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.

Good documentaries on human Prehistory

I just watched the documentary "First Peoples - Asia" (by NOVA) and found it quite good, discussing many of the issues that I and the readers of this blog have been following and discussing the last years on the settling of Asia (and geographical dependencies): the Zhirendong jaw, the Nubian points of Arabia, the archaic admixture events... 

The only issue is that for some odd reason (copyright masking?) interviewed people voices often have a too high pitch.

I hope the other four documentaries of the series are similarly good. I haven't watched them yet but the full playlist is embedded below beginning with the Asian colonization movie. For many readers it won't be that interesting personally (they already know all or most of it, maybe even better than what the movie explains) but it is still a promising tool to share your hobby with family and friends, so watch it in good company. 

Enjoy!

Update (Jan 9):

I've watched already four of them (Africa, Asia, Australia and Europe) and the European one is no doubt the worst: a superficial Neanderthal hybridization neo-myth spearheaded by John Hawks. Also the only map or description of the route followed by modern humans to Europe is absolute nonsense: directly from Africa via Palestine, when in fact it's extremely clear that at least most of the lineages went all the way to SE Asia and back before ever entering Europe. What happened to the spear in the rib of Zawi Chemi Shanidar man? What happened to the very fast replacement in the early Aurignacian, coincident with the Campanian Ignimbrite eruption? What about dogs? Not a word! Just whitewashing of the probably quite violent Sapiens-Neanderthal interaction. You can skip that one, really, it's pretty much nonsense.

Some hyper-hybridationism permeates all the documentaries but the others seem much better: the Asia one is quite good, the Africa one is not bad either (although could be much better if they paid more attention to archaeology, also Africa deserves 50% of the documentary space probably), the Australia one is OK but it simply ignores Papua and Wallacea altogether, what is a bit perplexing to say the least. The Europe one is just horrible: it has some facts but half of it its John Hawks' preaching his particular ideology about people being oh-so-nice that they probably used spears as toothpicks, Paabo making a lot of extra work for the cleaning crew (spectacular admittedly but should be in a separate Neanderthal docu, not in one dedicated to H. sapiens) and some real archaeology scattered around (but definitely not enough at all).

Ancient mitochondrial DNA from Alaska babies

Quickies

Two new ancient Native American mtDNA sequences from what is now Alaska and back in the day, some 11,500 years ago, was linked to Asia forming the Beringia isthmus.

Justin C. Tackney et al., Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia. PNAS 2015. Pay per view (free in 6 months) → LINK [doi: 10.1073/pnas.1511903112]

Abstract

Pleistocene residential sites with multiple contemporaneous human burials are extremely rare in the Americas. We report mitochondrial genomic variation in the first multiple mitochondrial genomes from a single prehistoric population: two infant burials (USR1 and USR2) from a common interment at the Upward Sun River Site in central Alaska dating to ∼11,500 cal B.P. Using a targeted capture method and next-generation sequencing, we determined that the USR1 infant possessed variants that define mitochondrial lineage C1b, whereas the USR2 genome falls at the root of lineage B2, allowing us to refine younger coalescence age estimates for these two clades. C1b and B2 are rare to absent in modern populations of northern North America. Documentation of these lineages at this location in the Late Pleistocene provides evidence for the extent of mitochondrial diversity in early Beringian populations, which supports the expectations of the Beringian Standstill Model.

A very good article in Spanish is available at Paleoantropología Hoy, which mentions that the only modern population to have both matrilineages are the Hualapai, who live in the state of Arizona (USA). 

Other populations carrying the C1b lineage are the Pima (Arizona), Delta Yuman (California), Ignacianos (Bolivia), extinct Tainos from Puerto Rico and the Norris Farm remains from pre-contact Illinois, as well as a few unspecificied "other tribes". 

B2 is more common, being found in some 37 populations, including Yakama, Wishram, Northern Paiute-Shoshone, Navajo, Zuni, Jemez (all these from North America), Quechua and Aymara (Peru, Bolivia). It was also common among the old Fremont and Anasazi populations of SW USA. 

