Gene flow from the Indian subcontinent to Australia: evidence from the Y chromosome

Gene flow from the Indian subcontinent to Australia: evidence from the Y chromosome.

Redd AJ, Roberts-Thomson J, Karafet T, Bamshad M, Jorde LB, Naidu JM, Walsh B, Hammer MF.
Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA.

Phenotypic similarities between Australian Aboriginal People and some tribes of India were noted by T.H. Huxley during the voyage of the Rattlesnake (1846-1850). Anthropometric studies by Birdsell led to his suggestion that a migratory wave into Australia included populations with affinities to tribal Indians. Genetic evidence for an Indian contribution to the Australian gene pool is contradictory; most studies of autosomal markers have not supported this hypothesis (; and references therein). On the other hand, affinities between Australian Aboriginal People and southern Indians were suggested based on maternally inherited mitochondrial DNA. Here, we show additional DNA evidence in support of Huxley’s hypothesis of an Indian-Australian connection using single-nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) on the nonrecombining portion of the Y chromosome (NRY). Phylogenetic analyses of STR variation associated with a major Australian SNP lineage indicated tight clustering with southern Indian/Sri Lankan Y chromosomes. Estimates of the divergence time for these Indian and Australian chromosomes overlap with important changes in the archaeological and linguistic records in Australia. These results provide strong evidence for an influx of Y chromosomes from the Indian subcontinent to Australia that may have occurred during the Holocene.

Y-chromosome-specific microsatellite variation in Australian aboriginals.

Y-chromosome-specific microsatellite variation in Australian aboriginals.

Vandenberg N, van Oorschot RA, Tyler-Smith C, Mitchell RJ.

Department of Genetics and Human Variation, La Trobe University, Bundoora, Victoria, Australia.

The frequency distributions of 4 highly polymorphic Y-chromosome-specific microsatellites (DYS19, DYS390, DYS391, and DYS392) were determined in 79 unrelated Australian Aboriginal males from the Northern Territory. These results are compared with those observed in worldwide populations at both the locus and the haplotype level. Common alleles in Aboriginals are DYS19*15 (49%), DYS19*14 (28%), DYS390*19 (39%), DYS390*24 (20%), DYS391*10 (72%), DYS392*11 (63%), and DYS392*13 (28%). No evidence of reduced gene diversity was observed for these Y-chromosome alleles. DYS390 exhibits the most complex arrangement, displaying a bimodal distribution composed of common alleles (*22-*26), and rare short alleles (*18-*20), with an intermediate allele (*21) being absent. DYS390*20, previously reported only in Papuans and Samoans, is observed for the first time in Aboriginals. Compared with a recent study of Aboriginals, our sample exhibits considerable diversity in the haplotypes associated with the rare DYS390*19 allele, indicating that this allele is of considerable antiquity, if it arose as a single deletion event. Combining all 4 Y-chromosome-linked microsatellites produced 41 unique haplotypes, which were linked using a median-joining network. This network shows that most (78%) of our Aboriginal haplotypes fall into 2 distinct clusters, which likely represent 2 separate lineages. Seven haplotypes are shared with haplotypes found in a recent study of Aboriginals, and 7 are shared with a Spanish population. The cluster of Aboriginal haplotypes associated with the short DYS390 alleles does not share any haplotypes with the Spanish, indicating that this cluster of haplotypes is unique to Australian Aboriginals. Limited data from 4 worldwide populations used to construct haplotypes based on 3 loci (DYS19, DYS390, DYS392) show that only 4 of these haplotypes are seen in Australian Aboriginals. Shared haplotypes may be the result of admixture and/or recurrent mutation at these loci. Expanding the haplotype analysis to include biallelic markers on the Y chromosome will resolve this issue.

 

 

Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis

Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis
Georgi Hudjashova, Toomas Kivisilda,b,c, Peter A. Underhilld, Phillip Endicotte, Juan J. Sanchezf, Alice A. Lind, Peidong Sheng, Peter Oefnerh, Colin Renfrewc,i, Richard Villemsa, and Peter Forsterj, 2007.

