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Ancient DNA from Clovis culture is Native American (also Tianyuan affinity mystery)

Figure 4 | [c] (…) maximum likelihood tree. 
A recent study on the ancient DNA of human remains from Anzick (Montana, USA), dated to c. 12,500 calBP, confirms close ties to modern Native Americans, definitely discarding the far-fetched and outlandishly Eurocentric “Solutrean hypothesis” for the origins of Clovis culture (what pleases me greatly, I must admit).
While this fits well with the expectations (at least mine), there is some hidden data that has surprised me quite a bit: it sits at the bottom of a non-discussed formal test graph in which modern populations are compared with both Anzick and Tianyuan (c. 40,000 BP, North China). See below.
Morten Rasmussen et al., The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 2014. Pay per viewLINK [doi:10.1038/nature13025]

Abstract


Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 14C years before present (bp) (13,000 to 12,600 calendar years bp)1, 2. Nearly 50 years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology3. However, both the origins and the genetic legacy of the people who manufactured Clovis tools remain under debate. It is generally believed that these people ultimately derived from Asia and were directly related to contemporary Native Americans2. An alternative, Solutrean, hypothesis posits that the Clovis predecessors emigrated from southwestern Europe during the Last Glacial Maximum4. Here we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705 ± 35 14C years bp (approximately 12,707–12,556 calendar years bp) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4× and show that the gene flow from the Siberian Upper Palaeolithic Mal’ta population5 into Native American ancestors is also shared by the Anzick-1 individual and thus happened before 12,600 years bp. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual.

Haploid DNA
The Y-DNA lineage of Anzick is Q1a2a1* (L54) to the exclusion of the common Native American subhaplogroup Q1a2a1a1 (M3). Among the modern compared sequences that of a Maya is the closest one.

The mtDNA belongs to the common Native American lineage D4h3a at its underived stage (root). 
For starters I must explain that these underived haplotypes can only be found within mtDNA and never in modern Y-DNA (common misconception) because this one accumulates mutations every single generation, while the much shorter mtDNA does only occasionally. Hypothetically we could find the exact ancestor of some modern Y-DNA haplogroup in ancient remains but that would be like finding the proverbial needle in the haystack. On the other hand, finding the underived stage in mtDNA, be it ancient or modern, does not mean that we are before a direct ancestor but just a non-mutated relative of her, who can be very distant in fact.


Autosomal DNA

In this aspect, the Anzick man shows clearly strongest affinities to Native Americans, followed at some distance by Siberian peoples, particularly those near the Bering Strait. 

Figure 2 | Genetic affinity of Anzick-1. a, Anzick-1 is most closely related to Native Americans. Heat map representing estimated outgroup f3-statistics for shared genetic history between the Anzick-1 individual and each of 143 contemporary human populations outside sub-Saharan Africa. (…)
However Anzick-1 shows clearly closer affinity to the aboriginal peoples of Meso, Central and South America (collectively labeled as SA) and less so to those of Canada and the American Arctic (labeled as NA). No data was available from the USA. 
This was pondered by the authors in several competing models of Native American ancestry:
Figure 3 | Simplified schematic of genetic models. Alternative models of the population history behind the closer shared ancestry of the Anzick-1 individual to Central and Southern American (SA) populations than Northern Native American (NA) populations; seemain text for further definition of populations. We find that the data are consistent with a simple tree-like model in which NA populations are historically basal to Anzick-1 and SA. We base this conclusion on two D-tests conducted on the Anzick-1 individual, NA and SA. We used Han Chinese as outgroup. a, We first tested the hypothesis that Anzick-1 is basal to both NA and SA populations using D(Han, Anzick-1; NA, SA). As in the results for each pairwise comparison between SA and NA populations (Extended Data Fig. 4), this hypothesis is rejected. b, Next, we tested D(Han, NA; Anzick-1, SA); if NA populations were a mixture of post-Anzick-1 and pre-Anzick-1 ancestry, we would expect to reject this topology. c, We found that a topology with NA populations basal to Anzick-1 and SA populations is consistent with the data. d, However, another alternative is that the Anzick-1 individual is from the time of the last common ancestral population of the Northern and Southern lineage, after which the Northern lineage received gene flow from a more basal lineage.
The most plausible model they believe is “c”, in which Anzick-1 is close to the origin of the SA population, while NA diverged before him. However model “d” in which Anzick-1 is close to the overall Native American root but NA have received further inputs from a mystery population (presumably some Siberians, related to the Na-Dené and Inuit waves) is also consistent with the data. Choosing between both “consistent” models (or something in between) clearly requires further investigation. 

