Locating Afro-Diasporan haplogroups within Africa

Dissecting the Within-Africa Ancestry of Populations of African Descent in the Americas (Stefflova et al., 2011)

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“Limitations of our study

Our database and analyses have several limitations. First, there remains limited data from W/WC Africa, where the published literature does not cover Ivory and Gold Coasts. Thus, the analysis of genotype data is limited by the available published data.”  […] 

“Second, mtDNA is a single locus that can inform us only about group maternal ancestry and needs to be complemented with study of NRY and AIMs. While NRY analysis is complicated by limited resolution and coverage of the published data in Africa as well as Bantu speakers’ migrations.” (Stefflova et al., 2011, p.7)

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The African Diaspora: Mitochondrial DNA and the Atlantic Slave Trade (Salas et al., 2004)

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“The results for the Americas overall accord broadly with the picture built up by historians, in attributing major contributions from both western and west-central Africa. The proportion of western African ancestry is not significantly greater than that of west-central Africa, and a significant southeastern African component is not detected at this level of analysis. Again in agreement with the historical evidence—and confirming the indications from the frequency profiles— the largest component in both North and Central America appears to derive from western Africa and to be somewhat greater in Central than North America. South America is, however, problematic.  […] This suggests that a major source region for South America remains unsampled; more data will be necessary to make further progress here.” (Salas et al., 2004, p. 457)

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In this blogpost i will be reviewing two scientific papers dealing with the haplogroups identified among several Afro Diasporic populations and correlating their frequencies with possible African source regions.

– The African Diaspora: Mitochondrial DNA and the Atlantic Slave Trade (Salas et al., 2004)
– Dissecting the Within-Africa Ancestry of Populations of African Descent in the Americas (Stefflova et al., 2011)

From these two studies the first one is the oldest and perhaps also least surprising in its reported outcomes. Because of limitations of available sampling in 2004 it also covers less populations. The second study provides a far more detailed overview, incl. Cape Verde & São Tomé & Principe!, plus a more historically refined yet still debatable explanation for its results. Despite several shortcomings this study offers a fresh perspective in sofar that it attempts to provide a more intraregional resolution for African origins, incl. ethnolinguistic ones! So i will start my discussion with this most recent and arguably more relevant study eventhough the first one was quite pioneering at the time of publication.

Below figure shows a good overview of how the main findings of both studies are actually still quite comparable. In accordance with slave trade records (see this page for screenshots from the Slave Voyages Database) West Africa is being shown as predominant for both the USA and the Caribbean while Brazil and Colombia show a greater share of Central & Southeast African. All countries however show a mix of African source regions.

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(Stefflova et al., 2011)

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Dissecting the Within-Africa Ancestry of Populations of African Descent in the Americas

Link to online article

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“Detailed description of mtDNA database
The African part of mtDNA database focused mainly on the West and West-Central parts of Africa, but included all other parts of Africa (North, North-East, South-West, South, East, and most importantly South-East). It includes the following states (the number of sequences in brackets): Angola (154), Botswana (19), Burkina Faso (97), Cameroon (1074), Central African Republic (C.A.R., 130), Chad (124), Democratic Republic of Congo (D.R.C., 62), Egypt (125), Equatorial Guinea (45), Eritrea (8), Ethiopia (262), Gabon (907), Guinea-Bissau (372), Kenya (154), Mali (204), Mauritania (64), Morocco (92), Mozambique (417), Niger (88), Nigeria (171), Senegal (280), Sierra Leone (277), Somalia (27), South Africa (74), Sudan (80), West Sahara (25)..” (Stefflova et al., 2011, suppplement, p.22)

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The African mtDNA database used for their analysis seems pretty impressive at first sight, however if you consult the supplement to Stefflova et al. 2011, and look closely into the countries as well as ethnic groups being covered there’s still some crucial African source populations missing:

• Ghana
• Benin/Togo
• Igbo, the 171 Nigerian samples being mostly from northern Nigeria, with only 31 Yoruba’s from southern Nigeria.
• Congo, the 62 DRC samples being mainly Mbuti Pygmies (52).