Published and new samples of Aboriginal Australians and Melanesians were analyzed for mtDNA (n = 172) and Y variation (n = 522), and the resulting profiles were compared with the branches known so far within the global mtDNA and the Y chromosome tree. (i) All Australian lineages are confirmed to fall within the mitochondrial founder branches M and N and the Y chromosomal founders C and F, which are associated with the exodus of modern humans from Africa ≈50–70,000 years ago. The analysis reveals no evidence for any archaic maternal or paternal lineages in Australians, despite some suggestively robust features in the Australian fossil record, thus weakening the argument for continuity with any earlier Homo erectus populations in Southeast Asia. (ii) The tree of complete mtDNA sequences shows that Aboriginal Australians are most closely related to the autochthonous populations of New Guinea/Melanesia, indicating that prehistoric Australia and New Guinea were occupied initially by one and the same Palaeolithic colonization event ≈50,000 years ago, in agreement with current archaeological evidence. (iii) The deep mtDNA and Y chromosomal branching patterns between Australia and most other populations around the Indian Ocean point to a considerable isolation after the initial arrival. (iv) We detect only minor secondary gene flow into Australia, and this could have taken place before the land bridge between Australia and New Guinea was submerged ≈8,000 years ago, thus calling into question that certain significant developments in later Australian prehistory (the emergence of a backed-blade lithic industry, and the linguistic dichotomy) were externally motivated.

Conclusions
The mitochondrial and Y chromosomal results presented here point toward one early founder group settling both Australia and NG soon after the exodus from Africa ≈50–70,000 years ago, at a time when the lowered sea levels joined the two islands into one land mass, necessitating sea travel only across narrow straits such as Wallace’s Line. The deep and specific phylogenetic lineages today within this former landmass indicate a small founding population size and subsequent isolation of Australia and, to a lesser extent, of NG, from the rest of the world. These founder events and the lack of contact could underlie the divergent morphological development seen in the Australian human fossil record and could also help explain the remarkably restricted range of Pleistocene Australian lithic industries and bone artifacts compared with contemporaneous cultures elsewhere in the world (55).

Estimated dates for mtDNA:

Region	Hg	N	ρ	SE	Age, yr
Aus/Mel	M	50	7,9	1,1	53,400 ± 7,500
Aus/Mel	Q’M29	27	6,6	1,4	44,300 ± 9,800
Aus/Mel	Q	22	4,7	1,0	32,000 ± 6,500
Mel	Q1	11	3,2	0,9	21,500 ± 6,100
Aus/Mel	Q2	4	4,5	1,4	30,400 ± 9,300
Mel	Q3	7	3,1	0,8	21,300 ± 5,500
Mel	M29	5	2,8	1,2	18,900 ± 8,300
Mel	M27	7	5,9	1,4	39,600 ± 9,800
Mel	M28	8	3,0	1,0	20,300 ± 6,500
Mel	M28a	6	1,7	0,7	11,300 ± 4,500
Aus	M42	6	6,0	1,3	40,600 ± 9,000
Aus/Mel	N	51	7,9	1,1	53,200 ± 7,300
Aus	N12	4	2,5	1,1	16,900 ± 7,200
Aus	S	12	3,8	0,8	25,400 ± 5,200
Aus	S1	4	3,3	1,1	22,000 ± 7,700
Aus	S2	4	2,3	0,8	15,200 ± 5,100
Aus/Mel	R	33	8,6	1,2	58,400 ± 8,400
Aus/Mel	P	31	7,6	0,9	51,700 ± 5,800
Mel	P1	6	4,5	1,0	30,400 ± 6,500
Mel	P2	7	1,9	0,6	12,600 ± 4,000
Aus/Mel	P3	5	5,8	1,2	39,200 ± 8,200
Aus/Mel	P4	8	9,8	1,9	65,900 ± 13,200
Aus	P4b	3	7,0	1,7	47,300 ± 11,700
Mel	P4a	5	3,8	1,1	25,700 ± 7,500

Y chromosomes in PNG and Aborigines.

Mitochondrial DNA variation in an aboriginal Australian population: evidence for genetic isolation and regional differentiation.

Mitochondrial DNA variation in an aboriginal Australian population: evidence for genetic isolation and regional  differentiation.

Huoponen K, Schurr TG, Chen Y, Wallace DC.
Laboratory of Genetics, Department of Biology, University of Turku, Turku, Finland.

