mtDNA C1e haplogroup (2026 update) (and C1f & C1g too)

I first posted about a unique and rare mtDNA haplogroup C1e found only in Iceland, back in 2014, hinting at a Neanderthal origin. Recently, I mentioned mythical voyages of mythical King Arthur to Iceland. Today I will review publications that mention C1e, since 2015.

C1e in Central Asia

This rare haplogroup has been reported in a paper by Järve, Mari et al. (2019), Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance. Current Biology, Volume 29, Issue 14, 2430 - 2441.e10. The article mentions this lineage casually, and then includes data in its Supplementary file, as Table 2: "All of the 31 individuals were successfully haplotyped (Table S2). Despite the small sample size, the 31 samples of this study exhibit a remarkable heterogeneity of mtDNA haplogroups (hgs) (Table S2)... with a few representatives of the rare hgs X, W and C1e (5/31)". Only one sample of the 31, was C1e, it is sample MJ-43, identified as ScySar_Su (Scythians and Sarmatians from the Southern Urals).

This sample belongs to a woman from the Early Prokhorovka period (4th century BC) from Sibai-1 from the northern periphery of the Prokhorovka area in Russia (more details on MJ-43 here) this spot can be seen in this map. These people were nomads who bred sheep and cattle, and were great horse riders. They buried their dead in large mounds.

The article describes this group: "Scythians and Sarmatians of the Southern Urals (group ScySar_SU) Due to its geographic position, the Southern Urals region became a contact zone of different ethnic groups at the beginning of the Early Iron Age. The prominent natural feature of the region is the mountain range of the Urals that divides the Eurasian steppe zone into its European and Asian parts. The relative proximity to the nations of Central Asia and the Near East, the abundance of natural resources and the existence of large centers of metallurgy made the region attractive for nomads, which culminated in the formation of a large-scale union of nomads in the 5th–4th century BC." How did the C1e go to Iceland from here, or reach this area from Iceland?

C1e in Xinjiang, China

Then there is the paper by Wang W, et al. (2021) (Ancient Xinjiang mitogenomes reveal intense admixture with high genetic diversity. Sci Adv 7: eabd6690) who mention the C1e haplogroup in its Supplementary file Table S1 as follows "WTL_M3B, Wutulan (WTL), Nilka County", China. This place can be seen in this Google map. It is dated at 2425-1942 BP. This is far from Iceland, and roughly 1,250 miles or 2,000 km from the Russian site, and very far from America.

A paper published last year by Cabrera V. (2025) suggests a back-migration from America into Asia: "Hg C1 comprises four common and well spread sub lineages, three of them (C1b, C1c, C1d) practicably exclusive of the Americas and one (C1a) with a wide Asian range, and several rare clades/isolates, the most ancient of which is represented by two identical sequences from Brazil (Simão et al. 2021) and Paraguay (Avila et al. 2019) that carries twelve mutations in its basal stem (Supplementary_Fig_S3.xls). Curiously, the other isolates have been detected in northwestern Eurasia instead of East Asia: C1e in Iceland (Ebenesersdóttir et al. 2011), western Russia (Järve et al. 2019), and western China (Wang et al. 2021); C1f in Tajikistan (Peng et al. 2018) and C1g in Mesolithic remains from western Russia (Der Sarkissian et al. 2014). As the oldest clades are found in the New World, the most parsimonious conclusion is that all the C1 branches in Eurasia resulted from retro migrations from America."

Name Change C1f → C1g

Cabrera refers to a C1g haplotype reported in 2014, in Russia, by Der Sarkissian et al. I quote this paper below. But note that the nomenclature has changed between this 2014 paper and now. The former C1f of 2014 is now C1g (Source).

A paper by Clio Der Sarkissian, et al.(2014) reporting another rare variant, mtDNA C1f haplogroup, found in Yuzhnyy Oleni Ostrov (see map), in NW Russia, discusses the American origin of the C1f and C1e variants:

"The Americas also remain under-sampled for complete mtDNA genomes and could be suggested as a potential geographical origin for the C1f lineage, as it has been for the Iceland-restricted C1e sub-clade. For C1e, an American origin through mating of Viking explorers with Native American women sometime earlier than 300 years ago was proposed. Among other hypotheses including that of a European origin, an American origin was favoured on the basis that most of the hg C1 diversity is found on the American continent, despite the fact that no sequence belonging to hg C1e could be detected in the Americas (or anywhere else). This lack of match was explained by under-sampling of the American mtDNA genome diversity. In any case, if admixture between Native Americans and Vikings did occur, it must have been limited, as no other American-specific lineage (e.g. hg A2, B2, D1, C1b, C1c, C1d) was detected in Iceland.
As for Mesolithic Europe, the possibility of a direct prehistoric genetic influence from the Americas is highly unlikely. However, in the eventuality that further sampling of complete mtDNA genomes in the Americas reveals the presence of additional haplotypes belonging to C1f, it would suggest an evolutionary history similar to that of mtDNA hg X2. Like hg C1, hg X2 displays relatively low frequencies albeit with a global distribution in the Northern hemisphere. For example, clade X2a was observed in Europe in the West, in the Near East, Europe, Central Asia, Siberia as well as North America [43]. One model for the present-day distribution of hg X2 suggests that clade X2a split early from the rest of the X2 lineages in the Near East, and reached east Siberia before participating in the second wave of migration into the Americas through admixture with Beringian populations [44]. A similar scenario involving an early split of the different C1 clades in Asia followed by their spread and subsequently isolated evolution could be considered as an explanation for the wide geographical distribution of hg C1 in general. However, this scenario currently lacks substantial support."

But the authors favor an Eurasian origin: "we suggest that the Icelandic-specific C1e sub-clade could have had a recent origin in northern Europe rather than an American origin. This hypothesis is relevant with regard to the origins of the Icelandic population, as Iceland was discovered and first settled by Scandinavian Vikings around 1,130 years ago. Vikings raids extended as far from their homeland in Scandinavia as France, Spain and Sicily, but their main expansion range comprised western Russia, the Baltic region, Scandinavia, and the British Isles [16]. The study of the mtDNA diversity of present-day Icelanders identified that most of the Icelandic mtDNA lineages had Norse (from Scandinavia) or Gaelic origins (from the British Isles) and that the Icelandic gene pool had strongly been impacted by genetic drift... Considering the Scandinavian origins of Icelanders and the identification of the sister clade C1f in Mesolithic North East Europe, it can be proposed that the Icelandic-specific C1e and C1f sub-clades might have both split from the common ancestors of the C1 lineages somewhere in Eurasia and later reached northern Europe during independent or similar migrations (before the Mesolithic for C1f). Therefore, the rare occurrence of the C1e and C1f sub-clades in Europe could be the result of their dilution within the pre-existing European mtDNA diversity when these lineages reached Europe... C1e might have been brought in by the Vikings who first colonised Iceland... While the C1e sub-clade might have been preserved at detectable frequencies in the Icelandic population due to the effects of founder event, it most likely has gone extinct in the source population in northern Europe as a consequence of its low frequency."

More Recent Developments

With the surge in genetic analysis, there have been more reports of C1f (see this source) that reports: 4 individuals in Iceland, 2 Native American, 1 German, and 5 individuals in another two countries (Italy and Tajikistan). A blog post from 2023. C1g has been reported in one ancient male individual, from Karelia (close to the Yuzhnyy Oleni Ostrov location), dated to 8,800-7,950 BP (Source).

A 2017 paper by Ming-Sheng Peng et al. adds some more C1g individuals to the map. In its Supplementary Table S4 it mentions two individuals with C1g haplogroup, PT35 and HM804483 the second has a note that reads "Origin_locality: USA Family Tree". Table S1 identifies the origin of PT35 as Pamir Tajik, the other sample seems to be an older one, used as a reference. This source gives full details, it is a C1, and back in 2009 it was a C1f (Source), now reanamed C1g.

More information is provided by https://www.yfull.com/mtree/C/, with 2021 data showing:

• C1f1, two individuals from Tajikistan, Gorno Badakhshan which includes Pamir.
• C1f2, one individual from India, Marathi, the other (id: YF132247) unspecified.
• C1g, one individual from Bolivia, ancient sample c.826-1049 BP, the other (id:JQ705835.1) unspecified.

I must admit, however, that I am confused by the nomenclagure, the Tajiks and the Indian are classed as C1f, but we have seen above that they are C1g! (?) geneticists have this persistent issue with changing codes and causing confusion!. Anyway the point is that this ratifies the Tajiks as C1g -or f- variants, and mentions an Indian subject, and a new ancient C1g in Bolivia, pre-Hispanic by its age.

