African genomes

African genomes

“We‘re all Africa,” according to a line from the official song of the 2010 Fifa World Cup held in South Africa, Shakira’s “Waka Waka (This Time for Africa)”. And unlike John F. Kennedy’s tenuous claim to Berlinerdom, this statement of global solidarity and unity actually has a very sound scientific foundation. There is now overwhelming evidence and agreement that modern humans originated in Afr...

A Challenge to the Ancient Origin of SIVagm Based on African Green Monkey Mitochondrial Genomes

While the circumstances surrounding the origin and spread of HIV are becoming clearer, the particulars of the origin of simian immunodeficiency virus (SIV) are still unknown. Specifically, the age of SIV, whether it is an ancient or recent infection, has not been resolved. Although many instances of cross-species transmission of SIV have been documented, the similarity between the African green...

Repair of Viral Genomes by Base Excision Pathways: African Swine Fever Virus as a Paradigm

Assessment of Genotype Imputation Performance Using 1000 Genomes in African American Studies

Genotype imputation, used in genome-wide association studies to expand coverage of single nucleotide polymorphisms (SNPs), has performed poorly in African Americans compared to less admixed populations. Overall, imputation has typically relied on HapMap reference haplotype panels from Africans (YRI), European Americans (CEU), and Asians (CHB/JPT). The 1000 Genomes project offers a wider range o...

African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana.

Over the past 20 y, many studies have examined the history of the plant ecological and molecular model, Arabidopsis thaliana, in Europe and North America. Although these studies informed us about the recent history of the species, the early history has remained elusive. In a large-scale genomic analysis of African A. thaliana, we sequenced the genomes of 78 modern and herbarium samples from Afr...