Patagonian mtDNA is quite unique!

A paper published in 2017 (Diferenciación regional de poblaciones nativas de América a partir del análisis de los linajes maternos, Intersecciones en Antropología 18: 271-282. 2017. ISSN 1666-2105. Josefina María Brenda Motti, Marisol Elisabeth Schwab, Julieta Beltramo, Laura Smeldy Jurado-Medina, Marina Muzzio, Virgina Ramallo, Graciela Bailliet, Claudio Marcelo Bravi), looks into the maternal genetic component of the Native American people of South America, analyzing their mtDNA.

Their data show that Patagonian natives have a unique set of haplotypes not found in the rest of South America. Table 1 in the paper is shown below, with the haplotypes found in Chilean and Argentine Patagonia (it has no data from the Province of Neuquén).

Haplogroup frequencies (%). Table 1 in Motti et al. (2017)

The authors point out the high frequency of certain variants in Argentina's Patagonia, namely, B2i2, D1g, D4h3a5 y C1b13. It suggests that the "notable unity" in Patagonia, both in Chile and Argentina with the preponderance of these haplotypes suggests that south of Latitude 40°S, as the Andes are lower in elevation, there could have been west-to-east mobility of migrating groups.

The authors also note that "these lineages are practically exclusive to Patagonia, as they are found at low frequencies in central Argentina, Uruguay, and northern Chile, and are absent from the rest of the continent. The homogeneity on both sides of the Andes Mountains is indicative of common ancestry."

They suggest that D4h3a5 reached the region along the Pacific, while the presence of B2i1 in the Amazon people like the Kayapó, a sister clade to Patagonia's B2i2 suggests the arrival of people along the Atlantic coast of South America.

mtDNA D1g is Ancient

Since D1g is around 18,000 year old, its age could hint that it was among the first to reach the area, followed by younger haplogroups B2i2 y C1b13, aged 10,800 BP and 12,000 BP, respectively. B2i2 is absent in the Island of Tierra del Fuego suggesting that it differentiated later.

Michelle de Saint Pierre (2017) suggested that D1g as well as D4h3a are ancient, and must have been present in the first wave of people to reach America, later overlaid by more recent arrivals. (de Saint Pierre, Antiquity of mtDNA lineage D1g from the southern cone of South America supports pre-Clovis migration. Quaternary International, Vol 444, Part B, 2017, p.19-25, ISSN 1040-6182, https://doi.org/10.1016/j.quaint.2017.05.054.). de Saint Pierre wrote:

"The age calculated for D1g, between 25,000 and 19,000 cal yr BP is extremely old for a South American mitochondrial subhaplogroup. The anomalous age of this haplogroup does not fit the currently accepted framework for the other mtDNA haplogroups in the Americas...
Of the exclusively Amerindian haplogroups, D4h3a has an age of 17.6 kyr. This is a good candidate to date the early peopling, since considerable evidence has shown it to be an ancestral haplogroup. D4h3a has been recovered from the late Pleistocene (12,707e12,556 cal yr BP) Anzick child (Rasmussen et al., 2014) and from a skeleton of an early Holocene individual from Alaska (Kemp et al., 2007), which is empirical evidence of the presence of this lineage in Paleoamericans. Also, D4h3a has a wide geographic distribution, being found low frequencies in populations across the continent, including the most southern native populations, the Patagonians"

See my post on D1g here, and the post on D4h3a here.

The Amazonian origin of the Mapuches

Back in 2012 (de Saint Pierre M, Gandini F, Perego UA, Bodner M, Gómez-Carballa A, Corach D, et al. (2012) Arrival of Paleo-Indians to the Southern Cone of South America: New Clues from Mitogenomes. PLoS ONE 7(12): e51311. https://doi.org/10.1371/journal.pone.0051311) had found that the sub-haplogroups B2i2 and C1b13 were exclusive to the southern tip of South America and noticed that B2i2 was found at high frequencies among the Mapuche people and related groups like the Pehuenche and Huilliche (26 to 39% frequencies) while admixture led to lower levels among the Tehuelches (14%). It was absent in northern Chile and also among the canoe people of Tierra del Fuego and Southern Chile (who rarely admixed with the Mapuches). Saint Pierre not only found th B2i group among the Amazonian Kayapó, they "identified only two additional mtDNAs, one from Brazil and one from northern Uruguay (both bearing the B2 control-region haplotype plus the B2i diagnostic transitions at np 430 and 485), thus preliminarily suggesting a geographic distribution of B2i1 limited to the northern and eastern part of South America/i>." This is interesting, and it is in line with the notion that the Mapuche originated in the Amazonian region and moved on, later into Chile.

