Major Guanche genetic influence in Puerto Ricans (guest article by Thierno)

Guest article by Thierno

A discussion on a study on Caribbean autosomal ancestry from 2013 by Andrés Moreno Estrada et al., "Reconstructing the Population Genetic History of the Caribbean,” was posted on this blog:

http://forwhattheywereweare.blogspot.com/2013/06/caribbean-autosomal-ancestry.html

There were two important elements of information to consider from said post.

1) The ADMIXTURE graphs displayed a "black" component, largely found in Caribbean Admixed Latinos but only poorly represented in South Europe, which suggested a "recent" founder effect some 500 years ago. [Note: "black" here refers to color coding of an autosomal component in Moreno 2013, not to Tropical African ancestry, that was color-coded as "green", please follow the link above for more details].

2) An interesting and informative discussion between a Puerto Rican named Charles, in search of his ancestry, and another blogger named Maju shed light on the little-known historical contribution of Canarian aboriginal Guanches (Berber) to the colonization of America. It is often referred to as the "Tributo de Sangre" (Blood Tribute).

https://es.wikipedia.org/wiki/Tributo_de_sangre

They concluded that the "black" component which was displayed on the ADMIXTURE graphs of the study most likely had a North African origin, by way of Canarian aboriginal Guanche ancestry.

K=4

This graph represents the stacked bar-plot of an unsupervised ADMIXTURE exercise which is aimed at studying the complex and intricate ancestral components of Puerto Ricans from Puerto Rico, based on samples that were collected from the 1000 Genomes panel.

The choice of populations that are represented in these ADMIXTURE graphs was firstly made to account for the major, historically known contributors to the Puerto Rican population: Iberians, indigenous Caribbeans, and former African slaves who are, respectively, represented by the "Maya" and "Yoruba" samples. 

Secondly, the presence of the merged North African samples in the dataset of these ADMIXTURE graphs serves as a formal test of comparison with the Iberian population in order to verify the aforementioned hypothesis.

The graph for K=4 clearly shows the "light-blue" component, represented in the Puerto Rican (PUR) samples, in addition to their Iberian (red), “Maya-like” (green), and “Yoruba-like” (purple) contributions. 

The "light-blue" component is largely restricted to the North African population and also mostly found in the Saharawi samples, making it a "Saharawi-like" component. In other words, it is the identifiable North African component of this ADMIXTURE exercise. 

This finding contrasts with the typically much lower North African scores of Hispanic Caribbeans that are reported in commercial autosomal DNA tests. I suspect that the use of Mozabite samples as proxies for North African may conflate their Berber ancestral component with the Iberian ancestral side of their complex genetic makeup.

I included Canarian samples because they still display a minor distinct variation of North African admixture relative to Iberians, although it is important to keep in mind that individuals from those samples, as well as present-day Canarians, are more similar to Iberians from an autosomal genetic standpoint. Moreover, studies that were done on Canarian autosomal DNA have shown disparities in the amount of Guanche (Berber) admixture among individuals who are located in different Islands of the archipelago. Canarians from La Gomera seem to have retained the most Guanche ancestry.

Maju had a blog post about a paper on the estimates of Guanche or Berber genetic influence of Canarians here:

https://forwhattheywereweare.blogspot.com/2011/04/canarians-nw-africans-iberians-etc-from.html

Hypotheses made in the recent past about a possible genetic link between Canarian aboriginal Guanches and Puerto Ricans, on the basis of the unknown role that the Canary Islands have played in the colonization of the Americas, are supported in these unsupervised ADMIXTURE runs. Hypothetically, they could have similar implications for some Admixed Latinos and specific Caribbean communities, but most notably for Hispanic Caribbeans.

Reasons for investigating this issue

I am a person of Fula descent. I wasn't predisposed to experiment on this issue, in the sense that I have a different ethnic history. With the help of the software ADMIXTURE, I decided to use my autosomal data and compare it with publicly available datasets, which include populations that are compatible with my genetic history. In addition to my Fula-specific and West African ancestral components, which were similarly detected in the populations studied by Henn et al. in 2012, I also scored a North African percentage.

I had noticed that my data matched up considerably with "New World" Afro-descendants but also, very intriguingly, with a large number of Hispanic Caribbeans.

