David Reich on who we are and how we got here

Over the last few weeks I have been binge watching YouTube videos about prehistory. I haven't been taking notes, simply immersing myself  in the latest content with a special focus on the latest results from DNA analysis. I suppose this approach lacks rigour, being more akin to the last minute approach I used to follow to get through exams, but I find that it works for me in providing structure and generating thoughts and linkages. 

As I listened, I thought how much our knowledge had changed and just how quickly.

This is a video of a talk given by Professor David Reich last year at Harvard: "Who we are and how we got here - Ancient DNA and the new science of the human past". This the second presentation I have seen on the same topic by Professor Reich, this is the link to the first. Both presentations follow  the release of his 2018 book of the same title.

The book has attracted some criticism not so much on the science but on some of the wording used. I haven't read the book, it seems to have got caught up in current preoccupations about language, but the presentation strikes me as scientifically rigorous and indeed quite fascinating.  It's quite a long video, over an hour, but will give you an insight into the way that scientific research is challenging our deeply held perceptions about the human past. 

New questions on the origin and spread of Australia's Aboriginal languages

Proposed Australian language tree

A University of Newcastle (UON) news item published on 21 March 2018, Indigenous language link reveals common ancestor, reported on new research on the history and structure of Australia's Aboriginal languages. As I have done before, I provide the information first while comments follow at the end.

The University of Newcastle piece reads:

"New research has found a ground-breaking link between Australian Indigenous languages, demonstrating for the first time that all Indigenous languages descend from one common ancestor. 

The unprecedented finding sheds new light on the origins of Australian language and has significant implications for the cultural history of Australia.

The result of a collaboration between the University of Newcastle (UON) and Western Sydney University (WSU), the finding is the first time the theory that all Australian languages derive from one language, Proto-Australian, has been proven. 

UON Chief Investigator and historical linguist, Associate Professor Mark Harvey, said the finding was an exciting culmination of a three-year project, which he hoped would enhance the understanding of Australian and human history. 

“Until now, it was speculated that Australia was significantly more linguistically diverse than somewhere like Europe, because it had not been proven that all Australian languages actually stemmed from the same lineage. 

“This is the first demonstration that all Australian languages are part of the same language family. This language family spread across all of Australia, presumably from a small area in Northern Australia. This spread is likely to have been carried out by at least some population movement whose material and genetic traces have remained somewhat elusive. 

“However, with further interdisciplinary research, this new linguistic evidence is likely to give us a more precise reconstruction of Australian prehistory from what is currently known,” Associate Professor Harvey said. 

The project used the standard method in historical linguistics to establish whether similarity between languages was due to inheritance from a common ancestor, as opposed to transfer from one language to another through human contact or chance. 

WSU Chief Investigator, Associate Professor Robert Mailhammer, said the findings revealed recurrent similarities between languages that were not in contact. 

“We discovered that the sounds of words we compared showed recurrent systematic differences and similarities across a set of languages that are spread out in a geographically discontinuous way, which makes it very unlikely that they are the result of chance or language contact,” Associate Professor Mailhammer said. 

While a multitude of Australian Aboriginal and Torres Strait Islander languages were spoken at the time of European settlement, the findings also imply that Indigenous Australian languages only spread after the end of the last ice age, some 10-12,000 years ago. 

“These findings show that Indigenous Australian languages were not the likely languages spoken by the first inhabitants of Australia, raising more questions around how the languages spread and how the linguistic findings connect to the genetic findings,” Associate Professor Mailhammer added. 

Both researchers recognise that work in this area will continue, with plans to publish a book on Proto-Australian and collaborate with other disciplines to inform what is known about the prehistory of Australia. 

Funded under an Australian Research Centre (ARC) 2014 Discovery Project, the key research was published in the leading journal of historical linguistics, Diachronica. 