Resulting in a disproportional share of Upper Guinean samples (Senegal, Guinea Bissau & Sierra Leone) as compared with Lower Guinean ones (Ghana, Benin, Nigeria). While the historically lesser important source regions of Cameroon & Gabon are overrepresented to an even greater extent (combined providing almost 2000 sequences out of a total of over 5000!).

Another thing to keep in mind is that the Afro-diasporic groups might show regional variation (substructure) within their populations which might be misrepresented by the sampling for this study. For example just like African Americans from South Carolina & Virginia might show a somewhat distinct ethnic/regional mix based on their specific slave trade patterns, also within Brazil (e.g. Bahia versus southern Brazil) and Colombia (e.g. the Pacific coast versus Cartagena) there might be regional differentiation which is not being specified in this study.

Of course all of this is because of understandable reasons of available sampling, however it’s good to be aware of these limitations of the database as it may explain some peculiarities in the results shown below. Going by a 3-way division (West, West-Central, Southeast) the results are not really shocking however when zooming in to greater localized detail we do see some unexpected and perhaps questionable outcomes.

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Comparing mtDNA findings with slave trade data

(Stefflova et al., 2011, Supplement)

It’s interesting to contrast above findings (based solely on a comparison of mtDNA sequences from a limited database) with documented slave trade numbers for all the countries mentioned. If you click on this link you get the same query variables i used in the Slave Voyages Database. I used Cartagena as a proxy for Colombia (named Spanish American Mainland below) and Caribbean is made up solely of the 6  Anglo-Carribbean islands covered by this study: Dominica, Grenada, St. Kitts, St. Lucia, St. Vincent, and Trinidad (Stefflova et al., 2011,  p.7). Cuba is shown separately in the second chart.

Trans-Atlantic Slave Trade Database (http://www.slavevoyages.org/)

Trans-Atlantic Slave Trade Database (http://www.slavevoyages.org/)

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Going from left to right in the first chart:

• Mozambique is shown for Brazil & Colombia, however it’s only Brazil that received a notable share of captives from Southeast Africa, 7% according to documented slave voyages. The Colombian findings are unaccounted for and might be suggestive rather of other Bantu speaking origins. Furthermore Cuba is shown with no Mozambique eventhough according to recorded slave trade history about 10% of all its slaves could have been hailing from there. Higher even than Brazil! Perhaps this lack of Mozambique reporting is caused by limited sampling from Cuba.The outcome for USA & the Anglo-Caribbean is compatible with the records. Actually for the USA a small % was detected as seen in the very first chart on top of this blogpost.

• Angola is most noticeable for Brazil as expected, also the %’s for the USA and the Caribbean are roughly in line with slave trade data for West-Central Africa although a bit overstated for the Caribbean. The Angola sampling was also done in Cabinda so it would contain Bakongo samples i suppose. Both Cuba & Colombia are shown with no Angola matches at all, this is contrary to widely documented evidence of Angolan presence in both countries. Again perhaps a local sampling issue.

• Cameroon is mentioned twice, its huge samplegroup being split up according to linguistic background. The Bantu speaking Cameroon samples seem to match especially with the USA & Cuba. I suppose this might be in line with Bight of Biafra origins and also in absence of Igbo samples it could be the next best thing. Although it’s surprising then that the Anglo-Caribbean are not shown with any %.

• Gabon & Equatorial Guinea are matched up with Brazil and Colombia. This is being covered by the almost 45% West-Central African slave imports for Colombia and almost 60% for Brazil. However these very sparsely populated countries are not known for having had any major share in Trans Atlantic slave trade. So most likely this outcome is caused because of the absence of Bantu speaking Congolese samples.

• Upper Guinea (Guiné Bissau, Sierra Leone, Senegal, Mali) is the only region which shows matches with all the Afrodiasporic populations. The percentages are clearly inflated though, possibly because of the absence of Lower Guinean samples (Ghana & Benin). Or else perhaps because of a founding effect reflecting the earliest wave of Upper Guinean slaves. Brazil only had a noticeable Upper Guinean slave trade in its northern states (Maranhão) otherwise it was neglible (below 3% according to the voyages database). Colombia and especially Cartagena actually did have a very significant input of Upper Guinean captives, dating mostly from the 1500’s/1600’s. The mtDNA % could still be inflated (63% versus 38.7%) however it seems correct that Colombia is shown with the highest share of Upper Guinean mtDNA matches. For Cuba, the USA and the Caribbean it’s difficult to disentangle any genuine connections with Upper Guinea.

