Guide to Patagonia's Monsters & Mysterious beings

I have written a book on this intriguing subject which has just been published.
In this blog I will post excerpts and other interesting texts on this fascinating subject.

Austin Whittall

Saturday, January 18, 2014

mtDNA D4h3a (Continued)

In my previous posts we have seen that along the west coast of America a rare mtDNA haplogroup (D4h3a) which is found there at much higher frequencies than elsewhere. In today's post we will look into this haplogroup in detail, and ask some questions.

How rare is the D4h3a haplogroup?

Map showing distribution of D4h3a in the Americas. Adapted from (2), by Austin Whittall

The map shown above gives an idea regarding the frequency at which this rare haplogroup is found in the Americas. On the left side, the original map from Perego et al. (2). Which is a rather "tricky" depiction since it portrays a gradual diffusion or decrease of the haplogroup across wide territories (Western U.S., Ecuador, Peru, Colombia and Amazon in Brazil; Chilean and Argentine Patagonia), which, if you check the tables below, is not exactly true.

The samples are discrete, not a continuum, taken at locations that cover the whole continent. They are discrete points and as such cannot "fade" or dissolve.

That is why I added the right side map, which shows the (red) current populations carrying D4h3a and in orange the remains of Paleoindians found carrying it. These pinpoint discrete points on the map, not vast territories.

The data also shows that one (yes 1) individual in each group (in the case of Mexico and Peru, carries D4h3a), that implies that there cannot be a "shaded" area on the map. In the case of Chile, Ecuador and the U.S., the natives lived in specific areas of a limited surface, not in large territories as is the case of modern nation-states.

So let's take a look at frequencies based on cases with this haplogroup out of a given population. The supplemental tables of Perego et al. (2) show that it is only found in:

Mixed extant Populations

  • 0.42% California
  • 1.50% North Mexico
  • 0.29% Central Mexico
  • 0.14% South Mexico
  • 1.88% Peru
  • 2.93% Chile
  • 0.48% Bolivia - Paraguay
  • 0.15% Brazil

It is absent in all the rest of the countries of the continent and in the US outside of California.

InNative American Groups its frequency is high in some groups, low in others and absent in most:

  • 21.67% Cayapa (Ecuador)
  • 16.00% Chumash (Ca. US)
  • 10.26% Fuegians (Chile)
  • 2.70% Mapuche (Chile)
  • 2.56% Klunk Mound
  • 1.82% Tarahumara (Mexico)
  • 1.28% Nahua (Mexico)
  • 0.40% Mixtek - Mixe - Zapotec (Mexico)
  • 0.95% Quechua (Peru)

It is absent in all other Native Americans sampled.

Clearly the canoe people (Cayapa, Chumash and Fuegians) have the highest frequencies. Mapuche very likely got it thorugh admixture with the now extinct Chono (who also carried it), under Spanish rule in northern Patagonia, at the Chiloé Island outpost.

The other groups in Mexico and Peru carry it at a frequency below 2%, all the North American native people except the Chumash and the Klunk Mound skeletal remains do not carry it.

Yes, as you can see there is one oddity: the Klunk Mound "hotspot", in Illiniois, U.S., it is far from the Pacific coast canoe people and was sampled from the bones of an ancient indian.

Klunk Mound Illinois

The image below shows where this non-coastal location is: Northern U.S.:

Table from (2) showing the Klunk Mound anomaly

The data indicates that out of 39 skeletal remains analyzed, only 1 carried the D4h3a haplogroup. (that is what the 2.56% frequency means). It is a low frequency, but it is real, and was found very far away from the coastal region.

