Population history of the Caribbean (Moreno-Estrada et al. 2013)

The placement of Caribbeans on a European "genetic map" is fairly interesting, as they appear to be "ultra-Iberian" (on the far left). The authors invoke drift as an explanation, which makes sense, given that a small portion of the Iberian gene pool entered into the composition of these populations.

On the other hand, it'd be nice to have Iberian data from a few centuries ago, to make sure, since Iberia, being a part of Europe may have had the opportunity to "right-shift" during the last few centuries due to gene flow, and even if it didn't there is a chance that gene flow within Iberia may have dulled population differentiation, while immigration to the Caribbean may not have originated from all parts of Iberia equally (and as I've shown, there is substantial population structure in Iberia down to this day).

arXiv:1306.0558 [q-bio.PE]

Reconstructing the Population Genetic History of the Caribbean

Andres 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, by making use of genome-wide SNP array data, we characterize ancestral components of Caribbean populations on a sub-continental level and unveil fine-scale patterns of population structure distinguishing insular from mainland Caribbean populations as well as from other Hispanic/Latino groups. We provide genetic evidence for an inland South American origin of the Native American component in island populations and for extensive pre-Columbian gene flow across the Caribbean basin. The Caribbean-derived European component shows significant differentiation from parental Iberian populations, presumably as a result of founder effects during the colonization of the New World. Based on demographic models, we reconstruct the complex population history of the Caribbean since the onset of continental admixture. We find that insular populations are best modeled as mixtures absorbing two pulses of African migrants, coinciding with early and maximum activity stages of the transatlantic slave trade. These two pulses appear to have originated in different regions within West Africa, imprinting two distinguishable signatures in present day Afro-Caribbean genomes and shedding light on the genetic impact of the dynamics occurring during the slave trade in the Caribbean.

Link

Effects of ancestry and admixture on human variation (Kidd et al. 2012)

AJHG Volume 91, Issue 4, 5 October 2012, Pages 660–671

Population Genetic Inference from Personal Genome Data: Impact of Ancestry and Admixture on Human Genomic Variation

Jeffrey M. Kidd et al.

Full sequencing of individual human genomes has greatly expanded our understanding of human genetic variation and population history. Here, we present a systematic analysis of 50 human genomes from 11 diverse global populations sequenced at high coverage. Our sample includes 12 individuals who have admixed ancestry and who have varying degrees of recent (within the last 500 years) African, Native American, and European ancestry. We found over 21 million single-nucleotide variants that contribute to a 1.75-fold range in nucleotide heterozygosity across diverse human genomes. This heterozygosity ranged from a high of one heterozygous site per kilobase in west African genomes to a low of 0.57 heterozygous sites per kilobase in segments inferred to have diploid Native American ancestry from the genomes of Mexican and Puerto Rican individuals. We show evidence of all three continental ancestries in the genomes of Mexican, Puerto Rican, and African American populations, and the genome-wide statistics are highly consistent across individuals from a population once ancestry proportions have been accounted for. Using a generalized linear model, we identified subtle variations across populations in the proportion of neutral versus deleterious variation and found that genome-wide statistics vary in admixed populations even once ancestry proportions have been factored in. We further infer that multiple periods of gene flow shaped the diversity of admixed populations in the Americas—70% of the European ancestry in today’s African Americans dates back to European gene flow happening only 7–8 generations ago.

Link