Researching in the field of Indigenous language, Dr Raymond Kelly from the University of Newcastle’s PURAI Global Indigenous and Diaspora Research Studies Centre said the findings would come as a welcome relief to many first nation people in the state of New South Wales (NSW) working at the coal face of language reconstruction, revival and renewal programs. 

“During the course of research for my own PhD, I also developed a similar conviction that Aboriginal languages in NSW are formed or drawn from a single source and expand beyond the state and territorial boundaries that we know exist today. These findings provide a healthy opportunity to re-evaluate the concept of connection and relationship for community,” Dr Kelly said."

The abstract of the :Diachronica article, the full article is behind a paywall,  reads:

"Evaluation of hypotheses on genetic relationships depends on two factors: database size and criteria on correspondence quality. For hypotheses on remote relationships, databases are often small. Therefore, detailed consideration of criteria on correspondence quality is important. Hypotheses on remote relationships commonly involve greater geographical and temporal ranges. Consequently, we propose that there are two factors which are likely to play a greater role in comparing hypotheses of chance, contact and inheritance for remote relationships: (i) spatial distribution of corresponding forms; and (ii) language specific unpredictability in related paradigms. Concentrated spatial distributions disfavour hypotheses of chance, and discontinuous distributions disfavour contact hypotheses, whereas hypotheses of inheritance may accommodate both. Higher levels of language-specific unpredictability favour remote over recent transmission. We consider a remote relationship hypothesis, the Proto-Australian hypothesis. We take noun class prefixation as a test dataset for evaluating this hypothesis against these two criteria, and we show that inheritance is favoured over chance and contact". 

Mark Harvey and Robert Mailhammer, Reconstructing remote relationships, Diachronica, Volume 34, Issue 4, 2017, pp 470 –515, Published online 09 February 2018

Comment

In The origins of Pama-Nyungan - a note on the implications for the history of New England's Aboriginal peoples (13 March 2018) I reported on new research by Professor Claire Bowern and her colleagues that concluded that all Pama-Nyungan languages, the dominant language family across Australia, emerged just under 6,000 years ago around what is now the Queensland town of Burketown and then spread across Australia as people moved in response to changing climate. This research appears consistent with those conclusions but goes further, suggesting that all Aboriginal languages were related to some common proto-language but only spread after the end of the last ice age, some 10-12,000 years ago.

My 13 March comment focused on the difficulty I was having in meshing the conclusions of  Professor Claire Bowern and her colleagues with my evolving conclusions on New England Aboriginal history. A particular difficulty was the pattern of language diffusion and replacement given my evolving thoughts on Aboriginal retreat and resettlement during the Late Glacial Maximum (LGM) and following Holocene period. To restate my views:

• We have a range of dates from the Hunter Valley, Liverpool Plains and at Wallen Wallen in SE Queensland suggesting occupation during the late Pleistocene (17,000 to 22,000 years ago)
• The LGM (Late Glacial Maximum) forced populations to shift to survive. Parts of the North Coast were not very hospitable, so I postulated a retreat north and south.
• As the new coastal environment began to form, people returned. Inland, the population spread from refuge areas along the slopes and plains. The Tablelands constituted an initial barrier.As the climate eased further and the environment changed the Tablelands were resettled primarily from the coast, but also onto the slopes from the West. I think that this pattern is reflected in later language differences.
• In terms of the patchy dates we have, we have earliest settlement in the Macleay around 9,000 years ago, a date of over 6,000 years ago for Seelands in the Clarence, around 5,500 years ago for Graman on the western slopes. My feeling was that by around 6,000 years ago, reoccupation of territory after the LGM was well underway.  
• from around 4000 years ago the number of dates begins to accelerate with accelerated population increase.

