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Category Archives: African Americans

Caribbean autosomal ancestry

Battle of Vertières (Haiti 1803)

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

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

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.
 

Cameroonian Y-DNA lineage A00 is older than Homo sapiens

The news has been floating around in the anthropology and human population genetic circles for some time but it was not formally confirmed until now: a very ancient Y-DNA lineage appears to be so old that it can hardly be considered to be strictly Homo sapiens at its ultimate origin. The lineage is extremely rare however and has only been found so far in two men: an African-American (from the USA?) and eight Mbo individuals from Western Cameroon.

Fernando L. Méndez et al., An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree. AJHG 2013. Pay per view (free 6 months after publication) → LINK [doi:10.1016/j.ajhg.2013.02.002]

Abstract

We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237–581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.

Figure 1. Genealogy of A00, A0, and the Reference Sequence
Lineages on which mutations were identified and lineages that
were used for placing those mutations on the genealogy are
indicated with thick and thin lines, respectively. The numbers of
identified mutations on a branch are indicated in italics (four
mutations in A00 were not genotyped but are indicated as shared
by Mbo in this tree). The time estimates (and confidence intervals)
are indicated kya for three nodes: the most recent common
ancestor, the common ancestor between A0 and the reference
(ref), and the common ancestor of A00 chromosomes from an
African American individual and the Mbo. Two sets of ages are
shown: on the left are estimates (numbers in black) obtained
with the mutation rate based on recent whole-genome sequencing
results as described in the main text, and on the right
are estimates (numbers in gray) based on the higher mutation rate
used by Cruciani et al.6

It could still be a very early diverging H. sapiens lineage, as is surely the case of the more recent and slightly more common A0 (former A1b, found in Cameroonian Western Pygmies, 8.3%, and among Algerian Mozabites, 1.5% – see here) but both are in the blurry zone of the time of birth of our species (judging from archaeological and paleoanthropological data) c. 200 Ka ago. The first documented “modern human” skull, Omo 2, is dated to 190 Ka ago and it shares locality with another one, Omo 1, which is rather H. rhodesiensis, so in that “dawn of modern humankind” there was surely not a very clearly drawn line between modern humans or Homo sapiens and archaic humans or Homo rhodesiensis (or whatever). Some of those proto-Sapiens lineages still remain among us at very low levels.

Their presence may also suggest minor admixture between the first migrant H. sapiens to arrive to Cameroon and their then still close relatives from previous flows, which we don’t consider H. sapiens because we have drawn a convenient, but as we see now somewhat blurry, anthropometric or paleoanthropological line at Omo 2 and later specimens close to us in skull shape. While there is some generic comparability, the fact of admixture between such closely related populations is much less impressive than the one of admixture with Neanderthals or, probably, Homo erectus (non-Neanderthal Denisovan relatives), more distant from us in the tree of Greater Humankind. 
As for the “molecular clock” estimate I suspect that this one is correct. I would have liked to explain it today but it will have to wait because it is a complex matter and I have been all day writing for this blog, so I am quite tired now.

Update (Mar 3): Kalupitero commented in another entry that this lineage has very distinctive STR markers and that he has spotted 9 Cameroonians and one French (probably of African ancestry) with it at the Sorenson Molecular Genealogy Foundation database.

Update (Mar 5): A reader directed me to a free copy of this paper, from where I selected fig. 1 (above) and fig. 3 (below). I realized that the number of sequences detected among the Mbo was not one as I originally said but eight. They also mention that the frequency of this lineage in Africa must be very low: c. 0.19% (CI: 0.11-0.35%).

Figure 3. Median-Joining Network of A00 Haplotypes
The network is based on haplotypes (constructed with 95 Y-STRs)
of eight Mbo and an African American (AA) individual. All mutations
are assumed to be single step and were given equal weight
during the construction of the network. Marker names are indicated
without ‘‘DYS’’ at the beginning.



See also:

 

Admixture in Latin America

The primary purpose of this new study is to test an ancestry informative marker (AIM) set for use in America, however the results are of general interest, as they surveyed much of South America, from Chile to Venezuela.

They selected a group of AIMs from Native American populations from Mexico, Peru and Bolivia and used Mestizo samples, together with others from Europe and Africa in order to refine their AIM set. Then they proceeded to test it in South American samples of Mestizo, Afroamerican and Native American self-identification.
The result is synthesized in figure 6:

Purple and red tags indicate American samples used in the generation of the AIM set

There is some more information in the text and figures of the paper, which you may find an interesting read.
 