2021 data on C1f and C1g. Source

The ages of the C1f branches in Asia are 4700 years BP are much younger than the 16200 years assigned to C1g, however, I must point out that Postillone and Pérez (2017) says that the Bolivian sample mentioned further up -it has the same id code- is C1c and not C1g! "KU523335.1 245.C1c C1c Bolivia." It also appears as C1c in the National Center for Biotechnology​database. So I have my doubts about it being C1g.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

D4h3a mtDNA revisited

Yu-Chun, lI et al. published a paper in 2023, that looked into the link between Native Americans (NAs) mitochondrial DNA (mtDNA) lineage D4h3a and the variant D4h3b which until now has been found only in East China and Thailand.

The authors noted that "D4h3 and its ancestor type D4h are relatively rare in contemporary populations (∼0.5%)" and estimated the age of the NA variant at 19,400 years (15.11 - 24.05 ky).

The interesting part is that they suggest that this haplogroup took a coastal route by sea from China to America, going through Japan's Islands. It didn't cross from Siberia and Beringia into America, walking.

"The coastal distributions of the NA (D4h3a) and Japanese lineages (D4h1a and D4h2), in combination with the Paleolithic archaeological similarities among Northern China, the Americas, and Japan, lend support to the coastal dispersal scenario of early NAs."

The authors highlight that this is a genetic source that is outside of Siberia, which provided mtDNA (a matrilineal lineage) to Native Americans. They stress that it is an "additional ancestral source for the ancestors of NAs beyond Siberia", and that "although only contributed to a small proportion of the mtDNA gene pool of NAs (D4h3a) [it] would be important in complementing the whole picture of origination histories of early NAs."

Below is an image from this paper:

Given the location of the original D4h variant, on the coast of Northern China, the authors suggest that it could have dispersed along the Pacific coastal rim: "we speculate that D4h would have documented LGM and post-LGM dispersals along the eastern Pacific coast. This echoes well with the dispersal D4h3a along the Pacific coastal path when the ice-free corridor was closed. Similarly, Y chromosome C-L1373, which probably radiated in parallel with mtDNA D4h, has also been reported in South Koreans (http://koreangenome.org/) and the Nivkh, thus lending support to a coastal population expansion scenario initiated from northern coastal China. This, together with the Paleolithic cultural affinities along the Pacific, e.g., stemmed points, and the palaeoecological feasibility of maritime dispersals (e.g., kelp highway hypothesis) lends further support to the coastal route hypothesis of early NAs."

It is also found along the coastal people in South America. Stuart J. Fiedel (source) in 2017 wrote that "D4h3a is a relatively rare clade of haplogroup D... it was reported mainly from coastal peoples, including the Fuegians of southernmost Chile, the Chumash of southern California, and the Cayapa of Ecuador The 10,300-year–old skeletal remains from On Your Knees Cave in coastal Alaska belonged to a derived clade of D4h3a."

However, Fiedel says that "the recent distribution of this clade is “deceptive” and has nothing to do with a hypothetical coastal migration".

He bases this argument on the fact that the Anzick baby had D4h3a mt DNA, and is roughly 12,900 years old, but it was found in south-central Montana, far from the Pacific coast, and that other remains are also from the interior of the continent like the Hopewell remains found in the Klunk Mounds in Illinois, and that this variant has been found in extant people of Native American origin in Peru, Bolivia, Brazil, and Mexico.

I had posted about D4h3a back in 2014 and pointed out the same idea:

"We see that the D4h3a tends to have a coastal distribution along the Pacific Ocean from Canada to Tierra del Fuego: Canada, California, Ecuador, Southern Chile and Argentina.
The Yaghan, Alakaluf, Chono, Cayapa, Chumash and the man from On Your Knees Cave, all had this haplogroup.
They all built sea-going craft: rafts, dugout canoes, bark canoes and "sewn plank" canoes.
Other groups also built canoes or rafts; the Changos in Northern Chile, the Pericú, and the Aleuts, though we cannot tell if they also carried this rare haplogroup.
But, as we will see in our next post, it is also found quite far from the Western Coast: as it was detected in ancient remains from the Klunk Mound (Illinois) and in Shandong, China.
Furthermore, the Ainu people of Japan also built "lashed-canoes" -like the Chono and the Chumash (as well as dugouts), and they may have a link with the Amerindians."

It pointed out the Chinese connection, the coastal route, and the original Japanese people, the Ainus. The second post in that 2014 series reported the Klunk Mound remains with this haplogroup variant and proposed that "This haplogroup was widespread across America (Pacific coast and well across the Rockies) and became extinct among all native groups being replaced by the other more common haplogroups now found in those groups (A, B, C, D). These surely migrated later into America." It also suggested a back-migration from America to Asia.

Let's see what future investigations find.

My nest post will be about the Cayapa people of Ecuador.

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

Siberians are not that close to Native Americans

Siberians are said to be the direct ancestors of Native Americans. These Siberians moved into the Beringian land bridge and from there crossed into North America and spread across the whole continent, peopling the Americas, or at least that is what the story says. But what are the facts?

A recent paper: The population history of northeastern Siberia since the Pleistocene, by Martin Sikora et al., Nature vol 570, pp. 182 June 13, 2019, https://doi.org/10.1038/s41586-019-1279-z, describes their findings after sequencing the genomes obtained from 34 ancient remains across Siberia. These genomes span ages ranging from 600 to 31,600 years ago.

These genomes also include the northernmost pleistocene remains found in Siberia, at Yana RHS: they are the earliest direct evidence of human presence in northeastern Siberia, a population that they refer to as Ancient North Siberians (ANS).

Their conclusions are interesting: (bold is mine)

"We find that—despite the complex pattern of population admixture throughout the past 40,000 years the first inhabitants of northeastern Siberia (represented by the Yana RHS individuals) were not the direct ancestors of either Native Americans or present-day Siberians, although traces of their genetic legacy can be observed in ancient and modern genomes across America and northern Eurasia.
These earliest ancient Siberians (the ANS) are known from a handful of other ancient genomes (those of the Mal’ta and Afontova Gora individuals); they are the descendants of one of the early modern human populations that diversified as Eurasia was first settled by our species, and are thus highly distinct.
The ANS were later partially assimilated with a group with East Asian affinity who formed the Ancient Palaeo-Siberians (represented by Kolyma1); this group also probably once had a wide geographical distribution across northern Eurasia. The genetic legacy of Ancient Palaeo-Siberians among present-day Siberians is more limited, being restricted to groups in northeastern Siberia."

They found that "Despite their extreme northeastern Siberian geographical location, the Yana RHS individuals are genetically closer to West Eurasians".

They have to look to a later date to find a Siberian that is closer to Native Americans: "We find that the Kolyma1 individual (dated to 9.8 ka) who represents a lineage that formed after about 30 ka, which we name ‘Ancient Palaeo-Siberian’ documents the first major genetic shift that we observe in the region ... Principal component analysis, outgroup-f3 statistics and mitochondrial DNA and Y chromosome haplogroups (G1b and Q1a1b, respectively) demonstrate a close affinity between Ancient Palaeo-Siberians and present-day Koryaks, Itelmen and Chukchis, as well as with Native Americans."

But Kolyma1 remains, found in northeastern Siberia, close to Beringia, are less than 10 ky old! So she cannot be an ancestor of the older American population which is now believed to have reached America at least 16 kya. Could Kolyma1 be the outcome of a backflow into Siberia, from America? Only about 66% of her genes is similar to that of Native Americans.

So Kolyma1 is the closest they could find to American Natives, however she isn’t an ancestor. Most of her genome belongs to the "Ancient Paleo-Siberian" lineage which split from that of the Native Americans some 24,000 years ago.

Interestingly, they report that "A signal of Australasian ancestry that has been observed at a very low frequency in some modern and ancient South American populations is not evident in any of the ancient Siberian or Beringian samples sequenced here, or in previous studies".

The study concludes that "the majority of Native American genetic ancestry is likely to have originated in northeastern Siberia rather than south-central Siberia, as has been inferred from modern mitochondrial and Y chromosome DNA."

To sum it up, the northernmost of the early Siberians (Yana) are not related to the people who supposedly peopled America. The later Kolyma woman is similar to but not an ancestor either, she is actually a later arrival in the area, when she died, America was already inhabited!

There is a paucity of remains between Yana and Kolyma1 which means that we have to wait for more remains to be discovered and studied before this issue is settled for good.

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

An ancient American origin of hepatitis B virus

Human hepatitis B viruses (HBV) are found in human populations all around the world. They can be grouped into ten genotypes named A to J (each with their own subgenotypes).

The genotypes have a distinct geographical distribution as you can see in the map below (Source):

Hepatitis B virus global distribution of genotyhpes.

A can be found in Africa, Asia, Europe and North America. B in Eastern and Southeastern Asia. C in the same region and Central Asia. D in India and western Eurasia. E a recent apparition, found exclusively in Africa (not taken to the Americas with slave trading and probably 200 years old only - read more).

F and H are exclusive to South and Central America.