Tianyuan and East Asian origins
All the above is very much within expectations, although refreshingly clarifying. But there is something in the formal tests (extended data fig. 5) that is most unexpected (but not discussed in the paper). 
The formal f3 tests of ED-fig.5 a to e fall all within reasonable expectations. Maybe the most notable finding is that, after all, the pre-Inuit people of the Dorset culture (represented by the Saqqaq remains) left some legacy in Greenland, but they also show some extra affinity with several Siberian populations (notably the Naukan, Chukchi, Koryak and Yukaghir, in this order) before to any other Native Americans, including Aleuts). 
But the really striking stuff is in figs. f and g, where it becomes obvious that the Tianyuan remains of Northern China show not a tad of greater affinity to East Asians (nor to Native Americans) than to West Eurasians. Also two East Asian populations (Tujia and Oroqen) are considerably more distant than the bulk of East Asian peoples to Tianyuan but also to Aznick.
Extended Data Figure 5 | Outgroup f3-statistics contrasted for different combinations of populations. (…) f, g, Shared genetic history with Anzick-1 compared to shared genetic history with the 40,000-year-old Tianyuan individual from China.
This is very difficult to explain, more so as Tianyuan’s mtDNA haplogroup B4’5 is part of the East Asian and Native American genetic pool, and the authors make no attempt to do it. 
The previous study by Qiaomei Fu et al. (open access) placed Tianyuan’s autosomal DNA near the very root of Circum-Pacific populations (East Asians, Native Americans and Australasian Aborigines) but after divergence from West Eurasians:
From Qiaomei Fu 2013
They even had doubts about the position of Papuans (the only Australasian representation) in that tree, which they suspected an artifact of some sort.
Since I saw that graph (h/t to an anonymous commenter at Fennoscandian Ancestry) I am squeezing my brain trying to figure out a reasonable explanation, considering that the formal f3 test has almost certainly more weight than the ML tree made with an algorithm. 
My first tentative explanation would be to imagine a shared triple-branch origin for Tianyuan, East Asians and West Eurasians, maybe c. 60 Ka ago (it must have been before the colonization of West Eurasia), to the exclusion of other, maybe isolated, ancient populations, whose admixture with the ancestors of the Tujia, Oroqen and Melanesians (maybe via Austronesians?) causes those striking low affinity values for these.
This would be a similar mechanism to the one explaining lower Tianyuan (and generally all ancient Eurasian) affinity for Palestinians (incl. Negev Bedouins) and also the Makrani, who have some African admixture and (in the Palestinian case) also, most likely, residual inputs from the remains of the first Out-of-Africa episode in Arabia.
However to this day we have no idea of which could be those hypothetical ancient isolated populations of East Asia. In normal comparisons such as ADMIXTURE analysis the Tujia and Oroqen appear totally normal within their geographic context, but this may be an artifact of not doing enough runs to reach higher K values, according to the cross-validation test, much more likely to discern the actual realistic components. 
The matter certainly requires further research, which may well open new avenues for the understanding the genesis of Eurasian populations, particularly those from the East.
 

Ancient Native Americans related to modern ones

Sequencing of ancient Native American remains from British Columbia (Canada), dated to c. 5-6000 years ago, shows that many modern local natives are their apparent descendants or otherwise related.
Yinqiu Cui et al. Ancient DNA Analysis of Mid-Holocene Individuals from the Northwest Coast of North America Reveals Different Evolutionary Paths for Mitogenomes. PLoS ONE 2013. Open accessLINK [doi:10.1371/journal.pone.0066948]
Abstract

To gain a better understanding of North American population history, complete mitochondrial genomes (mitogenomes) were generated from four ancient and three living individuals of the northern Northwest Coast of North America, specifically the north coast of British Columbia, Canada, current home to the indigenous Tsimshian, Haida, and Nisga’a. The mitogenomes of all individuals were previously unknown and assigned to new sub-haplogroup designations D4h3a7, A2ag and A2ah. The analysis of mitogenomes allows for more detailed analyses of presumed ancestor–descendant relationships than sequencing only the HVSI region of the mitochondrial genome, a more traditional approach in local population studies. The results of this study provide contrasting examples of the evolution of Native American mitogenomes. Those belonging to sub-haplogroups A2ag and A2ah exhibit temporal continuity in this region for 5000 years up until the present day. Of possible associative significance is that archaeologically identified house structures in this region maintain similar characteristics for this same period of time, demonstrating cultural continuity in residence patterns. The individual dated to 6000 years before present (BP) exhibited a mitogenome belonging to sub-haplogroup D4h3a. This sub-haplogroup was earlier identified in the same general area at 10300 years BP on Prince of Wales Island, Alaska, and may have gone extinct, as it has not been observed in any living individuals of the Northwest Coast. The presented case studies demonstrate the different evolutionary paths of mitogenomes over time on the Northwest Coast.

