginal Australians, New Guineans, Island Southeast Asians and Indians. Their work indicates an ancient association between Australia, New Guinea and the Mamanwa, a negrito group from the Philippines, and divergence times for these groups being 36,000 years ago, which supports the view that these populations are representatives of an early “southern route migration” out of Africa, with other populations in the region arriving by a separate dispersal. They also detected a signal that indicated substantial gene flow between the Indian populations and Australia long before European contact, which is contrary to the generally accepted view that there was no contact between Australia and the remainder of the world. The estimate arrived at by Pugach et al. is that the gene flow occurred during the Holocene, 4,230 years ago. They also point out that this is also the time when there were changes in tool technology, food processing and the arrival of the dingo, the evidence appearing in the archaeological record of Australia, which they suggest may be related to the migration from India.

It is suggested by genetic and archaeological evidence that anatomically modern humans (AMH) expanded from Africa (Ramachandran et al., 2005; Liu et al., 2006) to colonise all parts of the world, in the process replacing local archaic Homo populations, such as Neanderthals (Green et al., 2010) and Denisovans (Reich et al., 2010; Reich, 2011), with a limited degree of gene flow. Pugach et al. say it appears the anatomically modern humans proceeded by 2 routes: the northern route giving rise to the modern Asians 38,000-23,000 years ago (Gutenkunst et al., 2009; Rasmussen et al., 2011) and an earlier southern dispersal along the coast around the Arabian Peninsula and India to the Australian continent (Reich, 2011; Rasmussen et al., 2011). The ancestral Australian Aboriginal People and Papua New Guineans  diverging from the ancestral Eurasian population 75-62 ka (Rasmussen et al., 2011) and, based on evidence from archaeology, reached Sahul (the combined land mass of Australia, Tasmania and New Guinea) by at least 45 ka (O’Connell & Allen,2004; Kayser, 2010; Summerhayes et al., 2010). Subsequent additional gene flow to coastal New Guinea, though not to the highlands, from Asia, that was associated with the expansion of Austronesians (Kayser, 2010), though the extent of isolation of the Australian Aboriginals after the initial colonisation remains a subject of debate. There are some mtDNA and y chromosomal studies suggesting there was some degree of gene flow from the Indian subcontinent to Australia during the Holocene (Redd & Stoneking, 1999; Redd et al. 2002; Kumar et al., 2009), though according to the prevailing view that prior to the first European contact in the 18^th century there was little if any contact between Australia and the remainder of the world (Rasmussen et al., 2011; Hudjashov et al., 2007; McEvoy et al., 2010).

In this study Pugach et al. analysed genome-wide SNP data, finding that there was a significant signature of gene flow from India to Australia which they suggest was at about 4,320 years ago. Pugach et al. assembled genome-wide data from the across Northern Australia (AUA) (Reich et al., 2011; Redd & Stoneking, 1999), the highlands of Papua New Guinea (NGH) (Wollstein et al., 2010), 11 populations from island Southeast (SE) Asia (Reich et al., 2011), and 26 populations from India (Reich et al., 2009), which included Dravidian speakers from South India (Reich et al., 2011; Cordaux et al., 2003).  They also included data from Yorubans from Ibadan; Nigeria (YRI); individuals of northern and western European ancestry that were living in Utah (CEU); Han Chinese individuals from Beijing (CHB); and Gujarati Indians from Houston, TX (GIH) (Altshuler et al., 2010). There were 344 individuals in the final dataset; and following data cleaning and integration there were 458,308 autosomal SNPs for use in the analysis.

Genetic relationships between populations

See source

Discussion

An ancient ancestral association between Australia, New Guinea, and the Mamanwa (a negrito group in the Philippines), is suggested by the results of this study, with a divergence occurring at least 35 ka, which implies a common origin but early separation for these groups, and supports the view that these populations are representatives of the descendants of an early “southern migration route” (Reich et al., 2011; Rasmussen et al., 2011). Pugach et al. also found it striking that there was a signal of substantial gene flow between Indian and Australian populations prior to European contact. Pugach et al. estimated the data of this gene flow event to be 141 generations  ago which suggests that the gene flow may be associated  with the documented changes in the Australian archaeological record that occurred at about this time, which is around the time the dingo arrived I Australia.

Pugach et al. say the signal of Indian gene flow might not necessarily be from India directly; a scenario can be envisioned according to which the Indian ancestry comes indirectly to Australia, such as contact with island Southeast Asian populations.  Some trade between the northeast coast of Australia and Indonesia is believed to have taken place prior to European contact (Hiscock, 2008). There were 11 populations from island SE Asia included in this study, but the results showed no signal of recent gene flow from India into these populations or from those populations into Australia, which according to Pugach et al. renders the scenario of Indian ancestry by way of SE Asia unlikely.

It has been shown that there is patterning similar to those generated by admixture could be produced by ancient population structure (Eriksson & Manica, 2012). According to Pugach et al. even in the ancestral population of the AUA and the NGH, if this substructure existed, however, the suspicion that the gene flow detected in this study might be an artefact, that was attributable to this substructure, would require this ancestral age to be much older, old enough to predate the occupation of Sahul (Sankararaman et al., 2012). An argument against this possibility is the fact that the date obtained by this study is comparatively recent. Also the Australian Aboriginals shared approximately the same amount of Denisovan ancestry with Papua New Guineans that was shared between the Papua New Guineans and the Denisovans (Reich et al., 2011). As it is not expected that later mid-Holocene gene flow into Australia, though not into Papua New Guinea, should diminish the proportion of the Denisovan ancestry in the Australian Aboriginal People, though not in the ancestry of the Papua New Guineans, this might appear surprising. Given that the total Denisovan contribution to the ancestor of these populations is about 3-5 % (Reich et al., 2011), and the amount of the contribution from Indians is estimated to about 11 %, it is expected that the impact of Indian genetic material would be to decrease the Denisovan ancestry in the Australian genome by about 0.3-0.5 %, which is below the detection threshold of the data generated by this study.

Though the samples that have been presented in this study were collected from a broad geographical area across northern Australia, they might not be representative of the Australian Aboriginal People as a whole. As has been pointed out by others (McEvoy et al., 2010), it would be very helpful to have comprehensive studies of the genetic variation in Australian Aboriginal people in order to further understand their history which is increasingly complex.

Sources & Further reading

1. Pugach, Irina, Frederick Delfin, Ellen Gunnarsdóttir, Manfred Kayser, and Mark Stoneking. "Genome-Wide Data Substantiate Holocene Gene Flow from India to Australia." Proceedings of the National Academy of Sciences 110, no. 5 (January 29, 2013 2013): 1803-08.