.In the UON piece, the second researcher Professor Mailhammer states “These findings show that Indigenous Australian languages were not the likely languages spoken by the first inhabitants of Australia, raising more questions around how the languages spread and how the linguistic findings connect to the genetic findings,”

Then, in a comment on the findings, UON's Dr Kelly state that  they would come as a welcome relief to many first nation people in the state of New South Wales working at the coal face of language reconstruction, revival and renewal programs. He goes on: :

“During the course of research for my own PhD, I also developed a similar conviction that Aboriginal languages in NSW are formed or drawn from a single source and expand beyond the state and territorial boundaries that we know exist today. These findings provide a healthy opportunity to re-evaluate the concept of connection and relationship for community,” 

There is something of a tension between these views. The problem is that the linguistic evidence appears to be suggesting that the Aborigines in NSW/New England who survived the LGM were supplanted by/ absorbed by later groups. So the first nations of NSW may not be the first nations at all, but peoples who came millennia later. I'm not sure that that conclusion will provide much comfort.

Professor Mailhammer suggests that the research raises more questions around the way the languages spread and how the linguistic findings connect to the genetic findings. I think that we should add archaeological findings to the list.

Last year, I reported (When and where did the Australian Aborigines and the Denisovans meet? 17 September 2017) on a 2106 Nature article by Anna-Sapfo Malaspinas, Michael C. Westaway et al
A genomic history of Aboriginal Australia. The abstract to that paper reads:

"The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama–Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25–40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10–32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama–Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51–72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert."

As the title of my post indicates, my main focus was on the nature of DNA evidence and the linkages with the Denisovans. However, the broad conclusions as summarised in the abstract are broadly consistent with the latest linguistic evidence, with the spread of Pama–Nyungan by absorption and contact rather than occupation and replacement.  However, problems remain.

Since the Nature article was published, we have the latest results from the Madjedbebe Rock Shelter (The lessons and questions from Madjedbebe) pushing back the date of human occupation of Sahul to 62,000+ years ago.As noted before, on the assumption that the Aboriginal peoples were the first occupants a tension arises between the dates suggested by DNA analysis and those from archaeology. Further, each new piece of analysis suggested a far more complex picture in terms of out-of-Africa and the spread and mixing with other hominid species.

At this point I do not quite know what to think. I am documenting for later analysis and synthesis.

Beringia and the settlement of North America - DNA results from Alaska

This post is a reference note. It's outside my primary focus, but is recorded for reference purposes in the ever evolving world of prehistoric man.

In a paper in Nature, Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans that was published on-line on 3 January 2018, the authors' report on DNA analysis of Alaskan remains::

Despite broad agreement that the Americas were initially populated via Beringia, the land bridge that connected far northeast Asia with northwestern North America during the Pleistocene epoch, when and how the peopling of the Americas occurred remains unresolved. Analyses of human remains from Late Pleistocene Alaska are important to resolving the timing and dispersal of these populations. The remains of two infants were recovered at Upward Sun River (USR), and have been dated to around 11.5 thousand years ago (ka). Here, by sequencing the USR1 genome to an average coverage of approximately 17 times, we show that USR1 is most closely related to Native Americans, but falls basal to all previously sequenced contemporary and ancient Native Americans. As such, USR1 represents a distinct Ancient Beringian population. Using demographic modelling, we infer that the Ancient Beringian population and ancestors of other Native Americans descended from a single founding population that initially split from East Asians around 36 ± 1.5 ka, with gene flow persisting until around 25 ± 1.1 ka. 

The story is well covered in this Guardian piece by Jennifer Raff (hat tip to John Hawks) and in this more detailed story by Dr. Ben A. Potter, Ancient Beringians.The following diagram from DR Potter's piece suggests the evolution of the human population in North America. Comments follow the diagram.

No doubt the diagram will continue to evolve as we learn more. For the moment, a few comments from an Australian perspective. .

Beringia is the name given to the land bridge that joined Asia and North America during the period of very low sea levels. This land lies north of the main glaciation during the Last Glacial Maximum. We keep coming back to the LGM don't we?!

