See: Andres Moreno-Estrada!po=16.1017

Cubans are very interesting: they range from the least SSA admixed to among the highest SSA admixed.

"Mexicans cluster largely between European and Native American components, Colombians and Puerto Ricans show three-way admixture, and Dominicans principally cluster between the African and European components. Ours is the first study to characterize genomic patterns of variation from (1) Hondurans, which we show have a higher proportion of African ancestry than Mexicans, (2) Cubans, which show extreme variation in ancestry proportions ranging from 2% to 78% West African ancestry, and (3) Haitians, which showed the largest average proportion of West African ancestry (84%)"


This is interesting in terms of the European component:
Surprisingly, we observe another European-specific component emerge as early as K = 5 and remain constant through K = 15 (Figure S2). This component accounts for the majority of the Caribbean Latinos' European ancestry, and it only appears in Mediterranean populations, including Italy, Greece, Portugal, and Spain at intermediate proportions. Throughout this paper, we refer to this component as the “Latino European” component, and it can be seen clearly in Figure 1C (“black” bars represent the Latino European component, “Red” bars represent the “Northern European”, and pink the “Mediterranean” or “Southern European” component). At K = 8, when the clinal gradient of differentiation between Southern and Northern Europeans appears, the Latino European component is seen only in low proportions in individuals from Portugal and Spain, whereas it is the major European component among Latinos ."

This is how they explain it:

Importantly, when we applied ASPCA using the exact same reference panel of European samples but analyzing Mexican haplotypes of European ancestry (Moreno-Estrada, Gignoux et al., in preparation), we did not observe a deviated clustering pattern from the Iberian cluster: the effect is much weaker and not significant (bootstrap p-value = 0.099, see Figure S10). Furthermore, the deviation of the European segments of Mexican individuals from the distribution of the rest of Iberian samples is even smaller than the deviation of the Portuguese from the Spanish samples. We further evaluated whether the dispersion of the different subpopulations within the Caribbean cluster follow particular patterns along ASPC2, the axis driving the deviation from the Iberian centroid. We observed that Colombians and Hondurans tend to account for lower (more deviated) ASPC2 values compared to Cubans, Dominicans, and Puerto Ricans (Figure S11), suggesting a mainland versus insular population differentiation. We performed a Wilcoxon rank test to contrast ASPC2 for mainland (Colombia and Honduras) versus island (Cuba, Dominican Republic and Puerto Rico) populations, resulting in a highly significant p-value (1.5×10−15). Because >25% of European ancestry was required for inclusion in ASPCA, only two Haitian haplotypes were analyzed, and thus these were not included in the statistical analysis. Nonetheless, it is noteworthy that one of them clusters with the French, in agreement with historical and linguistic evidence regarding European settlements on the island."

"These results are in agreement with our cluster-based analysis focused on global ancestry proportions, where the European ancestry of Latinos is dominated by a shared Latino-specific component differentiated from both southern and northern European components, although shared to some extent with Spanish and Portuguese (Figure 1C). Bottlenecked populations may exhibit differentiation from their parental gene pool due to loss of genetic diversity and stochastic shifts in allele frequencies. One way of quantifying the extent of genetic drift is to compare FST estimates among the K = 8 ancestral clusters from Figure 1C. In the absence of drift, we would expect the southern-derived Latino component and the southern European component to show a very low level of FST. However, we observe an FST = 0.021 (Table S3). To put this into perspective, the FST of southern vs. northern Europe is FST = 0.02, meaning that the differentiation of the Latino-specific component with respect to southern Europeans is at least as high as the north-south differentiation within Europe."

Additionally, our data show a strong signature of assortative mating based on genetic ancestry among Caribbean Latinos, as suggested by previous studies [17]. In particular, we see a strong correlation between maternal and paternal ancestry proportions (Figure S5). To assess significance, we compared correlation of ancestry assignments among parent pairs to 100,000 permuted male-female pairs for each continental ancestry. All p-values were highly significant (p<0.00001, Table S2). It should be noted that these tests are not independent since the three components of ancestry by definition must sum to one. Further, apparent assortative mating could be due to random mating within structured sub-populations. To control for this, we performed permutations within countries of origin, and found significant correlations among individuals from every single population (p-value<0.05), except for Haiti. Although Haitians do show the same trend, with only two parent pairs, it is nearly impossible to assess significance."

The best-fit model for Colombians and Hondurans involves admixture between Native Americans and Europeans starting 14 generations ago, followed by a second pulse of European ancestry starting 12 and 5 generations ago, respectively. Of note is that between the first and second pulse of migration in Colombians, the proportion of European ancestry increased from 12.5% to 75% in two generations, implying that the European segments in today's Colombians date back to European gene flow happening in a short period of time; thus, tracing their ancestry to a smaller number of European founders compared to other Latino populations.In contrast with mainland population samples, the best-fit model for all four populations from the Caribbean islands involves older time estimates of the initial contact between Native Americans and Europeans. Namely, 17 generations ago for Cubans and 16 generations ago for Puerto Ricans, Dominicans, and Haitians. Historical records state that the first European colonies in the Antilles were established soon after the initial contact in 1492 [21]; that is, ∼500 years ago or 16.6 generations ago (considering 30 years per generation [22]), in excellent agreement with our time estimates. Another major distinction between mainland and Caribbean populations is that the best model for each of the latter involves a second pulse of African ancestry, occurring seven to five generations ago, with higher migration rates in Haitians and Dominicans, followed by Cubans and Puerto Ricans."

" Figure 4Ashows a closer view, in which Colombians and most Hondurans cluster closer to Chibchan-speaking groups from Western Colombia and Central America, including the Kogi, Embera, and Waunana. In contrast, most Caribbean islanders cluster with Amazonian groups from Eastern Colombia, Brazil, and Guiana. The closest ancestral populations include the Guahibo, Piapoco, Ticuna, Palikur, and Karitiana, among others, some of which are settled along fluvial territories of the Orinoco-Rio Negro basin. This location may have facilitated communication from the rainforest to the coast, explaining the relationship with Caribbean native components. Interestingly, the indigenous component of insular Caribbean samples seems to be shared across the different islands, suggesting gene flow across the Caribbean basin in pre-Columbian times."