Genome-wide patterns of population structure and admixture in West Africans and African Americans. Proc Natl Acad Sci USA

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 01/2010; 107(2):786-91. DOI: 10.1073/pnas.0909559107
Source: PubMed

ABSTRACT Quantifying patterns of population structure in Africans and African Americans illuminates the history of human populations and is critical for undertaking medical genomic studies on a global scale. To obtain a fine-scale genome-wide perspective of ancestry, we analyze Affymetrix GeneChip 500K genotype data from African Americans (n = 365) and individuals with ancestry from West Africa (n = 203 from 12 populations) and Europe (n = 400 from 42 countries). We find that population structure within the West African sample reflects primarily language and secondarily geographical distance, echoing the Bantu expansion. Among African Americans, analysis of genomic admixture by a principal component-based approach indicates that the median proportion of European ancestry is 18.5% (25th-75th percentiles: 11.6-27.7%), with very large variation among individuals. In the African-American sample as a whole, few autosomal regions showed exceptionally high or low mean African ancestry, but the X chromosome showed elevated levels of African ancestry, consistent with a sex-biased pattern of gene flow with an excess of European male and African female ancestry. We also find that genomic profiles of individual African Americans afford personalized ancestry reconstructions differentiating ancient vs. recent European and African ancestry. Finally, patterns of genetic similarity among inferred African segments of African-American genomes and genomes of contemporary African populations included in this study suggest African ancestry is most similar to non-Bantu Niger-Kordofanian-speaking populations, consistent with historical documents of the African Diaspora and trans-Atlantic slave trade.

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    • "). Previous studies have also shown the importance of genetic distance assessments, such as in inference of migration patterns (Li et al. 2008; Ramachandran et al. 2005; Deshpande et al. 2009 and Laval et al. 2010) as well as in the need to adjust for population stratification in association studies Bryca et al. 2010; Patterson et al. 2010; Miclaus et al. 2009 and Li et al. 2010). This study was conducted to infer the population structure of Malays that may or may not have shared ancestry from other study populations. "
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    ABSTRACT: The Malays consist of various sub-ethnic groups which are believed to have different ancestral origins based on their migrations centuries ago. The sub-ethnic groups can be divided based on the region they inhabit; the northern (Melayu Kedah and Melayu Kelantan), western (Melayu Minang) and southern parts (Melayu Bugis and Melayu Jawa) of Peninsular Malaysia. We analyzed 54,794 autosomal single nucleotide polymorphisms (SNPs) which were shared by 472 unrelated individuals from 17 populations to determine the genetic structure and distributions of the ancestral genetic components in five Malay sub-ethnic groups namely Melayu Bugis, Melayu Jawa, