New Paper: An early peopling of Australia

Update for my Oct. 5, 2025 post, Lake Mungo man revisited: maybe the Aboriginal people were not the first to reach Australia. A study published on Nov. 28, 2025 has uncovered interesting information on the date that humans reached Australia, and their interactions with archaic humans in Southeast Asia.

The paper is Francesca Gandini et al., (2025) Genomic evidence supports the “long chronology” for the peopling of Sahul. Sci. Adv. 11, eady9493 (2025).DOI:10.1126/sciadv.ady9493

The paper explores when modern numans settled in Sahul, a landmass that spanned Australia, Tasmania, Papua New Guinea, and smaller islands on the now submerged continental shelf (under the sea since ice melted at the end of the last Ice Age). It aimed at validating the "long chronology" with an arrival around 60 to 65,000 years ago, against the "short chronology" which proposed an arrival 47 to 51,000 years ago.

The authors analyzed DNA and used a genetic clock to time the arrival, which they place around 60,000 years ago. They also found that people arrived using two entry routes.

I have expressed my doubts about the accuracy of genetic clocks in several posts (See the useless genetic clocks), but let's look into this paper and its findings.

Near Oceania was peopled early

The authors found that " We also draw Oceania together with Sahul, finding that Near Oceania was first settled at around the same time as Sahul, followed by intense ongoing exchange." This is interesting as we find that people who used watercraft were already living in Near Oceania (New Guinea, Bismarck Archipelago, and the main Solomon Islands), 60,000 years ago. And would have had plenty of time to cross the Pacific Ocean and reach America!

The molecular clock

The time is set by the exit from Africa which this paper sets by defining the age of mtDNA haplogroup L3 "the African ancestor of all non-African mitogenomes" at 73 to 89,000 years old. This date "robustly precludes any contribution to the modern non-African mitochondrial pool from earlier dispersals before 90 ka, as proposed by some researchers." Which is a limitation. The ages could actually be older, humans left Africa in different waves over the past 200 ky.

The date for Y-chromosome haplogroups is similar; the paper states that "non-African lineages diverg[ed] from ~71 (63 to 81) ka."

The paper used ADMIXTURE tools to analyze genome-wide data (see my comment on this type of tool).

The authors admit the bias and the need to "define" initial parameters by hand: "The Bayesian approach has some problems that have received little attention. In practice, it gives extremely variable outputs, such that any given rate is hard to replicate. The outcome depends on precisely which samples are included in the calibration; even with similar sets of samples, the estimated rate can be very different, and biases appear toward the ages of the predominant samples used in the calibration. Moreover, in the cases of ages in the range 40 to 80 ka, there are few calibration points... In addition to age bias, there is also a profound geographical and phylogenetic bias: Only 2 out of 12 samples used were non-European, and only Tianyuan belongs to haplogroup N. Moreover, one sample (the Iceman) was inadvertently uncalibrated, reducing its age by >12%. Although subsequent calibration attempts have been made with more samples, these have exacerbated the biases."

In the "Materials and Methods" section the phylogenetic analyses and molecular clock dating assumptions and adjustments are explained, like: "We converted mutational distances (both ML and ρ) into years using the substitution rate of about one mutation every 3624 years for the entire mitogenome and correcting for purifying selection using the calculator provided by Soares et al."

The paper suggests a "Northern Route": from Borneo to Sulawesi (Celebes), Banda Archipelago and into Western Papua, and reaching Australia via the Cape York Peninsula in Queensland. The "Southern Route" went from Java, to Sumatra, Sunda, Flores, and Timor, reaching Australia through Arnhem Land and northern Western Australia.

It also mentions archaic admixtures: "The connection of Sahul populations to Aboriginal Philippine groups is reinforced by the presence of distinctively high levels of Denisovan-related archaic-related introgression in both, possibly relating to interbreeding with Homo luzonensis, in the Philippines, and Homo floresiensis, in Wallacea, or even within Sahul itself."

I always like to focus on the oddities, the things that authors point out as "remarkable"or, in this case, "notably", it is the following:

"We also included in this analysis our Iron Age sample from Sulawesi, which carries the Papuan mitochondrial Q1l lineage, alongside 17 further genomes from ancient Wallacea, including a pre-Neolithic sample from Sulawesi (41, 42) (fig. S8). Notably, despite its clear Papuan mtDNA ancestry, the Iron Age sample was the only archaeological sample from Wallacea to carry no discernible Oceanian autosomal ancestry. This result is confirmed by PCA (fig. S9). This indicates both that ancestry from New Guinea, while ancient (41), was not ubiquitous in prehistoric Wallacea, but possibly (at least, since the spread of the Neolithic) restricted to coastal regions, and that sufficient time had elapsed for the ancestry represented by the maternal lineage to have been “washed out” of the autosomal genome in this individual."

This means that the original, Papuan mtDNA was found in an Iron Age (1700 BP) person in Sulawesi, yet it lacked the autosomal (all the other chromosomes) that would mark it as an Oceanian, it carried the input of other non-Oceanian people that diluted its ancestral autosomal DNA. This seems quite obvious since the ancestors of modern Polynesians made their way across this region in recent times, on their way to the Pacific Islands.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2025 by Austin Whittall © 

Australia to America... via the Antarctic (Paul Rivet's Theory)

Paul Rivet (1876-1958) was a French anthropologist and ethnologist, founder of the Musée de l'Homme, who is well known for his theories about the peopling of America from Australia following a coastal Antarctic route, and Melanesia using a Trans-Pacific route. Both waves complemented the original Asian migration through Beringia.

Paul Rivet (1876-1958). Source

The idea of an "Oceanian" origin for the American Natives was first suggested by Benjamin Hornor Coates [4] in 1834, he mentioned the Malayan "race", a name used at that time that encompassed the people of the South Seas that we now call Polynesians. Below is a short quote from his work:

"The Malay. Scattered throughout a space of about one hundred and forty degrees of longi- tude, or about two-fifths of the circumference of the globe, from Madagascar to Easter Island, in the vicinity of America... this singular people have justly received the epithet Oceanic. Their colonies have been the most widely disseminated upon the face of the whole earth... We see nothing, therefore, in the features of the Indians which forbids their descent from Malay colonists."

John D. Baldwin (1872) analyzed who could have peopled America, contemplating the Phoenicians, the Lost Tribes of Israel, Atlantis, and of course, the Malayans (Polynesians): "Another hypothesis, much less improbable, though not satisfactory, is that civilization was brought to America in ancient times by the Malays." (online p.167).

Aleš Hrdlička (1869–1943) who championed the Beringian route, strongly criticized any other alternative migratory route. See his analysis and rebuttal of the Melanesian-Australian origin here in his article "Melanesians and Australians and the Peopling of America" (1935).

Others, however, in opposition to a single source for Amerindians, other scholars proposed a multiethnic origin (not only Siberians or Asians, but other "races"). They agreed that linguistic, cultural, and skeletal resemblances showed a link between Polynesians, Melanesians, Australians, and Amerindians.

This position was supported by De Quatrefages (source), who compared the Lagoa Santa skulls of Brazil with those of Melanesians, Ten Kate (source) who found similar coincidences with Southern Californian Pericue natives' skulls. There was also Richard N. Wegener, who believed that some Bolivian natives like the Siriono showed Melanesian traits. We also have Paul Rivet and Mendes Correia who proposed Melanesian and Australian origins for the Amerindians.

Antarctic Route

Portuguese anthropologist Antonio Mendes Correia (1888-1960) embraced the theory put forward by Wegener in 1912, that continents drifted apart after the breakup of an initial supercontinent, Pangea. Continental drift was rejected as no mechanism could be found to cause such colossal movements. It would take nearly 60 years for the plate tectonics theory to appear and explain the drift. Until then it was very difficult to explain (see this article as an example) how the Southern Beeches (Nothofagus) and the Monkey Puzzle species (Araucaria), as well as some marsupials and the Galaxiidae fish lived in Patagonia and in Australia, Papua New Guinea, and Melanesian Islands.

