July 26, 2014

Ancestry of Cubans

PLoS Genet 10(7): e1004488. doi:10.1371/journal.pgen.1004488

Cuba: Exploring the History of Admixture and the Genetic Basis of Pigmentation Using Autosomal and Uniparental Markers

Beatriz Marcheco-Teruel et al.

We carried out an admixture analysis of a sample comprising 1,019 individuals from all the provinces of Cuba. We used a panel of 128 autosomal Ancestry Informative Markers (AIMs) to estimate the admixture proportions. We also characterized a number of haplogroup diagnostic markers in the mtDNA and Y-chromosome in order to evaluate admixture using uniparental markers. Finally, we analyzed the association of 16 single nucleotide polymorphisms (SNPs) with quantitative estimates of skin pigmentation. In the total sample, the average European, African and Native American contributions as estimated from autosomal AIMs were 72%, 20% and 8%, respectively. The Eastern provinces of Cuba showed relatively higher African and Native American contributions than the Western provinces. In particular, the highest proportion of African ancestry was observed in the provinces of Guantánamo (40%) and Santiago de Cuba (39%), and the highest proportion of Native American ancestry in Granma (15%), Holguín (12%) and Las Tunas (12%). We found evidence of substantial population stratification in the current Cuban population, emphasizing the need to control for the effects of population stratification in association studies including individuals from Cuba. The results of the analyses of uniparental markers were concordant with those observed in the autosomes. These geographic patterns in admixture proportions are fully consistent with historical and archaeological information. Additionally, we identified a sex-biased pattern in the process of gene flow, with a substantially higher European contribution from the paternal side, and higher Native American and African contributions from the maternal side. This sex-biased contribution was particularly evident for Native American ancestry. Finally, we observed that SNPs located in the genes SLC24A5 and SLC45A2 are strongly associated with melanin levels in the sample.



LivoniaG said...

"The analysis of mtSNPs indicates that 34.5% of the mtDNA haplotypes have Native American ancestry, 38.8% African ancestry, and 26.7% Eurasian ancestry...With respect to the maternal Native American proportions, the highest were found in Holguín (59%) and Las Tunas (58%)"

Aside from the matter of "sex-biased gene flow," these mtDNA results are interesting from the point of view of that high mtDNA number assigned to Native Americans. There was some insistence in the past that there was no such ancestry left in Cuba, and there was no true "mestizo" element.
It's possible that the admixture contribution may actually higher. (from the report: "the precision for the Native American ancestral component is probably substantially lower (r2<0.4)."

Unknown said...

Some good stuff in here. Nice maps of the female and male ethnic contributions by province.

35% of the population have native maternal haplogroups as opposed to a tiny native paternal signal (0.5). The African men did a bit better.

"We estimated the average maternal Native American proportion to be 34.5% in the sample, in sharp contrast to the autosomal (8%) and paternal (0.5%) proportions. The African maternal, autosomal and paternal proportions were estimated to be 39%, 20% and 18%, respectively.

There are believed to have been 3 tribes present in Cuba at the time of colonization,Guanahatabeyes (indigenous, non Arawak language), Ciboneyes (Cuban Arawak tribe of ) and the Taínos (technologically advanced Arawaks fleeing Caribs marauding up from Venezuela).

However the maternal haplogroup signal is overwhelmingly A2(64.2%). A2i (4.4%), B2 (7.8%), C1 (13.4%), D1 (10.3%).

Problematic as extinct Tainos were 75%C and 25%D, whereas the Ciboney were 60% C, 33% D and 0.07% A (Lalueza-Fox 2001 and 2003). Makes me wonder quite how many native slaves were brought over from Yucatan during the colonial period.

The female Eurasian haplogroups are weird too. More U and N than I expected. 28% H, 22% U, 11.5% N, 11.5% J. The U is the weirdest.

The sole native Cuban Y haplogroup was Q1a2a1a1

tew said...


"The U is the weirdest".

That U is probably mostly from the Canary Islands, where a U lineage was the most common Guanche haplogroup, and which was very important in the early peopling of Latin America. So not really surprising.

Unknown said...

I should have said:

"Problematic as PRE-COLUMBIAN Tainos were 75%C and 25%D, whereas the Ciboney were 60% C, 33% D and 0.07% A (Lalueza-Fox 2001 and 2003).

The Taino bones are from the Dominican Republic La Caleta site.

"The bones dated from 650, 750 and 840 AD."

On thinking about it more recent waves of folk up from Venezuela could also be the source of the A2 (and B). Caribs for example. Hopefully more archaelogy should clarify the situation.

The two Lalueza papers do however add weight to the idea that C and D were the first haplogroups to arrive in the Americas. At least this part of the Americas.

Unknown said...

"That U is probably mostly from the Canary Islands"

Makes sense.

tew said...

"waves of folk up from Venezuela could also be the source of the A2 (and B). Caribs for example"

I think that is unlikely, though - Major Carib migrations/raids/invasions were taking place at the very time of contact with the Spaniards, so there is good historical record of that event, and we know that it was essentially men who migrated, assimilating local women. For a short time, there was even a curious situation of diglossia recorded in which women would speak Taino while men spoke Carib.

Maybe the high percentage of A is rather a signal of the migration of mestizos from continental Central America (Cuba was a major colonial center and a magnet for "internal" migration as well).

