Category Archives: Latin America

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].


Caribbean autosomal ancestry

Battle of Vertières (Haiti 1803)

A very interesting study on Caribbean populations’ autosomal ancestry is in the oven (pre-publication at arXiv).

Andrés Moreno Estrada et al., Reconstructing the Population Genetic History of the Caribbean. arXiv 2013 (pre-pub). Freely accessibleLINK [ref. arXiv:1306.0558v1]


The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, by making use of genome-wide SNP array data, we characterize ancestral components of Caribbean populations on a sub-continental level and unveil fine-scale patterns of population structure distinguishing insular from mainland Caribbean populations as well as from other Hispanic/Latino groups. We provide genetic evidence for an inland South American origin of the Native American component in island populations and for extensive pre-Columbian gene flow across the Caribbean basin. The Caribbean-derived European component shows significant differentiation from parental Iberian populations, presumably as a result of founder effects during the colonization of the New World. Based on demographic models, we reconstruct the complex population history of the Caribbean since the onset of continental admixture. We find that insular populations are best modeled as mixtures absorbing two pulses of African migrants, coinciding with early and maximum activity stages of the transatlantic slave trade. These two pulses appear to have originated in different regions within West Africa, imprinting two distinguishable signatures in present day Afro-Caribbean genomes and shedding light on the genetic impact of the dynamics occurring during the slave trade in the Caribbean.

The most synthetic graph is the following one:

Figure 1: Population structure of Caribbean and neighboring populations. A) On the map, areas in red indicate countries of origin of newly genotyped admixed population samples and blue circles indicate new Venezuelan (underlined) and other previously published Native American samples. B) Principal Component Analysis and C) ADMIXTURE [12] clustering analysis using the high-density dataset containing approximately 390K autosomal SNP loci in common across admixed and reference panel populations. Unsupervised models assuming K= 3 and K=8 ancestral clusters are shown. At K=3, Caribbean admixed populations show extensive variation in continental ancestry proportions among and within groups. At K=8, sub-continental components show differential proportions in recently admixed individuals. A Latino-specific European component accounts for the majority of the European ancestry among Caribbean Latinos and is exclusively shared with Iberian populations within Europe. Notably, this component is different from the two main gradients of ancestry differentiating southern from northern Europeans. Native Venezuelan components are present in higher proportions in admixed Colombians, Hondurans, and native Mayans.

As expected, Mexicans and most Colombians and Hondurans cluster mostly between Europeans and Native Americans, while Cuban, Dominicans and Haitians do between Europeans and Africans instead, with Puerto Ricans and some Colombians and Hondurans showing tripartite ancestry. 
A most notable issue is that the bulk of Caribbean Latin American ancestry from Europe forms a distinctive component that the authors suggest is a founder effect from the early colonization almost 500 years ago but that I feel that deserves a closer look.
The authors provide also the full ADMIXTURE results for up to K=15, with cross-validation data, what is certainly appreciated by this blogger.

Figure S3:
ADMIXTURE metrics at increasing K values
based on Log-likelihoods (A)
and cross-validation errors (B)
for results shown in Figure S2.

Using table B, the best fit is K=7:

From Fig. S2 (ADMIXTURE results)
Here we see a generic Mediterranean presence in Europe of the “black” component. Would it be just a simple reflection of European structure, then we should expect that the European component in Latin Americans would be c. 70% “red” and just 30% “black”. But nope, not even in Cubans, who are the ones with the most recent European input overall (because it was a colony until a century ago). 
This may indeed have the explanation that the authors suggest: that it is the result of a “recent” founder effect some 500 years ago in the early moments of the Castilian conquest and colonization of America. But still something does not ring correct. At the very least I have some doubts. 
An alternative possibility that should be eventually tested could be that what we identify as “European” ancestry is in fact something European-like but not exactly European, for example North African and/or Jewish ancestry. There could be various sources for this trans-Mediterranean flow into America: on one side it has often been speculated (but never really proven) that a lot of Muslim and Jewish converts migrated to the colonies in the hope to escape the Inquisition. A major problem here is that most Muslim Iberians should be identical or nearly identical in ancestry other Iberians (Jews were not numerous enough probably anyhow).
But another interesting possibility is that many North Africans (including Canarian Aborigines or Guanches) may have been enslaved early on to supply the plantations of the Caribbean. Initially the excuse for slavery was not “racial” (an Illustration development in fact) but “religious”. There are known many Papal edicts insisting that Canarian converts would not be enslaved, something that the Portuguese (first colonial power in the archipelago) did anyhow again and again. It is plausible (but ill-documented) that North African conquest campaigns and raids by Portugal first and Castile later would also capture many slaves in those areas, slaves that would probably end up in America in many cases, where they may have been emancipated eventually, becoming part of the Mestizo backbone of the Castilian colonial empire. 
I know I am speculating a bit here but it is an interesting alternative to explore. In this regard I really miss North African control populations, because they would shed light on this intriguing matter.
Another issue the paper explores is the origin of African ancestry, finding that the oldest ancestry is mostly from westernmost Africa (Mandenka, Brong as reference populations), while more recent ancestry is mostly from the Nigeria-Angola arc (Yoruba, Igbo, Bamoun, Fang and Kongo). 
The study also tries to reconstruct population history but some of their results are perplexing and highly unlikely.