In 1926, Correa wrota about an Antarctic link between Australia and America which humans could have crossed: "There remained the possibility of human passage, which would more easily traverse small straits and channels and take advantage of isthmuses, peninsulas, and islands that marked, as some still do today, the previous continuity of these continental masses. "[1]

That same year (1926), Paul Rivet [2] put forward the same idea, adding that the larger ice cap covering Antarctica during the last Ice Age would have provided additional support for the trip across the South Pacific. Rivet stated that:

"Certainly, the definitive adoption of my hypothesis requires prior objective documentation of human use of this route. However, it is to be hoped that such documentation will be obtained in the future, many of which are perhaps buried beneath the mysterious ice of the Antarctic lands.
...
I do not dispute the conjectural nature of several of my considerations. One would not dare to present as already established the transit route whose hypothesis I have put forward. But I do not hesitate to consider it legitimate and very likely."

Polynesians or Melanesians in America?

We know that the human beings reached the region of Melanesia (New Guinea, Fiji, Vanuatu, Solomon Islands, and New Caledonia) and Australia and Tasmania some 50,000 years ago. These were the dark-skinned Australian aboriginals and Papuans (Australasians). Much later, c.3,500 years ago, Austronesian farmer groups reached the area. These would later expand eastwards to discover and populate Polynesia. So there is a long period of time for the ancient Melanesians to have moved across the Pacific into America.

There are some (see this blog) who believe that Melanesians may have reached New Zealand and even the Chatham Islands (becoming the Moriori people there) long before the arrival of the Maori people c. 1250-1300 AD. However this theory, acceptable in the early 1900s, is now disputed, and considered pseudoscience and possibly racist as it denies the Maori their "first people" status.

I have posted about Polynesians in America on several ocasions, to which I will add another bibliographic reference: Nordenskjöld, who wrote in 1931 about the "Oceanian" artifacts in South America including a Table with 49 coincidences between Amerindian and Oceanian cultures [3]:

" As is well known, we find in South America quite a number of culture elements of which parallels are found in Oceania. These we may call "Oceaman", although this certainly does not imply any proof that they have been wmported into America from Oceania. These "Oceanian" culture elements may derive their origin from the crew of some weather-driven vessel, because the possibility of such having landed upon the coasts of America is not entirely to be disregarded, as Friederici has fairly convincingly shown. Some of them may also originate directly from actual immigrations of exceedingly remote date into South America from across the ocean.
...
In Table II hereto appended are enumerated a number of such elements as might possibly be “Oceanian”’ because of their occurring both in Oceania and America."

Is the Antarctic Route Feasible?

The Antarctic route seems to be dangerous and almost impossible: glaciers, ice sheets, frigid rough ocean, no food or wood to light fires. Was the Antarctic route viable?

Back in 2012 I post on this subject: Circling Antarctica and getting into America. Today I will revisit it with more information.

Convey and Stevens (2007) suggest that there is evidence to "support the existence of ice-free biological refuges at least from 1.8 million to 10,000 years ago. Evidence preserved from volcanic eruptions below the ice now also allows for the possibility of low-altitude ice-free land at glacial maxima." There has been Grass in the Antarctic for at least 120 ky (or even 300 ky) according to genetic data, and even bugs like springtails and chironomids have survived for millions of years in its icy landscape.

In 1985, the remains of a Yamana woman aged 21, were found on Livingston Island, 62°3'S 60°30'W, 809 km (503 mi.) south of Cape Horn, it forms part of the South Shetland islands on the Antarctic Peninsula. In 1977 two stone spear points in 1977 were also found there, though they were later said to have been planted there and therefore fake. (Source), the remains however were authentic. Her skull was found later (Source) and dated to the early 1800s. The authors suggest the woman was part of a sealing expedition and either died at sea, and her body washed ashore, or was buried there by the crew. However, it could be possible she was on a canoe that drifted (or was deliberately taken) there from Tierra del Fuego across the treacherous choppy waters of the Drake Passage.

In my book, while discussing the Warrah Wolf-Fox of the Falkland⁄Malvinas Islands, I pointed out that there is archaeological evidence showing that the islands, located 450 km (280 mi) from the Patagonian mainland, were visited by Paleo-Indians or even Fuegians. "A 2021 study supports that humans visited the island before their discovery by Europeans based on different pieces of evidence, such as Darwin’s comment that “the old canoes which are occasionally now stranded, show that the currents still set from Tierra del Fuego.” There are fossil charcoal remains, some 4,800 years old, suggesting man-made hearths, and a stone arrowhead discovered in 1979 made from local stone using Fuegian native stone knapping techniques."

The Fuegian canoes were sturdier than we imagine, and probably there is more evidence out there in the Antarctic and the islands that surround it (South Georgia, South Orkney, and South Sandwich Islands).

There are some references on the internet about Fuegian myths regarding the Antarctic as you can see in this example: "The Fuegian Amerindians Aush, who, upon migrating from other lands to the southern Fuegian region, found the "land of ice," which could be the archipelagos located north of the Antarctic coast." But when I checked my library (Canclini, Arnoldo, Leyendas de Tierra del Fuego - Mitos de los onas y yaganes, aborigenes fueguinos, and Beauvoir, José María, Aborígenes de la Patagonia. Los Onas: tradiciones, costumbres y lengua), I didn't find any legends or a refrence to this Aush-Antarctic myth.

In Oceania, the Polynesians occupied, and later abandoned the Auckland Islands, some 465 km (289 mi.) south of New Zealand's Southern Island (50.7°S 166.1°E), this was the southernmost point reached by the Maori navigators. However, a 2021 paper gives creedence to Maori stories about the frozen continent: "It may have been about our year 750 that the astonishing Hui-Te-Rangiora, in his canoe Te Iwi-o-Atea, sailed from Rarotonga on a voyage of wonders in that direction (South): he saw the bare white rocks that towered into the sky from out the monstrous seas, the long tresses of the woman that dwelt therein, which waved about under the waters and on their surface, the frozen sea covered with pia or arrowroot, the deceitful animal that dived to great depths – ‘a foggy, misty dark place not shone on by the sun’. Icebergs, the fifty foot long leaves of bullkelp, the walrus or sea-elephant, the snowy ice fields of a clime very different from Hui-Te-Rangiora’s own warm islands – all these he had seen. The Maori of Aotearoa."

Argentine anthropologist, Profesor Augusto Cardich, was quoted in an article published in 2001 (The First Americans: Were they Australians? Mammoth Trumpet vo. 16 No.2 p.4). He pointed out that the southern ice shelf advanced north from the Antarctic and reached a low latitude of 55° S, touching Tierra del Fuego during the LGM. People from Tasmania sailed along the shelf and reached America. He also noted that the South Pacific was much warmer and also calmer than the North Pacific during the Late Pleistocene. Considering that the ancestors of the Australian aboriginals sailed to reach their continent-island, Cardich considers "all this evidence makes me think crazy atl all to think they might have sailed from Australia to South America." Cardich published a book on this subject: Fueron los australianos los primeros americanos?, Augusto R. Cardich, Lima : Universidad Nacional Mayor de san Marcos (2001).

The suggestion that the climate was warmer and that stormtracks had moved closer to the equator some 13,000 to 9,000 years ago is supported by scientific evidence (see Late Pleistocene and Holocene paleoclimate and glacier fluctuations in Patagonia, 2004).

The map below shows the LGM and current summer and winter maximum extension of the sea ice around the Antarctic continent. South America is upper left, the western tip of Australia is lower right; Africa and Madagascar top. New Zealand is out view as is eastern Australia. Adapted from: Reconstruction of past sea ice extent (2013). I added the red dashed line marking the migratory route, and the name of the continents.

I find it hard to believe that a group of people, well adapted to tropical and subtropical environments, would deliberately move on, south, into the freezen polar region, somehow master the new environment, and after hunting penguins and sea wolves, survive a trip of roughly 9,000 km (5,600 mi) through an unknown territory. It seems highly improbable.

Resources

[1] Mendes Correa (1926), Nouvelle hypothese sur le peuplement primitif de l'Amerique du Sud. (↺)

[2] Rivet (1926), Les Malayo-Polynesiens en Amerique. (↺)

[3] Erland Nordenskjöld, (1931).Origin of the Indian Civilizations in South America (↺)

[4] H. B. Coates, (1834). On the origin of the Indian population of America.(↺)

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2025by Austin Whittall © 

Click Language may not be the "first" language of mankind

In previous posts I have written about languages, their diversity, out-of-Africa and the peopling of America.

I recently read an interesting article published several years ago in Scientific American (Social Clicks: Sounds Associated with African Languages Are Common in English) by Anne Pycha -February 1, 2012.