And here is the unusual thing, thse F and H genotypes are distinct from all the other ones: they branch from the phylogenetic tree as a separate and earlier branch as can be seen in the following trees from different authors:

HBV phylogenetic tree.Credits

HBV, another phylogenetic tree Note location of chimps and gorillas.Credits

HBV, a phylogenetic tree. See the branch of the woolly monkeys by the American F and H genotypes.Credits

So where did HBV originate? And here is the difficult question which cannot be answered by the usual Out of Africa theory (originated in African apes and passed on to humans there, spreading out of Africa as our ancestors migrated across the globe, reaching America last).

This time the evidence does not point towards a clear African origin. It seems that the oldest and most distant branch is rooted in America.

Margaret Littlejohn, Stephen Locarnini, and Lilly Yuen describe the five theories about HBV's origin and their shortcomings:

• New World origin (out of South America), and then reached the Old World after European discovery in 1492.
• Cospeciation: evolved in parallel in certain primate species over the past tens of millions of years.
• Coevolution as anatomically modern humans (AMH) migrated out of Africa. Caveat: "it does not fit with the close genetic relationships observed between primate and human HBV. Another inconsistency is that Native Americans predominantly have genotype F infections, whereas northeast-Asians, who are their closest relatives genetically, have genotypes B and C infections."
• Cross-species transmission, between human and nonhuman primates.
• Bat origin

The authors interestingly point out that "Given the arguments for and against each of these five theories, it is probable that HBV evolution cannot be explained by any single theory. The reality probably involves cospecies evolution within birds, rodents, and bats, followed by a series of cross-species transmission events to explain the close relationship between human and nonhuman primate HBVs observed today. Challenges for any unifying theory include the high level of genome divergence observed between HBV sequences of New World woolly monkeys and other nonhuman primates, w hich cannot be explained by the cross-species transmission theory, and also that HBV has only been detected in rodent species of the New World. If HBV coevolved with avian, rodent, and primate species, then why is it not found in all rodent and primate species? In addition, if HBV emerged out of Africa with AMH, then why are people from the New World, who are genetically most closely related to humans in the Far East, predominantly infected with HBV genotypes F and H rather than the genetically unrelated HBV genotypes B and C that are found in the Far East?"

As you can see, the American F variant and its presence in the New World woolly monkeys stand firmly against an Out of Africa origin.

Finally the paper mentions archaic hominins (Neanderthals, Denisovans and our admixing with them): "The influence of these various groups of archaic humans on the evolutionary history of HBV would be difficult to decipher. However, the possibility that human HBV may have originated, at least in part, from these archaic humans should not be discounted."

It is likely that it originated in the Americas in an Archaic (H. erectus) group and then moved into Asia and Africa (the most recent variant "E" is African after all!).

But Out of Africa is hard to beat. The author of a paper that studied HBV found in 7,000 year-old remains in Eurasia, is quoted here as follows:

"... it is still unclear how old HBV actually is. "It could be much older. It could even be coming out of Africa, which would explain why chimpanzees and gorillas fall together with the oldest HPV genomes" he adds. "That could be one explanation, but we also find it in the new world and new world monkeys and old world monkeys separated 60 million years ago, so it's very unlikely it's that old. There's lots of open question marks here."

But, he is mistaken, the gorillas and chimpanzees HBV does not align with the "oldest" groups (see second tree image further up), they lie closer to the more recent Eurasian variants..."

As usual, when an odd thing appears in the Americas which confronts the Out Of Africa theory, orthodox science finds it hard to explain them away and support the OOA theory.

Merry Christmas and Seasons Greetings to all our readers. And a Great 2019 for everyone!

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

On the direction and root of phylogenetic trees

When I see a phylogenetic tree (also known as an evolutionary tree), I always wonder why do we believe that those branches, trunk and the root which anchors it, are correct. I ask myself why is it assumed that the mutation took place in one direction and not the other. And this trivial question is fundamental because the branches open up from other branches based on the differences between the DNA as you move along them.

Below is a very simple example of what I mean. Imagine we reach a planet, and come across a species whose DNA is sequenced and reveals the folowing genes: A, B and C.

We then take a sample of individuals, and sequence their genome. The nine individuals in our sample come from different continents and the "order" of the genes is different in each individual:

AAAAA, AACAA, BAAAA, BAAAB, BBAAA, CACAA, AACAB, BAACB and BABAB.

We assume that mutations take place at random so a B can spontaneously mutate into C or A, an A into B or C and a C into A or B. So, a group of scientists after looking at the genomes assumes that AAAAA is the oldest group of that species and that the other populations are the result of mutations that modified the original genome. They build tree (1) shown below. The most distant population is the one with the BABAB genome.

The red arrow marks the "founding" population and the green arrow the "newest" group, descended from them.

But another group of scientist based on some ancient remains and other assumptions, says "No, the original population is not AAAAA, it is the people carrying the BABAB genes" (exactly the opposite to what the first group of scientists have proposed and proven in Tree (1).

The second group builds Tree 2, where as we can see (the green arrow shows the original population and the red one shows us where they place the population AAAAA. For this second group of scholars, populations AACAB and CACAA are the "most recent" populations. The tree below shows the mutated gene in red:

Two different trees built from the same genome samples. Copyright © 2018 by Austin Whittall

The scholars could then identify haplogroups where the A to C or the B to A mutation marks a haplogroup and theorize on how these haplogroups evolved one from the other... Does this sound familiar? Yes, it is how the mtDNA and the Y chromosome DNA haplogroups were created -by adopting certain mutations as key indicators for branches and defining that it took place in a certain way (in our DNA, for instance, an aadenine (A) switch for a cytosine (C) may mark a haplogroup. A for C but, we could also -as in our thoretical planet imagine that the C switched for an A and that the supposed parent genome is actually the child and not the other way round.

Thus the "new" American genomes could actually be the oldest and the African ones the youngest (like switching from tree 1 to 2 above).

This is of course an oversimplification, but we do have the DNA of Neanderthals, Denisovans, Homo sapiens from different sites around the world, and anchors from our ape relatives, the chimps. But often, when I look at the sequences (CGACGGAATACG... and so on - see this image below (from Nature where a standard human sequence -top row "Reference"- is compared to Neandertal sequences in the bottom two rows), I wonder how true and accurate are our "reconstructions". Which base mutated first, which later?...

And also See this image, which compares Denisovan, Neandertal and some apes and monkeys.

Trees are created by computer programs that use "assumptions" and theoretical considerations built into them by the scientists that programmed them. They supposedly work using statistically sound calculations, which are so complex that I doubt anyone can verify them without the help of computer software... so maybe some bias is built into them, for instance assuming that AAAAA is the "original" genome in our distant planet, or here, assuming that the DNA of an African is "older" than that of an Amerindian...

I don't believe in snake oil, but I do believe that we should look at facts with open eyes (like the two trees that can be built using those nine sequences in our distant planet. Same data different conclusions) and not be biased by a prejudice (prejudice = Pre Judgement, we use the data to prove what we believe to be true, not to prove the facts...).

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

Tianyuan Man's DNA (40 ky old) linked to present South American Natives

I have read online that an analysis of the remains of the "Tianyuan Man", from China, dating back to 40,000 years ago, have revealed some unexpected findings.

I will quote Phys.org below: (I highlighted part of the text in bold)

"... With a close relationship to present-day Asians, they expected him to be similar to present-day Asian populations with respect to Europeans. It was a surprise when they found that a 35,000-year-old individual from Belgium, GoyetQ116-1, who in other ways seemed to be an ancient European, shared some genetic similarity to the Tianyuan individual that no other ancient Europeans shared.
...
A second unexpected result sheds some light on human genetic diversity in prehistoric East Asia. In 2015, a study comparing present-day populations in Asia, the Pacific and the Americas showed that some Native American populations from South America had an unusual connection to some populations south of mainland Asia, most notably the Melanesian Papuan and the Andamanese Onge. That study proposed that the population that crossed into the Americas around 20,000 years ago could not be thought of as a single unit. Instead, one or more related but distinct populations crossed at around the same time period, and at least one of these groups had additional ties to an Asian population that also contributed to the present-day Papuan and Onge.
No trace of this connection is observed in present-day East Asians and Siberians, but unlike them, the Tianyuan man also possesses genetic similarities to the same South Americans, in a pattern similar to that found for the Papuan and Onge. The new study directly confirms that the multiple ancestries represented in Native Americans were all from populations in mainland Asia. What is intriguing, however, is that the migration to the Americas occurred approximately 20,000 years ago, but the Tianyuan individual is twice that age. Thus, the population diversity represented in the Americas must have persisted in mainland Asia in two or more distinct populations since 40,000 years ago."

A simple answer for the "intriguing" finding is that either:

(a) The ancestors of Tianyuan man came from South American stock, crossed North America before it was peopled by later Siberian-origin humans, and entered Asia via Bering heading south and peopling China, Melanesia and the Andamans first, and then heading west into Europe where the ancestors of the GoyetQ116-1 remains picked up these genes.