At first, I attributed it to the fact that West Africa was a region from which slaves were sent to the Americas.

However, when I tried to identify what specific ancestral components I share with some of those Hispanic Caribbean matches, a common restricted Northwest African ancestry seemed to emerge as a pattern with several of them. After reading the blog-post of Maju on Caribbean autosomal ancestry - several years after he posted it - and the possible Northwest African hypothesis of Hispanic Caribbeans, I figured I would try to verify it and maybe, at the same time, manage to elucidate some of my questions.

K=5

[Note (update Dec-31-2020): the sharing of this very drifted (PUR) component between the complex admixed Puerto Rican samples and my sample is difficult to interpret precisely, and from a historical standpoint, as the Lawson et al. paper makes very clear (please see the last update from 2 years ago). Comments below are clues for follow-up research.]

 

The graph for K=5 indicates a green specific homogenization of the Puerto Rican samples (PUR) in comparison to the other populations, which suggests a recent founder effect that most likely took place over the past few centuries. 

Very intriguingly, my North African component is replaced by this PUR specific component instead of the yellow North Africa. It suggests that the "Guanche-Berber" side of the Puerto Ricans overlaps with my Northwest African component. 

I would say that it indicates some complex genetic links between the Guanches and, possibly, other Northwest African populations.

I hope that these unsupervised ADMIXTURE exercises can be of help to those interested in the autosomal genetic links between Hispanic Caribbeans and Canarian aboriginal Guanches.

Thierno

Appendix

I used publicly available datasets to perform these ADMIXTURE exercises.

The first one contains a combined dataset of populations from both the 1000 genome project and HGDP unrelated samples, for a total of 162,645 SNPs. It has been filtered and re-arranged by its contributors who are Peter Carbonetto and Amir Kermany.

It belongs to the Ancestry DNA workshop on Github.com.

All the repositories can be accessed here: https://github.com/Ancestry

It was publicly available until a year ago and was utilized during the Computational, Evolutionary and Human Genomics (CEHG) Symposium.

The PUR (Puerto Ricans in Puerto Rico), IBS (Iberians from Iberia), the Maya and The Yoruba samples were selected from this dataset.

The second dataset is from the Henn et al. study from 2012, “Genomic Ancestry of North Africans Supports Back-to-Africa Migrations.” It contains the North African samples that I used for the exercises. I merged them with the dataset that contains the PUR samples, and intersected 44,804 SNPs.

This is the link to access it: http://biologiaevolutiva.org/dcomas/north-african-affy-6-0-data-henn-et-al-submitted/

The third dataset is from the Botigué et al. study from 2013, “Gene flow from North Africa contributes to differential human genetic diversity in Southern Europe.”

It has Spain_S (Andalucians), Spain_NW (Galacians), and Canary Islanders. I also intersected 44,804 SNPs with the first and the main datasets.

The link to access it is here: http://biologiaevolutiva.org/dcomas/north-african-affy-6-0-data-henn-et-al-submitted/

I used the software PLINK to update the physical and genetic positions of the SNPs from the second and third dataset, in order to properly merge them with the ones from the first dataset. I also made sure to merge only SNPs that were already found in the selected dataset (1000 genome and HGDP).

Lastly, I intersected my personal data with the dataset (1000 genome and HGDP), for a total of 161,764 SNPs.

The software ADMIXTURE was used to estimate ancestry.

R was used to plot the estimates.

Update (Oct 30th): 

I would like to briefly elaborate on the sampling strategy. The first ADMIXTURE runs that I produced contained additional continental European populations, as well as other West Asian samples. The display showing the distinctive ADMIXTURE coded colors between North African and European samples of the dataset appeared at higher K values, with their respective higher standard errors of the cross-validation error estimate.

I had asked for Maju’s insight on admixture analyses in the past, as I was interested in how his posts on West African and Berber genetics related to my personal autosomal DNA. I did the same for this analysis.

I followed Maju’s recommendations to limit the selection of the reference population to be analyzed to just 4: Iberians, West Africans, Mayans, and Northwest Africans. This resulted in the clear and distinctive display of Berber and Iberian components, starting at K=4 which has a lower standard error. I later added Canary Islander samples.