He also mentions that the archaeological data for the remains was described by Potter et al. 2014. The two babies are post-natal and pre-natal deaths respectively and were carefully buried with ochre paint on their bodies, arrow points (bow and arrows originally, I presume) and organic remains (food). Then a hearth was built over the tomb, which had absolutely normal use, including disposing of food remains (although it can be speculated that they were additional food offerings), except for another baby that was apparently cremated at it in later times. The deaths of the two babies took place in summer, judging from the animal remains of the burial context.

Ket genetics: strong "ANE" and a paleo-Eskimo link

Quantity over quality series.

Pavel Flegontov et al. Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry. BioRxiv 2015 (pre-pub). Freely accessible → LINK [doi: http://dx.doi.org/10.1101/024554]

Abstract

The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal'ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralic-speaking Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, determined mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that the Kets belong to the cluster of Siberian populations related to Paleo-Eskimos. Unlike other members of this cluster (Nganasans, Ulchi, Yukaghirs, and Evens), Kets and closely related Selkups have a high degree of Mal'ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed.

Atlas of Inuit trails

An anthropological and geographical resource that may be of interest:

→ Pan Inuit Trails

The atlas seems so far mostly limited to Nunavut and other parts of Northern Canada.

From the Introduction:

The Atlas provides a synoptic view (although certainly incomplete) of Inuit mobility and occupancy of Arctic waters, coasts and lands, including its icescapes, as documented in written historical records (maps of trails and place names). 

The documents that form the foundation of this Atlas consist of both published and unpublished accounts of Inuit engagement with cartography during the 19th and 20th centuries. All documents are held in public libraries or archives. The focus of the Atlas in this initial project is on material from the Eastern and Central Canadian Arctic. It is hoped that the Atlas can be further developed in subsequent phases to present material of other Inuit groups such as the Inupiat, Inuvialuit, and peoples of Nunatsiavut (Labrador) and Nunavik. 

Delineations of trails and place names play a critical role in documenting the Inuit spatial narratives about their homelands. To show where these trails lead and connect to other trails, the historical records used in making this Atlas are being relationally linked, referenced geospatially, and displayed on a base map.

Partial image of the atlas

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.

13,000 years old Mexican remains confirm genetic continuity from Paleoamericans

New ancient mtDNA from an underwater cave in Yucatan confirmed that there are no obvious differences between the so-called Paleoamericans and modern Native Americans.

James C. Chatters et al., Late Pleistocene Human Skeleton and mtDNA Link Paleoamericans and Modern Native Americans. Science Magazine 2014. Pay per view → LINK [doi:10.1126/science.1252619]

Abstract

Because of differences in craniofacial morphology and dentition between the earliest American skeletons and modern Native Americans, separate origins have been postulated for them, despite genetic evidence to the contrary. We describe a near-complete human skeleton with an intact cranium and preserved DNA found with extinct fauna in a submerged cave on Mexico’s Yucatan Peninsula. This skeleton dates to between 13,000 and 12,000 calendar years ago and has Paleoamerican craniofacial characteristics and a Beringian-derived mitochondrial DNA (mtDNA) haplogroup (D1). Thus, the differences between Paleoamericans and Native Americans probably resulted from in situ evolution rather than separate ancestry.

The Hoyo Negro girl, whose skeleton was preserved underwater for millennia, after she apparently fell into the cave and died as consequence, belonged to haplogroup D1, one of a handful found in modern Native Americans (all them within A, B, C, D and X2). 

The radiocarbon date for the skeleton is c. 12,800 BP, while the upper limit of her death (inferred from calcite formation on the bones, dated via thermoluminiscence) is of c. 12,000 BP. 

Overall there are already four mtDNA and two Y-DNA Paleoamerican sequences from the 13-10,000 BP bracket, all of which fit perfectly with modern Native American DNA. See map to the right.