• Niger/Nigeria/Cameroon is based mostly on Chadic and Volta speaking samples from the north. It might perhaps capture some connections with interior slave trade in these countries. However since the sampling from southern Nigeria was rather lacking in this study it could again represent a rather misleading picture. As also to be seen from the quite high %’s for almost all Diasporans.

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Correlating colonial history with African origins

(Stefflova et al., 2011, Supplement)

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“the within-Africa maternal ancestry reflects the diverse colonial histories of the slave trade. We have confirmed that there is a genetic thread connecting Africa and the Americas, where each colonial system supplied their colonies in the Americas with slaves from African colonies they controlled or that were available for them at the time. This historical connection is reflected in different relative contributions from populations of W/WC/SW/SE Africa to geographically distinct Africa-derived populations of the Americas, adding to the complexity of genomic ancestry in groups ostensibly united by the same demographic label.” (Stefflova et al., 2011, p.1)

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The above statement seems plausible to some extent when explaining the differences observed in the African mtDNA frequencies for various Afro-diasporic populations. Afterall it’s known from the Slave Voyages Database that each destination in the Americas seems to have had its own regional “sourcing” mix of slaves from within Africa. However it’s also misrepresenting the complexity of slave trade patterns and partially anachronistic. Generally speaking it’s not so much the reliance on any single provenance zone in Africa that makes the slave trade patterns for any disembarkation region unique but rather the relative share of several provenance zones combined! Across the Afro-Diaspora there’s a great deal of overlap and shared African ancestry! There’s hardly any slave trade region within Africa that was visited exclusively by only one particular European slavetrading nation throughout the long history of Trans Atlantic Slave Trade. Also slave traders from a particular European country might sell their slaves in American colonies ruled by a different European country

Colonial control along the African coast was very relative and restricted to a few European forts up till the age of Imperialism, and this period only started after the abolition of slave trade! The map above is misleading therefore as it shows the situation in the Americas circa 1763 but in Africa it looks rather like a depiction of the situation in the early 1900’s (post WW1)! Untill the late 1800’s when European Imperialism got started the slave ports along the Bight of Benin or the Slave Coast were always under local African control and visited by all European slavetrading nations. The same goes for the slaveports along the Bight of Biafra although here the English buyers did indeed predominate (at least till 1807). But not so along the socalled Loango coast, to the north of Angola, which was visited in near equal measure by English, Dutch and French traders during the 1700’s. In Upper Guinea and along the Gold Coast there were more European forts already in the 1600’s however they were under control of several slave trading nations (England, France, Netherlands and Portugal), so again not the exclusive domain of just one colonial power. Mozambique and Angola (Luanda and southwards) are perhaps a more convincing case. Portuguese control of the coastal areas was somewhat more tighter here but again not perfectly so. And even here there’s been reports of contraband trade by especially the French in Mozambique.

Also the Portuguese were an important supplier of slaves to the Spanish colonies within the Americas. Just like the English, Dutch and to some degree also the French engaged in extensive intercolonial trade which clouds a straightforward overview based on the Slave Voyages Database. This much is alluded to by the authors when discussing Colombia however it seems again they simplify things by not mentioning how the English and the Dutch took over the Asiento in the late 1600’s from the Portuguese. Their explanation for the surprising Mozambique score of Colombia as a result of a supposedly late Portuguese slavetrade seems unconvincing therefore. Their discussion of the Brazilian results is more in line with known slave trade history but they skip over the fact that Brazil is known to have imported far greater numbers from the Bight of Benin (which was not under Portuguese colonial control!) than from Upper Guinea (Stefflova et al., 2011, p.7).