Note: I have also been asked to replace Yoruba with Senegambian Mandinka samples to check for potential differences. This is something that I had already checked, but I didn't notice any difference in either the Berber percentage in Puerto Ricans or in their homogenization, which indicated a recent founder effect.

Thierno



Update March 14th 2019:

After this article was posted last October, I received a lot of interesting feedback on the admixture analyses and suggestions for different ancestral contributions of Hispanic Caribbeans, both in private messages and in the comment section of this post/both publicly and privately. In light of this, I would like to go over some aspects of the analysis again. 

A note of caution in the interpretation of estimates

The estimates of the clusters from ADMIXTURE are not to be interpreted literally. The different ancestral k components are not “real” populations. They are designed to help identify differentiation between populations.

Both supervised and unsupervised analyses will produce FSTs between the designated populations or between the clusters. They serve to evaluate “approximately” possible genetic variations. In this type of analysis, as we can observe in the graphs contained in this post, moderate amounts of the components that are less divergent from each other overlap across populations which share lower FSTs. Considering that FSTs between North Africans and West Eurasians is usually around 0.06, there will inevitably be a shared overlapping effect. As a result, it isn’t possible to obtain a very precise delineation between North African and Iberian samples. So, essentially, this is an evaluation of variation and not an accurate system of measurement. 

Intuitively, it seems that analyses which contain populations or clusters that are separated with higher FSTs will be more robust. It also seems that when FSTs fall below 0.05, the degree of differentiation in the displayed clusters is difficult to evaluate or make sense of. This may explain why analyses of intra-European/Mediterranean populations with FSTs that are around 0.01 are difficult to evaluate with ADMIXTURE. Other steps can be taken to mitigate the effects of linkage disequilibrium, as was the case for the dataset that was used for the analysis in this post.

ADMIXTURE works better for recently admixed groups who derive their ancestry from distinct populations. For obvious historical reasons, African Americans and Hispanic Americans have recent ancestries that most admixture analyses can detect fairly well.
Evidently, the total complexity and chaotic processes of ancient migrations which are not static, but rather dynamic cannot realistically be captured by ADMIXTURE. The complete reconstruction of such patterns on the basis of present-day populations would obviously be misleading.

Daniel J. Lawson, Lucy van Dorp and Daniel Falush wrote a paper called, “A tutorial on how (not) to over-interpret STRUCTURE/ADMIXTURE bar plots” (2018) in which they warned against some of the pitfalls of admixture analyses.

While it’s not possible to make exact predictions from tools that are used in the field of population genetics, when interpreted correctly, some interesting information can still be extracted from various analyses.

 
Previous research on the possible Canarian legacy in America, including the examination of historical records, had been conducted prior to the publication of the Moreno et al. (2013) paper. With regard to the genetic affinity of the aboriginal inhabitants of the Canary Islands, a similar analysis was done more recently on the autosomal DNA of ancient Guanche samples that may have lived between the 7th and the 11th century and is discussed in a paper by Rodrı́guez-Varela et al. (2017). The authors conclude that a Northwest African-specific ancestry component makes up the majority of their autosomal ancestry, as well as other Berber populations from North Africa. Additionally, Y-DNA E1b-M81, which is found at high frequencies in Northwest Africa, was also detected in these samples.

In the study from Arauna et al. (2016) on how “Recent Historical Migrations Have Shaped the Gene Pool of Arabs and Berbers in North Africa,” the authors expressed doubts about the use of Mozabite samples as the sole proxy for North African genetic diversity. 

Considering that the paper from Moreno et al. didn’t have North African samples, the focus of this post was to explore potential variations by including Northwest African samples such as Moroccans and Saharawis.

Naturally, to exactly what extent inhabitants of the Canary Islands – whose gene pool could have already been affected by the DNA of Iberian settlers - may have impacted the genetic pool of Hispanic Caribbeans is a question which would require further and more diversified analyses.


mtDNA L(xM,N)

Several studies have reported mtDNA L(xM,N) among various Latin American communities. They strongly suggest recent African ancestry in the context of the recent colonization of the New World. The uncommon L(xM,N) lineages that have formed variant specific subclades which are not native to Africa but rather found in other continents or regions are extremely rare, it seems.