Figure 3: Demographic reconstruction since the onset of admixture in the Caribbean. We used the length distribution of ancestry tracts within each population from A) insular and B) [not shown] mainland Caribbean countries of origin. Scatter data points represent the observed distribution of ancestry tracts, and solid-colored lines represent the distribution from the model, with shaded areas indicating 68.3% confidence intervals. We used Markov models implemented in Tracts to test different demographic models for best fitting the observed data. Insular populations are best modeled when allowing for a second pulse of African ancestry, and mainland populations when a second pulse of European ancestry is allowed. Admixture time estimates (in number of generations ago), migration events, volume of migrants, and ancestry proportions over time are given for each population under the best-fitting model. The estimated age for the onset of admixture among insular populations is consistently older (i.e., 16-17) compared to that among mainland populations (i.e., 14).

The really perplexing issue here is that in Haiti and Cuba particularly, the latest and quite notable arrival of African ancestors corresponds to a mere four generations ago, what means (as the approx. generation length is of c. 30 years, not longer because then the earliest European arrival would be before Columbus’ feat) a mere 120 years ago, i.e. around 1890. 
The reality is that Haiti became independent in 1791-1804 and no relevant demographic inflow has happened since then. Similarly the last major batch of slaves to Cuba (from Spain, where slavery was being outlawed, as well as from Haiti itself) was in the earliest 19th century (however slavery would not be abolished in Cuba until 1884, although human trade was declared illegal in 1835 under British pressure). 
Therefore there must be an error of some sort in these reconstructions, which generate more recent African inflows that are realistically possible.

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.

Archaeologists: Dakar rally in Chile is a crime against patrimony

The College of Archaeologist of Chile has risen their voice against the Rally Dakar 2014 (which is not anymore held in Africa after much controversy but in South America) because it impacts and destroys many archaeological sites. 
According to the Chilean archaeological guild the rally is a clear crime under the article 38 of law 17288, which should be persecuted by the Council of Defense of the State (CDE). However this entity “has its hands tied” because the Rally is promoted by the National Sports Institute (IND). 
The Council of National Monuments (CMN) has documented not less than 207 archaeological sites damaged by previous editions of the rally up to 2012 (all rallies since 2009 have gone through Chilean, as well Argentine and sometimes Peruvian lands).
Since 2009 five legal actions have been initiated against this destructive competition, all of which have been dismissed by the courts. 
Source[es]: Diario de Antofagasta (via Paleorama).
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Posted by on May 11, 2013 in archaeology, Chile, ecology, Latin America


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]

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.
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).

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. 

Polynesian mtDNA in extinct Native American population

The evidence seems to accumulate in favor of some Polynesian impact in South America:
Vanessa Faria Gonçalves et al., Identification of Polynesian mtDNA haplogroups in remains of Botocudo Amerindians from Brazil. PNAS 2013. Pay per view (six months embargo) → LINK [doi:10.1073/pnas.1217905110 ]


There is a consensus that modern
humans arrived in the Americas 15,000–20,000 y ago during the Late
Pleistocene, most probably
from northeast Asia through Beringia.
However, there is still debate about the time of entry and number of
migratory waves,
including apparent inconsistencies between
genetic and morphological data on Paleoamericans. Here we report the
of mitochondrial sequences belonging to
haplogroups characteristic of Polynesians in DNA extracted from ancient
skulls of
the now extinct Botocudo Indians from
The identification of these two Polynesian haplogroups was
confirmed in independent
replications in Brazil and Denmark,
ensuring reliability of the data. Parallel analysis of 12 other Botocudo
individuals yielded
only the well-known Amerindian mtDNA
haplogroup C1.
Potential scenarios to try to help understand these
results are presented
and discussed. The findings of this study
may be relevant for the understanding of the pre-Columbian and/or
peopling of the Americas.

Maize was common in Peru 5000 years ago

It has been confirmed, after decades of debate, that the people of coastal Peru did not just live on fishing but also on farming.
Jonathan Haas et al., Evidence for maize (Zea mays) in the Late Archaic (3000–1800 B.C.) in the Norte Chico region of Peru. PNAS 2013. Pay per view (for six months) → LINK [doi: 10.1073/pnas.1219425110]


For more than 40 y, there has been an active discussion over the presence and economic importance of maize (Zea mays) during the Late Archaic period (3000–1800 B.C.) in ancient Peru. The evidence for Late Archaic maize has been limited, leading to the interpretation that it was present but used primarily for ceremonial purposes. Archaeological testing at a number of sites in the Norte Chico region of the north central coast provides a broad range of empirical data on the production, processing, and consumption of maize. New data drawn from coprolites, pollen records, and stone tool residues, combined with 126 radiocarbon dates, demonstrate that maize was widely grown, intensively processed, and constituted a primary component of the diet throughout the period from 3000 to 1800 B.C.