Another aspect not mentioned by the authors is the impact of post-slavery migrations interfering with a straightforward interpretation of documented slave trade patterns. The study reports a rather high Upper Guinean percentage for São Tomé but fails to mention that in fact a considerable proportion of its population is consisting of relatively recent migrants from Cape Verde, who arrived there in the last 100 years or so as socalled contract labourers. It might very well be that they or their descendants were disproportionately among those sampled for São Tomé, which is a reminder of how samplegroups are not always per se representative.

About the USA they mention the following:

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” A different distribution of African ancestry was observed in Philadelphia, a former British colony. The ancestry of African Americans from Philadelphia draws its mtDNAs mainly from the Bight of Biafra and Benin regions (37% Nigeria-Niger-Cameroon and 15% Cameroon Bantu in Philadelphia compared to 25% and 14% in the US overall, respectively). Ancestry from Guinea Bissau-Mali-Senegal-Sierra Leone predominates in other United States African American populations compared to Philadelphia alone (43% vs. 22%). Despite the differences in coverage and sampling, this pattern may be attributed to a significant contribution of slaves from British colonies in Africa to the British-controlled Philadelphia region compared to a more diverse contribution to other parts of the United States from French, Spanish, and Dutch colonies.”(Stefflova et al., 2011, p.7).

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I’m again not really convinced by this argument they are proposing to explain the differences between Philidelphia and the rest of the USA. It’s generally known that the slave trade to the USA was carried out overwhelmingly by English and American owned vessels. The combined share of French, Dutch and Spanish trade, even with Louisiana and Florida included,  amounting to a mere 3% of the total slave trade to the US according to the box in the lower left corner of this chart.

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Source: http://abolition.nypl.org/

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I suspect it’s rather differences in regional preferences and timing of slave trade to Virginia & the northern States versus South Carolina which might explain the results, especially those for the Gullah. However both the domestic slave trade and post-slavery migrations by African Americans across the USA might again complicate a straightforward correlation.

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“Another example of these differences is the Gullah/Geechee populations from South Carolina/Georgia that have 78% of their source from the Guinea Bissau-Mali-Senegal-Sierra Leone region (data not shown), corresponding to the ‘‘Rice coast’’ around Sierra Leone that was the major source of slaves drawn by the United States in the later period of the slave trade” . (Stefflova et al., 2011, p.7)

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Specifying within-West African origins

Despite the several limitations and points of disagreement i’ve discussed sofar i do think this study made a very useful attempt to provide more specification of African origins in a framework that’s applicable to the whole Afro-Diaspora.  Another informative part of the study (but beyond the scope of this blog) concerns the comparison of African Americans with “black” Brazilians on page 3, as well as page 8 of the supplement, aside from mtDNA, also valuable data is given on Y-DNA frequencies and even an autosomal breakdown (see this figure). For me the most interesting part of the study however concerns the within-West Africa analysis which goes beyond the usual treatment of West Africa as one monolithic region. But instead seems to suggest the existence of a separate distinct Upper Guinean cluster. This can be seen for example in this figure:

(Stefflova et al., 2011, Supplement)

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Even more intriguing for me personally is the way Cape Verdean’s  breakdown is being shown as 100% NorthWest African, incl. a minor share of Mauritania. Not too surprising given it’s geographical location however still an important confirmation.

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“Our admixture analysis indicated that the current population of Cabo Verde derives solely from West Africa (,100% from W/WC, not including Bantu speakers or Pygmy), namely from West Niger-Congo speakers of Guinea-Bissau, Senegal, and Sierra Leone (,90%) and Semitic/Berber speakers of Mauritania, Mali and Western Sahara (,10%).”  (Stefflova et al., 2011, p.3)

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(Stefflova et al., 2011, Supplement)

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The authors of the study appply three different methods for specifying the West African portion, in all cases the sum of the breakdown will correspond with the total of W/WC geography in the very first chart posted on top of this blogpost. Only for Cape Verde it will be 100% therefore. It’s noteworthy that besides Cape Verde only the Colombian samples show any affinity with Berber/Semetic mtDNA. Perhaps a legacy of the early slave trade connections between Cape Verde and Cartagena (see “Shared Upper Guinean roots between Cape Verdeans and Latin Americans“). In the first breakdown according to language it’s again Cape Verde and Colombia and also São Tomé which don’t score any % for “Volta/Chadic/Nilo Saharan” which quite possibly acts as a proxy for Lower Guinean origins.