In 2012 Cerezo et al. published a paper on subject which is titled, “Reconstructing ancient mitochondrial DNA links between Africa and Europe.”

Another study, published by Ricardo Rodriguez-Varela and his colleagues, is called “Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans.”

More recently, a paper called “Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands” was published by Rosa Fregel with the mtDNA sequencing of 48 ancient individuals. Out of all of the L(xM,N) lineages that were analyzed, only the newly defined L3b1a12 was identified as a new Canarian-specific lineage.

It appears that European and Canarian autochthonous mtDNAL(xM,N) lineages form subclades which correspond to specific mutations that are less likely to be found in Africa.

In the case of Puerto Ricans, there was a project from National Geographic called “Genographic Project DNA Results Reveal Details of Puerto Rican History” (2014). After sampling 326 individuals from southeastern Puerto Rico and Vieques, they found that 80% of Puerto Rican men carry West Eurasian (or European) Y-DNA paternal lineages, while 60% of Puerto Ricans carry maternal lineages of Native American origin. This may shed some more light on the findings of Moreno et al., (2013), who wrote of the “Latin-European” component which seemed to indicate a founder effect.

In contrast, it would be interesting for future research to sample Hispanic Caribbean communities where African ancestry may have been retained in higher proportions and, in the process, collect more mtDNA and Y-DNA.

Thierno

Caribbean Taino ancient DNA still alive in admixed populations

Taino Native Americans also had a very high genetic diversity, comparable to other continental large native populations such as Andeans or Amazonians, what speaks of high mobility in the Caribbean islands before European colonization.

The mitochondrial lineage B2 was sequenced, although it is today rare in the region.

Hannes Schroeder et al., Origins and genetic legacies of the Caribbean Taino. PNAS 2018. DOI:10.1073/pnas.1716839115

The Caribbean was one of the last parts of the Americas to be settled by humans, but how and when the islands were first occupied remains a matter of debate. Ancient DNA can help answering these questions, but the work has been hampered by poor DNA preservation. We report the genome sequence of a 1,000-year-old Lucayan Taino individual recovered from the site of Preacher’s Cave in the Bahamas. We sequenced her genome to 12.4-fold coverage and show that she is genetically most closely related to present-day Arawakan speakers from northern South America, suggesting that the ancestors of the Lucayans originated there. Further, we find no evidence for recent inbreeding or isolation in the ancient genome, suggesting that the Lucayans had a relatively large effective population size. Finally, we show that the native American components in some present-day Caribbean genomes are closely related to the ancient Taino, demonstrating an element of continuity between precontact populations and present-day Latino populations in the Caribbean.

Fig. 2.

Taino demography. Total estimated length of genomic ROH for the Taino and the Clovis genome (13) and selected Native American and Siberian genomes (15, 31, 32) in a series of length categories. ROH distributions for modern individuals have been condensed into population-level silhouettes (SI Appendix, section 14).

A 14.000 year old human settlement in Argentina

Quickies

Although the paper claims this site as the signature of arrival of our species to the South Cone (southern region of South America), there is another site with quite apparently older dates: Monte Verde (Chile), that cannot be ignored. In any case, it is a quite interesting data point for the peopling of America and the oldest one known East of the Andes.

Gustavo G. Politis et al., The Arrival of Homo sapiens into the Southern Cone at 14,000 Years Ago. PLoS ONE, 2016. Open access → LINK [doi:10.1371/journal.pone.0162870]

Abstract

The Arroyo Seco 2 site contains a rich archaeological record, exceptional for South America, to explain the expansion of Homo sapiens into the Americas and their interaction with extinct Pleistocene mammals. The following paper provides a detailed overview of material remains found in the earliest cultural episodes at this multi-component site, dated between ca. 12,170 14C yrs B.P. (ca. 14,064 cal yrs B.P.) and 11,180 14C yrs B.P. (ca. 13,068 cal yrs B.P.). Evidence of early occupations includes the presence of lithic tools, a concentration of Pleistocene species remains, human-induced fractured animal bones, and a selection of skeletal parts of extinct fauna. The occurrence of hunter-gatherers in the Southern Cone at ca. 14,000 cal yrs B.P. is added to the growing list of American sites that indicate a human occupation earlier than the Clovis dispersal episode, but posterior to the onset of the deglaciation of the Last Glacial Maximum (LGM) in the North America.