(b) The Asian ancestors of South Americans entered America at least 40,000 years ago, before Siberian-Asians peopled North America. This eliminates the need for a persistance in Asia of "two or more distinct populations since 40,000 years ago".

According to Science:

"... Tianyuan Man inherited about as much Neandertal DNA—4% to 5%—as ancient Europeans and Asians of similar age. That’s a bit higher than the 1.8% to 2.6% of Neandertal DNA in living Europeans and Asians. The Tianyuan Man did not have any detectable DNA from Denisovans...
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. They inherited about 9% to 15% of their DNA from an ancestral population in Asia that also gave rise to the Tianyuan Man. "

Or rather the Tianyuan man "inherited" this DNA from the American ancestors of the present Amerindian populations in South America.

The lack of Denisovan DNA is interesting and we should find out how come Melanesians which have a very high content of Denisovan DNA also have a very close link to Tianyuan man which has no Denisovan genes!

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2017 by Austin Whittall © 

Into Africa: sub-Saharan genetic diversity is due to introgression with archaics

Following up on my previous post, I want to share some more papers on the subject of the admixture of Homo sapiens and archaic hominins in Africa, which may be the cause of the "genetic diversity" which is the main evidence supporting an African origin of modern humans.

This paper (Genetic evidence for archaic admixture in Africa, by Michael F. Hammera, August E. Woernera, Fernando L. Mendezb, Joseph C. Watkinsc, and Jeffrey D. Walld) reached the following conclusions:

"Extensive simulation results reject the null model of no admixture and allow us to infer that contemporary African populations contain a small proportion of genetic material (˜2%) that introgressed ˜35 kya from an archaic population that split from the ancestors of anatomically modern humans ˜700 kya."
...
"Th[is] suggests that one such introgression event may have taken place in central Africa (where there is a very poor fossil record). Interestingly, recent studies attest to the existence of Late Stone Age human remains with archaic features in Nigeria (Iwo Eleru) and the Democratic Republic of Congo (Ishango)"

The authors cite This paper (Allsworth-Jones, P., Harvati, K. and Stringer, C. (2010) The archaeological context of the Iwo Eleru cranium from Nigeria and preliminary results of new morphometric studies. In: Allsworth-Jones, P., (ed.) West African Archaeology New developments, new perspectives. BAR, S2164 . Archaeopress , pp. 29-42. ISBN 978 1 4073 0708 4):

""... results highlighted apparent archaic aspects in the specimen in its long and rather low cranial shape, and although modern overall, it also resembled fossils such as Omo Kibish 2 and Ngandong in certain respects. New studies... establish the relatively archaic shape of the vault, and confirm that this Late Stone Age individual was markedly different from succeeding populations.".

So we have archaic humans living relatively recently, and, the recent studies on Homo naledi also show that it was contemporary to the earliest modern humans (but it did not live -as far as we know in Central or Western Africa, but in South Africa:

In This paper we see that Homo naledi, is quite primitive but also relatively recent (The age of Homo naledi and associated sediments in the Rising Star Cave, South Africa. Paul HGM Dirks. https://doi.org/10.7554/eLife.24231.001):

""We... establish[ed] that all sediments containing Homo naledi fossils can be allocated to a single stratigraphic entity ... interpreted to be deposited between 236 ka and 414 ka. This result has been confirmed independently by dating three H. naledi teeth with combined U-series and electron spin resonance (US-ESR) dating. Two dating scenarios for the fossils were tested ...: a maximum age scenario provides an average age for the two least altered fossil teeth of 253 +82/–70 ka, whilst a minimum age scenario yields an average age of 200 +70/–61 ka. We consider the maximum age scenario to more closely reflect conditions in the cave, and therefore, the true age of the fossils... we have constrained the depositional age of Homo naledi to a period between 236 ka and 335 ka. These age results demonstrate that a morphologically primitive hominin, Homo naledi, survived into the later parts of the Pleistocene in Africa, and indicate a much younger age for the Homo naledi fossils than have previously been hypothesized based on their morphology."

In other words dating range from 139 to 414 ka but the authors selected intermediate dates. They too seem surprised by its archaic appearance at such a late date.

And it was indeed "archaic" as attested by this paper (Human Evolution: The many mysteries of Homo naledi, Chris Stringer) which says:

"...Berger et al. describe how the collection displays a unique combination of primitive and derived characteristics (Berger et al., 2015). For example, the small brain size, curved fingers and form of the shoulder, trunk and hip joint resemble the prehuman australopithecines and the early human species Homo habilis. Yet the wrist, hands, legs and feet look most like those of Neanderthals and modern humans. The teeth have some primitive features (such as increasing in size towards the back of the tooth row), but they are relatively small and simple, and set in lightly built jawbones. Overall, to my eye, the material looks most similar to the small-bodied examples of Homo erectus from Dmanisi in Georgia, which have been dated at ~1.8 million years old".

Interesting that H. naledi resembles more primitive Homo erectus with an age of 1.8 million years when it is only roughly 200 ka old!.

Another Paper (Genome Research Published in Advance February 17, 2016, doi: 10.1101/gr.196634.115 Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies, PingHsun Hsieh et al.) supports this idea of an archaic introgression, but this time, in Pygmies!:

"... our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing model-based whole genome-level evidence of African archaic admixture. Our inferences also suggest a complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH (anatomically modern humans), likely within the last 30,000 yr."

These findings plus that of an early presence of Homo sapiens in Morocco - In this paper (New fossils from Jebel Irhoud, Morocco and the pan-African origin of Homo sapiens, Jean-Jacques Hublin et al. Nature 546, 289–292, 2017):

"...We identified a mosaic of features including facial, mandibular and dental morphology that aligns the Jebel Irhoud material with early or recent anatomically modern humans and more primitive neurocranial and endocranial morphology. In combination with an age of 315?±?34 thousand years (as determined by thermoluminescence dating)3, this evidence makes Jebel Irhoud the oldest and richest African Middle Stone Age hominin site that documents early stages of the H. sapiens clade..."

An age which clearly overlaps that of H. naledi

These findings may lead to an overhaul of the Out Of Africa theory as it is not implausible that H. sapiens originated in Eurasia or even America from other Out Of Africa migrants that departed long ago (Neanderthal ancestors or even H. erectus), and then they peopled Africa recently from North to South and mixed during their Into Africa journey with archaics like Naledi or Iwo Eluru, picking up genetic diversity and carrying it into sub-Saharan Africa with them.

Maybe archaic DNA will be recovered from Naledi and clarify the situation.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2017 by Austin Whittall © 

Homo naledi is far too young...

Homo naledi, a very primitive looking hominid, once believed to be a very ancient relative of modern humans, has been dated to a very recent period, in this paper (The age of Homo naledi and associated sediments in the Rising Star Cave, South Africa, by Paul HGM Dirks et al., DOI: http://dx.doi.org/10.7554/eLife.24231, published May 9, 2017 Cite as eLife 2017;6:e24231) some 236 to 335 kya. And the abstract concludes:

"...We have constrained the depositional age of Homo naledi to a period between 236 ka and 335 ka. These age results demonstrate that a morphologically primitive hominin, Homo naledi, survived into the later parts of the Pleistocene in Africa, and indicate a much younger age for the Homo naledi fossils than have previously been hypothesized based on their morphology."

Primitive

A second paper (New fossil remains of Homo naledi from the Lesedi Chamber, South Africa, John Hawks, et al., DOI: http://dx.doi.org/10.7554/eLife.24232 Published May 9, 2017 Cite as eLife 2017;6:e24232) points out its really primitive crania, which has a smaller size than that of H. habilis. And this creature lived side by side with our purported African ancestors!

H. naledi (R) seems to have shared southern Africa with distinct human species, such as Kabwe man (L)

Apparently there are two theories to explain H. naledi:

1. It is a ancient relative of H. habilis and retained its primitive morphology in a branch that survived into the times of modern humans.
2. It split later on, after H. habilis, maybe from Homo erectus and reverted into a primitive form.

Could these primitive hominids have admixed with Africans and enriched their genome with "diversity"? adding genes and variety that did not appear out of Africa because H. naledi were constrained to their Sub Saharan location?

An out of Africa origin of modern humans Asian (or even, an American) origin for modern humans, who later reached Africa and admixed with H. naledi would surely yield the current genetic variability.

Since Naledi is so young, perhaps viable DNA could be obtained and sequenced. Who can tell what that information will tell us!

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2017 by Austin Whittall © 

Denisovans, Inuit and Native Americans

An article, which you can read here Arctic Inuit, Native American cold adaptations may originate from extinct hominids from Dec. 2016, tells us something about the Inuit, Amerindians and Denisovans or some other now extinct archaic hominid... (the original paper is here).