This underlines that anthropometric estimates are not really reliable to determine ancestry, at least in the long run, because there has been much speculation about these not supporting continuity between the first settlers of America (Paleoamericans) and modern Native Americans, however ancient DNA consistently supports continuity. 

One thing is the genotype and another the phenotype. And although they are somehow related for the greatest part, this relationship is not always straightforward, at least with our current knowledge.

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

Siberian genetics with focus on Yakutia

Informative study on the populations of Sakha Republic (Yakutia) and Siberia in general:

Sardana A. Fedorova et al., Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): implications for the peopling of Northeast Eurasia. BMC Evolutionary Biology 2014. Open access → LINK [doi:10.1186/1471-2148-13-127]

Abstract

Background

Sakha – an area connecting South and Northeast Siberia – is significant for understanding the history of peopling of Northeast Eurasia and the Americas. Previous studies have shown a genetic contiguity between Siberia and East Asia and the key role of South Siberia in the colonization of Siberia.

Results

We report the results of a high-resolution phylogenetic analysis of 701 mtDNAs and 318 Y chromosomes from five native populations of Sakha (Yakuts, Evenks, Evens, Yukaghirs and Dolgans) and of the analysis of more than 500,000 autosomal SNPs of 758 individuals from 55 populations, including 40 previously unpublished samples from Siberia. Phylogenetically terminal clades of East Asian mtDNA haplogroups C and D and Y-chromosome haplogroups N1c, N1b and C3, constituting the core of the gene pool of the native populations from Sakha, connect Sakha and South Siberia. Analysis of autosomal SNP data confirms the genetic continuity between Sakha and South Siberia. Maternal lineages D5a2a2, C4a1c, C4a2, C5b1b and the Yakut-specific STR sub-clade of Y-chromosome haplogroup N1c can be linked to a migration of Yakut ancestors, while the paternal lineage C3c was most likely carried to Sakha by the expansion of the Tungusic people. MtDNA haplogroups Z1a1b and Z1a3, present in Yukaghirs, Evens and Dolgans, show traces of different and probably more ancient migration(s). Analysis of both haploid loci and autosomal SNP data revealed only minor genetic components shared between Sakha and the extreme Northeast Siberia. Although the major part of West Eurasian maternal and paternal lineages in Sakha could originate from recent admixture with East Europeans, mtDNA haplogroups H8, H20a and HV1a1a, as well as Y-chromosome haplogroup J, more probably reflect an ancient gene flow from West Eurasia through Central Asia and South Siberia.

Conclusions

Our high-resolution phylogenetic dissection of mtDNA and Y-chromosome haplogroups as well as analysis of autosomal SNP data suggests that Sakha was colonized by repeated expansions from South Siberia with minor gene flow from the Lower Amur/Southern Okhotsk region and/or Kamchatka. The minor West Eurasian component in Sakha attests to both recent and ongoing admixture with East Europeans and an ancient gene flow from West Eurasia.

The matrilineal mitochondrial DNA pool is dominated by  C4, C5, D4 and D5, with some instances of other lineages (see fig. 1). All these and most of the rest are common Siberian lineages of East Asian roots. 

In the odd zone, the extremely rare haplogroup R3 has been found among North Yuhaghirs in this study (previously only in Jordan that I know with any certainty). They mention that R3 and R1 are derived from the same root, sharing two coding region mutations, and therefore they proceed to rename R3 as R1b. R1 is an also rare Indian matrilineage. 

The patrilineal Y-DNA pool (see fig. 2) is massively dominated by N1c, which also dominates most Uralic-speaking peoples. This is unusual for a Turkic-speaking population but it was known since long ago. Other still important lineages are C2 (former C3, typical of NE Asia and some North American populations), N1b and R1a. Some instances of I, E1b1b1, J, O, F and L are also reported. C2 is more important among the Northern (non-Turkic) populations of Sakha Republic, reaching to 30-40%.