Patrilineages of Panama

Quickies

Viola Grugni et al., Exploring the Y Chromosomal Ancestry of Modern Panamanians. PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0144223]

Abstract

Geologically, Panama belongs to the Central American land-bridge between North and South America crossed by Homo sapiens >14 ka ago. Archaeologically, it belongs to a wider Isthmo-Colombian Area. Today, seven indigenous ethnic groups account for 12.3% of Panama’s population. Five speak Chibchan languages and are characterized by low genetic diversity and a high level of differentiation. In addition, no evidence of differential structuring between maternally and paternally inherited genes has been reported in isthmian Chibchan cultural groups. Recent data have shown that 83% of the Panamanian general population harbour mitochondrial DNAs (mtDNAs) of Native American ancestry. Considering differential male/female mortality at European contact and multiple degrees of geographical and genetic isolation over the subsequent five centuries, the Y-chromosome Native American component is expected to vary across different geographic regions and communities in Panama. To address this issue, we investigated Y-chromosome variation in 408 modern males from the nine provinces of Panama and one indigenous territory (the comarca of Kuna Yala). In contrast to mtDNA data, the Y-chromosome Native American component (haplogroup Q) exceeds 50% only in three populations facing the Caribbean Sea: the comarca of Kuna Yala and Bocas del Toro province where Chibchan languages are spoken by the majority, and the province of Colón where many Kuna and people of mixed indigenous-African-and-European descent live. Elsewhere the Old World component is dominant and mostly represented by western Eurasian haplogroups, which signal the strong male genetic impact of invaders. Sub-Saharan African input accounts for 5.9% of male haplotypes. This reflects the consequences of the colonial Atlantic slave trade and more recent influxes of West Indians of African heritage. Overall, our findings reveal a local evolution of the male Native American ancestral gene pool, and a strong but geographically differentiated unidirectional sex bias in the formation of local modern Panamanian populations.

Fig 1. Spatial distributions of Y-chromosome components in Panama.

Bars show Native American (violet), West Eurasian/North African (green), sub-Saharan African (yellow) and South Asian (light blue) components in each province or comarca. In grey the Y-chromosome portion with discordant haplogroup predictions.

Archaeologists studying Monte Verde claim an age of 18 Ka BP and add some detail

Quickies

I'm going in this and upcoming short entries through my backlog. You are warned.

New archaeology from Monte Verde (Chile) suggests a date of 18 Ka BP (slightly older than the oldest known North American site) and also that it was a transiting site for highly mobile peoples and not a main base, as they were not using superior local lithics but bringing their own.

Tom D. Dillehay et al. New Archaeological Evidence for an Early Human Presence at Monte Verde, Chile. PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0141923]

Abstract

Questions surrounding the chronology, place, and character of the initial human colonization of the Americas are a long-standing focus of debate. Interdisciplinary debate continues over the timing of entry, the rapidity and direction of dispersion, the variety of human responses to diverse habitats, the criteria for evaluating the validity of early sites, and the differences and similarities between colonization in North and South America. Despite recent advances in our understanding of these issues, archaeology still faces challenges in defining interdisciplinary research problems, assessing the reliability of the data, and applying new interpretative models. As the debates and challenges continue, new studies take place and previous research reexamined. Here we discuss recent exploratory excavation at and interdisciplinary data from the Monte Verde area in Chile to further our understanding of the first peopling of the Americas. New evidence of stone artifacts, faunal remains, and burned areas suggests discrete horizons of ephemeral human activity in a sandur plain setting radiocarbon and luminescence dated between at least ~18,500 and 14,500 cal BP. Based on multiple lines of evidence, including sedimentary proxies and artifact analysis, we present the probable anthropogenic origins and wider implications of this evidence. In a non-glacial cold climate environment of the south-central Andes, which is challenging for human occupation and for the preservation of hunter-gatherer sites, these horizons provide insight into an earlier context of late Pleistocene human behavior in northern Patagonia.

Notice that Monte Verde is quite towards the south and, in Ice Age contexts, it was a rather extreme environment, barely outside of the glaciers. I wonder what they looked for in such a remote place, even if they probably only went there in summer.