Two genes, TBX15 and WARS2 seem to be critical in how the body deals with fat in cold climates to generat heat. The article points out the following:

" The Inuit DNA sequence in this region matches very well with the Denisovan genome, and it is highly differentiated from other present-day human sequences, though we can't discard the possibility that the variant was introduced from another archaic group whose genomes we haven't sampled yet," said Fernando Racimo, lead author of the study.
The authors found that the variant is present at low-to-intermediate frequencies throughout Eurasia, and at especially high frequencies in the Inuits and Native American populations, but almost absent in Africa. TBX15 is a gene known to affect the human body's response to cold, and is associated with a number of traits related to body fat distribution. The authors speculate that the archaic variant may have been beneficial to modern humans during their expansion throughout Siberia and across Beringia, into the Americas."

Allow me to suggest another option: the archaic variant evolved in Homo erectus in high latitude Asia, they had reached this part of the world at least 1 million years ago. They hunted big game (mammoths and hairy rhino lived there and did so for millions of years). What would stop them from following the heards into America? Thanks to this adaptation they could. And this is why, their descent, the Amerindians carry it. Later after Homo sapiens evolved in America, it back migrated into Siberia and Eurasia and reached -though diluted- Africa when it was peopled by modern H. sapiens from Asia and America.

This explains the cline from a peak in America to a low in Africa. As you moved into hotter regions it became less of an advantadge (actualy a fatty layer in a hot climate is a disadvantage).

Sources
Archaic Adaptive Introgression in TBX15/WARS2 Fernando Racimo David Gokhman Matteo Fumagalli Amy Ko Torben Hansen Ida Moltke Anders Albrechtsen Liran Carmel Emilia Huerta-Sánchez Rasmus Nielsen Mol Biol Evol (2017) 34 (3): 509-524. DOI: https://doi.org/10.1093/molbev/msw283 Published: 22 December 2016

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2017 by Austin Whittall © 

Into Africa, some proof on an Out Of America origin of modern Homo sapiens

Regarding my previous post where I mentioned a paper on the non-African origin of modern humans, I have come across another very interesting paper: "Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa" by Michael DeGiorgio, Mattias Jakobsson and Noah A. Rosenberg (Proc Natl Acad Sci U S A. 2009 Sep 22; 106(38): 16057–16062. Published online 2009 Aug 17. doi: 10.1073/pnas.0903341106) which offers an interesting model which can explain the greater diversity of Africans and at the same time make them the "most recent" humans instead of the oldest ones.

The usual argument for an Out of Africa origin of Homo Sapiens is the higher diversity in Africa versus that of non-African populations. A typical example used as proof is the graph showing how Heterozygosity decreases with the distance to Africa (there are countless of these on the internet, with the Y axis showing Heterozygosity and the X axis showing the distance from Addis Abbaba), below is one of them:

A typical heterozygosity vs. distance to Ethiopia. From Fig. 2 in [1]

Notice the negative gradient of the graph (shown by the dashed line in the figure -Fig. B, on the right). Heterozygosity falls from left to right.

The paper by DeGiorgio, Jakobsson and Rosenberg which caught my attention explores a models to explain this fact. In doing so they analyze different alternatives. And the one they discard because it does not fit the current idea of an Out of Africa model, is precisely the one that explains the data, if you accept a non-African origin of mankind. Allow me to explain:

Archaic Persistence Model

The team developed this "archaic persistence model" in which an archaic population evolved-mutated and originates modern humans (Homo sapiens). And as this first original and most ancient Homo sapiens population expands outwards from its homeland, it spreads gradually forming colonies which move into a "collection of preexisting archaic populations". For instance Denisovans, Neanderthals or even surviving yet unknown Chinese hominds -or Homo erectus descendants...

In the words of the authors, this is what they observed as the populations moved away from the original nucleous, the first modern human population:

"Heterozygosity increases, LD decreases, and the ancestral allele frequency spectrum slope increases with increasing colony number. These results can be understood from the fact that in the long time since the initial divergence, the K archaic populations have enough time to develop distinctive localized variants. As the migration wave travels through them, it accumulates diversity, gathering new variants from each population through which it passes. Thus, heterozygosity increases with increasing colony number in the same way that it increases in the archaic admixture model at the population in which admixture occurs. The difference between models lies in the fact that in the archaic persistence model, archaic admixture occurs in every population, so that heterozygosity increases at each step rather than at a single location. This occurrence of archaic admixture at each step also explains the decrease in LD and increase in the slope of the ancestral allele frequency spectrum that occur at each step...

In other words they observed that if the original, the "first real" human group, was in Africa, as we moved further away from there we should find more heterozygosity, which we don't. Hence the model is wrong and despite having originated in Africa we did not go through this type of admixture.

But lets just look at this with a more open mind:

Turn it around!

However if the original home of modern humans (Homo sapiens) was in America and not Africa, then, as they migrated outwards from America, into Asia, Oceania, Europe and went through each of the archaic populations in the old world, adding diversity and finally reached Africa mixing with the archaics there, the heterozygosity would be lowest in America and grow towards Africa, which is exactly what their model finds and which coincides with the observed heterozygosity cline in modern humans.

So It all makes sense if you invert the origin of the first humans: form Africa, to America.

Below is the image showing how heterozygosity grows as you move away from the original H. sapiens population if you assume the Archaic Persistence Model, the authors discard it because the actual observed heterozygosity falls as you move away from Africa:

From Fig 6 in DeGiorgio, Jakobsson and Rosenberg, adapted by A. Whittall

Now let's turn this same figure around and the result is a graph with a negative gradient which is exactly the same as the first graph we used in this paper (the distance to A. Abbaba & heterozygosity):

Same figure as above but we change the location of the first modern humans
Adapted by Austin Whittall

As an engineer, I sometimes get the feeling that Anthropology and those who study the origins of humanity are like the late 1800s Physicists who despite all the evidence kept on pushing the notion of ether or fiddle with the data to uphold classic mechanics. It took Einstein and Plank to change the paradigm with their Relativity and Quantum theories. Something similar took place in the 1500s, with Copernicus explaining with graceful simplicity the movement of the planets, doing away with the complex Ptolomean system. A shift in mindset is needed to look at the same data to find the necessary changes and to avoid adhering to theories that contradict that data.

Sources

[1] Verdu P, Pemberton TJ, Laurent R, Kemp BM, Gonzalez-Oliver A, Gorodezky C, et al. (2014) Patterns of Admixture and Population Structure in Native Populations of Northwest North America. PLoS Genet 10(8): e1004530. doi:10.1371/journal.pgen.1004530

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

An intersting paper on the NON AFRICAN orign of mankind

Seems it is an Out of Asia after all...

This is a very interesting -at least it goes against the grain of most orthodox papers, positing an out of Asia orign of mankind- paper: WORLD SCIENCE EN ROUTE FROM OUT-OF-AFRICA TO OUT-OF-AMERICA: FIRST STOP IS OUT-OF-ASIA.

By the way, Happy 2017!! I have the feeling that this year will bring us surprises galore, and not only from some Neanderthals (with my apologies to our great and dignified ancestors) who have recently taken up their lodging in Washington DC.

May reason, sensible discussion of ideas, open-mindedness and above all, Western values such as respect, freedom to dissent, freedom of religion, thought and above all, freedom of speech, prevail above any populist sleazy politicians and their demagoguery. On both sides of the Anglo-Saxon Atlantic (i.e. Brexit supporters). Respect, chivalry and rationality must prevail over bigotry, prejudice and Medieval witch-hunting. Racism belongs with the 1940s fascists, not in the XXIst century.

And if you post any insidious comments I will publish them even if I disagree -of course-, no foul language please.

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

HPV16 and Humans, Neanderthals, Denisovans and the Out Of Africa theory

Short comment. I have just read this paper: Transmission Between Archaic and Modern Human Ancestors During the Evolution of the Oncogenic Human Papillomavirus 16 by Ville N. Pimenoff, Cristina Mendes de Oliveira and Ignacio G. Bravo. Mol Biol Evol (2016), doi: 10.1093/molbev/msw214, First published online: October 7, 2016.

I am trying to see how it fits in with a non African origin of mankind because the authors are trying to fit their finding that the oldest and most diverse haplogroups of HPV 16 are not found in Africa, but out of it (the African variants of HPV are newer and less diverse) within the Out of Africa theory. And it may not be the case.

Above a map showing distribution of the main clades and below. Some quotes from the paper:

"HVP16A (fig. 2) (is), the most basal HPV16 lineage, in all continents and in all indigenous populations, except in sub-Saharan Africa"

"Moreover, for indigenous populations in South America, for instance, the increased presence of HPV16A lineage variants has been proposed to reflect the influence of recent European occupation (Picconi et al. 2003). However, such a rapid selective sweep of the putative pre-Columbian HPV16 genetic diversity would require strong selection forces for the viral dynamics in very short time scale, which are not compatible with our current understanding of PV evolution"

These Amerindians always have some oddity regarding their genetics, don't they?

