Reconstructing the history of Indigenous American populations from the Thousand Genomes Project admixed populations of the Americas

ZAKHARIA F; MUZZIO M; SANDOVAL K; MORENO-ESTRADA A; GRAVEL S; BYRNES JK; GIGNOUX CR; RODRIGUEZ-FLORES JL; MAPLES BK; GUIBLET W; DUTIL J; KENNY EE; BIGHAM AW; SHRIVER MD; THE 1000 GENOMES CONSORTIUM; RUIZ-LINARES A; OLEKSYK TL; MARTINEZ-CRUZADO JC; GONZALEZ BURCHARD E; BUSTAMANTE CD

San Francisco

Congreso; 2012 Meeting ASHG; 2012

ASHG

The Americas exhibit a rich cultural and biological diversity, including many countries with different languages, and have been deeply affected by historical events such as the arrival of the Europeans in the late 15th century. Yet little is known about the original peopling of the Americas, or about the interactions that may have taken place between the early settlers. The Thousand Genomes Project (TGP) has generated low coverage whole genome sequence, high coverage exome sequence and high quality genotype calls for three admixed populations from the Americas: Puerto Rico (PUR), Colombia (CLM), and Mexico (MXL). This dataset not only provides novel insights into these admixed populations, but also offers a unique opportunity to explore the genetics of their respective Indigenous American (IA) ancestors. To this end, we performed local ancestry deconvolution to identify tracts of IA ancestry in each of the admixed individuals in the sample. We found that the PUR, CLM and MXL populations contain an average 12%, 24%, and 47%; IA ancestry, respectively, and that 99.9%; of genomic sites are covered by at least one IA chromosome, with an average coverage of 17X, 35X, and 54X IA chromosomes for the PUR, CLM, and MXL respectively. We developed ancestry-specific (AS) extensions of both PCA and ADMIXTURE (PCA-AS and ADMIXTURE-AS) to analyze population structure considering only the IA components of ancestry in the admixed TGP genomes. We trained these methods using a large dataset comprising 493 participants from 52 IA populations across the Americas, genotyped at high density. We found that IA components in admixed individuals cluster with different linguistic groups, with the MXL and CLM appearing to be closest to Northern Amerind and Chibchan-Paezan speaking groups respectively, and the PUR near Equatorial-Tucanoan speaking populations endemic to the Amazon. Finally, we used the joint site frequency spectra of the admixed populations to make novel inferences about the demographic history of their IA ancestors. Preliminary results estimate an initial split of the MXL ancestors from the others around 12.5 kya, followed by the divergence of the PUR and CLM ancestors around 8 kya. We also found evidence of strong bottlenecking events in the PUR and CLM lineages, consistent with the low levels of heterozygosity observed in these populations.