Mexico's Native American diversity

Interesting study on Mexico's Native American diversity:

Andrés Moreno Estrada et al., The genetics of Mexico recapitulates Native American substructure and affects biomedical traits. Science 2014. Freely available with registration → LINK [doi:10.1126/science.1251688]

Abstract

Mexico harbors great cultural and ethnic diversity, yet fine-scale patterns of human genome-wide variation from this region remain largely uncharacterized. We studied genomic variation within Mexico from over 1000 individuals representing 20 indigenous and 11 mestizo populations. We found striking genetic stratification among indigenous populations within Mexico at varying degrees of geographic isolation. Some groups were as differentiated as Europeans are from East Asians. Pre-Columbian genetic substructure is recapitulated in the indigenous ancestry of admixed mestizo individuals across the country. Furthermore, two independently phenotyped cohorts of Mexicans and Mexican Americans showed a significant association between subcontinental ancestry and lung function. Thus, accounting for fine-scale ancestry patterns is critical for medical and population genetic studies within Mexico, in Mexican-descent populations, and likely in many other populations worldwide.

Fig. 1-D

First of all it has to be highlighted that the sentence "some groups were as differentiated as Europeans are from East Asians" is a bit misleading. It refers to the raw FST parameter (Fixation Index) which in these cases is caused by extreme drift, product of isolation and small number endogamy.

Otherwise the Seris (Comcaac), who are the only population affected by the claim, are clearly derived not only from the same root as the rest of Native Americans but more specifically from the ancestor population of the Tarahumaras (Rarámuri), as fig.1-D reflects (right). 

The Seris are a small population of coastal Sonora who add up to less than one thousand people and have remained proudly distinct, not only from the colonial population but also from other fellow Native Americans. In spite of this long extreme isolation that makes the appear "as differentiated as Europeans are from East Asians", it is apparent that they must derive from the Uto-Aztecan populations of NW Mexico (and maybe also across the border). 

K=9 (fig. 2-B-part)

Other very isolated and heavily drifted populations are the Lacandon and Tojolabal Mayas. Again, in spite of their radical isolation, they seem related to other Mayas by origin. In these cases their languages are recognized as members of the Maya family, while the Seri language is considered an isolate. 

Actually the extreme FST scores only apply between these extremely drifted populations: FST{Seri-Lacandon}=0.136, FST{Seri-Tojolabal}=0.121. 

This reference is interesting because it explains how subcontinental levels of differentiation can happen in relatively short time if the founder populations are small and isolated for some 20 Ka. It is a warning call against reaching to too many conclusions based only on populations with a long history of isolation.

Otherwise the Seri FST scores are high but more normal: 0.087 to 0.096.  See table S-4 for further details. 

The tree is interesting also because it suggest a main division separating the Nahuas from the rest of the Uto-Aztecan meta-population (Saris included). The Nahuas, who approximately correspond to the the ancient Aztecs, are actually divided in several groups, which seem rather akin to their immediate neighbors and not so much among them or their linguistic relatives. 

This implies that, as the ancestors of the Nahuas migrated southwards, they assimilated so many locales that they largely lost their distinctiveness. In the ADMIXTURE graph to the left, we see that they do keep a variably small fraction of Uto-Aztecan affinity (not just them, also the Purepecha and Totonac, whose languages are distinct). 

Otherwise Mexican Natives have two main components at K=9: the main Mexican one (blue) and the Maya one (orange). The Maya division is also apparent in the tree. 

However it must be mentioned that the ADMIXTURE run available in the supp. materials (fig. S-10) reaches down to K=20, showing further differentiation between the various Mesoamerican populations dominated by the blue components at K=9. 

For comparison, in the European segment only the Basque component shows up as distinct in all those runs (since K=10). So we are talking about a fairly diverse population compared with European relative homogeneity.