The Pete Klunk Mound group is located in a north-south line on the bluffs of the Illinois River, this north of the town of Kampsville (39° 18' 14" N, 90° 36' 7") in Calhoun Cty., Illinois, U.S. See the map below:


The Pete Klunk group is made up of fourteen mounds which were excavated in 1960-61 by Gregory Perino. The remains, affiliated with the Illinois Hopewell cultural phenomenon date to 1,825 +⁄- 75 YBP. (Very young compared to the other remains descrbed in this post). (3)

The Klunk Mound remains can mean two things:

  1. 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.
  2. The Klunk mound person was from the West Coast and migrated across the U.S. to Illinois.

Option 1 is the most reasonable explanation, and is supported by Cui et al. (1):

They detected a sub-haplogroup (D4h3a7) in the remains of a Paleoindian from Lucy Island, Canada, about 200 km (125 mi) south of "On Your Knees" Cave. They dated it to 5.710 +⁄- 40 BP.

You will recall that the first sample of D4h3a was found at "On Your Knees " Cave in southern Alaska, and dated at 10.3 kya. The fact it was found in a paleoindian on an island points towards ancient "canoe" people.

It seems quite prevalent in this area among ancient -now defunct- Native Americans.

Cui's paper adds that "Sub-haplogroup D4h3a is not identified in any ancient or living individuals on the Northwest Coast after approximately 6000 years BP... This suggests that sub-haplogroup D4h3a is either in extremely low frequency or has gone extinct in living populations of the Northwest Coast...." (1)

They point out that in the past it was more prevalent, since "two of seven (29%) early-mid Holocene skeletal remains from different archaeological sites continent-wide exhibit mitochondrial sub-haplogroup D4h3a" (1).

Its current absence in the area is attributed to "the result of random genetic drift in situ and/or the result of population movements into the geographic region..." (1).

In other words they support the idea that it was widespread and was replaced by newcomers' mtDNA.

The First People in America

It is quite probable that the original first peopling wave of H. sapiens carried D4h3 with them (I deliberately left the "a" and went a step backwards, towards the root for reasons I will explain later on in this post), the entered America, occupied the whole continent from Bering to Tierra del Fuego.

The clade mutated into subclades hence D4h3 became D4h3a and this in turn mutated into the variants we find today (D4h3a1, a2.... a7).

Then came other wave/s of migrants from Asia, they overcame the first wave who mixed, fell prey to the diseases these new Asians brought, were killed in tribal warfare or being much inferior in number were diluted by the new mtDNAs into non-existence.

Only those living in specialized ecological niches: i.e. canoe people in a geographical setting with islands (Fuegia, Southern Chile, Santa Catalina islands in California) survived, the others perished (the remains of the Klunk Mound, Lucy Island and "On Your Knees" men prove it).

And now we look at the area occupied by D4h3a it seems that they came with a group of canoe people who paddled down the Pacific Ocean's coastline settling here and there.

We should not infer population patterns from the areas that they currently occupy.

The Chinese connection

An interesting point is that D4h3 is not exclusively American, the D4h3a subclade is found exclusively in the Americas, but the other subclade, D4h3b was identified in one Chinese individual Qingdao, Shandong province, Eastern China. (2) You can read the original paper by Yao et al. (4) if interested (individual is QD8153).

This is a very important piece of information. Its extreme rarity in Asia is estimated at 1 x 10-4 (1 : 10.000) by Perego et al., but instead of exploring the reasons for this, they use it, as expected, to buttress the "Out of Africa" theory and currently accepted timelines.

Perego's paper states that this Chinese branch poses an: "... upper limit for the most recent common female Asian ancestor of D4h3." (2). So to fit in the Beringian migration c. 15 kya they calculate the following timelines: (Below is the tree with its branches and the dates that they calculated - From Figure S1 in (2) - see the image further down).

  • D4 (40.4 - 34.1 kya)
  • D4h (no date)
  • D4h3 (40.9 - 36.6 kya) [*]
    • D4h3b (no date)<< The Chinese clade
    • D4h3a (18.0 - 14.3 kya)
      • D4h3a1 (18.4 - 11.8 kya) [*]
      • D4h3a2 (11.5 - 9.6 kya)
      • D4h3a3 (10.5 - 3.3 kya)
      • D4h3a4 (1.5 - 0.1 kya)
      • D4h3a5 (25.3 - 30.6 kya) [*]
      • there are more branches.