The mitochondrial DNA (mt-DNA) variation of in the Walbiri tribe of the Northern Territories, Australia, was characterized by high resolution restriction fragment length polymorphism (HR-RFLP) analysis and control region sequencing. Surveying each mt-DNA for RFLPs with 14 different restriction enzymes detected 24 distinct haplotypes, whereas direct sequencing of the control region hypervariable segment I (HVS-I) of these mt-DNAs revealed 34 distinct sequences. Phylogenetic analysis of the RFLP haplotype and HVS-I sequence data depicted that the Walbiri have ten distinct haplotype groups (haplogroups), or mt-DNA lineages. The majority of the Walbiri RFLP haplotypes lacked polymorphisms common to Asian populations. In fact, most of the Walbiri haplogroups were unique to this population, although a few appeared to be sub-branches of larger clusters of mt-DNAs that included other Aboriginal Australian and/or Papua New Guinea haplotypes. The similarity of these haplotypes suggested that Aboriginal Australian and Papua New Guinea populations may have once shared an ancient ancestral population(s), and then rapidly diverged from each other once geographically separated. Overall, the mt-DNA data corroborate the genetic uniqueness of Aboriginal Australian populations.

More on Aborigines, showing a population movement from PNG into Australia.

Peopling of Sahul: mtDNA variation in aboriginal Australian and Papua New Guinean populations

Peopling of Sahul : mtDNA variation in aboriginal Australian and Papua New Guinean populations.
A J Redd and M Stoneking

We examined genetic affinities of Aboriginal Australian and New Guinean populations by using nucleotide variation in the two hypervariable segments of the mtDNA control region (CR). A total of 318 individuals from highland Papua New Guinea (PNG), coastal PNG, and Aboriginal Australian populations were typed with a panel of 29 sequence-specific oligonucleotide (SSO) probes. The SSO-probe panel included five new probes that were used to type an additional 1,037 individuals from several Asian populations. The SSO-type data guided the selection of 78 individuals from Australia and east Indonesia for CR sequencing. A gene tree of these CR sequences, combined with published sequences from worldwide populations, contains two previously identified highland PNG clusters that do not include any Aboriginal Australians; the highland PNG clusters have coalescent time estimates of approximately 80,000 and 122,000 years ago, suggesting ancient isolation and genetic drift. SSO-type data indicate that 84% of the sample of PNG highlander mtDNA belong to these two clusters. In contrast, the Aboriginal Australian sequences are intermingled throughout the tree and cluster with sequences from multiple populations. Phylogenetic and multidimensional-scaling analyses of CR sequences and SSO types split PNG highland and Aboriginal Australian populations and link Aboriginal Australian populations with populations from the subcontinent of India. These mtDNA results do not support a close relationship between Aboriginal Australian and PNG populations but instead suggest multiple migrations in the peopling of Sahul.

One of the other studies in this blog puts one of the M clades from SE Asia at about 87k old. The origin of Aborigines has been under debate for quite a while, with Southern India having some support as onepoint of immigration into Australia.along with PNG. This is going to be subject for a few posts. This stuff directly impacts on the OOA date, as genetic dating of Aborigines can set a lower limit to the migration date. 55k minimum for an entry into Northern Oz as a minimum now, so add about 15k for transit time and you are looking at about 70k absolute minimum (it’s probably a hell of a lot bit older). The changes in paleo-vegetation in Australia date it earlier, about 65k, so another 10k could be easily added to this.