Pycha writes that:

"[English language] Speakers, it turns out, use clicks for a previously overlooked purpose: as a form of verbal punctuation in between thoughts or phrases. Melissa Wright of Birmingham City University in England recently analyzed click sounds in six large sets of recorded English conversations. She found that speakers used clicks frequently to signal that they were ending one stretch of conversation and shifting to a new one. For example, a speaker might say, “Yeah, that was a great game,” produce a click, then say, “The reason I’m calling is to invite you to dinner tomorrow.”
This pattern, which occurred for both British and American speakers, suggests that clicks have a meaning similar to saying “anyway” or “so.” That is, clicks provide us with a phonetic resource to organize conversations and communicate our intentions to listeners...".

Why is this important? Because Click languages, which are only spoken in Africa, are often portrayed as ancient languages, the "original" mother tongue of human beings.

This video shows what a Xhosa sounds like speaking in his click language.

See these scholarly articles as an example of the above notion of a primeval African click language:

• Ancient Roots for an African Language?
• History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation

However if clicks were overlooked in English, were they also ignored among other languages?

There was one other language outside of Africa, spoken on Mornington Island, Australia. It was called "Damin", nobody speaks it now, it became a lost language. It was spoken in until the 1800s by the initiated men of the Lardil aboriginal tribe (read more here).

The idea that click languages are the original tongue of mankind is based on a weak assumption: since these languages are used by the South African hunter-gatherers, and these people are also (see my recent post on this subject) said to be the oldest group of humans based on their mtDNA, then it must be the primeval language. But are we expected to believe that these people kept their original language while elsewhere it evolved at a rapid pace, diversifying? Why would the click-languages remain static or evolve slower?

I side with Tom Güldemann who wrote: "The idea that modern click phonemes have their ultimate origin in the linguistic feature of a very ancient human language remains just one among several speculative hypotheses."

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2019 by Austin Whittall © 

Humans but not AMH in Australia 125,000 years ago?

My previous post mentioned the currently accepted window for the entry of humans into America, roughly some 15,000 years ago. A similar situation occurs with Australia: the peopling of the vast southern continent-island is tied to the purported "Out of Africa" dates meaning that nobody accepts an earlier entry date than roughly 50,000 years ago.

But there seems to be some evidence of early human activity in Australia. I will mention two of them.

Charcoal 120,000 years old at Moyjil

Fire is a good indication of human activity. Of course, natural events can also start fires. A paper published in 2018 (Ian J. McNiven et al., The Moyjil site, South-West Victoria, Australia: Excavation of a last Interglacial charcoal and burnt stone feature - Is it a Hearth?, Proceedings of the Royal Society of Victoria 130(2):94, January 2018, DOI: 10.1071/RS18008), looks into the charcoal found at a site in NSW, Australia.

I will highlight the paper's main points: "The oldest dates for human occupation of Sahul (Australia and New Guinea) based on radiocarbon dating are a little under 50 ka...
we present excavation results for a small deposit containing charcoal and darkened stones (some clearly burnt) at Moyjil...
The potential for Moyjil to re-write the early human history of Australia is not new, as claims have already been made that a marine shell deposit at the site dating to at least 60‒80,000 years ago (since redated to 120‒125,000 years old — see Sherwood et al. 2018a) could be cultural in origin (Sherwood et al. 1994; Nair & Sherwood 2007)...
On balance, the broad range of discrimination criteria marginally point more towards CBS1 representing a cultural hearth and not exclusively a naturally burnt feature. As such, some evidence exists for CBS1 representing a ~120,000 year old hearth. However, the evidence for CBS1 as a hearth must be definitive and irrefutable for such a substantial claim to be considered credible, given the significant implications that this would have for world history. At this juncture, CBS1 does not meet this high level evidential threshold.".

So the evidence exists but as it isn't "irrefutable", for the time being it will not be considered as being the result of human activity.

For those interested on the shell midden deposit dated to 120-125 kya, the full text paper is here.

Lake Eyre Skull Fragment

The book The First Boat People by Steve Webb, Cambridge University Press, 2006, addresses the issue of an early peopling of Australia (you can read it online following the link above).

Webb provides plenty of evidence to back his ideas. I will just mention the skull fragment found at Lake Eyre, (pages 161 to 172) which was dated to an age of 121 - 162 kya via fluorine analysis and to 132 kya by uranium series method.

Webb states that these dates... "strongly suggests it lies well within the last interglacial, probably towards the middle (?80–100 ky). These results are, therefore,taken to indicate that humans were certainly in this region during the lastinterglacial and well before the onset of the last glaciation."

Which is what we mentioned in our post, yesterday. Dates of initial peopling of America could be from the Interglacial. And Webb finds that feasible for Australia too.

Webb summarizes the situation as follows: "Finally, we cannot ignore the fact that humans lived next door to Australia for nearly two million years before they arrived here. The fossil evidenceindicates that they constituted a viable population living at the edge of theinhabited world, in Java and China. Their viability stretches beyond theirfossil remains and into the realm of exploration as they explored beyond Java to Flores Island almost one million years ago, and that required a capability to cross at least two 22 km water gaps. The idea that this was an aberrant group and one that does not count in any assessment of regional human evolution is difficult to accept and, indeed, it does not take into consideration the will and determination of this erstwhile group of humans. Consider, if they made that inter-island crossing so long ago, what would have stopped them from continuing to the end of the archipelago and even further during the next 700 ky? These people or their descendants were the most obvious to be the first Australians, long before the 'advent' of anything called anatomically modern human. Why should we invoke a people from half way round the world to reach here first when this successful population thrived and explored their archipelago only a few hundred kilometres away from our continental shelf or little more than a hundred kilometres away during low sea levels? It isnot possible that this persistent and successful group did not attempt to enter Australia and eventually succeed in doing so. They may have done this out of pure curiosity, probably tens, possibly hundreds of thousands of years before anybody else came anywhere near their new homeland. For me, the question is not did they arrive here, it is when did they arrive here."

I fully agree with Dr. Webb.

The map below shows current continental shores (gray line), the ice age coastline (gray shade), the Homo erectus would have had to cross the same open stretches of water our Homo sapiens ancestors crossed, from Flores Island to Sahul:

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2019 by Austin Whittall © 

Australasian signal in the DNA of Amerindians

BBack in 2015 (Skoglund P, Mallick S, Bortolini MC, et al. Genetic evidence for two founding populations of the Americas. Nature. 2015;525(7567):104–108. doi:10.1038/nature14895) an article showed that " show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent or at all in present-day Northern and Central Americans or a ~12,600 year old Clovis genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.".

This is quite a remarkable discovery, and the authors quickly clarified that "These results do not imply that an unmixed population related anciently to Australasians migrated to the Americas. While this is a formal possibility, an alternative model that we view as plausible is that the 'Population Y' (we use 'Population Y' after Ypykuéra, which means 'ancestor' in the Tupi language family spoken by the Suruí and Kartiana) that contributed Australian related ancestry to Amazonians was already mixed with a lineage related to First Americans at the time it reached Amazonia."

They concluded that "he genetic data allow us to say with confidence that Population Y ancestry arrived south of the ice sheets anciently: the fact that the geographically diverse Andamanese, Australian and New Guinean populations are all similarly related to this source suggests that the population is no longer extant, and the absence of long-range admixture linkage disequilibrium suggests that the population mixture did not occur in the last few thousand years."

Last year another study (Reconstructing the Deep Population History of Central and South America Posth C. et al., (2018) Cell, Vol 175:5 P1185-1197.E22, Nov. 15, 2018) looked into the peopling of America but didn't manage to find this Australasian signal in "ancient remains" that they analyzed:

"failure to find significant evidence of Australasian or Paleolithic East Asian affinities in any of the ancient Central and South American individuals raises the question of what ancient populations could have contributed the Population Y signal in Surui and other Amazonian groups and increases the previously small chance that this signal—despite the strong statistical evidence for it—was a false-positive."