On the autosomal DNA pool, the heatmat (fig. 4) shows that among all sampled populations the Selkup are particularly isolated. Koryaks and Chukchis from the far NE Siberia form a small cluster of their own and so do Shors and Kets (West Siberians). Native American populations also show great individual isolation in comparison with most Eurasians.

Otherwise there are three major clusters: West/South/Central Eurasians, East Asians and Siberians, who generally also cluster with East Asians.

Some of this is also apparent in the PCA (fig. 5) although not as neatly:

PCA of the native populations of Sakha in the context of other Eurasian and American populations.

Maybe more illustrative is the ADMIXTURE analysis:

ADMIXTURE plots. Ancestry proportions of the 758 individuals studied (from 55 populations) as revealed by the ADMIXTURE software at K = 3, K = 4, K = 6, K = 8, and K = 13.

The analysis reveals, from K=6 upwards, the following clusters: West Eurasian (dark blue), South Asian (green), East Asian (orange, also light green at K=13) and several Siberian and Native American specific clusters (yellow, light and dark brown, red, etc.)

The persistance of the blue West Eurasian component in Aleutians and Greenlanders should raise some eyebrows. However, Greenlanders do not really cluster with West Eurasians in the heatmap, so this is almost certainly an artifact that indicates that a much greater K-depth should be achieved in order to properly classify this most diverse human sample. Thirteen clusters are obviously not enough.

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 view → LINK [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.

The Mal'ta aDNA findings

The recent sequencing of ancient DNA from the remains of a Central Siberian young boy, corresponding to the Gravettian site of Mal'ta, West of Lake Baikal, dated to c. 24,000 years calBP, has caught the interest of many anthropology enthusiasts. During my hiatus of more than two months, most people who asked me to retake blogging with an specific request, talked of these findings. Let's see:

Maanasa Raghavan et al., Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 2013. Pay per view → LINK [doi:10.1038/nature12736]

Abstract

The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians^{1, 2, 3}, there is no consensus with regard to which specific Old World populations they are closest to^{4, 5, 6, 7, 8}. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia⁹, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers^{10, 11, 12}, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages⁵. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians^{2, 13}. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago¹⁴, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.

Haploid lineages

The Mal'ta boy, MA-1, carried distinct yDNA R* and mtDNA U* lineages. While both are clearly related to those dominant in Europe and parts of Asia (West, South) nowadays, they are also distinct from any specific dominant lineage today.

R* (yDNA) is neither R1 nor R2 but another distinct branch of R. This kind of R(xR1, R2) is most rare today and found mostly in and around NW South Asia. Following Wikipedia, this "other R" is found in:

• 10.3% among the Burusho
• 6.8% among the Kalash
• 3.4% among the Gujarati

However I must say that I recall from old discussions that some R(xR1) is also found among Mongols and some North American Natives. I would have to find the relevant studies though (maybe in an update).

U* (mtDNA) is also quite rare today but has been found in Swabian Magdalenian hunter-gatherers, as well as in some Neolithic samples, although it may well be a totally different kind of U* (I could not discern the specific markers in the paper nor the supplementary materials and it must be reminded that the asterisk only means "others").

Autosomal DNA

The study also shows some statistical inferences from the autosomal (or nuclear) DNA of the Mal'ta boy:

Figure 1 [b & c]
b, PCA (PC1 versus PC2) of MA-1 and worldwide human populations for which genomic tracts from recent European admixture in American and Siberian populations have been excluded19.
c, Heat map of the statistic f3(Yoruba; MA-1, X) where X is one of 147 worldwide non-African populations (standard errors shown in Supplementary Fig. 21). The graded heat key represents the magnitude of the computed f3 statistics.

Here we can appreciate that MA-1 is closest to Native Americans but still rather intermediate between them and South and West Eurasians. Interestingly East Asians are quite distant instead, suggesting that MA-1 was still not too much admixed with that continental population, unlike what happens with Native Americans, who are essentially East Asian in the autosomal and mtDNA aspects. So this kid appears to be some sort of a "missing link" in the Paleolithic ethnogenesis of Native Americans.