The "American" haplogroup is dated at 18 - 14.3 kya, a nice fit for orthodoxy's 15 kya for entry into America. And though the Chinese clade is not dated it falls somewhere between 40 and 18 kya

I marked with [*] those branches that are older than the branch from which they arise. Seems wrong to me that a branch be older than a root....

The calculation is unclear, please take a look at the image below which displays the mutations:


Detail from Figure S1 in (2), D4 hg and its branches, mutations and estimated timeline

The authors originally state that "Time estimates shown for clades are averaged distance (?) of each haplotype to the respective root. The first value has been obtained by considering one coding-region substitution every 4,610 years, while the second one assuming 7,650 years per synonymous transition." (2).

But that is not what the image shows:

  • D4h3a1 has one "synonymous transition" (which I will abbreviate as: st) so should be 4.61 ky younger but, instead, it is older than D4h3a.
  • D4h3a2 also has one st but is 6.5 ky younger instead of 4.61 ky.
  • D4h3a4 also has one st but is 16,5 ky younger instead of 4.61 ky.
  • The root of all, haplogroup M is dated at 62.4 kya. After 2 st's it branches into D4 which the authors date at 40.4 kya (yes, 2 st's would be 9.22 ky but they calculate that as 22 kya).

I am an engineer and maths is straightforward for me, but this kind of maths baffles me. It feels as if they were forcing the data to make it fit with the required into-America-across-Beringia timeline.

This genetic mtDNA clock ticks at variable rates.

Haplogroup subclades

The D43Ha haplogroup is not the same among all Native Americans sampled, there are several subclades:

  • The Chilean group carried D4h3a1 and D4h3a2. These have accumulated a lot of internal variation
  • The Mexican and Californian (and one Chilean) carry D4h3a3.
  • The Lucy island man had another sublcade: D4h3a7 (5.7 kya).
  • What subclade did the Klunk Mound man carry? Below is a detail from (3):
    • KlunkMound 16223, 16241, 16301, 16318, 16342
    • Chumash 1d 16223, 16241, 16301, 16342
    • Chumash 2d 16223, 16241, 16301, 16342

    So it only differed in the HVR polymorphism 16318 from the some of the Chumash people's Haplogroup. (3)
  • The ca. 10,3 ky old "On Your Knees" man also had D4h3a... (which subclade?)
    He had a HVR polymorphism 16092 (3), which is found among the Chumash, Fuegians and a Nahua in Mexico, meaning it is close to the root of the subclades. But I have not seen it classified.

There is a lot of variation here among the different subclades and to me that spells a long time (each mutation requires a tick in the clock, more mutations = more ticks), but for Perego (2) it spells something different:

The rapid dispersion of D4h3a southward along the Pacific coast is supported by two deep subclades (D4h3a1 and D4h3a2), found exclusively in Chile, and by its spatial distribution.... Overall, these mtDNA findings make plausible a scenario positing that within a rather short period of time during the pre-Bølling interstadial (15.8 to 14.9 kya) and during the warmer Bølling interstadial (14.5 to 13.9 kya), the ice-free corridor may have opened for successful southward migration, whereas the Pacific coastal path may have been feasible somewhat earlier, but not before 17 kya, allowing for successive small-scale migrations of Beringian groups." (2)

Why does two "deep subclades" in Chile, with a lot of variations suggest a "rapid dispersion", baffles me.

What does "speed" have to do with subclade variations?

Actually, when a population is expanding (more offspring survive), it is more likely that mutations passed on from mother to daughter survive in the following generations and, with a larger quantity of women having children, there is more chances of random mutations taking place, thus creating even more variety and Haplogroup subclades. When a bottleneck occurs and populations contract, many mutations are lost as they are not passed on to anyone (bearer dies or all its offspring die).

