Reconstructing the population genetic history of the Caribbean.
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.
Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America.
Andrés
A
Moreno-Estrada
Simon
S
Gravel
Fouad
F
Zakharia
Jacob L
JL
McCauley
Jake K
JK
Byrnes
Christopher R
CR
Gignoux
Patricia A
PA
Ortiz-Tello
Ricardo J
RJ
Martínez
Dale J
DJ
Hedges
Richard W
RW
Morris
Celeste
C
Eng
Karla
K
Sandoval
Suehelay
S
Acevedo-Acevedo
Paul J
PJ
Norman
Zulay
Z
Layrisse
Peter
P
Parham
Juan Carlos
JC
Martínez-Cruzado
Esteban González
EG
Burchard
Michael L
ML
Cuccaro
Eden R
ER
Martin
Carlos D
CD
Bustamante
D044383:Black People / Q000235:genetics*; D017691:Caribbean Region; D004272:DNA, Mitochondrial / Q000235:genetics; D003710:Demography; D051456:Gene Flow; D005828:Genetics, Population; D023281:Genomics; D006239:Haplotypes; D006630:Hispanic or Latino / Q000235:genetics; D006801:Humans; D007198:Indians, North American / Q000235:genetics*; D044465:White People / Q000235:genetics*
D004272:DNA, Mitochondrial