Figure 2 | Admixture graph for MA-1 and 16 complete genomes. An admixture graph with two migration edges (depicted by arrows) was fitted using TreeMix21 to relate MA-1 to 11 modern genomes from worldwide populations22, 4 modern genomes produced in this study (Avar, Mari, Indian and Tajik), and the Denisova genome22. Trees without migration, graphs with different number of migration edges, and residual matrices are shown in Supplementary Information, section 11. The drift parameter is proportional to 2Ne generations, whereNe is the effective population size. The migration weight represents the fraction of ancestry derived from the migration edge. The scale bar shows ten times the average standard error (s.e.) of the entries in the sample covariance matrix. Note that the length of the branch leading toMA-1 is affected by this ancient genome being represented by haploid genotypes.

Even if I am not too keen of TreeMix, in this case the results seem consistent.

We can appreciate here that a sample of Native Americans (the Karitiana, maybe not as "pure" as the Xavantes but still very much so) show up in a different branch from MA-1, reflecting their overwhelmingly East Asian ancestry, mostly by the maternal side (mtDNA). MA-1 instead hangs from the South-West Eurasian branch, soon after the split between South Asians and West Eurasians. Both have extremely drifted branches, surely indicating the small size of their founder populations, typical of the Far North. 

In addition to this basic tree, two admixture events are signaled: one is the already known Denisovan (H. erectus?) weak one into Australasian Natives (represented by Papuans) and the other one, quite more intense, is the one hanging from upstream of MA-1 to Native Americans (Karitiana), reflecting the partial South-West Eurasian ancestry of Native Americans (noticeable also in their dominant paternal ancestry: haplogroup Q). 

The fact that the admixture signal stems from quite upstream of MA-1 indicates that this boy (or rather his relatives) were not direct ancestors of Native Americans in any significant way but rather a different branch from the same trunk. Probably proto-Amerindians were already in this period at the North Pacific coasts, not sure if in Beringia or around Okhotsk or what but certainly they had already separated from the Mal'ta population.

What did we know of Native American genesis before this finding?

There are three principal lines of evidence:

1. Y-DNA, which among Native Americans is essentially haplogroup Q (plus some C3, which is from NE Asia). By phylogenetically hierarchical diversity, haplogroup Q must have coalesced in West or Central Asia (or maybe South Asia?), very possibly in or near Iran. The NE Asian and Native American branches are clearly derived, even if more important numerically today.
2. mtDNA, which among Native Americans is essentially from NE Asia (A, C, D), middle East Asia (B) but also in a small amount from West Asia (X2). 
3. Archaeology: we can track, more or less directly, the proto-NAs by means of following the Upper Paleolithic sequence in Siberia and nearby areas. 
1. C. 47,000 years ago (calBP) H. sapiens with Aurignacoid technology (i.e. linked to West Eurasian earliest Upper Paleolithic) reached Altai, displacing the Neanderthals to the Northern fringes of the district.
2. C. 30,000 years ago, Upper Paleolithic ("mode 4") technology with roots in Altai reached other parts of Siberia, Mongolia and North China, from where it expanded eastwards and southwards gradually in a process of, probably, cultural diffusion. 
3. By c. 17,000 years ago they were already in North America and c. 15,000 years ago in South America. In the LGM they were probably in Beringia already (but this is only indirectly attested so far). 

So we already had a good idea about the origins of Native Americans: their ultimate roots, at least patrilineally, seem to be in Altai (where they were part of the wider West Eurasian colonization at the expense of Neanderthals with Aurignacian-like technology and dogs). Then, probably around 30,000 years ago they expanded eastwards through Siberia and maybe nearby areas, entering in intense and intimate contact with the already existent East Asian populations, with whom they admixed once and again, mostly by the female side. 

It would seem therefore that their society was already patrilocal because otherwise their patrilineages would have just got dissolved among the locals and would have never reached Beringia nor America in such dominant position.