A group of canoe people cannot be taken as an example of booming populations, and even if they paddle quickly to Tierra del Fuego, they will still be a small band of people in canoes restricted in their population size by the natural maritime resources they can exploit. All canoe populations have been small due to this reason.

So, let's try to offer an alternative explanation:

Another Explanation

The Chinese sublcade is not Asian, it originated in America and back-migrated into Asia, that is why (above) I suggested that the D4h haplogroup entered America and diversified there. The population expanded, new subclades arose. The Dh4b people went back to Asia, the others carrying the Dh4a clade marched on to occupy America, and their expanding population generating new sublcades.

They did not paddle along the coast, they walked, occupied the continent, leaving their mtDNA all across it.

Then, as explained above, other wave/s of modern humans arrived and replaced the original people, reducing them to marginal coastal areas where the pre-existing canoe people survived with their D4h3a mtDNA.

More to be posted on this subject....


(2) Perego, Ugo, A. et al., (2009). Distinctive Paleo-Indian Migration Routes from Beringia Marked by Two Rare mtDNA Haplogroups. Current Biology 19, 1-8, 2009 p. 2 doi 10.1016/j.cub.2008.11.058
(1) Cui, Yinqui, et al., (2013) Ancient DNA Analysis of Mid-Holocene Individuals from the Northwest Coast of North America Reveals Different Evolutionary Paths for Mitogenomes. Published: July 03, 2013, doi: 10.1371/journal.pone.0066948
(3) Kemp, Brian, et al. (2007), Genetic Analysis of Early Holocene Skeletal Remains From Alaska and its Implications for the Settlement of the Americas. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 132:605–621
(4) Yao, et al. (2002), Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Am J Hum Genet 70:635–651.

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


  1. Hi Austin, thanks for the nuanced and thorough writeup. As of late, I'm of the opinion that "The Chinese sublcade is not Asian, it originated in America and back-migrated into Asia." As I pointed out in one of the online forums, there seems to be an interesting pattern whereby a number of East Asian mtDNA clades contain versions of specifically Amerindian kind. At the same time, some of the more obviously East Asian clades such as the various M lineages or hg G are not found in the Americas. We can build a plausible back migration argument (and it's not just me but a number of academic authors) for hg C1 in Japan and Amur, A2a for extreme northeast Asia and now D4h3 for China. It's highly unlikely that one single D4h3 lineage was cherry picked in China and carefully carried to the Americas all the way down to Tierra del Fuego. It's more likely that it was much more frequent and diverse in the Americas in the past and that it at some point back migrated into China.One thing I'm struggling with is whether this back migration for recent (12,000 years ago) or ancient. It's possible that the mtDNA phylogeny is inaccurate and these Amerindian lineages should be thought of as basal in their respective clades. In this case, they would be retentions from a remote past, with all other A, C and D lineages found in Asia derived from them after the back migration.

  2. German,
    Thanks for you comment, I agree.

    I have been reading about the issue of how the mtDNA clock has been set, and I have some serious doubts about the accuracy since it seems based on assumptions and then checked against other assumed figures (like the date of entry into America of roughly 15 kya).

    But when you look at the accumulated mutations along haplogroups you see that they have no relationship whatsoever with the divergence times!

    i.e. there does not appear to be a ratio of "n" mutations per year. It seems variable.

    It is quite logic to propose a early peopling of America, long before 12 kya and back-flow into America.

  3. Actually, isn't the extant proportion quite high in Terra del Fuego? I think it is also inland in South Argentina. Yes, it does look like a hemispheric distribution that admixed over time, with the most inaccessible places (far south and islands) admixing least. You are seeing the result of back migration of the remnant from the islands on the west coasts. This according to:
    Enigma at Beringia, which I think is a must read for someone like yourself. It sounds similar.


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