In the second breakdown of “Ethnic groups 1” it’s notable how only the Caribbean and the USA score any % for Fulbe/Mende, the Fulbe samples being taken from Burkina Faso, Cameroon and Chad and the Mende from Sierra Leone. In the third breakdown of “Ethnic groups 2”  it’s fascinating how the Senegalese ethnic groups of the Lebou and Wolof are only appearing for Cape Verde, São Tomé, Brazil and Colombia. The USA is however unique in being matched up with the Fulbe from Cameroon, Niger and Burkina Faso.

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(Stefflova et al., 2011, Supplement)

The African Diaspora: Mitochondrial DNA and the Atlantic Slave Trade

Link to online article

The findings of this study from 2004 are mostly speaking for themselves so i will not bother with much commentary. Except that eventhough the outcomes might not be that surprising it’s still important that this kind of confirmation of slave trade data is being reported (based on mtDNA). Also the inclusion of Dominican samples for “Central America/Caribbean” might be noteworthy.

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“The results for the Americas overall accord broadly
with the picture built up by historians, in attributing
major contributions from both western and west-central
Africa. The proportion of western African ancestry is
not significantly greater than that of west-central Africa,
and a significant southeastern African component is not
detected at this level of analysis.” (Salas et al., 2004), p.457)

“However, in agreement with the historical evidence, the
contribution of northern Africa (which includes many western
Eurasian sequence types [Rando et al. 1998, 1999;
Macaulay et al. 1999]) to the American gene pool appears
to be very minor.“(Salas et al., 2004), p.459)

“Several common and widespread American types are shared
with eastern Africa as well, but none are shared uniquely
with eastern Africans alone. A number are also shared with
south-eastern Africans; again, however, all of these types
are also present in western Africa. A largely western African
provenance, with a possible minor southeastern African
contribution, seems to be the simplest explanation for
this pattern.” (Salas et al., 2004), p.460)

” A few haplogroup L3f types in America match those
of eastern Africans—again, however, never uniquely;
they are also shared by western Africans, southeastern
Africans, or both. At the same time, several L3f types
are shared uniquely by western Africans only. L3f is
likely of eastern African origin (Salas et al. 2002), but
the derived subhaplogroup L3f1 is also present in west-
ern Africa, and it is this component that is most com-
monly found in Americans.” (Salas et al., 2004), p.462)

“Some mtDNA clades are notable for their absence (or
virtual absence) in the Americas. Neither of the Khoisan-
specific haplogroups, L1d and L1k, are found in America,
nor are the eastern African haplogroups, L1e and L1f.
This supports the historical view that neither Khoisan-
speaking populations nor eastern Africa contributed sig-
nificantly to the Atlantic slave trade.” (Salas et al., 2004), p.462)

“However, the eastern African haplogroup L3g is found in
several American individuals, implying either a small
eastern African influence (Thomas 1998, p. 706), more
recent immigration from Africa into America, or hitherto
undetected gene flow into western or southeastern Africa
and thence to the Americas. ” (Salas et al., 2004), p.462)

” Population Samples
We compiled a database from 481 individuals carrying
African mtDNAs belonging to seven available American
samples harboring a major African component. The
sample from North America included 101 African Americans
from the United States (HvrBase database; for details,
see Handt et al. 1998). The sample from Central
America/Caribbean included 8 from Mexico (Green et
al. 2000), 25 Carib from Belize (Monsalve and Hagelberg
1997), 112 from the Dominican Republic (Torroni
et al. 2001; A.T., unpublished data), 41 Choco´ from
Columbia, and 37 Garı´funa from Panama and Belize (A.
Salas, M. Richards, M.-V. Lareu, S. Silva, M. Matamoros,
V. Macaulay, and A. Carracedo, unpublished
data). The sample from South America included 157
Brazilians: 29 from the study by Bortolini et al. (1997),
68 from the study by Alves-Silva et al. (2000), and 60
from the study by Santos et al. (2002)..”  (Salas et al., 2004), p.455)

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(Salas et al., 2004)

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(Salas et al., 2004)