A possible 60,000 year old human presence in Australia

The rock shelter at Nauwalbila

Radiocarbon analysis of the early archaeological site of Nauwalabila I, Arnhem Land, Australia: implications for sample suitability and stratigraphicintegrity
Auteur(s) / Author(s)
BIRD M. I. ; TURNEY C. S. M. ; FIFIELD L. K. ; JONES R. ; AYLIFFE L. K. ; PALMER A. ; CRESSWELL R. ; ROBERTSON S. ;
Résumé / Abstract
This study presents the results of an extensive radiocarbon dating program at the Nauwalabila I site in northern Australia. The results show that the radiocarbon chronology at Nauwalabila is reliable to ∼130 cm depth, but below this depth coarse charcoal has been variably altered during a period in the early Holocene when an ephemeral groundwater table reached close to the ground surface of the time. Below ∼150 cm none of the radiocarbon ages can be considered to indicate reliably the age of deposition of the sediments. Luminescence dates near the surface and at 110 cm are concordant with the radiocarbon chronology in the upper part of the sequence, and hence the aberrant radiocarbon results below ∼ 150 cm do not constitute a reason to doubt the accuracy of the luminescence chronology deeper in the stratigraphy. A conservative estimate of the age of the sequence, based on extrapolation of results from that portion of the sequence where the radiocarbon chronology is considered to be reliable, is consistent with the chronology proposed previously from luminescence dating. Both chronologies therefore suggest occupation of the site before 50,000 years. Based on sediment characteristics and the distribution of quartz, chert, quartzite and quartz crystal’ artefacts, there is no evidence that there has been significant vertical displacement of artefacts relative to the surrounding sand matrix. Both chemical alteration and physical translocation of charcoal contributed to the aberrant ages at depth in the deposit. The results point to the need for careful assessment of the suitability of charcoal for radiocarbon dating prior to analysis and to the dangers of relying on a small number of radiocarbon dates in the development robust site chronologies. Strategies for screening samples for suitability include (i) microscopic examination, (ii) not analysing samples unless they survive the full ABOX pretreatment, (iii) not analysing samples unless the material is significantly larger than the sediment matrix, (iv) using CHN analysis on both untreated and pretreated material to check for organic contamination and (v) using stepped combustion to check for concordancy in the ages of carbon released at successively higher temperatures.

A very old, but not impossibly old, date for Aborigines in Northern Australia. 65,000 isn’t an impossibility. I’ve had a look around and the thermoluminesence dates from the site seem to agree with the 50,000 date, as do dates from Malakunanja II

The case of Roberts et al. has been recently been significantly strengthened by their announcement of a similar age for the basal deposits of a second Arnhem Land site, Nauwalabila I, 65-70 km south of Malakunanja II. This site contains ‘securely stratified’ artefacts in a rubble base below the sand deposits dated by the related but different luminescence technique, optically-stimulated luminescence (OSL) (Jones 1993; 114; Roberts et al. 1993; Roberts et al. in press). At Nauwalabila I a sequence of five OSL dates are also in stratigraphic order The three oldest samples are 30,000+2400 years (OxODK166) from 1.70-1.75 m depth below surface; 53,400+5400 years (OxODK168) from 2.28-2.40 m; and 60,300+6,700 years (OxODK169) from 2.85-3.01 m. This latter date is below both the rubble layer and the lowest artefacts, while the date of 53,400+5400 years dates the sands immediately above the rubble layer.

 Implications

The central issue is whether Malakunanja II and Nauwalabila I are really >15,000 years older than any other known Australian site as these dates imply. Luminescence dates measure calendrical years and for that part of the radiocarbon range for which we can calibrate radiocarbon determinations against other dating techniques, uncalibrated radiocarbon determinations mainly underestimate calendrical years. Stuiver et al. (1991: 10) suggest this underestimation is c. 2000 at 14,000 years ago. Mazaud et al. (1991) propose a maximum underestimation of 3000 years between 18,000 years ago and 40,000 years ago and a negligible difference between 45,000 years ago and 50,000 years ago. Bard et al. (1993) indicate that a determination of 18,000 radiocarbon years represents almost 22,000 calendar years. Stuiver & Reimer (1993) use this last date as the oldest in their most recent calibration program. In western NSW, Bell (1991: 48) compared four paired radiocarbon determinations and thermoluminescence dates for separate hearths each c. 30,000 years old, where the TL dates were between 3500 and 5100 years older than radiocarbon determinations. However, substantial comparative sequences of radiocarbon determinations and dates produced by alternative radiometric techniques for the crucial period between 20,000 and 40,000 radiocarbon years are not yet available from anywhere in the world.

From this discussion of the dating of Australian sites. It’s entirely possible that humans were in Oz at this time, as there’s some evidence of contemporary occupation in Asia (Luijiang, at 68,000 years old). So a 60,000 year old entry date to Australia is completely possible.