But shortly after another paper was published in Science (Early human dispersals within the Americas, Moreno-Mayar et al., Science 07 Dec 2018: Vol. 362, Issue 6419, eaav2621 DOI: 10.1126/science.aav2621) that sequenced the DNA of ancient remains from all across America, Alaska to Patagonia and found that prior to the main migration into America, there was an earlier one, with Australasian traits:

"... there are genomic and archaeological hints of an earlier human presence. How these early groups are related or structured, particularly those with Australasian ancestry, remains unknown.... [there were] multiple independent, geographically uneven migrations into South America. One such migration provides clues of Late Pleistocene Australasian ancestry in South America, [which] contributed to present-day South American ancestry."

"... we find that the Amazonian Surui share a larger proportion of alleles with Australasian groups (represented by Papuans, Australians and Andaman Islanders), with respect to Mixe. Lagoa Santa yielded similar results to those obtained for the Surui. When compared to Mesoamerican groups (Mixe and Huichol), Lagoa Santa also shares a larger proportion of alleles with Australasian groups but not with other Eurasians."

Remarkably, these first wave individuals with Austronesian genes somehow reached South America without leaving any traces in North America: "[a populaton] that harbored an Australasian signal in the Late Pleistocene and reached South America, yet left no apparent traces in North America".

-- New, Sept. 4, 2019 --

I had originally written:

So the facial reconstruction of "Luzia", one of the 12,500 year-old Lagoa Santa crania (and almost lost in the fire that razed the Rio de Janeiro National Museum -fortunately the skull survived) which originally depicted her with an African look now has her looking more Asian:

One of Luzia's relatives - African look has gone. Source

Luzia before, more "African".

Reader feedback:

D. Parker wrote an e-mail to me with the following text:

your source: http://agencia.fapesp.br/the-new-face-of-luzia-and-the-lagoa-santa-people/29168/. Notice caption ^^^ does not say that that picture is Luzia.
The Brazilian researchers’ contribution to the study was fundamental. Among the 49 individuals from which fossil DNA was taken, seven skeletons dated to between 10,100 and 9,100 years ago came from Lapa do Santo, a rock shelter in Lagoa Santa. A new bust has replaced Luzia in the Brazilian scientific pantheon. Caroline Wilkinson, a forensic anthropologist at Liverpool John Moores University in the UK and a disciple of Neave, has produced a facial reconstruction of one of the individuals exhumed at Lapa do Santo. The reconstruction was based on a retrodeformed digital model of the skull.
Estudos genéticos dão nova cara ao Povo de Luzia Representação do fóssil humano mais fa...
Facial reconstruction of the People of Luzia by Caroline Wilkinson of Liverpool John Moores University in England, based on a retroformed digital skull model of the Lapa do Santo archaeological site. The skull used as a reference is from a young man, cataloged as Burial 26.
Also in regard to the Caroline Wilkinson reconstruction. None of the articles, not the one you sourced said the Caroline Wilkinson reconstruction. looks more Asian. The eye fold is not depicted Asian. None of the features are particularly Asian. The nose is not as flat as many Asians. It's true that the ancestors of Native are believed to be Asian but the reconstruction is intended to depict someone looking Native American and though they have Asian ancestry they dont always look exactly like,Asians. People have said it looks racially ambiguous or could even pass for a dark skinned European or Middle Eastern person, Nevertheless these reconstructions include speculation from the forensic artist
regards,
D. Parker

I thank Mr. Parker for his comments. And I promise to write a specific post on these Brazilian remains (the whole group).

See this post here:Lagoa Santa sites and remains: old and odd

.

My remark on the features of the reconstructed face still stands however. The overall impression of the original bust is that of an African, now it is more Eurasian, it does not look like the typical Amerindian people one sees -today- in South America which have distinct features.

-- end of comment--

So the question remains open: where did this signal come from? And why is it not present in North America or Asia? Below is a map from Skoglund's 2015 paper, and the white circles show this lack of Australasian DNA in those regions, and the red and yellow cicles indicate their presence in South America:

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2019 by Austin Whittall © 

The "unsampled population" in America: archaic hominins?

I want to share an excellent article from "Ancient DNA Era", published on Nov. 27, 2018 by Alberto (Early human dispersals within the Americas – Moreno-Mayar et al. 2018).

In this article Alberto discusses a recent paper (Early human dispersals within the Americas, J. Victor Moreno-Mayar, Lasse Vinner, Peter de Barros Damgaard, Constanza de la Fuente et al, Science 08 Nov 2018 DOI: 10.1126/science.aav2621) which deals with "multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, and a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America."

Moreno-Mayar mentions:

"We sequenced 15 ancient human genomes spanning Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans (NA), including an Ancient Beringian individual, and two morphologically distinct "Paleoamericans." We find evidence of rapid dispersal and early diversification, including previously unknown groups, as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, and a later Mesoamerican-related expansion."

Alberto focuses on the "previously unknown groups" and the "Australasian genetic signal" and he quotes the original paper:

"...further SFS-based modeling indicates that Mixe most likely carry gene flow from an unsampled outgroup […] Hereafter we refer to that outgroup as 'Unsampled population A' (UPopA), which is neither AB, NNA or SNA [Ancient Beringians, Northern Native Americans or Southern Native Americans], and which we infer split off from Native Americans ~24.7 ka, ranging from 30-22 ka (95% CI; this large range is a result of the analytical challenge of estimating divergence and admixture times in the absence of UPopA genome data).[…] Under a model with a pulse-like gene flow, we inferred a probability of ~11% gene flow from UPopA into Mixe ~8.7 ka (95% CI: 0.4-13.9 ka; the wide interval potentially reflects unmodeled continuous migration)"

Alberto then reasons as follows: (I quote him extensively below)

" When they say "unsampled", they mean unsampled. So no, we’re not talking about potentially "anyone", but quite specifically about a population that does not only seem to be an outgroup to NA, but also an outgroup to Eurasians.
If this is true, then who can be an outgroup to Eurasians? Basically there are 4 options:
– An African population (meaning a population that went Out of Africa after the main OoA event that gave birth to most Eurasians, and that somehow reached Central America some 9 kya). This one is the least likely, really.
– An early OoA population (meaning a population that went OoA before the main OoA event). We know from archaeology (and with some support from genetics) that such early events did occur but they hardly contributed to later Eurasian populations (maybe a tiny bit to some SE Asian/Australasian populations?). So this one would mean that such population made it to the Americas and survived somewhere around Central America until the second major wave arrived.
– Archaic hominins. Like Neandertals or Denisovans. A small admixture from such groups (on top of what other NA already have) would make the shared drift of Mixe with all other AMH be lower. So is it possible that some form of archaic hominin lived in America and survived until some 9 kya?
– A fourth option would be an early "generic" Eurasian population, something similar to Ust-Ishim samples from 45 kya, but not directly related to Ust-Ishim."

I favor option three "Archaic hominins" but Alberto believes option four is the most likely one.

Finally Alberto remarks: "Using qpGraph, this Australasian admixture is estimated to be around 3% in these samples (and modern Surui). How it got there (if it’s real, that it well could be) is unknown at this point, but it’s important to keep in mind that it was already present at least 10.4 kya, so it cannot be from any kind of Holocene migration of Australasians to South America. The possibility is that there was a small (?) population of Australasian origin at the arrival of the migrants of NE Siberian origin."

Skoglund already noticed the Australasian link in Native American DNA (See paper here and the other paper here) back in 2015.

In my book Monsters of Patagonia y point out the similarity between Australian and Patagonian native myths (read more), and conclude " Human remains discovered in Brazil show a very strong resemblance to modern South Pacific people, suggesting that America was first colonized by the generalized human (Homo sapiens) population that inhabited East Asia in the Late Pleistocene. These people arrived in America in very ancient times long before the Mongolid morphology of the forbearers of the Clovis had evolved."

We will have to wait for more evidence to learn about the unsampled population and the Australasian migrants.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

On an Archaic hominin introgression in Africa and an earlier date for the peopling of Australia

Today I have come across two brand new and very interesting papers:

The first one tells us that modern Homo sapiens reached Australia much earlier than formerly believed: 65,000 years ago. (Chris Clarkson et al., "Human occupation of northern Australia by 65,000 years ago", Nature 547, 306–310, 20 July 2017, doi:10.1038/nature22968).

The authors point out that "This evidence sets a new minimum age for the arrival of humans in Australia, the dispersal of modern humans out of Africa, and the subsequent interactions of modern humans with Neanderthals and Denisovans.".