Maternal ancestry of Jamaicans

Jamaican slave revolt of 1759 (source)
There is a new study on the mitochondrial DNA of Jamaicans, shedding some light on the ancestry of this Caribbean nation:
I must certainly commend the historical introduction, which is not just comprehensive but also easy to follow and understand and well integrated with the information provided by the mitochondrial DNA findings. 
While there are a handful of lineages rooted in Native America or North of the Sahara (but not European), the overwhelming majority of the more than 400 Jamaican matrilineages studied in their HVS-I region have their roots in Africa. 
The most informative findings are however those about the regional origins within Africa of  the ancestors of modern Jamaicans. The Gold Coast and Bight of Benin regions (between Assini and the Niger Delta per fig. 1) are the main sources of Jamaican ancestry. Other West African regions (Sierra Leone, Bight of Biafra and West-Central Africa) were secondary sources only, while South and East Africa is almost not represented. 
This last appears to have surprised the authors, who expected more impact of the late slave trade based largely on the Indian Ocean coasts, similarly they seem a bit perplex by the relatively low influence of the Bight of Biafra, another major late source of African slaves. They argue that greater traveled distances may have hurt the chances of survival of people being transported from farther away (a documented fact) and that creole slaves, those born in the Caribbean, had much better chances of survival and even some chances of upward mobility.
See also: African ancestry of the Noir Marron of the Guianas, a previous example of the same approach cited in this paper. In that case however the bulk of the ancestry was from the Biafra area.
 
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Posted by on February 25, 2012 in African Americans, African genetics, America

 

Echoes from the Past (Feb 2)

Lots of links that I think of interest but I do not have time, knowledge or enough discipline to deal with in greater detail.
Truly sorry about the format (or lack of it); I’m drowning in information.
Middle Paleolithic
Levallois core and flake (replica)
Neanderthal-made rock art?

Upper Paleolithic & Epipaleolithic

El joven de la cueva del Mirón fue enterrado hace 18.500 años[es] (the young man of El Mirón cave, Asturias, was buried 18,500 years ago)
Una sentencia da la razón a Zeleta S.L. y pone en peligro a Praileaitz[es] (tribunal puts Praileaitz cave, Basque Country, at even more risk)
Neolithic & Chalcolithic
Russian fish trap findings
Diversidad LBK y relaciones entre Neolíticos y Cazadores-Recolectores[es] (LBK diversity and relationships between Neolithic and hunter-gathererer peoples).
Modelos generales del Neolítico versus datos arqueológicos[es] (general modeling of Neolithic versus actual archaeological data)
Metal Ages and History
 
Malta inscription
«Tartessos no era un pueblo de catetos. Eran sensibles y técnicamente capacitados»[es] (Tartessos was not a redneck people: they were sensible and technically capable – there’s been some Tartessos conference these days in Andalusia, with nothing new).
Aparecen en Liédena los restos de un poblado de la transición entre la Edad de Bronce y la de Hierro[es] (settlement from the Bronze-Iron ages’ transition discovered in Liedena, Navarre)
Excavation of Bosnian Sun Pyramid given green light (remember the Bosnian “pyramid”? – it is back!)
Human genetics and evolution
Fig. 2 – PCA (BAM stands for Bamileke)
Master controller of memory identified (this is kind of scary: they wiped out memories in mice!)
Study Reveals Possible New Key to Human Evolution (synapsis making in early childhood allows for extreme learning)
Bonobos’ unusual success story (like humans bonobo males are more successful at mating with relatively low testosterone levels).
Other
 

Brazilians are much more homogeneous than ‘racial’ categories suggest

This is a very revealing paper on Brazilian genetic makeup and the shallowness of racial classification in general:
Abstract
Based on pre-DNA racial/color methodology, clinical and pharmacological trials have traditionally considered the different geographical regions of Brazil as being very heterogeneous. We wished to ascertain how such diversity of regional color categories correlated with ancestry. Using a panel of 40 validated ancestry-informative insertion-deletion DNA polymorphisms we estimated individually the European, African and Amerindian ancestry components of 934 self-categorized White, Brown or Black Brazilians from the four most populous regions of the Country. We unraveled great ancestral diversity between and within the different regions. Especially, color categories in the northern part of Brazil diverged significantly in their ancestry proportions from their counterparts in the southern part of the Country, indicating that diverse regional semantics were being used in the self-classification as White, Brown or Black. To circumvent these regional subjective differences in color perception, we estimated the general ancestry proportions of each of the four regions in a form independent of color considerations. For that, we multiplied the proportions of a given ancestry in a given color category by the official census information about the proportion of that color category in the specific region, to arrive at a “total ancestry” estimate. Once such a calculation was performed, there emerged a much higher level of uniformity than previously expected. In all regions studied, the European ancestry was predominant, with proportions ranging from 60.6% in the Northeast to 77.7% in the South. We propose that the immigration of six million Europeans to Brazil in the 19th and 20th centuries – a phenomenon described and intended as the “whitening of Brazil” – is in large part responsible for dissipating previous ancestry dissimilarities that reflected region-specific population histories. These findings, of both clinical and sociological importance for Brazil, should also be relevant to other countries with ancestrally admixed populations.