Sequence of further components or distinctions showing at depths greater than K=9:

• K=12: Tarahumara
• K=14: Nahua-Purepecha-Totonac
• K=15: Tepehuan
• K=16: Purepecha + Jalisco-Nahua
• K=18: Triqui
• K=20 Totonac

Mestizo ancestries

An issue worth mentioning, particularly in relation to the so far unconfirmed but quite plausible Canarian origin of a large share of the "European" ancestry in the Caribbean region, is that the European ancestry of Mexicans seems essentially Iberian, as shown in fig. S-14:

I am anyhow awaiting for a sensible geneticist to address this question properly. When dealing with Mexicans and other Latin American populations of complex colonial ancestry, it seems quite apparent that so diverse European samples are in excess and that instead a North African control is surely missing instead.

A more regionalized approach to Iberian ancestry could also be interesting.

Regarding the Native American share of the ancestry, a finding of this study is that there is important regional variation: Yucatan and Campeche Mexicans have clearly strong Maya ancestry, while in Sonora it is something more like Tarahumara and in the core of Mexico it seems Nahua-like or from other "central" populations like the Zapotec or Totonac. See fig. 2A for details.

There is also very minor Tropical African ancestry across the board, somewhat more relevant in Guerrero and Veracruz, states which historically hosted the main port cities of New Spain and still have some small Afrodescendant populations.

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 accessible → LINK [ref. arXiv:1306.0558v1]

Update (Nov 15): formally published at PLoS Genetics (open access → LINK). No apparent major changes.

Abstract

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.


Update (3 Nov): Canary Islands were a major source of Caribbean "white" ancestry.

A very interesting and informative discussion with a Puerto Rican in search of his ancestry arose recently at my old blog Leherensuge. Charles provided very useful information on this matter and told me about aspects of the history of the colonization of America, and very especially the strategical (but economically less important) islands of the Greater Antilles.

A very unknown historical element is that Castile (not as much as Portugal but still) lacked great amounts of willing settlers in its free (non-serf) population and that therefore it had to look for assimilated colonists in odd places like the Canary Islands, where the clannish Guanches (the distinctive aboriginal islander Berbers) seem to have served that purpose by grade or force.

For example, in 1678 the Castilian Government issued a decree (cédula) that has become popularly known as Tributo de Sangre[es] (Blood Tribute) by which the Canarian oligarchs were imposed a "tax" of nine families to be moved to the Caribbean for each 1000 tons of local exports to America. There are some historians who criticize[es] this concept as "a myth" but what seems very clear is that, either way, Canarian Aborigines contributed heavily to the settlement of "Spanish America", very especially the Dominican Republic, Puerto Rico and Cuba.

So it seems I was correct in imagining a North African origin of this "black" component of Caribbean European-like ancestry. Of course, it still awaits a formal test of comparison with North Africans but I am pretty much persuaded now.

This is an interesting example of settlement with a culture (Castilian/Spanish in this case) different from the genetic roots of the population (largely Aboriginal Canarian). A similar example can well be that of the Irish (partly forced) settlement of Australia, carrying an "English" language and identity but effectively being from a different origin. In the case of Quebec it is also very probable that most original settlers came from some specific region of the French state and surely not from the "core France" around Paris (Southwest? - still untested but there is a very clear founder effect in any case).

I wonder how many other such cases have happened also in prehistory. For example: how genuinely "Indoeuropean" (by blood) were the Celts or other invaders of the Metal Ages. The likely answer is: probably not much. This has probably happened a lot but is in most cases undocumented. Only careful and dispassionate genetic research can give us some answers.


Update (Feb 16 2014): Charles has found another very interesting study, with plenty of data, which illustrates the continuous flow of Canarians to the Spanish possessions in the Caribbean. It is in Spanish language however:

Juan Manuel Santana Pérez, Isleños en Cuba y Puerto Rico (del siglo XVIII a mediados del XIX). Cuadernos Americanos nº 126, 2008 → LINK (freely accessible PDF).


Update (Oct 12 2018): Independent research just published HERE shows that about half of the ancestry of Puerto Ricans is Berber (North African) rather than Iberian and thus that the Guanche or Canario ancestry hypothesis posited by Charles is almost certainly correct.

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).

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 access → LINK [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. 

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 ]

Abstract

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 identification of mitochondrial sequences belonging to haplogroups characteristic of Polynesians in DNA extracted from ancient skulls of the now extinct Botocudo Indians from Brazil. 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 post-Columbian 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]

Abstract

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.

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.

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

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]

Abstract

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