The other paper by Duo Xu et al ("Archaic hominin introgression in Africa contributes to functional salivary MUC7 genetic variation", Molecular Biology and Evolution, 2017; DOI: 10.1093/molbev/msx206.) tells us that an archaic hominin interbred with sub-Saharan Africans.

This is an extremely interesting conjecture which the authors state as follows "...we conclude that a divergent MUC7 haplotype likely originated in an unknown African hominin population and introgressed into ancestors of modern Africans...".

This introgression could explain why there is so much diversity in sub-Saharan Africans: they got it from an archaic human (I posted this same idea Here, where I wrote: "This leads me to ask, what if African heterozygosity was enriched by recent admixture with other hominins in Africa? an inflow of different relic alleles elevated African diversity above that of non-Africans" and Here where I wrote: "These ancient African humans carried the A00 lineage in them, mated with AMH (within the last 195 ky)").

The second paper is interesting and I will post on it later because it has some "orthodoxy" influencing its hypothesis, see this for instance, where the authors look into the introgressed halpogroup, (E):

"However, introgression of haplogroup E from Neanderthals or Denisovans is unlikely, because haplogroup E is exclusively found in sub- Saharan African populations, whereas introgression events between Neanderthals or Denisovans with modern humans happened after modern humans migrated out of Africa (Vernot and Akey 2014) (Figure 5A, Figure S5). As such, we hypothesize that an archaic hominin, at that time still roaming in Africa, contributed haplogroup E to the ancestors of extant Africans."

They are assuming that H. sapiens originated in Africa and moved "Out" of Africa. If they had move "Into" Africa from Eurasia, then Neanderthals or Denisovans could have been the origin of the haplogroup...

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

NRY haplogroup C, part 2. Eurasia and Homo erectus

Y chromosome Haplogroup C is perhaps the oldest and therefore earliest indicator of the presence of modern human males in Eastern Asia. It is found at a relatively low frequencies across most of Asia, reaching its highest frequencies in North Eastern Asia (Mongolia, Siberia); it declines in Japan, Korea, China, India, Southern Asia, but risies in Eastern Indonesia, Polynesia and Australia. It is absent in Africa, found at moderate frequencies in North America and very low frequencies in Europe and South America. [1] (see map below)

As we will see below, it has distinct geographically-specific haplotypes of which C3 is the most widespread one spanning Asia and America.

Map showing global distribution of C haplogroup, frequencies and official dispersion routes. Adapted from [2]

This extended range and low frequency coverage underlying more recent Eurasian haplogroups clearly indicate that it arose very early in Asia, among first humans that left Africa, during their trek across Western Asia and before they reached Eastern Asia.

In today's post I will summarize its regional haplotypes and frequencies and, close the post with a discussion on their origin and dispersal. I will go over the data and the "orthodox" point of view and later will suggest some non-orthodox ideas regarding C hg. and its origin. To skip the region by region information click here to go to the analysis part of this post.

A Regional Analysis of NRY Haplogroup C

We will detail the C haplogroup's haplotypes and their frequencies of in the following regions:
Australia, Melanesia, Polynesia and Papua New Guinea, Indonesia, Indian subcontinent, China, Japan, Korea, Northwest Asia and Siberia, Persian Gulf, Europe, North America, (South America was discussed in a previous post.

C haplogroup across Southeastern Asia, Australia and Polynesia

To get your bearings in our regional analysis, the following map will come in handy. It shows the frequencies of the different C haplotypes in East and Southeast Asia, PNG, N. Zealand, Polynesia and Australia:

Y chromosome C haplogroup, Range and frequencies in Asia, Australia and Polynesia. Adapted by A. Whittall from [3]

The map clearly shows how hg. C is present in the region at noticeably differing frequencies and with very distinct haplotypes in the each of the geographic locations:

• C3 (M-217). North Asia (Mongolia, Korea, China) and the Americas
• C1 (M-8). Only found in Japan and Ryukyu
• C*. In South China and S.E. Asia, but this is a Paragroup and may conceal yet unknown haplotypes.
• C2 (M-38). From East Indonesia and across Melanesia, Polynesia and New Zealand, but with two distinct haplotypes in the West and the East of this vast region.
• C4 (M-347). Unique to Australia
• C5 (M-356). Not shown in the map, but unique to India, Nepal and Pakistan

As you can see, there is a clearly geographic distribution of haplotypes with little or no overlap.

The following table gives some numerical data for the whole of Asia (including Greater India, not shown in the map above and North America):

Table with C haplogroup frequencies Asia and America. Adapted from [4]

This of course mirrors what we have mentioned above: discrete regional distributions and an overlaid C* paragroup at low frequencies (highest in South East Asia) which will have to be resolved into other new haplotypes once their markers have been identified.

Below we will review each region in detail and then try to reach some conclusions.

The Australian Aboriginals - C4

Austrailian natives have their own unique haplogroup, C4, defined by SNP M347; C4 has two haplotypes: C4a (with STR DYS390 deleted) and C4b with M210.

This is the original, ancient haplogroup that arrived in Australia during its peopling wave, which took place some 50 kya and was followed by "considerable isolation after the initial arrival" [4].

The original migrants came from the southern tip of mainland Asia: "Sunda" (encompassing the main Indonesian islands and Malaysia). The "Wallace Line", a strip of sea with many minor islands forming "Wallacea" (Sulawesi, Lombok, Sumbawa, Flores, Sumba, Timor, Halmahera, Buru, etc.) separated it from the other landmass of "Sahul", which was formed by Australia and Near Oceania -New Guinea (NG) and Melanesian Island. The migrants trekked across this now submerged land (sea levels rose after deglaciation c. 9 kya) and rafted across the Wallace Line, reaching Australia.

Interestingly, the other C haplogroups and paragroup C* did not enter Australia (one study detected some C* in Arnhem which may reflect modern arrivals), or if they did, disappeared without a trace.

Despite my hopes that Homo erectus admixed with this Paleolithic migratory wave that peopled Australia and New Guinea (NG), the mainstream science does not support this notion: ""local H. erectus or archaic Homo sapiens populations did not contribute to the modern aboriginal Australian gene pool" [4].

One thing that surprised me is that the time it took the human groups to move across Sahul and Sunda was so long in comparison to what orthodoxy attributes to the peopling of America event:

• Australia. "...the migration from southwestern Asia to Australia would have taken <5,200 years ... This migration speed is in the same order of magnitude as estimated for other prehistoric continental settlements" [4]
• Americas. " the Paleo-Indian spread along the entire longitude of the American double continent might have taken even <2000 yr." [5]

Note that to cross America from Alaska to Cape Horn is about twice the distance compared to the trek from Malaysia to Tasmania yet we must believe that they did it in less than half the time. Did the Paleoindians move four times faster than the Australian Aboriginals' ancestors? Something is not quite right with these numbers. Most likely the American peopling event is far too short, but since orthodox science has to have people in Monte Verde, Chile c. 13 kya and they supposedly entered the New World 15 kya., the absurdly short 2 kya figure appears... Another example of fiddling with the dates to make them fit with preconceptions.

C2: Melanesia, Polynesia and New Guinea (NG)

Melanesia and New Guinea (NG) were settled in the same wave that peopled Australia over 42 kya [6], but later waves of humans reached this area and account for over half the Y chromosome haplogroups in the Region. Nevertheless, haplogroup C is widespread and found at a ㅏ% frequency in Indonesia, indicating its ancient origin [3]. It is found with different haplotypes:

• C* [C-RPS4Y*(xM38, M217, DYS390.1del]. This paragroup is the oldest (50 kya) lineage in Sunda and Sahul [6]. It is very rare in Melanesia and only appears in some coastal NG samples.
  It is "notably absent from the NG Highlands and Taiwan and the Philippines" [6], reaching only 3.4% in the latter (Taiwan and Philippines are mentioned because they are apparently the ancestral home of many Melanesians, but seemingly not the C* carriers). [8]
• C2.
  