According to Wikipedia, Beringia, like most of Siberia and all of North and Northeast China, was not glaciated because snowfall was very light.. It was a grassland steppe, including the land bridge, that stretched for hundreds of kilometres into the continents on either side. It became, in effect, a refuge area that allowed some people and animals to survive and to enter what would become North America. More and more, I think that we need to understand the possible pattern of refuge areas in Sahul (Australia) that might have facilitated human survival on this content during the LGM.

In looking at the diagram, I was struck by the short time horizons involved in the evolution of particular groups compared to the history of Aboriginal occupation of this continent.We know, I think, that the Papuans and Aborigines come from the same base, that the genetic differences between South West and North East are perhaps as great as those between Asian and European populations, that there were some specific genetic mutations that emerged in adapting to differing environments. We also know that there were considerable differences in physical appearance between differing Aboriginal groups over space. But I don't think that we understand the pattern here. Certainly I don't.

 I think that it would be interesting to find that out.

A note on the latest DNA results for Tianyaun Man.

Regular commenter JohnB pointed me to this piece by Ann Gibbons in Science that I had missed, Was this ancient person from China the offspring of modern humans and Neandertals?
(Oct. 12, 2017).

Tianyuan Cave (photo) is near modern Beijing. In 2007 researchers found human remains radio carbon dated to between 42,000 and 39,000 years ago. That is well after the first groups of Aboriginal people arrived in Australia. Now the results of new DNA analysis have been published in Current Biology. The formal summary of results follows. Further comments follow the summary.

Summary 

By at least 45,000 years before present, anatomically modern humans had spread across Eurasia, but it is not well known how diverse these early populations were and whether they contributed substantially to later people or represent early modern human expansions into Eurasia that left no surviving descendants today. Analyses of genome-wide data from several ancient individuals from Western Eurasia and Siberia have shown that some of these individuals have relationships to present-day Europeans while others did not contribute to present-day Eurasian populations. As contributions from Upper Paleolithic populations in Eastern Eurasia to present-day humans and their relationship to other early Eurasians is not clear, we generated genome-wide data from a 40,000-year-old individual from Tianyuan Cave, China, to study his relationship to ancient and present-day humans. We find that he is more related to present-day and ancient Asians than he is to Europeans, but he shares more alleles with a 35,000-year-old European individual than he shares with other ancient Europeans, indicating that the separation between early Europeans and early Asians was not a single population split. We also find that the Tianyuan individual shares more alleles with some Native American groups in South America than with Native Americans elsewhere, providing further support for population substructure in Asia and suggesting that this persisted from 40,000 years ago until the colonization of the Americas. Our study of the Tianyuan individual highlights the complex migration and subdivision of early human populations in Eurasia. 

Melinda A. Yang, Xing Gao, Christoph Theunert, Haowen Tong, Ayinuer Aximu-Petri, Birgit Nickel, Montgomery Slatkin, Matthias Meyer, Svante Pääbo, Janet Kelso, Qiaomei Fu, 40,000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia, Current Biology, Volume 27, Issue 20, p3202–3208.e9, 23 October 2017

Recognising my knowledge limitations, I drew the following main points from the latest results. My indebtedness to Anne will be clear if you look at her article. :

• The date ranges mean that Tianyaun Man. is probably at least 20,000 years younger than the first Aboriginal occupation of Sahul, the name given to the bigger Australian continent when sea levels were lower.
• The DNA results show elements of Neanderthal genes but no trace of the Denisovan genes to be found in Aboriginal DNA. On the basis (as seems to be the case) that the Denisovans were reasonably widely spread across Eurasia, this suggests to my mind that  Tianyaun Man came from a later migration wave,
• Tianyuan Man shares DNA with one ancient European—a 35,000-year-old modern human from Goyet Caves in Belgium. But he doesn’t share it with other ancient humans who lived at roughly the same time in Romania and Siberia—or with living Europeans.
•  Tianyuan Man is most closely related to living people in east Asia—including in China, Japan, and the Koreas—and in Southeast Asia, including Papua New Guinea and Australia.This suggests that the Tianyuan Man was not a direct ancestor, but rather a distant cousin, of a founding population in Asia that gave rise to present-day Asians. 
• Tianyuan Man was a distant relative of Native Americans living today in the Amazon of South America, such as the Karitiana and Surui peoples of Brazil and the Chane people of northern Argentina and southern Bolivia. But he is not an ancestor to ancient or living Native Americans in North America, which suggests there were two different source populations in Asia for Native Americans. 