I have posted about a common origin for Mapuche and the Amazonian Guaraní people (and again here), and that the Mapuche were late arrivals in the Patagoian region, so I welcome additional evidence that supports this theory.

Variant C1b13, on the other hand, is found beyond Patagonia, among people like the Atacameño of NW Chile's Atacama desert region, and the Alakaluf and Yamana canoe people, and surely spread to these people from the Mapuche homeland in Central Chile, and is of recent origin there, from an older C1 root.

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The Inca Child from Argentina and a new haplogroup C1bi

The third and last post of the day deals with a novel mtDNA sub clade found in the mummified (due to the high dry altitude of the Andes) remains of a child sacrificed by the Inca people about 500 years ago. The child's mtDNA is similar to that found in some very old remains in Upward Sun River, Alaska.

The paper (see below [1]), reports that this new variety of C1b haplogroup and that it is very ancient: The authors believe it originated some 14,000 years ago along the Andes in South America. As it is rare nowadays they suggest that either (a) it is due to a bias in sampling -so it has not been detected in large frequencies, or (b) it has become extinct in many parts due to the mass deaths caused by the turmoil of European discovery and conquest during th 1500s. They write:

" the phylogenetic patterns of C1bi point to a geographic origin in the Andean side of the South American sub-continent approximately 14 kya. The haplotype found in the Inca child from the Cerro Aconcagua, interpreted in the light of present-day variation in South America and together with the different archaeological and anthropological findings, supports the existence of demographic movements along the Pacific coastline during the Inca period. The fact that C1bi is very uncommon in present-day populations from South America could be explained by insufficient sampling of modern populations (although the present-day haplotype databases of mitogenomes and partial mtDNA sequences are very large). Alternatively, this rarity could reflect important changes in the gene pool of South America since the period of the Inca civilization. Further research on modern and ancient South American populations" [1]

Regarding the age, those 14 kya are maybe even too recent, their confidence intervals are rather wide, from 5 to 23.6 kya. The child was sacrificed 500 years ago during an Inca rite on the highest mountain located outside of Asia, the Aconcagua.

They point out that " C1b most likely arose relatively early, either in Beringia or at a very initial stage of the Paleoindian southward migration [...] While some C1b sub-clades were exclusively observed in Mesoamerica or in South America, a few of them were found in both territories." The map published in the paper shows the distribution of C1b across America: it is strongly concentrated in Mexico, Peru and strangely, in Puerto Rico.

C1b distribution heat map. From [1]

The child has a new clade named C1bi (where "i" stands for "Inca") and is similar to the clade "C1b13. The TMRCA of this sub-clade is 11.8 (8.6–15.1) kya; it is virtually absent from North-Central America and its geographic location is mainly centered in Chile", which fits in the same geograpic area of C1bi.

The clade is very rare: "By querying large databases of control region haplotypes (>150,000), we found only a few C1bi members in Peru and Bolivia (e.g. Aymaras), including one haplotype retrieved from ancient DNA of an individual belonging to the Wari Empire (Peruvian Andes)." [1]

I have already written about the loss of diversity in America not because of a Beringinan or Out of Asia bottleneck but due to the high death toll that virtually wiped out the Native Americans when they were contacted by the European navigators after 1492. Interestingly, my post cites a paper which points out that Hg C suffered a greater impact of lost diversity (with Hg D) than either haplogroups A or B.

In another post I tried to link mtDNA hg. C1 with the Neanderthals. In this post I mention that hg C1 spans Eurasia and America, closely following the Neanderthal homeland.