Figure 2. Phylogeny of complete mitochondrial genomes sequenced in this study.
Mutations
are transitions unless specified. Transversions are indicated by an A,
G, C, or T after the nucleotide position. Insertions are indicated by an
“i”, deletions are indicated by a “d”, recurrent mutations are
underlined, and mutations back to the rCRS nucleotide are designated by a
“@”. The C stretch length polymorphism in region 303–315 was
disregarded in the tree. The sample “Haida 9″ was analyzed in Schurr et
al. (2012). All other samples were analyzed in this study.
 
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Posted by on July 7, 2013 in aDNA, America, mtDNA, Native Americans, Paleolithic

 

New Maya city discovered

Archaeologists have discovered the ruins of a long lost Maya city in the jungle SE of Campeche state (Yucatan Peninsula, Mexico), in the historical Maya region of the central lowlands. 

The newly discovered city, Chaktún, occupies some 22 Ha. and is believed to have been an important local power between 600 and 900 CE. It was hidden in the northern area of the Biosphere Reserve of Calakmul, near the Guatemalan border.

Source: Paleorama[es].

 

Maya pyramid destroyed in Belize… to get gravel

The machinery of a construction company has destroyed one of the most important archaeological treasures of Belize with the most idiotic possible purpose: to get gravel from it. 

The pyramid of Nohmul was erected some 2300 years ago and are part of the most important patrimonial set of Belize, located not far from the Mexican border. 
Belizean police claims to be investigating the incident and may lay charges against the vandals.
 

OSL dating: Brazilian site is 22,000 years ago

Toca da Tira Peia is the new name of American prehistory, providing an OSL date for the layer of scattered stone tools of c. 22,000 years BP. Located near the also controversial Pedra Furada site, the date seems to give some support to those who dare to think outside the box on the early peopling of America.
Christelle Lahaye et al., Human occupation in South America by 20,000 BC: the Toca da Tira Peia site, Piauí, Brazil. Science 2013. Pay per view LINK [doi:10.1016/j.jas.2013.02.019]

Abstract


When and how did the first human beings settle in the American continent? Numerous data, from archaeological researches as well as from palaeogenetics, anthropological and environmental studies, have led to partially contradictory interpretations in recent years, often because of the lack of a reliable chronological framework. The present study contributes to the establishment of such a framework using luminescence techniques to date a Brazilian archaeological site, the Toca da Tira Peia. It constitutes an exemplary case study: all our observations and measurements tend to prove the good integrity of the site and the anthropological nature of the artifacts and we are confident in the accuracy of the luminescence dating results. All these points underline the importance of the Toca da Tira Peia. The results bring new pieces of evidence of a human presence in the north-east of Brazil as early as 20,000 BC. The Toca da Tira Peia thus contributes to the rewriting of the history of the peopling of the American continent.

There are slightly older sites in North America, however they are all surrounded into some degree of controversy: Topper in South Carolina is dated to c. 23,000 cal-BP (C14) while some sites in Alberta, located in the Mackenzie “ice-free corridor” have also dates under the LGM layer (i.e. > 21 Ka BP).
There’s actually nothing impossible about such early dates in my understanding.

See also:

 

Southern Native American Y-DNA: no correlation with language, extensive info on haplogroup C3

Genetics does not necessarily correlate with linguistic families. It often does not. This seems to be the case with Native Americans as well.
Lutz Roewer et al., Continent-Wide Decoupling of Y-Chromosomal Genetic Variation from Language and Geography in Native South Americans. PLoS Genetics 2013. Open accessLINK [doi:10.1371/journal.pgen.1003460]

Abstract
Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans.
There’s only so much to say about language families and patrilineages: that they do not agree in any obvious way:

Table 1. Correlation between Y-SNP haplogroup and language class.
However the paper also address the interesting matter of NE Asian and Native American paragroup C3(xC3b), which is almost only found among Ecuadorean Natives (Kichwa and Waorani speakers). The only other known case among Native Americans, according to the authors, is an individual of Southern Alaskan native ancestry. 
Figure 1. Origin of male native South American samples.
For
each sampling site, its geographic location as well as the size
(proportional to the circle area) and Y-SNP haplogroup composition of
the respective sample are shown. Blue lines: major aquatic systems;
dashed gray lines: current national boundaries.