Postscript 28 October: 2017

Current Anthropology has an interesting article by Professor Robin Dennell, "Human Colonization of Asia

in the Late Pleistocene: The History of an Invasive Species" (Current Anthropology Volume 58, Supplement 17, December 2017) The summary reads:

 Narratives of “Out of Africa 2”—the expansion of Homo sapiens across Asia—emphasize the pattern of human dispersal but not the underlying processes. In recent years, the main debates have been over the timing and frequency of dispersal. Here, I treat these issues as subordinate to biogeographic ones that affected the behavior of humans in Asia as an invasive species that colonized new environments and had negative impacts on indigenous hominins. I suggest that attention should focus on three issues: (i) geographic factors that molded human dispersal across Asia, (ii) behavioral changes that enabled humans to overcome previously insurmountable barriers, and (iii) demographic considerations of human dispersal and colonization of Asia, including interactions with indigenous competitors. Although a strong case can be made that humans dispersed across southern Asia before 60 ka, this should not detract from attention on the underlying processes of dispersal and colonization.

I found the article provided a useful summary framework. The geographic analysis in particular filled a gap in my knowledge The MIS in the paper, by the way, stands for Marine isotope stage. I wasn't really familiar with the term so looked it up. According to Wikipedia:

 Marine isotope stages (MIS), marine oxygen-isotope stages, or oxygen isotope stages (OIS), are alternating warm and cool periods in the Earth's paleoclimate, deduced from oxygen isotope data reflecting changes in temperature derived from data from deep sea core samples. Working backwards from the present, which is MIS 1 in the scale, stages with even numbers have high levels of oxygen-18 and represent cold glacial periods, while the odd-numbered stages are troughs in the oxygen-18 figures, representing warm interglacial intervals. 

A note on the Sunghir DNA results from an Australian perspective

ANCIENT NETWORKERS  DNA from four Stone Age people — including the two shown here as they looked when excavated, top, and at the time of death, bottom — suggests that hunter-gatherers have long formed groups with few close relatives. Aside from discouraging inbreeding, that social structure encouraged cooperative ties among groups and rapid cultural advances, scientists say. 

Interesting piece in Science News by Bruce Bower, Ancient humans avoided inbreeding by networking (5 October 2017) on the results of DNA analysis of four individuals from the Sunghir site in Russia, Sunghir is situated about two hundred kilometres east of Moscow, on the outskirts of Vladimir, near the Klyazma River.

The story is based on an article that appeared in Science. If you follow the link through you can access the original article, You will need to register, but that is free. The article's abstract reads:  

Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding. When these wider social networks evolved among HGs is unknown. Here, we investigate whether the contemporary HG strategy was already present in the Upper Paleolithic (UP), using complete genome sequences from Sunghir, a site dated to ~34 thousand years BP (kya) containing multiple anatomically modern human (AMH) individuals. We demonstrate that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that UP social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network.

Martin Sikora1, Andaine Seguin-Orlando, Vitor C. Sousa, Anders Albrechtsen, Thorfinn Korneliussen, Amy Ko, Simon Rasmussen, Isabelle Dupanloup, Philip R. Nigst, Marjolein D. Bosch, Gabriel Renaud, Morten E. Allentoft, Ashot Margaryan, Sergey V. Vasilyev, Elizaveta V. Veselovskaya, Svetlana B. Borutskaya, Thibaut Deviese, Dan Comeskey, Tom Higham, Andrea Manica, Robert Foley, David J. Meltzer, Rasmus Nielsen, Laurent Excoffier, Marta Mirazon Lahr, Ludovic Orlando, Eske Willerslev, "Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers", Science 05 Oct 2017. eaao1807, DOI: 10.1126/science.aao1807