In [1], the authors found one sample "...that belongs to haplogroup C1b13b sampled in a Spanish individual, although born in Talagante (Chile); therefore we labeled it here as originating in America" [1], in other words a person of European origin born in America carried a European variant of C1. They assumed perhaps that this individual had some Amerindian admixture, I believe that it is just a coincidence that this man has C1 and by chance his ancestors migrated to America.

The hot spot in Puerto Rico is very interesting and requires some explanation. The local Carib - Taino natives were wiped out early during the discovery period. So where did the C1b found there come from?

Sources
[1] The complete mitogenome of a 500-year-old Inca child mummy Alberto Gomez-Carballa, Laura Catelli, Jacobo Pardo-Seco, Federico Martinon-Torres, Lutz Roewer, Carlos Vullo y Antonio Salas Scientific Reports 5, Article number: 16462 (2015). Nature, Nov. 12, 2015 doi:10.1038/srep16462

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

The age of the mtDNA from Upward Sun River in Alaska

The paper by Justin C. Tackney et al., (2015) Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia, PNAS doi: 10.1073/pnas.1511903112, published today has found that the remains of a stillborn baby and a very young infant that were buried at the same time in a grave in Upward Sun River, Alaska 11,500 years ago, belong to Mitochondrial DNA types C1b and B2, and these "allowing us to refine younger coalescence age estimates for these two clades. C1b and B2 are rare to absent in modern populations of northern North America. Documentation of these lineages at this location in the Late Pleistocene provides evidence for the extent of mitochondrial diversity in early Beringian populations, which supports the expectations of the Beringian Standstill Model.".

Though it is behind a paywall, the information published online indicates the ages of "about 12,800 years ago for C1b and 12,000 years ago for B2" and that one of the paper's co-authors "O'Rourke suspects the real times were even earlier, but that nonetheless both 11,500-year-old infants were at or near the root of their respective genealogical trees".

Additionally, O'Rourke said "'You don't see any of these lineages that are distinctly Native American in Asia, even Siberia, so there had to be a period of isolation for these distinctive Native American lineages to have evolved away from their Asian ancestors. We believe that was in Beringia,'".

This value of 12 to 12.8 kya is interesting. Why not 20 or 25 kya? It is convenient that the these 12,000 years situate the origin of these haplotypes at the time of a purported Beringian standstill. Lets see how they were calculated.

The Supplemental information, on page 4 tells us that "... Mutational distances were converted into years using a corrected molecular clock proposed by ref. 27 or a whole-genome substitution rate of 2.67 × 10−8 sub per site per year".

And this is a critical point, because based on this mutation rate is that the authors have estimated the age of these mtDNA haplotypes.

However this mutation rate is questinable. For instance a value of 0.43 × 10−9 per site per year was reported for the 45,000 year old shin bone from Ust’-Ishim.

The difference between 0.43 x 10-9 and 2.67 x 10-8 (which I will express as 26.7 x 10-9) is 62 times!

I eliminated the previous paragraphs because I was using autosomal and mtDNA mutation rates and they are not comparable. (see the comment below dated 27/Oct.) However, the following is valid. Because as I mention in Comments below, the mtDNA mutation rates estimated by different authors vary and considerably, from 1.3 to 3.2 x 10-8. Even the range for a 95% Confidence Interval is too wide for my liking, so...

Fidgeting with mutation rates one can get a wide range of coalescence dates...and that means you can get mistaken ones too.

I posted in June 2014 about mtDNA C1 haplogroup and in that post, I cited a paper that gave the following age to C1b: 17.9 +⁄- 2.3kya. Which is at odds with the figure calculated by Tackney's team.

In that post, besides questioning the molecular clock (I always seem to be irked by this subject), I wrote: "Interesingly, C1 has a high values for nucleotide diversity indices, and show a South to North cline (with most variations in South America), indicating that it has deeper roots in the southern part of the New World or that bottlenecks reduced its diversity in the North. In my opinion in points at an older date of entry into America than those mentioned above.", which again seems to be at odds with such early (12 kya) dates and a late Beringian standstill.

A Map showing the mtDNA C1 haplogroup current and probable archaic range
Copyright © 2015 by Austin Whittall

Let's wait and see if they can get a Y chromosome haplogroup from the remains (but it seems both were girls).

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