"...most common HPV16A lineage haplotypes were observed mostly in Eurasian populations while most common HPV16B, C and D lineage haplotypes were observed mainly in African populations...
Neanderthals/Denisovans may have carried essentially the ancestral HPV16A. Evolution of HPV16 genomes in ancestral Hominin populations remaining in Africa, instead, would have lead to HPV16B and CD lineages (fig 4). The virtual absence of HPV16B outside Sub-Saharan Africa is parsimoniously explained if in the last out-of-Africa expansion, the modern human ancestors that left Africa probably lost the ancestral HPV16B lineage by a lineage sorting event ..."

And the above is the theory put forth by the authors to explain the anomaly of less diverse HPV in Africa vs. the Rest of the World.

"After the modern human dispersal, the HPV16CD ancestor generated in allopatry the HPV16C lineage in the populations remaining in Africa, and the HPV16D lineage in the populations outside Africa (fig. 4). During their expansion in Europe and in Asia, modern human ancestors experienced limited admixture with Neanderthal and Denisovan populations, and were exposed to the HPV16A lineage, most likely through sexual contact..."

But this is all conjectures, there is no physical evidence of HPV in Denisovans or Neanderthals:

"... there is hitherto no evidence of the presence of any PV sequences from ancient human samples. Indeed, we analysed the currently available Neanderthal and Denisovan pre-assembly sequence data, and we could not find any significant traces of any known HPVs in these data sets"

"... that the HPV16A1-3 lineage predominated in Europe, South Asia and Central/South America, and was also present in all other continental subgroups, albeit with very low prevalence in sub-Saharan Africa (fig. 2). HPV16A4 was the most prevalent lineage in East Asia and was also present in North America, but was virtually absent elsewhere. Variants B and C were largely restricted to Africa and were especially prevalent in Sub-Saharan Africa, although they were also observed in North America. Variant D was present in all continents, displaying low prevalence in Sub-Saharan Africa, and the highest frequency in Central/South America.·"

Why is "D" highest in the Americas if it is supposed to have originated in Africa (see further up)... slave trade by Europeans? We'd need to see Karitiana or Coya, Pima haplogroups...

Then we have the time frame!! (rather wide): "Depending on substitution rate priors, divergence times of extant HPV16 lineages showed to be between 260 kya and 4.8 Mya"... early enough to be older than our oldest relatives. It may also leave the window open for an Homo Erectus migartory event into Asia carrying the ancestral HPV16A root. And the diversity issue also seems odd: "Although HPV16A was thus always the basal clade, divergence within HPV16A showed to be lower than within HPV16BCD" So the oldest group with A type haplos are less diverse among them than the BCD are.. maybe some ancient bottleneck in the A groups?.

And the diversity again: " East Asian and Central American HPV16 isolates showed higher average number of pairwise differences compared with sub-Saharan African isolates, even after accounting for intralineage diversity.", what? something in America more diverse than in Sub-Saharan Africa... why?

"... although HPV16A is the oldest lineage, the tmrca for the HPV16BCD variants (197kya, 95% 121-291kya) was older than the tmrca for the HPV16A lineage (88kya, 95% HPD 50 – 134kya), and the HPV16A lineage encompasses less genetic diversity than the sister HPV16BCD lineages." This is odd, again the diversity issue (bottleneck) but the split is younger in the "oldest" lineage?? That sounds odd.

I will keep on trying to make sense of this, and post later on this finding.

New 03 Nov. 2018, following a recent paper published two days ago, I have added a new post on this subject: HPV Neanderthals, Africans and the early peopling of America

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

Humans in Siberia 10,000 years earlier than formerly believed,

Seems like human beings have been on the move for much longer than formerly believed. A paper published in Science (Early human presence in the Arctic: Evidence from 45,000-year-old mammoth remains Vladimir V. Pitulko, Alexei N. Tikhonov, Elena Y. Pavlova Pavel A. Nikolskiy, Konstantin E. Kuper, Roman N. Polozov, Science 15 Jan 2016:Vol. 351, Issue 6270, pp. 260-263 DOI: 10.1126/science.aad0554), mentions their discovery of a butchered mammoth, with clear signs of pre and post-mortem wounds caused by intelligent beings. The date is 45000 years ago, and pushes back the presence of humans in the area some 10,000 years.

The free-access text says:

"Earliest human Arctic occupation
Paleolithic records of humans in the Eurasian Arctic (above 66°N) are scarce, stretching back to 30,000 to 35,000 years ago at most. Pitulko et al. have found evidence of human occupation 45,000 years ago at 72°N, well within the Siberian Arctic. The evidence is in the form of a frozen mammoth carcass bearing many signs of weapon-inflicted injuries, both pre- and postmortem. The remains of a hunted wolf from a widely separate location of similar age indicate that humans may have spread widely across northern Siberia at least 10 millennia earlier than previously thought.
Abstract
Archaeological evidence for human dispersal through northern Eurasia before 40,000 years ago is rare. In west Siberia, the northernmost find of that age is located at 57°N. Elsewhere, the earliest presence of humans in the Arctic is commonly thought to be circa 35,000 to 30,000 years before the present. A mammoth kill site in the central Siberian Arctic, dated to 45,000 years before the present, expands the populated area to almost 72°N. The advancement of mammoth hunting probably allowed people to survive and spread widely across northernmost Arctic Siberia."

The place is well north of the Arctic Circle, at 72° north. Location map.

So they were there longer ago than expected which means they were equipped to reach America via the Arctic earlier than expected too. or Move out of America into Asia at an early date... After all, who said they were Homo sapiens? They could be Denisovans, archaic Asian or even archaic American hominins.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2016 by Austin Whittall © 

More evidence of archaic humans in Asia ca. 100-200 kya.

A paper published in Nature, two days ago: Earliest hominin occupation of Sulawesi, Indonesia by Gerrit D. van den Bergh et al., Nature 529, 208–211 (14 January 2016) doi:10.1038/nature16448, reports an interesting finding in Indonesia:

"Sulawesi is the largest and oldest island within Wallacea, a vast zone of oceanic islands separating continental Asia from the Pleistocene landmass of Australia and Papua (Sahul). By one million years ago an unknown hominin lineage had colonized Flores immediately to the south1, and by about 50 thousand years ago, modern humans (Homo sapiens) had crossed to Sahul. On the basis of position, oceanic currents and biogeographical context, Sulawesi probably played a pivotal part in these dispersals. Uranium-series dating of speleothem deposits associated with rock art in the limestone karst region of Maros in southwest Sulawesi has revealed that humans were living on the island at least 40 thousand years ago. Here we report new excavations at Talepu in the Walanae Basin northeast of Maros, where in situ stone artefacts associated with fossil remains of megafauna (Bubalus sp., Stegodon and Celebochoerus) have been recovered from stratified deposits that accumulated from before 200 thousand years ago until about 100 thousand years ago. Our findings suggest that Sulawesi, like Flores, was host to a long-established population of archaic hominins, the ancestral origins and taxonomic status of which remain elusive.

The Bold, part that I highlighted above is very clear: archaic humans lived in this part of Sulawesi between 200 and 100 thousand years ago. They were not Homo sapiens, who arrived there about 50,000 years ago. So what are these "elusive" people?

The evidence of a non-African ancestral human group is growing. Could they be Denisovans? Homo erectus? We will just have to wait and see.

Did they move further north, into China, Eastern Siberia and, maybe the Americas? Or did they come from there in an Out-Of-America dispersal?

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2016 by Austin Whittall © 

Pre-Columbian skull with Middle Eastern mtDNA?

I have just come across a very brief "Paper" which details a study conducted on a skull found in Idaho, U.S., which was dated by radiocarbon to an age of about 600-700 years BP and is therefore older than the arrival of Europeans (Columbus) to America. The startling finding is that: "Forensic Mitochondrial DNA Haplogroup R0a1a identified, although it is not associated with known Native American populations. Area where Haplogroup R0a1a originated is from the Arabian Peninsula or western Eurasia" [1] of course the authors find that rather difficult to explain so they added that: "Forensic mitochondrial DNA identified haplogroup R0a1a which originated on the Arabian Peninsula; this is not consistent with the rest of the data in the study. Future work will include. Additional trace element analysis from the bone to provide constraints to the duration of burial independent of C-14 dating. A secondary ancient DNA analysis to confirm or disprove the initial findings".

That is check if the skull is younger and therefore admixture with an Arabian could be more plausible or, the mtDNA was wrongly identified and therefore the skull is old and Amerindian.

The map shows where R0 hg is more prevalent: Middle East, Balkans, Horn of Africa and East AFrica....

I am interested in following up on their following studies.