Bruce's report focuses on what the results might show us about mating patterns among hunter gatherers (HG). I looked at the results from a slightly different perspective. First to summarise some key points as I understood them:

• The DNA of four individuals was analysed. The remains dated from around 34,000 years ago.
• The DNA of the three individuals buried together share both mitochondrial and Y-chromosome lineages  That is, they formed part of the same group. However, none of them were closely related (that is, third degree or closer). Third degree relationships includes first cousins, great grandparents and great grandchildren. 
• Modelling provided a refined estimate of the time since admixture with Nenaderthals at 770 generations (95% CI 755-786). Accounting for the uncertainty of both the admixture estimate and 14C ages, this corresponds to an admixture date between the ancestors of Sunghir and Neanderthals of between 53.6 and 58.1 kya (at 29 years/generation. However, the results from one individual suggested that there could have been a more recent admixture.

.The Aborigines arrived in Australia perhaps 60-65,000 years ago. That is before the estimated admixture date between the Sunghir and Neanderthals. They too carry Neanderthal genes, although they also carry Denisovan genes, suggesting a later mixing with Denisovan peoples. So the evidence continues to suggest that we are dealing with long and overlapping periods of interaction between different hominin species.

 I am not quite sure what conclusions to draw from the DNA results so far as breeding patterns within the Sunghir group are concerned. However, it would not be surprising if they had kinship arrangements designed to prevent in-breeding.. Aboriginal kinship arrangements have that effect while also fitting people into social structures. Those arrangements probably evolved with time. We cannot assume that those holding among Aboriginal people at the time of European occupation were the same as those holding 65,000 years before.

Too a degree, too, this type of arrangement depends upon population size. In-breeding is more common among smaller groups.    

New evidence of possible early (c220,000 years ago) Neanderthal Homo Sapiens interbreeding

Interesting story in Science by Ann Gibbons (Neandertals and modern humans started mating early  Jul. 4, 2017 , 11:00 AM). The piece begins:

For almost a century, Neandertals were considered the ancestors of modern humans. But in a new plot twist in the unfolding mystery of how Neandertals were related to modern humans, it now seems that members of our lineage were among the ancestors of Neandertals. Researchers sequenced ancient DNA from the mitochondria—tiny energy factories inside cells—from a Neandertal who lived about 100,000 years ago in southwest Germany. They found that this DNA, which is inherited only from the mother, resembled that of early modern humans. 

After comparing the mitochondrial DNA (mtDNA) with that of other archaic and modern humans, the researchers reached a startling conclusion: A female member of the lineage that gave rise to Homo sapiens in Africa mated with a Neandertal male more than 220,000 years ago—much earlier than other known encounters between the two groups. Her children spread her genetic legacy through the Neandertal lineage, and in time her African mtDNA completely replaced the ancestral Neandertal mtDNA.

Anne's article is based on a 4 July 2017 report in Nature Communications, Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals by Cosimo Posth, Christoph Wißing, Keiko Kitagawa, Luca Pagani, Laura van Holstein, Fernando Racimo, Kurt Wehrberger, Nicholas J. Conard, Claus Joachim Kind, Hervé Bocherens and Johannes Krause.

I suggest reading Anne's piece first and then the source article. This includes some very interesting material, including methodology and qualifications.  

New DNA results shed light on African migration patterns

Researchers in Malawi examine bone fragments whose DNA provided input into a significant study of African migration patterns. Photo New York Times. 

There is an interesting article in Cell, Reconstructing Prehistoric African Population Structure. The summary reads:

"We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers 8,100–2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers 1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a 3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a 1,200-year old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations"

The New York Times (21 September 2017) carried a useful story by Carl Zimmer, Clues to Africa’s Mysterious Past Found in Ancient Skeletons, which provides some useful supplementary material.