  • C2-M38*(xM208). It is almost absent west of the Wallace Line, its highest frequencies are found in East Indonesia, Moluccas Nusa Tenggara (51 - 44%) [9], coastal NG and Cook Islands.
    It is the most common haplogroup in Northwestern NG (34.6%) and the second most frequent haplogroup in New Guinea (avg. 12.8%). Since its STR diversity his highest in NWNG (Bird's Head region) it very likely originated there (or in Wallacea as the oldest hg. (42 - 61 kya) [6] , expanding east across Melanesia and NG into Polynesia (although rarely observed there); and also West, into Eastern Indonesia. [10][8]
  • C2b-M208. Found at high frequencies in the West Papua highlands and among Cook Islanders, it is old: mean age 46.2 ky [6] but had a much more recent expansion into Polynesia (5 - 2.2 kya) [8], where it is found at high frequencies (34%) and also among the New Zealand Maori (77%). [11] [10]
    Is a low frequency hg. in Northwest NG (2.5%) and NG (avg. 6.8%). [10]

A variety (originally named C6) with the P55 marker was reported [6] but is now considered as a Private SNP due to lack of positive testers [2] or a familial group of related males [12] so the C6 haplotype has been dropped and reassigned to European lineages. Three other haplotypes are absent in the region : C5, C3 and the Australian Aboriginal C4 [6].

Rest of Indonesia

• C*. Has a patchy distribution across the Asian region, it is found at high frequencies in East Indonesia (29.2% in Flores and 22.8% in Lembata) and, as mentioned above, is absent in Melanesia and Polynesia. Further north it appears in China (Yao, 20%). [3]
• C2-M38*, is absent in Western Indonesia but grows to an average of 33.5% in Eastern Indonesia (from 11% in Sulawesi to 57% in Sumba); it is found at very low frequencies in Polynesia and Melanesia. [3]

The Indian Subcontinent and the C5 clade

Haplogroup C was detected in India and had been initially classified as C* until Sengupta S. et al., (2006) [14] analysed the paragroup and identified a new haplotype, C5-M356. Almost 85% of the Indian C* individuals were assigned to the new subclade. Which is only found in the Indian subcontinent. [14]

Ancient and autochthonous

C5 is a pan-Indian lineage, absent in the rest of the world yet found at very low frequencies in India (1.4%) where it is widely distributed: It "occurs in all linguistic groups and in both tribes and castes. It also occurs in one Dravidian Brahui in Pakistan" [14]. For this reason, it "is an ancient hg... most plausibly arose in situ within the boundaries of present-day India" [14].

Unsurprisingly, The C3-M217 hg. frequent in Eastern and Central Asia has not been detected in India (it did appear in Pakistan though) [14], neither have C2 or C4.

The data regarding C hg. in India and Pakistan is the following [14] (notice the very low frequencies):

• India
  
  • C*-M216 (RPS4Y) 0.27%
  • C5-M356 1.51%
• Pakistan
  
  • C3-M217 6.82%
  • C5-M356 0.57%

Tamils of Southern India

The Tamil people inhabit southern India and northern Sri Lanka. A study [15] that sampled tribes, some of which are still foragers, found that haplogroup C was present in 19 out of the 31 groups sampled at relatively high frequency of 4.4% (avg). 90% of them were C5 and the remaining 10% were C*. C hg exhibited a high variance (0.80) suggesting a local origin for its prevailing haplotype.

China

C haplogroup is unevenly spread across China, it is scarce along the eastern coast and more frequent in the North, South and West. The C* paragroup is common in the South and East, and C3 in the North and West.

• Southeast. (Yao, 20% - C*). [3]
• Northeast. Heilongjiang (Manchu, 44.0%) and Hezhe 6.7%, Inner Mongolia (Mongolian, 52.2%; Oroqen, 61.3%), Outer Mongolia (52.8%) [2]
• Northwest. Xinjiang (Hazak, 75.5%) [2]
• Center. Miao 1.7%, Hui 6.7%, Tujia 8.2% (C-RPS4Y*), Han 6% (C-M217), Tujia 18,3% (C-M217)[7] [2]
• South. C*: Mulau 9.1% and Shui 6.9% [2]

Neolithic archaeological remains 6.5 - 2.7 kya from West Liao River valley in Northeast China carried the C3e - P53.1 haplotype. These people are believed to have originated in the northern China steppe, a region where extant populations still carry C3e at a 23.8% frequency. [[17]]

Japan and its C1

C haplogroup is found in Japan at low frequencies, and it has a local haplotype, C1 exclusive to Japan. The values are: [18]

• C1 - M105, the local haplotype, 1.5%
• C3 - M217, originated in the mainland, 2.2%

Korea - C3*

The prevalent C haplogroup in Korea is C. The values differ according to the source: [20] indicated a 12.6% frequency of C-RPS4Y (that is C*, very likely C3*). Another [7] indicated a 16.2% frequency of C3* (xC3c) and yet another [14] 9.6% of C3*.

C3* is also found in neighboring Manchuria at moderate frequencies: higher than in Southeast Asia yet lower than Northeast Asia suggesting an expansion from Mongolia or Siberia into Korea.

Siberia and Northwest Asia

The North Asian haplotypes are (always from the orthodox point of view) relatively recent: C3 as a whole (4.1 to 14.9 ky), and its subclusters are even younger still: C3c (1.6 to 5.9 ky) and C3d (0.5 to 2.0 ky). Notice how wide spread these dates are, which shows the uncertainty originated by the mutation rates used in the calculations. [14]

These are the C lineages found in Northern Asia:

• C3c. (M-48) Prevails among Manchurians, Evens, Kalmyks and Evenks. All of which are Mongolic-Tungusic peoples. [19]
• C3d. Is frequent among Mongol speaking peoples: Mongols, Khamnigans and Buryats.
• C3*. Paragroup with high frequencies (+30%) among Koryaks and Mongols it is also found in North America.

Trivia: history

There is a Genghis Khan "star cluster" (part of paragroup C3*) which is said to have originated 1 kya ago in Mongolia and spread by the Khan's relatives due to their "social status" (a neat sinophylic way of saying that the Mongol hordes raped their way across Eurasia). It now ranges from 35% among Mongols to between 3 and 8% among Buryats, Kazaks, Tuvinians, Shors and Altaians. It is between 0.27 to 2.8 ky old, so it may be related to Genghis Khan and his male relatives. [14][19] Nevertheless, the Kereys tribe in Kazakhstan have the highest frequency (76.5%) of this C3* star cluster and it is unlikely that it is due to Genghis Khan's clan. [19] So maybe these people are the original source of it.

Persian Gulf region

This in Southwestern Asia, the region where haplogroup C first appeared in Asia after leaving Africa. It is found at very low frequencies:

Iran [21]:

• C*. 0.1%. Only appears among the Zoroasterians of Yazd province (2.9%).
• C3. 0.4%, is found in 4 out of 20 ethnic groups, from 0.8% (Bandari) to 2.9% (Zoroasterian).
• C5. 0.5%, appears in 3 groups, From 1.5% (Bandari) to 2.8% (Mazandarani). This is the Indian clade, did it back-migrate into Iran recently or is this a relict?

No apparent pattern, just a patchy distribution: C3 and C5 in the north cicum-Caspian area; C3 and C* in central Iran, C3 and C5 by the Persian Gulf. Perhaps the remnants of the ancient dispersal or are they recent movements of people? [21]

Other Gulf Countries: we also have C* (C-M216) at low frequencies in: Oman 3.3%, Saudi Arabia 1,3% and the UAE 1,2%. [21]

European C6

There is a very rare Southern European haplotype within C hg. The nomenclature for this European C-V20 haplotype has changed: it is now named C6 (originally named C7, but since the NG P-55 became a private marker, C6 was reassigned to Europe). It is characterized by markers V20, V7, V86. V182. V184, V219, V222.

Very few samples were known, a recent study [22] found 1 (one) person carrying C6 out of a sample of 1965 individuals! The paper indicates that "Further studies are needed to establish whether C7 [they use the old notation] chromosomes are the relics of an ancient European gene pool or the signal of a recent geographical spread from Asia.". If the latter, the C6 hg. has yet to be identified in Asia; I am inclined towards an ancient origin in Europe.