Overall this is the quite clear notion that I have on Native American earliest genesis and for me there is no reasonable doubt about this narrative (except maybe in the fine details). However I must reckon that some individuals have reacted very negatively against it. But no matter how much they yell, I fail to see their arguments. 

How does this new finding affects this narrative?

It simply confirms it with further evidence. By 24,000 calBP the proto-NAs were surely already, as I said before, in NE Asia close to the Pacific coasts, so this Mal'ta population is a branch left behind in their migration (plus whatever new inflows from the West, which we can't evaluate). The very low affinity level with East Asians, in spite of its quite Eastern location, shows that early East Asians had not yet reached, at least in significant numbers, so far North. If they had, they probably did only at more eastern longitudes, probably near the sea, where resources were more plentiful.

In other words: the first Central Siberians were of South+West Eurasian stock and the current East Asian genetic and phenotype hegemony in that area reflects post-LGM flows, mostly lead by yDNA N1. 

Early Native Americans were the product of admixture of these earliest Siberians with NE Asians, admixture that surely happened East of Lake Baikal, although the exact details are still unclear. 

What does MA-1 say about the West?

His mtDNA is generally consistent with other common U-derived lineages found in West Eurasian Upper Paleolithic, so not much other than he was somehow related, what is confirmed by autosomal analysis. 

His yDNA is more interesting maybe, nonetheless because it is probably the oldest sequence of this kind but also because it belongs to haplogroup R. It certainly discards whatever "molecular clock" guesstimates for R that are shorter than this site's age but on its own it is not able to set a real age other than a bare minimum. 

So for example Eupedia's estimate of 29 Ka for R as such could still be valid, although I would say that extremely unlikely. 

Indirectly however it does say something by confirming the overall narrative of Native American origins as above and that means that Eupedia's estimate of a mere 24 Ka age for haplogroup Q is almost certainly wrong by a lot. 

Using that tree, we would have to at least double the age of Q in order to fit with the Altai narrative (which begins at c. 47 Ka ago), what, extrapolating, implies an age for R of at least 58 Ka. I have estimated some 48 Ka of age for R1 and 68 Ka for P, so it makes good sense after these so necessary corrections. The exact ages we may never know but the approximate ages should be something like these. 

And that's about all I can say. More in comments (and/or updates) if need be.



Update (Dec 6): R* and P* (and other rare clades) among Central Asians

A reader sent me copy of the study by Wei-Hua Shou et al. (2010) titled Y-chromosome distributions among populations in Northwest China identify significant contribution from Central Asian pastoralists and lesser influence of western Eurasians, published by Nature (doi:10.1038/jhg.2010.30).

While it is not the bit of info I was recalling above, it does add some information about unmistakable R(xR1,R2) and P(xQ,R) among Central Asian populations (from P.R. China territory). In detail:

• R* is found in 5/31 Tayiks, 1/41 Kazakhs and 1/50 Uyghurs.
• P* is found in 1/31 Tayiks and 1/43 Kirgizes. 

Also of interest should be the presence of:

• Q(xQ1) in  8/35 Dongxiang (a Mongol ethnicity), 1/45 Kirgizes and 1/50 Tu (another Mongol ethnicity).
• F(xG,H,I,J,K) in 2/32 Yugu (Yugurs, a distinct Uyghur sub-ethnicity), 2/41 Kazakh, 1/31 Tayiks and 1/50 Tu.
• K(xN,O,P) in  32/533 total (i.e. 6% in Easternmost Central Asia), among which are most notable: 9/50 Uyghurs, 6/23 Uzbeks, 6/27 Bao'an (another small Mongol ethnicity), 3/32 Xibo (a Tungusic ethnicity), 2/32 Yugu and 2/5 Mongols. I guess that it is possible that this is a distinct K subclade, although it can well be either part of MNOPS (NO*?) or also belong to LT (L?).
• R2 in 1/31 Tayiks and 2/27 Bao'an.

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 access → LINK [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.

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.