When and where did the Australian Aborigines and the Denisovans meet?

Back in September 2016, a paper in Nature rather dryly titled “A genomic history of Aboriginal Australia.” reported on the results of a comparative genomic study of Australian Aboriginals and Papuans.  Genomics applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes (the complete set of DNA within a single cell of an organism).

The results were quite striking,  so striking that they attracted global media attention. “Indigenous Australians most ancient civilisation on Earth, extensive DNA study confirms” read one UK headline.

Some care must in fact be exercised in interpreting the results, for the statistical techniques used give you date ranges, a central date and then a confidence interval, a range within which the actual date might fall. These can be large, 20,000+ years, something that can be quite frustrating when you are trying to match dates to understand a pattern. That said, the results were remarkable.

They suggest that Aboriginal Australians and Papuans are more closely related to each other than to anyone else on earth. They also suggest that the Aboriginal-Papuan population diverged from Eurasians following a single out-of-Africa migration 51,000 to 72,000 years ago. See what I mean about date ranges.

In their long travels, that small band or bands of Australo-Papuans appear to have mixed with two related archaic human species. The first were the Neanderthal, something shared with Eurasians. Between one and six per cent of modern Eurasian’s genes derive from the Neanderthal, a percentage higher in some individuals depending on their exact family lineage.

Much later, the travelers mixed with the Denisovans, with about four per cent of the Aboriginal genome traceable to that admixture. We did not discover the existence of the Denisovans, a group named after Denisova Cave in the Altai Mountains in Siberia, until excavations that began in 2008. Subsequent work suggests that the cave had also been inhabited by Neanderthals and modern humans over 125,000 years of intermittent occupation.

Speaking of the meeting with the Denisovans, study leader Professor Eske Willerslev is reported as saying: "We don't know who these people were, but they were a distant relative of Denisovans, and the Papuan/Australian ancestors probably encountered them close to Sahul."

Now comes this interesting piece in The Siberia Times (Olga Gertcyk, Extinct Denisovans from Siberia made stunning jewellery - but did they also discover Australia?, 14 September 2017). The UK Daily Mail carried a rather more sensationalised verson.(Will Stewart and Tim Collins, Were ancient Denisovans the first to discover Australia? Scientist believes traces of their DNA found in Aboriginal people suggest they beat homo-sapiens to the continent, 15 September 2017). Hat tip to regular commenter JohnB for pointing me to the Siberia Times story.

While the stories have a beat-up tone, the recent discoveries do raise the question of just when and where the ancestors of the modern Australians did meet the Denosovans. If, as the present consensus seems to suggest, they met them near Sahul, the extended continent that became Australia as the sea levels fell, the Denosovans must have been wide spread.    

In an earlier 2013 paper in Science,  Alan Cooper and Chris Stringer posed the question Did the Denisovans Cross Wallace's Line?. The summary of the paper reads:

The recent discovery of Denisovans (1, 2) and genetic evidence of their hybridization with modern human populations now found in Island Southeast Asia, Australia, and the Pacific (3) are intriguing and unexpected. The reference specimen for the Denisovan genome (4), a distal phalanx from a young girl, was recovered from the geographically distant Denisova Cave in the Russian Altai mountains. Three Denisovan mitochondrial genomes have been generated from material in the cave, dated by poorly associated fauna (5) at more than 50,000 years old. The diversity of these genomes indicates that the Denisovan population had a larger long-term average size than that of the Neandertals (6, 7), suggesting that the Denisovans were formerly widespread across mainland East Asia. However, interbreeding with modern humans only appears to have occurred in remote Island Southeast Asia, requiring marine crossings and raising questions about the distribution and fossil record of Denisovans in Island Southeast Asia.