Archaic La Braña C6 individual

C6 has been identified in the 7,000 year old remains of a Mesolithic man, discovred at the La Braña site in Spain, supporting its ancient origin. However, with the usual caution of a scientific paper, the authors indicate that: (bold mine):

"... La Braña 1 sample belongs to either haplogroup C or F. When mutations defining those haplogroups were checked, only ancestral alleles were found in the haplogroup F-defining mutations, whereas seven C-defining mutations (M130, M216, P255, P260, V183, V199 and V232) showed only derived alleles. Thus, La Braña 1 most likely belonged to haplogroup C [...] The fact that we found ancestral alleles in mutations defining C1, C2, C3 and C4 (Table S9), together with their actual phylogeographic distribution restricted to Asia, Oceania and the Americas suggests that our individual does not belong to any of these branches. Rather, a new branch within haplogroup C (C6, originally named C7) has recently been identified in several men from Southern Europe, suggesting this could be an ancient European clade. Importantly, mutation V20 showed one read with the derived allele (A), which points to C6 as the most probable sub-clade for La Braña 1 sample. It could also be possible that this G to A mutation is a result of DNA damage. Other less likely haplogroup affiliations are C* and C5 (no read covered SNP M356), both found mainly in present-day India." [23]

North American C3b

Haplogroup C is present in North America at moderate frequencies in a unique haplotype found only in that part of the New World: C3b (P39). The details of the frequencies among the native people: [24]

Tanana (Alaska): 41.7%, Cheyenne: 15.9%, Sioux: 11,4%, Apache: 14.6%, Navajo: 1.3%. It was not detected among any other population across North or Central America.

See my previous post on C3* in South American natives.

Analysis and Discussion

Above I pointed out that Y chromosome hg C is absent in Africa; this means it originated outside of Africa. Conventional mainstream science will therefore place this origin after the OoA (Out of Africa) migration of Modern Homo sapiens some 60 kya.

1. Origin

The accepted theory is that Haplogroup C originated with the split from the hypothetical Haplogroup CF -or CF(xDE). Its marker is SNP P143, which is ancestral to F and C hgs. This split took place somewhere in Southwestern Asia, perhaps on the shores of the Persian Gulf 60 kya.

2. Dispersal across Asia

Men carrying hg. C are believed to have taken an eastern "coastal" route along the coast of the Arabian Sea, reaching the mouth of the Indus River. I see no objections to the possibility that they also advanced inland along the main rivers of this area, but the official dispersal theory sticks to a coastal route (perhaps to tie in the timing of the OoA event and the peopling of Australia, a quick march along the coasts of Asia is required).

2.a. India

From the Indus, C entered the Indian subcontinent, we can suppose that the typically Indian C5 arose later, from those who stayed behind in India, because it is unlikely that C mutated and only those with the C5 marker stayed in India and all the rest, with the non-mutated version kept on moving. Another option is that the mutations arose later from some other region and back- ispersed into India, where it is now prevalent. But this needs us to explain why it became lost in its point of origin.

2.b. Into Austronesia

These migrants pushed on south towards Cape Comorin and Sri Lanka, and then north along the Bay of Bengal and across modern Bangladesh, Myanmar and down into Malaysia, till they reached the edge of the emerged continental shelf in Indonesia: (during the Ice ages sea level was lower so all East Indonesian islands were joined into the Sunda landmass). They boated across the Wallace Line, a stretch of deep seas that blocked access of placental mammals southwards into Australia and New Guinea (NG) -as well as marsupial migrations towards the north. They finally reached Sahul the joined continent of NG and Australia.

Peopling of Sahul and Southeast Asia. Adapted from [25]

The map above shows the current continental area and the emerged continental shelves (in grey), the red arrow shows the migration into Sahul.

It was during these moves that C2 appeared in Wallacea (Western Indonesia and NG) and stayed there while C4 appeared in Australia and also stayed there... why? what kept them from expanding and overlapping in a unified landmass?

The answer: Culture and Topography. Swamps, jungle, valleys and mountain ranges, deserts, rugged shores have kept NG people physically isolated. Tribal societies with their cultural imprint also kept them separated. Current language diversity is a clear indicator of isolation in NG. It is likely that these factors plus population bottlenecks may have kept PNG and Australian natives isolated after the initial single-wave peopling event allowing them to develop their own specific haplotype mutations without any furhter admixture. (Further reading on the peopling of Sahul, McEvoy et al., 2010).

Only much later did another migratory spasm take C2 across the vast Pacific Ocean to people Polynesia and New Zealand but this was a new C2 subclade (C-M208).

2.c. Northwards

We have not considered that these people may have crossed India via the Narmada (by this river, remains of H. erectus were unearthed) and Ganges Rivers or advanced upstream and inland along the Indus, Sutlej, Brahmaputra, Irrawaddy or Saleween rivers, reaching Tibet and Central China or that they may have gone across the continent from Dhaka (Bangladesh) to Hanoi (Vietnam) along the Tropic of Cancer (yellow arrow in map above) and from there advanced inland too (Mekong and Pearl rivers).

No, we have supposed that they took the long tortuous coastal route proposed by orthodoxy, which, in an Ice Age World is shown above (red arrow along Sunda and Blue one northwards towards S.E. Asia). Don't ask me why we must stick to the coast.

I bet that if populations in the interior, in North of Myanmar, Thailand, Yunnan and Laos are sampled, C* and maybe C5 will appear at low frequencies.. maybe this is the homeland of C* from which all others radiated and C5 back-migrated into India.

The following map shows all these possible routes (actually these make more sense than the coastal route for the North Asian populations):

Entry and dispersal routes of C haplogroup in Asia. Copyright © 2014 by Austin Whittall. Data from [13]

The Green route is the official route. In blue, my suggested change, following the rivers (this explains why it is not so frequent along the East China Sea), a radically different route but also feasible is the Red route, across the Indus, Tian Shan, Altai and Southern Siberia into Manchuria.

I will cite a very interesting paper by Derevianko and Shunkov (2011) [27] which deals with the OoA theory it is worth reading it:

"Early human migration was a slow process, not a relay race. It is hard to conceive why the migrants should have moved directly to the east along the narrow coastal line rather than exploring the banks of the rivers which flow into the ocean and thus moving far to the north, where favorable ecological niches were available." [27]

Having said this, we will assume that, as per Zhong et al., [19] they moved in a "single coastal northward expansion route... in China about 32 to 42 thousand years ago."

2.d. China

They reached Southern China, and the paragroup C* formed here some 36 kya; the migrants continued along the coast (once again we must explain why C* stayed behind and the others moved on), part entered Taiwan (and from there Japan), the others and kept on towards North China leaving barely a trace in the coastal areas of Eastern China (now isn't that strange?).

In North China (Liaoning, Heilongjiang) the C3 haplotype appeared (33 to 20 kya) and dispersed widely: Eastwards, from Manchuria into Korea and Japan. West into Mongolia and South-Central Siberia, Western China, Altai, etc. (20 to 8 kya), and finally as the ices receeded at the end of the last Ice Age, (15 kya) Northwards into Northeast into Eastern Siberia, Beringia and... finally, America.

Another group entered Japan via Ryuku from Taiwan and originated the local C1 haplotype there.

And this is the end of the Orthodox dispersal version.

3. Sub-haplogroups

We have seen above that C hg. has various discrete subhaplogroups (C1, C2, C3, C4, C5 and C6 plus a paragroup C*) each with a specific geographical distribution. Common sense indicates that they "have undergone long-time isolation" [2]. But little is said about how they originated without spreading into other regions.

Below I adapted Fig. 2, from Redd A., et al., (2002) [26]; at that time the C5 haplotype from India was not known and the C4 among Australians was not shown in the tree, so I added the C4 dotted line around the yellow Aboriginal dots; I also wrote C5? around the green Indian dots within C* paragroup (top part). C3 in this figure does not include Native Americans and surely contains a lot of paragroup C3*. So I included on the right hand side, the C3* data for Asia and America from Roewer et al., (2013) [19], correlating the regions to the color code of Redd et al. (I added the South American natives in pink), but I maintained the individual data dots with their original colour (key is on upper right corner).

Also see C3* phylogenetic tree in my previous post.

C haplogroup unrooted tree. Adapted from [26] and [19]

The tree is quite revealing as it shows a central core of C* from which the other branches appear. Actually, a closer look at the tree reveals that this central C* as per Redd et al., is Indian, and it is linked to the probable root in the form of the branch joining it with haplogroup B (on the left).

The most central branches of the tree are the Australian C4 (left-center) tightly gathered in the middle, and Indian C5 (center and top-center) with the other branches located further apart:

• C2. (bottom left). Is diverse as can be judged from its spread branches, and it arises from C4
• C1. (upper left). Is quite diverse and arises from C*
• C3. (upper right). Is diverse and is also born from C*
• C*. (middle and bottom center). Is diverse. The main branch on the bottom is mainly South East Asian, but there are also some Indian in it. It is very spread and closely linked to the root of C2 and C4, which suggests that this South Asian C* and the Austronesian lineages C2 and C4 are the very old lines of the C hg. peopling wave.