Source

Watkins, Jennifer K.; Alanko, Gordon A.; Blatt, Samantha H.; Bradbury, Cynthia A.; Kohn, Matthew J.; Lytle, Marion; Lacroix, Deborah; Taylor, Joanna; Dudgeon, John; Hazard, Rebecca E.; O’Leary-Jepsen, Erin; and Butt, Darryl P., "A Transdisciplinary Approach to Determining the Provenience of a Distorted, Pre-Columbian Skull Recovered in Rural Idaho" (2015). College of Engineering Presentations. Paper 5. http://scholarworks.boisestate.edu/eng_15/5

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall © 

On Y chromosome Hg. C in South America

Hello again. I have taken a short break and vacations (winter here in Argentina, but vacations were needed!), and are back online posting again.

One year ago I wrote about Y chromosome's haplogroup C, one of the oldest ones, found in S.E. Asia, Melanesia, Micronesia, Polynesia, East Asia and only very rarely among Native Americans (Y chromosome haplogroup C Part 1 - C hg. in America - seeking a link with Homo erectus). I revisited the subject again this week and was interestingly surprised to find two new developments:

New Paper on the Ecuadorian natives

A paper titled "Insights into the origin of rare haplogroup C3* Y chromosomes in South America from high-density autosomal SNP genotyping", by Massimo Mezzavilla, Maria Geppert, Chris Tyler-Smith, Lutz Roewer, Yali Xue (DOI: http://dx.doi.org/10.1016/j.fsigen.2014.11.005) looks into different explanations for the unusual prevalence of hg C3* among two groups of Ecuadorian natives and concludes that:

"Our simulations revealed good power to detect recent admixture, and that ≥5% admixture 6 Kya ago could be detected. However, in the experimental data we saw no evidence of gene flow from Japan to Ecuador. In summary, we can exclude recent migration and probably admixture 6 Kya as the source of the C3* Y chromosomes in Ecuador, and thus suggest that they represent a rare founding lineage lost by drift elsewhere."

Which is in line with my conjectures put forth in my post one year ago: "It seems to me that there are several different haplotypes hidden in the C3* paragroup that have yet to be identified, but the Americans, but, it clearly indicates no relationship between Japanese or Koreans and the Amerindians...
It is extremely likely that the current patchy distribution and the extremely low frequences of C3* paragroup in South America reflects the remains of a once widespread lineage later overlaid by more recent migrants from Asia and which was seriously reduced due to the bottleneck provoked by the Conquest of America that began in the Sixteenth Century.".

Which is interesting as it indicates that a very "old" Y chromosome haplogroup is present in America. But wait, there is some more evidence:

The Botocudos of Brazil

A recent article at DNAeXplained, "Botocudo Ancient Remains from Brazil" tells about the odd discovery that took place in 2013 that detected a Polynesian mtDNA among some Botocudo skulls that were analyzed. It also adds some new information gleaned from a paper that was recently published. The skulls' Y chromosome was sequenced and it indicated that "...their Y haplogroups are C-P3092 and C-Z31878, both equivalent to C-B477 which identifies former haplogroup C1b2.". Note that the paper does not mention Y-chromosomes. The above is a conclusion of someone who checked the paper... so you can take that with a pinch of salt until ratified by some other source.

So, rhey are citing a paper which I read and checked, but found no reference to the Y-chromosome. (see it here). It does say that these individuals nuclear DNA as well as their mtDNA Bot15 and Bot17 are strongly Polynesian and lack any kind of Amerindian, African or European admixture. They then conjecture about possible origin for these odd individuals (slave trade of Polynesians via Peru, Madagascar slave trade to Brazil, Spanish or Portuguese ships bringing Polynesians to Brazil and a Trans-Pacific contact (strange as the genes appeared on the Atlantic coast of Brazil...). They are stumped and conclude: "Whether brought by Europeans or the result of the Polynesian expansion, the fact remains that some Brazilian Botocudos carried distinctive Polynesian genetic signatures. We hope that further sampling will provide a more definitive answer to this intriguing finding."

These Native Americans were considered backwards and primitive (see my post on them and the theory that they represented an authoctonous American "race"), below is an image of a Botocudo (and he looks anything but backwards or primitive...).

Their name came from the Portuguese word "botoque" (wooden disk) that they used as a personal decoration in earlobes and lower lip.

An article written in 2005 by Reinaldo Jose Lopes (read it here in Portuguese) stated that (my translation): "according to investigators of the University of Sao Paulo, everything indicates that the most typical representatives of the race of the first Americans were those known as Botocudos...". Lopes then explains that the cranial measurements of the Botocudos are closer to those of Paleo Indians and Africans or Melanesians

This was written in the context of the discovery of "Luzia" a woman's skull in the state of Minas Gerais, at Lagoa Santa (by the way, the Botocudos identified as Polynesians by their DNA were also from Minas Gerais). Luzia was dated at 11,500 years old. Below is a reconstruction of her face. Very African or Australian Aboriginal...

Closing Comments

So here we have some interesting facts: some Botocudos of Brazil have a very rare Y-chromosome haplogroup (C) in America, found among a group of Native Americans deemed as the closest to Paleo Indians and to very old remains that actually look Melanesian... The mtDNA and nuclear DNA of these Botocudos are almost pure Polynesian. And also some Ecuadorian natives also have Y Chromosome C Hg., which may belong to a now extremely rare "founding group".

Put together we could conjecture that the old human lineage that peopled Asia reached the New World long before later East Asian or Siberian waves got there. That they are found in some secluded parts of America. They are old, and linked to Melanesia, Australia (whose inhabitants recently moved across the Pacific peopling Polynesia).

In previous posts I have hinted that C hg may actually have a Homo erectus origin (you can read about this it here go down to "Some crazy ideas"), and these recent papers may indirectly support that notion.

Having said this, I also want to give another more critical point of view, a big "BUT..."

I have a suggestion for this oddity, based on the "dog principle": if it has a tail, wags it and barks, its a dog.

So if these skulls have Polynesian mtDNA, Y chromosome unique to Polynesia, nuclear DNA that is 100% Polynesian -and this is the real key- so they did not admix with the Native Americans or Europeans or Africans. These guys were Polynesians. Not American Natives with Polynesian ancestors. No. Pure Polynesians.

Since the papers above clearly indicate that the only possible routes used by these people to get to Brazil are highly improbable, there is only one possible explanation: The skulls belong to Polynesian individuals, picked by some scientific expedition to Polynesia, taken back to Rio de Janeiro, deposited there and incorrectly labeled as Botocudos.

I am going to wait for a formal paper assigning them to Y-chromosome's haplogroup C before considering them seriously.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall © 

Not he usual "Out of Africa" cline

A paper (Hai et al., 2012) [1] analized a very special and unconventional gene, miR-941, it immediately drew my attention because it goes against the usual decreasing gradient of variability from Africa outwards, which shows lower variability in the fringe regions that are further away from our purported Eden in Africa. This post will look into this oddity and its implications.

microRNAs or miRNA

Genes usually are in charge of producing proteins or RNA strands (i.e. tRNA) that in turn interact with gene expression pathways. But this is not the case with micro RNAs (miRNAs) which have very important roles in gene expression. miRNAs are short single-strands of RNA (20 to 24 nucleotides long), hence the name "micro".

The appearance of a new miRNA can impact on the expression of hundreds of genes, so for this reason, the the authors of the paper [1] set out to detect a human-specific miRNA and then tried to figure out its evolution and impact on modern humans. They sought microRNAs (miRNAs) specific to the human genome.

The older (archaic or more ancient) miRNAs tend to have higher expression levels than those that have appeared more recently, and a survey of several human-specific miRNA showed just that: low expression levels, a sure signal that they are quite recent. But there was an exception: miR-941 which was found in the human brain at very high expression levels, higher than other miRNAs found in humans and primates.

miR-941

More interesting was the fact that its expression was absent in macaques and chimpanzees showing that it evolved in the hominid line after we split from the chimps some 6 million years ago (Mya). Its upper limit is given by Denisovans, who do also carried it, and this split took place about 1 Mya. So the miR-941 evolved in our hominin ancestrors between 6 and 1 Mya.

What is exciting is the fact that it interacts with our brains, and the human intellect began to evolve during that time span: the "Human-specific effects of miR-941 regulation are detectable in the brain and affect genes involved in neurotransmitter signalling." [1] it is active in the cerebellum and the prefrontal cortex, which are two processing regions within our brains.

The media hyped up this paper based on its role as "making us human" and its impact on our brain-power, but, as we will see below its role is much deeper than that.