So far we still have only one known Denisovan site, the original at one at Altai. Based on the material remains there, they have appear to have been an advanced hunter-gatherer group. It seems unlikely that the Altai Denisovans "discovered" Australia. It is more likely that there were a number of Denisovan migration paths with possible northern and southern migration routes. But we just don't know. As Professor Richard 'Bert' Roberts, Director of the Centre for Archaeological Science at the University of Wollongong suggested in the Siberia Times piece, We need deep study of ancient migration routes to understand how the Denisovan DNA exists to this day in the native people of Australia. More broadly, we just need more information about them!

We also need, I think, to consider the latest results from the Madjedbebe rockshelter in the Northern Territory,  something I wrote about in The lessons and questions from Madjedbebe, which showed occupancy as well as a sophisticated tool kit from around 65,000 years ago. Recognising my own lack of professional expertise, there is an apparent tension now between some of the date ranges generated by genomic analysis and archaeological analysis.

I have no idea how these conundrums will be resolved, nor what picture we will find at the end of the process. I suspect that it will be as different from current knowledge as current knowledge is from the world view holding even thirty years ago. .      .  .

New DNA results challenge Indian pre-conceptions

The thorniest, most fought-over question in Indian history is slowly but surely getting answered: did Indo-European language speakers, who called themselves Aryans, stream into India sometime around 2,000 BC – 1,500 BC when the Indus Valley civilisation came to an end, bringing with them Sanskrit and a distinctive set of cultural practices? Genetic research based on an avalanche of new DNA evidence is making scientists around the world converge on an unambiguous answer: yes, they did. Tony Joseph, Hindu Times

Interesting piece in the Hindu Times again illustrating the way that DNA analysis is re-shaping our view of the world.

I have absolutely no expertise in the question of Indo-Aryan migration, nor am I familiar enough with Indian politics to know how how questions of the direction of migration play out domestically. I had always assumed that part of the ethnic difference between the north and south of the country lay in the different migration patterns, with the north open to waves of migration from elsewhere in Eurasia. The latest data would appear to support that view.

Until recently, only data on mtDNA (or matrilineal DNA, transmitted only from mother to daughter) were available and that seemed to suggest there was little external infusion into the Indian gene pool over the last 12,500 years or so. New Y-DNA data has turned that conclusion upside down, with strong evidence of external infusion of genes into the Indian male lineage during the period in question.

Tony Joseph suggests that the reason for the difference in mtDNA and Y-DNA data is obvious in hindsight: there was strong sex bias in Bronze Age migrations. In other words, those who migrated were predominantly male and, therefore, those gene flows do not really show up in the mtDNA data. On the other hand, they do show up in the Y-DNA data:

In fact, about 17.5% of Indian male lineage has been found to belong to haplogroup R1a (haplogroups identify a single line of descent), which is today spread across Central Asia, Europe and South Asia. The Pontic-Caspian Steppe is seen as the region from where R1a spread both west and east, splitting into different sub-branches along the way. Genetic analysis suggests that the Indian versions of R1A split of between 2,000 and 1,500 BC.

Postscript 21 June 2017

Ramana, my Indian blogger friend, pointed me to this rebuttal of the Joseph piece, Genetics Might Be Settling The Aryan Migration Debate, But Not How Left-Liberals Believe. My first reaction was that  Anil Kumar Suri appeared to be wielding a rather hatchet in what was clearly an ideological dispute that I did not properly understand.

I need to go back to to the Joseph piece and look at the detail of DNA material provided to try to determine what is factual as compared to ideological positioning on both sides. Meantime, some one may be able to explain just what the apparent ideological and political dispute really is..

On a different topic, regular commenter Johnb has pointed me to yet another DNA study, First complete genome data extracted from ancient Egyptian mummies. For later reference.

Postscript 30 June 2017

Ramana  pointed me to another article on the same topic, Here We Go Again: Why They Are Wrong About The Aryan Migration Debate This Time. He also commented: "As you are probably aware, I am a student of Vedanta and as such have studied some of our old texts. The word Aryan is used in Sanskrit to describe people of noble character and not a race or tribe or caste.".

There is a whole Indian back story  in the controversy that I am simply not properly aware of.