Overall distribution of Y-DNA C3* (yellow), which I understand to mean C3(xC3b) for this study:

Figure 4. Prevalence of Y-SNP haplogroup C-M217 (C3*) around the Pacific Ocean.
Light blue: previous studies; dark blue: present study; yellow: relative frequency of C-M217 (C3*) carriers.

The most interesting information anyhow may be in the haplotype network:

Figure 5. Median-joining network of
167 different Asian and American Y-STR haplotypes carrying Y-SNP
haplogroup C3* (from this and previously published studies).

The
median-joining network is based upon markers DYS19, DYS389I,
DYS389II-DYS389I, DYS390, DYS391, DYS392, DYS393 and DYS439 (see
Materials and Methods for details). ALA: Alaskan; KOR: Korean; CHI:
Chinese, including Daur, Uygur, Manchu; MON: Mongolian, including
Kalmyk, Tuva, Buryat; ANA: Anatolian; INDO: Vietnamese, Thai, Malaysian,
Indonesian, Philippines; JAP: Japanese; TIB: Tibetan, Nepalese; ALT:
Altaian, including Kazakh, Uzbek
; SIB: Teleut, Khamnigan, Evenk, Koryak;
ECU: Ecuadorian, including Waorani, Lowland Kichwa, COL: Colombia,
including Wayuu
; RUS: Russian.
The network clearly shows that the Native American C3* haplotypes are mostly or totally related to a cluster of Altaian, Mongol and Chinese roots. The Altaian connection is particularly strong for all but one of the lineages. This is very much concordant with a proto-Amerind patrilineal origin in Altai (where NE Asian and American Y-DNA Q and mtDNA X2 variants surely originated in the early Upper Paleolithic) which traveled to Beringia via Mongolia or nearby regions, spreading the mode 4 (blade tech) to East Asia c. 30,000 years ago.
This is not the view of the authors but mine. The authors instead speculate with (i) a late wave or (ii) even naval contact between East Asia and South America. I find both hypothesis lacking merit and I lean for a founder effect model instead.
On the other hand, the C3b presence in NW North America, critically among Na-Dene speakers, may still represent a second wave: that of Na-Dene speakers, whose “recent” linguistic connections to Siberia (Yenisean family) have found strong support in the last years. 
 

Rock art from Baja California dates to c. 9,000 years ago, maybe even older

Catalan researchers from the IPHES have been studying the impressive rock art of the caves of Baja California Sur (Mexico) and concluded that some of the art is from c. 8-9,000 years ago. However contextual dates are sometimes older, of c. 10-11,000 years ago. 

Source: El Universal[es], which has many more photos.
For decades it was believed, following the pioneer work of Clement Meighan, that the art was from the 13th century CE. However in the 1980s the more in-depth research by Catalan scientists revealed that it is in fact from much older dates, at least 5,000 years ago. These days it has been revealed that they are even older in some cases. 
The rock art is distributed by many areas of Baja California Sur, very especially the Sierra de San Francisco, which alone hosts more than 250 sites. These sites were often occupied through millennia, until the 18th century CE in some cases. Even later they have been used as shelters for sheep, however nowadays they do enjoy state and UNESCO protection. 
The most outstanding cave, La Pintada (the painted one), appears to have indications of astronomical knowledge. In the words of Viñas Vallverdú:
In the particular case of La Pintada there are many markings of astronomical type, spots where it is indicated that the Sun illuminates in certain time of the year, signaling a date in their calendar. That way they knew that, when the Sun hit one of those marks, it was time to collect the pitahaya or that the rain period was nearing.
The research is part of an international project by IPHES and the Instituto Nacional de Antropología e Historia (INAH) of Mexico, which is surveying the prehistory of the North American federation. 
The study will be published as the doctoral thesis of lead researcher Ramón Viñas Vallverdú (IPHES).

Source: El Universal[es] (includes a very beautiful photo-gallery).