Unknown said...

We really need the results from the other islands also.

I recently (today) found this data for the English speaking Caribbean (Crawford et al, 2014). Most of the data so far is for the Spanish-speaking Caribbean, and the English-speaking Caribbean has received different post colonial population flows.

"The Carib Reserve of Dominica contains the highest proportion of Native American maternal genes (mtDNA RFLPs and sequencing HVS1) in Caribbean populations with 58%, and 16% African. This estimate is based on the 50% of the mtDNA haplogroups are C, and the remainder 8% belong to the A haplogroup."


"Krwaczak (2012) indicated that among the Black Caribs of St. Vincent Island 44% of the haplogroups are Native American (similarly A and C) and 47% African. The African component was detected by the presence of L0, L1 and L2 mtDNA haplogroups. " This is a PhD so I cant get at the exact proportions but the implication is that the results are very similar to those for Dominica.

So in this reputedly Carib population (Dominica), for the Amerindian component:

Haplogroup C = 86%
Haplogroup A = 14%

Presumable this result chiefly represents the pre-Carib women of these islands. I would expect population flows to travel up the island chain from Trinidad with incoming A reducing as it travels up the coast.

So how does Cuba have 69% A2 and Puerto Rico 56% A?

My working hypothesis is that C got to the Caribbean first, most probably given the technology from South America. Haplogroup D arrived next in pre-Columbian times from the north travelling from Cuba (33%)to Hispaniola (25%). Haplogroup B has only been reported in modern day Cuban populations so far, so perhaps it arrived from the north in post Columbian times.

I suspect a small amount of pre-Columbian A travelled up the chain of islands from Trinidad to St Vincent (?%), Dominica (14%), Cuba (pre-Columbian 0.08%) with or before the Caribs.

So the bulk of the A2 in Cuba and Puerto Rico probably arrived recently from the north (Central America?) either as a very, very recent pre-Columbian migration or more likely as Kes's mestizo post Columbian migrants. If so we would expect A2 to be largely absent from the English-speaking islands.

Moreno (2013) has a nice ethnic comparison for the Spanish-speaking islands (Cuba, Haiti, Dominican Republic, Puerto Rico). Haiti appear to have obliterated their Amerindians. This paper includes Yukpa (Cariban), Bari (Chibchan) and Warao (Arawakan) population groups for comparison. But to me the islands just look a lot like Central America but with more Africans and Europeans diluting things out. This fits with a recent influx from Central America to these islands.

I would love to see the the Vincentians, folk from Dominica and the Santa Rosa Trinidadian Caribs in this comparison. Also the Maroon-descended Jamaicans. Maroons are rumoured to have picked up a bit of Amerindian blood during their period of isolation. They certainly picked up a lot of Arawak culture.

Puerto Rico Data:
"Haplogroups A and C cover 56.0% and 35.6% of the Native American mtDNAs, respectively. No haplogroup D "

In summary Caribbean Cs nd Ds have a good chance of being Arawakian Tainos or Ciboney. The Cs might also be descendants of the Caribbean aboriginal folk (possibly including the Guanahatabey with their non-Arawak language and hunter gather lifestyle). Most A2s and all Bs look to have been something else, genetics should tell us eventually where they came from. My guess is Florida if pre-Columbian and Central America migration if post-Columbian chiefly as I do not think they had the technology to get from Central America to Cuba in pre-Columbian times but Florida seems possible.

A few A2 will be old (Carib or Arawak)in the Caribbean and are likely to have unusual genotypes related more to the South Americans.

Mark D said...

This study shows what can be ascertained from adequate sampling and methodology; a nice cross-section of both local and regional populations. I applaud those involved.

As for the predominance of mtDNA haplogroup A, I believe this has been reported on in past studies. I have seen the same here in South Florida amongst Cuban-Americans, even those who fled Cuba in the early 1960s. A Cuban-born friend of mine, light skinned and blue eyes with reported 93% European ancestry has mt haplogroup A2d1. This is not uncommon, and probably reflects what the authors correctly report as the early history of both Cuba and Puerto Rico. What is needed is more aDNA from these islands.

Kepler said...

There were more migrations from Venezuela than male Caribs.

After 1510, when native American slaves were dying like flies in Cuba and Hispaniola, Spaniards started to raid the coasts of Venezuela, all the way from Goajira to the East, capturing thousands of Indians - women and men, Arawak and Caribs, to use them as servants in the islands.
Later the Welser traders sold several thousands, mostly to the same area (that was in the thirties and early forties of the XVI century). So: this was a new flow of genes.

David Jacobson said...

The concept that there is such a thing as Native American genetic ancestry is very problematic. The thousand genome data fairly clearly establishes a significant distinction between sequences of SNP's found in African, European, and Asian populations. The American populations are largely an admixture of the other three. It is a reasonable assumption that the Asian contribution came with the original arrival of the founding Native American populations. The European contribution is more problematic. Likely a large part of that contribution is due to historical arrival of European's in the new world. But, there is no reason to believe that the founding population was purely Asian. The distinct European SNP frequencies and sequences could have easily appeared among humans evolving on the North side of the Himalayan mountains as the Y chromosome haplotypes seem to have done. The founding Native American population could have easily included an admixture of Asian and European preponderant SNP's.