Cuba 1: previous 4.3% TA, now: 2.5% TA
Cuba 2: previous 6.5% TA, now: 3.6% TA

*TA = Tropical African (or whatever the Yoruba component means).

For comparison Utah Whites show 2.1% TA, what makes the Cuban case a bit confusing after all (there’s also French ancestry in Cuba for example or it could even be “Moorish”, Morisco, Jewish…). Of course I do think that there is small Tropical African admixture but not sure exactly how much anymore, not with that “artifact” over there (Utahns are after all also Creoles, much like Cubans).

I do agree in any case that “an algorithm is just an algorithm” and that the results must be taken with a pinch of salt, very specially for very small apportions such as these.

Edit: Upon second look, I feel that now the Yoruba component acts as partial proxy for the Indian one, after the Gujarati samples were removed. The Indian component was somewhat larger among North Europeans than Iberians and it is these who now show anomalous Yoruba component. This may also influence Cuba 2 (but not Cuba 1).

I wonder if Tropical/Southern African samples can act that way, i.e. as de-facto representative of “other human” when the specific ancestry is not well represented. It was not so obvious when it acted as semi-proxy for North Africans, who do have some apparent TA admixture, but that’s not the case in India and yet the Yoruba component seems to make up partly for the lack of the Gujarati component in Northern Europeans.

Curious to say the least.

1) i will probably run a very narrow ADMIXTURE run with a lot of markers at some point to see if your admixture is “real” or not. as you suggest, your levels are low enough that there’s ambiguity, and we just can’t say with any confidence. do you have any citations on the number of canarians proportionally which came to cuba? an N = 2 is really not large enough to separate them from other iberians, so that is as far as i can go there.

2) i may be able to phase your genotype and try and figure out WHEN/if admixture occurred. if it is canarian or iberian it should be older, but i might not be able to get enough precision….

This is interesting. It looks to me that at K=6 admixture run I show more red than the average Utah, white American, and that the only thing my husband is showing that is certainly large for Iberian peninsula standards is the Amerindian (light purple) component, yet it is no more than twice that of what the average CEU shows. As for the African, it is just slightly more than what those two Canary Islanders show, and for all we know if we had more Canary Islander samples, he could align easily with them. There are some interesting things to mention about the K=7 run in regards to the Basques, which other posters have commented.

The results of Cuban 1, or me, is certainly more in line with what I would expect most white Cubans to show, particularly those from the western side of the island. I think if other Cubans submit their data you will see data more like mine, if not more European.

https://docs.google.com/open?id=0B8Tdg8RZEWOOalNMT2Flb0tDZTg

Castilla y Leon 1KG (12)
Spanish (I supposed this comes from Behar et al.) (12)
Castilla La Mancha 1KG(6)
Extremadura 1KG (8)
Cantabria 1KG (6)
Pais Vasco 1KG (7)
Catalonia 1KG (8)
Valencia 1KG (10)
Islas Baleares 1KG (6)
Andalucia 1KG (4)
Aragon 1KG (6)
Galicia 1KG (8)
Islas Canarias 1KG (2)

So the total number of Iberians used amount to 95. I do wonder why Murcia 1KG (8) wasn’t included on this run?

Anyways, I presume the Basque individuals are actually the French Basque from HGDP which are 24. Now what puzzles me the most is that both Spanish and French Basque are coming out in the 7-10% North African (Blue component), which is unlike anything I have ever seen before. Also I wonder how big the CEU(Utah, Whites) and Orcadian samples were combined, that the red component(European) is actually centered around Orcadians and to a lesser extent CEU. Also puzzling is the presence of a West African(orange) component in Russians, Orcadians and CEU at levels that are twice that found in Extremadura and Galicia, and still larger than the one found in the Canary Islands. The rest of Iberian populations display no West African(Orange) component, but larger than previously observed values of North African, specially the Spanish Basques. I wonder if you could consider the introduction of a Sardinian sample, to see if the North African showing in Spanish Basque is indeed North African, or if is the previously found Mediterranean component which peaks in Sardinians.