The paper suggests that our extended life span and a higher tendency to developing cancer (compared to chimpanzees and macaques) is probably due to this microRNA. So we should thank miR-941 not only our higher reasoning abilities but also our unusually long life span (yes, cancer is a terrible collateral effect). The authors put it this way:

"It is, therefore, appealing to speculate that emergence of miR-941 enhanced the maintenance of adult stem cell populations, thus supporting longer human lifespan, but rendering human cells more prone to malignant transformation. The role of miR-941 in the regulation of insulin signaling adds support to this notion. The insulin-signaling pathway was consistently implicated in lifespan regulation in many species, including humans. Notably, experimentally verified targets of miR-941 within this pathway include genes directly shown to be involved in lifespan extension in model organisms: IRS1, PPARGC1A and FOXO140 (ref. 40). Furthermore, FOXO1 was linked to extended human longevity." [1]

Not the usual cline though

Unlike many genetic markers which show a high diversity in Africa and then a decreasing gradient as you move away from our purported homeland, miR-941 shows quite a different picture:

Although it is found in all humans, the number of precursor copy-number, or repeats is quite variable: it ranges from 2 to 11 copies. This variaton is linked to geographical location too. Although there is a clear indication that the usual decreasing cline is not present in miR-941, orthodoxy compels the authors to affirm that there is a higher African variability and a West to East cline!:

"The average pre-miR-941 copy number decreased from the west to the east: from eight copies in sub-Saharan Africans to six copies in Eastern Asians. miR-941 precursor copy number variation was also significantly higher in sub-Saharan Africans compared with 'out of Africa' populations, with the exception of Oceanians and native Americans
[modern human carry] 2–11 copies of miR-941 precursor, with an average of 8 copies found in sub-Saharian Africa, an average of 7 copies in Europe, America, Oceania and most of Asia, and an average of 6 copies in East Asia." [1]

Look at the figure below (from [1]) and make up your own mind; it shows miR-941 precursor copy repeats in different populations:

The upper part of the image (c) shows that the variability is highest among South American Karitiana (5 to 9 counts), Papuans and Palestinians (4 to 7) folllowed by San (6 to 9). In other words, it is not higest among Sub-Saharan Aficans!

In the case of the Amerindians, it is a surprising find since they are, according to orthodoxy, supposedly a bottleneck population "lacking the diversity of the Africans" , the other Eurasian people -purported ancestors of the American Natives have less variability than Amerindians.

Part d reflects this, showing the average of each region with the highest count numbers in Oceania, Africa and among Native Americans. All other populations have a lower count.

The Variance (in part e) clearly shows the highest variances in Africans and Native Americans. This does not depict a west - east cline, actually it drops off in the middle and grows again as you move on east.

This is clearly at odds with the accepted notion that diversity drops off with distance to Africa, with the New World populations being the less diverse! The authors actually state this mainstream notion in their abstract: "... shows a trend for decreasing copy-number with migration out of Africa" [1] which is not what the facts in their paper shows. (preconceptions are so hard to erase aren't they?).

So even though the main text shows that diversity drops in Eurasia but increases in Oceania and America the authors overlook it and don't even try to seek an explanation for it.

Speculations and Copy-number variation (CNV)

The paper points avoids controversy and does not analyse the significanse of the different Copy-numbers, it merely points out that a different amount of repeats "is not unexpected, given general instability of genomic regions formed by tandem repeats" [1].

But it is not chance that is at play here but natural selection the authors point out tha when a new miRNA appears (obviously its initial appearance is due to chance), it may wreak havoc in the established network due to negative changes in gene expression. So the forces in natural selection would quickly get rid of it or modify the binding sites that produce negative effects. In the case of miR-941, since it was not eliminated, what changed were its binding sites, which were lost.

So if Amerindians have a higher Copy-number variation (CNV), there must be a selective pressure at work. Actually this is the case:

"The "high-degree of copy-number variation (CNV) ... among contemporary human ethnic populations, suggest[s] a high degree of functional variability even among humans. New cell biological funcions acquired because of the appearance of mR-941, for example, new controls over sonic hedgehog and insulin-signaling pathways (Hu et al., 2012), are likely to be important as CNV-dependent determinants of human-specific adaptations to the environment and to disease." [2]

In other words, CNV is important and should not be overlooked.

It is clear that Amerindians and Papuans have a wide range of CNV than Europeans or Asians, and comparable to those of Africans. Yet they are always depicted a population that originated from a founder effect and later went through a bottle neck which reduced its genetic diversity even further. Why is CNV higher among them?

I am at a loss to explain this, but it the high CNV in Oceanians and American natives is a well known phenomenon, and is an incongruity that is explained away as a sampling bias! [3]:

"higher-frequency CNVs were more common especially in Oceania and the Americas... in contrast with their usual reduced variation, populations from Oceania and the Americas had more CNV loci and more previously unobserved loci than most other populations." [3]

The authors try to explain this anomaly as due to "some bias may exist in CNV detection" and go into an elaborate explanation on sampling. Then they simply ignore this large variability in CNVs compared to the usual Out of Africa cline of decreasing diversity and conclude that: [3]

"despite a difference from SNPs in the frequency spectrum of the copy-number-variants (CNVs) detected - including a comparatively large number of CNVs in previously unexamined populations from Oceania and the Americas- the global distribution of CNVs largely accords with population analyses for SNP data sets of similar size..." [3]

The image below, from [3] actually shows the opposite (peaks in America, Oceania and the Kalash -from Pakistan):

Since African CNV is low, it shows that the high CNV in the Americas is not due to admixture with Africans brought to the New World as slaves. It is due to another cause.

So why do Papuans and Amerindians have a higer CNV diversity?

CNVs can have a negative effect on health and provoke diseases (these will tend to be selected against as the carriers will have a burden which may impede them from having children). Other CNVs have a positive effect and may protect the carrier against disease and "other copy number variants carried by healthy individuals that seem to have no function might actually be evolutionarily retained in populations if they provide a selective advantage." [5]

Could the American and Oceanian variety in CNVs be due to the forces of natural selection retaining CNVs that have been lost by other populations?

Or did they receive these variants from other archaic populations that lived in these areas and admixed with them, receiving these extra CNVs which conferred them a selective advantage?

If so, then the archaic people were already living in America and Sahul when humans reached those regions.

More on the decreasing diverstity myth

When a population with a given diversity (Population A in the image above; diversity is shown by the different colored circles) splits and a sub-population (Population B) moves away, -shown in stage 1- diversity will decrease. In this case we took B as having the same mix as A, but it could have been different, reducing diversity even further (see Population C for instance). The smaller population is more prone to genetic drift which reduces diversity and will also be less likely to evolve new mutations as its size is smaller. It will also be subject to the risk of extinction or loss due to natural calamities than a larger population spread out over a wider territory. So even if the migrating group grows at the same pace as the original population (stages 2 and 3), the outcome will be a reduced diversity.

The acepted theory suggests that variation within a population is proportional only to n (the effective population size) and μ (the mutation rate) which should be the same across all human groups (is it?). [4] So size influences variation: bigger sizes, more variation. Which makes me ask (as an explanation to the higher CNV observed in the New World and Sahul): Did America and Oceania have a larger population in the past which later became extinct? Well, we know that the Americas suffered a devastating impact after its discovery by Europeans in 1492: its population was decimated and its diversity plummeted. Did something simila happen in Oceania? Probably not, as an Old World population they were well adapted to Old World diseases.

Another factor is that, before mutation-drift equilibrium is reached, the age of a population influences its diversity: older populations accumulate more variations. So could the observed CNV diversity be due to an early peopling of America or Oceania by one of our ancestors (Homo erectus? Neanderthal? Denisovans?). This would extend the timeline well beyond the accepted 50 kya for the OoA event or the 15 kya for the peopling of America and allow for diversity to develop.

And, as a closing grand finale look at these two images from Seielstad et al., (1999) [4], which also depict a close relationship between Africans and Americans instead of the usual "decreasing gradient away from Africa":

Yes, the paper (which looks into Y chromosome STR diversity), dates back to 1999 and its figures are extremely unsual but the paper nevertheless echoes the well known mantra of orthodoxy:

"A recent African origin for all humans is supported by a robust corpus of evidence. This evidence takes three major tracks: (1) increased genetic diversity in Africa versus the rest of the world, (2) phylogenetic analyses placing the deepest branches between African and non-African populations, and (3) indications that the age of the “genetic most recent common ancestor” is very young. The Y chromosome, like mtDNA and the autosomes, appears to support a recent African origin." [4]

Sources

[1] Hai Yang Hu, et al., (2012). Evolution of the human-specific microRNA miR-941. Nature Communications 3, Article number: 1145 doi:10.1038/ncomms2146
[2] Antonio Noronha, Changhai Cui, Robert Adron Harris, John C. Crabbe, editors. (2014). Neurobiology of Alcohol Dependence. Elsevier, May 2, 2014. pp 500
[3] Mattias Jakobsson et al., (2008) Genotype, haplotype and copy-number variation in worldwide human populations. vol. 451 doi:10.1038/nature06742
[4] Mark Seielstad, Endashaw Bekele, Muntaser Ibrahim, Amadou Touré, and Mamadou Traoré, (1999). A View of Modern Human Origins from Y Chromosome Microsatellite Variation. Genome Res. Jun 1999; 9(6): 558–567.
[5] Lobo, I. (2008) Copy number variation and genetic disease. Nature Education 1(1):65

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