Comments:

The bottom clusters are basically a widely divergent C2 sprouting from the Australian C4, and C* in S.E. Asia

The top clusters are C1, C5 and C3 all sprouting from the archaich core.

Redd's original root from Hg. B, anchors in Indian C* (green dots). I have no way of telling apart the C5 and the C* of (See data above: Indian origin), my guess is that the upper cluster is genuine C5 while the green dots in the central part of the tree and the bottom are actually C*.

The core from which C1, C5, C3, C* and C4 sprout from are green Indian subcontinent dots... surely C* from India. Only C2 is clearly rooted in one line of C4

1. Origins

C2. Arose in Wallacea from an ancestral lineage of C (which must be the original C M-130 variety) carried by the group that would move into Australia and Melanesia. Part of them moved on into Australia forming C4, the other proto-C people remained in Wallacea and formed derived clades: paragroup C-M38* and haplogroup C-M208, which remained in this territory located East of the Wallace Line and much later moved into Polynesia. Topography, tribal structure and bottlenecks kept C2 and C4 apart.

C4. See above, the "ancestral C stock" from Wallacea entered Australia and remained there in isolation.

Of course the ancestra C line is ancestral to current C* in S. E. Asia, and the C4, C5, C1 and C3 lines. C* is still found in India and other parts of S.E. Asia, it is represented by the green dots in the central part of the image. These will prove to be a new haplotype (H7?) when their marker is found. This is the ancestral lineage, from which all others sprout, it is Indian.

This may help explain some of the questions we posed during the haplotype analysis:

C5 originated from this ancestral C in India, the ancestral C people are the original peopling wave, they moved north and became C3 and C1, they moved south and became C4 in Australia and C* in S.E. Asia, a yet to be discriminated haplogroup (H8?) It

The European C6 is not placed in the tree but it is surely a group that split early in Asia and marched West into Europe.

Clearly further analysis is necessary to breakdown C* into newer sub-clades.

C* in Indonesia has a very high STR variance: this means that it has had plenty of time to mutate; it is very old. In Indonesia it is more frequent in the East, because a "continual eastward migration of the initial settlers (i.e., settlements were not permanently established in western Indonesia) or later waves of (partial) replacement." overlaid it. [3] This corroborates is antiquity.

As we can see in the Table of C haplotype distribution, above, haplotype C3 is concentrated in Northern Asia and has a decreasing cline towards the south (absent in Australia, NG and Polynesia) and west, it is found in North America at relatively high frequencies (C3b - P39, unique to the New World) and in South America in a patchy C3* distribution (see my previous post on C3* in South America.

A sinophile paper [19] proposes that this cline is due to its Chinese origin some 42 to 32 kya, and a coastal north route of expansion, it adds that the highest STR diversity for C3 is found in Southeast Asia. This, in my opinion corrobrates its origin from the ancestral C group, but not in China; it appeared in a region that is central to the other Haplotypes:

The region currently occupied by Myanmar, North Thailand, East India and Yunnan in China.

From there it irradiated and became the current regional haplotypes.

Some Crazy ideas

Having given the official story and facts, allow me to let my imagination fly and suggest an alternative scenario based on these same facts.

The area where C hg. is found with a highest diversity in Asia is precisely the area where Homo erectus lived for over 1.5 million years: Southern and Eastern Asia (from China and Korea in the North, to India and Indonesia in the south).

Haplogroup C's coastal route is precisely the one supposedly taken by our distant H. erectus ancestor.

The OoA theory with H. sapiens originating in Africa and peopling the world, totally replacing previous extant populations (if they existed), is so widely accepted that it dealt a death blow to the multiregional theory (H. sapiens evolved in different regions from a common archaich ancestor). But recent genetic discoveries of admixture with Neanderthals, Denisovans and mysterious "X" hominins as well as some remains in China with a mosaic of archaic and modern features have put fresh wind in the sails of the Multiregional theory.

For instance, Derenko and Shunkov (2011) question the OoA theory and support the Multiregional hypothesis in which an "independent formation of anatomically modern humans occurred", this took place in three regions with four subspecies all of which merged into modern humans:

• East and South East Asia, with Homo sapiens orientalensis
• Rest of Eurasia, with Homo sapiens neanderthalensis and Homo sapiens altaiensis (Denisovans)
• Africa, with Homo sapiens africanensis

Among other things, they also use the evidence of a distinct post-Middle Paleolithic South East Asian lithic industry that was different to that of Europe and Asia, with an "autochthonous development of the Upper Paleolithic,"[27]

They go a step further and suggest a Homo erectus evolution into modern humans in Asia:

"...population of anatomically modern humans descended from Homo erectus locally. .... progressive biological traits are due to parallel evolution. Both in East Asia and in Africa, anatomically modern humans apparently originated from the same ancestral species – Homo erectus sensu lato. ...The totality of evidence speaks in favor of a progressive in situ evolution of Homo erectus in East Asia over a span of more than one million years. This does not preclude the immigration of small populations from adjacent regions, small-scale gene flow, or admixture." [27]

If this is the case, then the C haplogroup found among South East Asians is in fact the one carried by H. erectus from Africa into Asia and later mutated in situ in Asia.

But this would contradict the accepted notion that our Y chromosomes are exclusively human, and that our ancestors (and their Y chromosomes) split from those of H. erectus long ago. Their genes disappeared with them and therefore do not appear in us.

But a study has already suggested an ancient origin for human Y chromosome: (Mendez et al, 2013) it reports the discovery of a novel Haplogroup named A00, which gave a very old age: "338 thousand years ago (kya) (95% confidence interval = 237-581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils..." [16]. In other words this "human" Y chromosome haplogroup is older than humans!

Which of course has been criticised by OoA proponents as using incorrect mutation rates that pushed the dates too far into the past.

I wonder, (read my previous posts criticising the mutation rate calculations) if actually the mutation rates for this (and All other) haplogroups is not underestimated by a factor of three or four, which would mean that the dates could be 711 - 2,381 ky, more than enough to accomodate H. erectus in the picture.

This means that Y chromosomes mutate far slower than currently accepted. And that when we look at the current distribution of NRY hgs. we are seeing the ancient migrations of pre-sapiens men across the globe.

Current C hg. distribution reflects the migration of Homo erectus out of Africa 1.8 Mya. A band of a few hundreds of people walking into Asia with the CF haplogroup, splitting in the Persian Gulf by acquiring the M130 marker, and thus forming C haplogroup. They moved across South Asia keeping their C hg. identity during their long trek (note that since mutation rates are slower than accepted, no mutations arose during this period).

Finally reaching the Homeland from which it differentiated into its current haplogroups, in the North of S. E. Asia. From there they spread out. Some moved into NG, Australia mutating (slowly) into C2 and C4. Others went back into India and mutated to C5. The core in S.E. Asia evolved into C* while others went north forming C1 and C3.

A group did not take the Eastern route and went West into Europe forming C6 there. Maybe it will be sequenced someday from the bones at Sima de los Huesos...

Erectus entered America long ago, and the patchy C3* distribution in South America is what remains of a once widespread coverage of H. erectus in the New World, and not a recent transpacific junk with Jomons from Japan shipwrecked on the shores of Ecuador.

Of course this could be proved or rejected if DNA could be sampled and sequenced from H. erectus remains (maybe impossible due to DNA decay). Maybe in the future it could be done, who knows?

Sources

[1] Chuan-Chao Wang and Hui Li, (2013). Inferring human history in East Asia from Y chromosomes. Investigative Genetics 2013, 4:11 doi:10.1186/2041-2223-4-11
[2] Hua Zhong et al., (2010). Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia. Journal of Human Genetics doi: 10.1038/jhg.2010.40
[3] Tatiana M. Karafet et al., (2010). Major East–West Division Underlies Y Chromosome Stratification across Indonesia. Mol Biol Evol (2010) 27 (8): 1833-1844. doi: 10.1093/molbev/msq063 First published online: March 5, 2010
[4] Georgi Hudjashov et al., (2007). Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis. vol. 104 no. 21, 8726–8730, doi: 10.1073/pnas.0702928104
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