November 15, 2013

Population history of the Caribbean

PLoS Genet 9(11): e1003925. doi:10.1371/journal.pgen.1003925

Reconstructing the Population Genetic History of the Caribbean

Andrés Moreno-Estrada et al.

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse—which today is reflected by shorter, older ancestry tracts—consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse—reflected by longer, younger tracts—is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub-continental source populations with far greater resolution than previously thought, even when limited pre-Columbian Caribbean haplotypes have survived.



Mark D said...

Isn't this essentially the same as the one published in June?

I noticed that the charts were identical, but haven't put them side by side to compare verbiage.

Kepler said...

No, it is not.
I would like to see further what they mean by saying that the Waraos are particularly linked to the Mayas. Can there be a tentative timing?

A couple of remarks from a Venezuelan:
1) we know there were Carib and Arawak groups migrating from Venezuela's coast towards the Caribbean islands for a long time. Still,
2) between 1492-1498 and 1560 approximately there was a dramatic collapse of the indigenous population of the Caribbean islands and the Europeans decided from the start to enslave natives from the Venezuelan coast and take them to those islands to keep on the work. They were soon to be replaced by Africans. But in any case: thousands upon thousands of native Americans were transported by Europeans during those first decades.

3) I don't know what they really mean by saing Yukpas being "isolate". They are from the Carib family group, even if they have been isolated from the Carib speaking region for a long time. Their language is quite distinct but still part of the Carib language family like that of the Pemon, the Karina, the Yek'uana.

It would be interesting if more comparisons were made between the now completely mixed Venezuelan population along the whole Venezuelan coast and the Waraos, who speak an isolated language. Most archaeologists now think that virtually the whole central and eastern Venezuelan coast but for the Orinoco was Carib area and the Waraos were where they are now. Still, it could be conceivable that the Waraos had "colonies" or the like.
Alexander von Humboldt said the natives of Margarita, the Waikeri, told him their great-grandparents spoke a language like the Waraos (in 1800 they all spoke Spanish only). But now most consider the Waikeri (now extinct) were part of the Carib language family.

All this might be taken into account to consider whom to compare with.

MOCKBA said...

Early colonization-times Spaniards were supposed to have been enriched by Moorish and Sephardic element, while the Iberian population left behind would have been relatively depleted / "cleansed"? Adding Maghreb and Sephardi samples to the analysis may offer a direct test to the hypothesis

Grey said...

If the sugar plantation model was first developed on the West African islands and then exported to the Americas a mixed Creole population created on those islands may have been exported too. They would (may?) have had an advantage over European colonists (more resistance to tropical diseases) and an advantage over African slaves (color-based social status) so might (?) over time have become a larger percentage of the total population than they were originally.

Mark D said...

I commend the authors for the sampling criteria used, one of the issues I've noted in the past,

"A total of 251 individuals representing six different Caribbean-descent populations were recruited in South Florida, USA. Participants were required to have at least three grandparents from their countries of origin, thus limited ethnographic and anonymous pedigree information was collected."

A friend of mine here in South Florida was unable to participate since, while he and both his parents were born in Cuba, his paternal grandparents emigrated early last century from Galicia, Spain. Nevertheless, his admixture shows 5% Native/95% European, and his mtDNA haplogroup is A2d1, clearly Native American.

I find it extremely interesting the dichotomy in gender lineages among Hispanics.