When did humans first arrive in greater Australia and why is it important to know?
James F. O’Connell, Jim Allen
 
James O’Connell is Professor of Anthropology at the University of Utah. He has conducted ethnographic and archaeological fieldwork in central Australia, western North America and East Africa, and has published extensively on modern hunter-gatherer ecology, ethnoarchaeology, and Greater Australian and North American prehistory. Jim Allen is currently an Australian Research Council Senior Research Fellow in the Archaeology Department, La Trobe University, Melbourne. Prior to this he was the Foundation Professor of the same department. He has conducted extensive archaeological fieldwork in various parts of Australia and Tasmania and in Papua New Guinea since the mid-1960s. Since 1984 he has concentrated on the Pleistocene archaeology of those countries and published widely on that research.

Abstract
Until recently, archeologists have generally agreed that modern humans arrived on Australia and its continental islands, New Guinea and Tasmania (collectively, Greater Australia), about 35,000 to 40,000 years ago,1 a time range that is consistent with evidence of their first appearance elsewhere in the Old World well outside Africa.2,3 Over the past decade, however, this consensus has been eroded, first by dates of 50,000 to 60,000 years from two sites in Arnhem Land and then, dramatically, by dates of 116,000 to 176,000 years from a third site on the eastern margin of the nearby Kimberley region. If accurate, these dates require significant changes in current ideas, not just about the initial colonization of Australia, but about the entire chronology of human evolution in the late Middle and early Upper Pleistocene. Either fully modern humans were present well outside Africa at a surprisingly early date or the behavioral capabilities long thought to be uniquely theirs were also associated, at least to some degree, with other hominids. Deciding whether these dates are accurate and associated with definite evidence of human activity thus becomes critically important. We think there are good reasons to be skeptical, not only on the basis of the dates and their alleged associations, but because of their mismatch with established sequences, both in Greater Australia and elsewhere. Until these issues are resolved, adjusting the broader global picture to accommodate these early dates is premature. © 1998 Wiley-Liss, Inc.

However, I’m suspicious of a date over 100,000 years. I think it’s rather more likely there was another hominid group (Erectus) in that locale, and Mungo man agrees with me.

Humans caused mega fauna extinctions in Oz, not climate.

Extinction ‘by man not climate’

The extinction of many ancient species may be due to humans rather than climate change, experts say.

Large prehistoric animals in Tasmania may have been wiped out by human hunting and not temperature changes, a team of international scientists argue.

This pattern may have been repeated around the globe on islands such as Great Britain, the scientists say.

The findings were published in the American scientific journal – Proceedings of the National Academy.

For many years, scientists have been arguing about the causes of widespread extinctions of vast numbers of species at the end of the last Ice Age.

What has caused the most debate has been the fate of megafauna – large bodied creatures in Australia that included three-metre tall giant kangaroos and marsupial lions.

It is sad to know that our ancestors played such a major role in the extinction of these species – and sadder still when we consider that this trend continues today Professor Chris Turney, University of Exeter

Humans arrived in Tasmania about 43,000 years ago, when the island became temporarily connected by a land bridge to mainland Australia.  It had been thought that many megafauna were already extinct by this stage.  But using the latest radiocarbon and luminescence dating techniques, the British and Australian scientists say they were able to determine the age of the fossilised remains of the megafauna more accurately than ever before.

They discovered that some of the giant animals survived for 2,000 years after humans arrived, and at a time when the climate was not changing dramatically.  The researchers concluded that these species were driven to extinction by hunting.

Human blame?

Professor Chris Turney, from the University of Exeter, the lead author on the research paper, said that 150 years after the publication of Charles Darwin’s seminal work The Origin of Species, the argument for climate change being the cause of this mass extinction had been seriously undermined.

“It is sad to know that our ancestors played such a major role in the extinction of these species – and sadder still when we consider that this trend continues today,” he said.

Given Tasmania’s history as an island, the research findings should help to disentangle the role of humans and climate change in other island environments, such as Britain, the scientists said.

Previous research had found that on mainland Australia some 90% of megafauna disappeared about 46,000 years ago – soon after humans first settled on the continent.
Story from BBC NEWS:

Does this surprise anyone? Nope, humans are very hard on their prey species.