See also: Science Daily.

Posted by on February 27, 2013 in Latin America, Neolithic, Peru


5000 years old temple found near Lima, Peru

Archaeologists have uncovered one of the oldest temples of America in El Paraíso, a rich archaeological site located 40 km northwest of Lima. 
The pyramidal structure is estimated to be c. 5000 years old (although awaiting radiocarbon dating), much much older than the Incas and rather contemporary of the pyramids of Egypt, for example. It confirms that the area of Lima was a ceremonial center for the ancient peoples of Peru.
The Temple of Fire, as it was nicknamed by the discoverers, contains a hearth at its center, which they suspect was a key part of their rituals. It is built of stone covered in fine yellow clay, which shows some indications of having been painted in red colors.
The ritual site is located close both to the coast and to the valley, allowing for it to interact with both the coastal fishing economy and the beginnings of agriculture in the interior, they say. The prehistorical period of this building is known as the Pre-Ceramic Age (c. 3600-1800 BCE). 
Sources: BBC, El Universo[es] (via Pileta).

Update: see the interesting comments below by Raimo Kangasniemi, who argues that several sites (Áspero, La Galgada, Caral, all them in Peru) are roughly contemporary of this one, indicating a growing dedication of resources to ritual/religious buildings already in the Pre-Ceramic Period V, also elsewhere.


Posted by on February 13, 2013 in America, Latin America, Native Americans, Neolithic, Peru


Alert: Brazilian mining project to destroy dozens of archaeological sites in the Amazon

At least 24 caves, which hold major archaeological relevance for the understanding of the early inhabitation of the Amazon basin, will be destroyed by a gigantic iron mine project in the region of Carajás (Pará, Brazil). 
While the area is a national forest and the Brazilian law demands in principle that archaeological sites be preserved, the government has given Vale, the Brazilian mining giant, what amounts to a blank license for the destruction of whatever stands in their way.
Not just that, but Vale holds control over what ongoing research can disclose of the importance of the caves:
Renato Kipnis, a respected archaeologist in São Paulo whom Vale hired to
survey the caves of Carajás, said that Vale had prohibited him from
discussing their archaeological significance, because of a
confidentiality agreement Vale had required him to sign. Later, a Vale
spokeswoman allowed Mr. Kipnis to be interviewed by e-mail, but only if
the company was allowed to vet his replies. 

In written replies screened by Vale, he marveled at the importance of the caves. 
Source: New York Times
NASA image of the already existing Carajás mine
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Posted by on December 19, 2012 in America, archaeology, Brazil, Latin America, Native Americans


The Xavantes as genuine unmixed Native Americans

Xavantes (cc Agência Brasil)
A new paper proclaims that Xavantes appear to be one of the less mixed and or more genetically distinctive Native American people of present day.
Patricia C. Kuhn et al., Genome-Wide Analysis in Brazilian Xavante Indians Reveals Low Degree of Admixture. PLoS ONE 2012. Open access ··> LINK [doi: 10.1371/journal.pone.0042702]


Characterization of population genetic variation and structure can be used as tools for research in human genetics and population isolates are of great interest. The aim of the present study was to characterize the genetic structure of Xavante Indians and compare it with other populations. The Xavante, an indigenous population living in Brazilian Central Plateau, is one of the largest native groups in Brazil. A subset of 53 unrelated subjects was selected from the initial sample of 300 Xavante Indians. Using 86,197 markers, Xavante were compared with all populations of HapMap Phase III and HGDP-CEPH projects and with a Southeast Brazilian population sample to establish its population structure. Principal Components Analysis showed that the Xavante Indians are concentrated in the Amerindian axis near other populations of known Amerindian ancestry such as Karitiana, Pima, Surui and Maya and a low degree of genetic admixture was observed. This is consistent with the historical records of bottlenecks experience and cultural isolation. By calculating pair-wise Fst statistics we characterized the genetic differentiation between Xavante Indians and representative populations of the HapMap and from HGDP-CEPH project. We found that the genetic differentiation between Xavante Indians and populations of Ameridian, Asian, European, and African ancestry increased progressively. Our results indicate that the Xavante is a population that remained genetically isolated over the past decades and can offer advantages for genome-wide mapping studies of inherited disorders.

The Xavantes, comprising today some 10,000 people, have suffered repeated hostility from the Western civilization in Brazil since centuries ago. In spite of all they have managed to remain proud and distinct.

Fig. 2 three-dimensional global PCA with emphasis in American populations

Fig. 3 (edited by me: only the labeling): neighbor-joining global tree