Real ancestry of various regional populations divided by racial self-description (fig. 2):

It is I think quite interesting to realize that racial categories are often meaningless in representing the real ancestry of individuals collectives. This is specially true for the brown (pardo) and black (preto)  categories but, in the north specially, it is also very true for the category white (branco). In this sense, the Brazilian census would probably do well dropping racial categories altogether, as they are obviously without meaning. 
Overall Brazilians seem mostly of European ancestry (60-80%), with some lesser regional variability, as is very apparent in figure 3:

Native American ancestry is rather homogeneous by regions, making up 7-10% of the ancestry except in the North (Amazon) region, where it’s double (19%). African ancestry is somewhat more important and also regionally variable: 10% to 29% (this last in the Northeast).
Notice anyhow that the samples were collected in six specific cities and that specially the vast Amazon region is probably under-represented (as the only sample comes from Belem, a large city of the coast). I’d dare say that the vast Brazilian interior (all samples are from the coast) must be stronger in Native American ancestry, even if we do not consider the surviving aboriginal populations, but only the creoles.
 

Exploring the ancestry of African-Americans

Preliminary note: in this post African-American means people of African descent living in America (aka the Americas), not just people from the USA.
The authors acknowledge that they find difficulties in tracking regional African ancestry because of the limited genetic data available for this continent, with some important countries in the Atlantic slave trade, like Ivory Coast or Ghana, being still largely not researched. The situation may be even worse for Y-DNA and autosomal markers.
I’d say that this sad situation is product of several factors: first of all lack of interest by Western or Asian researchers, then unequal access to the DNA pools of the continent, often for political reasons (this happens elsewhere, specially in parts of Asia but also in France), other factors are the huge size and diversity of Africa and its population and the relative lack of obvious structure, with many lineages scattered across the continent. This last element actually seems to demand greater research and finer-grained haplotyping but this only comes in small drops. 
Inter-continental admixture, the well known sex-bias
A simpler analysis can be done in regards to inter-continental admixture (fig. 1):

Fig. 1 – Ancestry of African-Americas: (a) mtDNA, (b) Y-DNA and (c) autosomal DNA
We can see in these maps, for example, that Afro-Brazilians are largely of European and Native American ancestry (c), even if African descent is still dominant.  We can also see that European ancestry is overwhelmingly of male lineages (b), while Native American one instead is almost only of female origin (a). 
This seems quite peculiar of Afro-Brazilians, with no other American population displaying such pattern. Although it may be arguable in the case of Afro-Caribbeans. The population displaying most European female ancestry are African-Americans from Philadelphia.
Notice that minor European and Native American components are present in the autosomal samples of pure West Africans, indicating that these minor amounts are actually imprecisions of the clustering method. 
In the reverse direction, there is a map (fig. S1) in the supplementary materials that shows important African and Native American ancestry among white Brazilians, again showing sex-bias in the admixture, with nearly all being attributable to female ancestry. Some admixture is also apparent in white Philadelphians but it is much smaller.
African regional ancestry estimates
But the greatest effort of the authors of this paper is trying to unravel the African regional ancestry of these populations. For this they had to resort to mitochondrial DNA, which is admittedly just part of the whole picture and is often not sufficiently well structured by regions anyhow:

Fig. 3 regional African ancestry estimates (mtDNA)
The impression we get is that SE African (Mozambique) and Gabonese ancestry is restricted to South America. Instead Cameroon ancestry is concentrated towards the North of the new continent. Angolan and West African ancestry are widespread, however there is no detected Angolan ancestry in the former Spanish colonies. 
The authors argue some of these differences based on the chronology of the Atlantic slave trade, that in its first phase almost exclusively preyed in Westernmost Africa and Angola, while looking for other sources West-Central Africa and Mozambique in its late phases.

West African insular peoples

A map available in the supplemental material, fig. S6, also addresses the matrilineal ancestry of the populations of Cape Verde and São Tomé, two insular areas uninhabited before the colonial period and settled essentially with slaves from the continent (though Cape Verdeans  specially also have some important European admixture, less important probably in São Tomé). Cape Verde African ancestry is exclusively from Westernmost Africa, including Mauritania, instead São Tomé shows a mixture of Westernmost Africa and Central Africa (Gabon, Angola), to the exclusion of the Nigeria-Cameroon area.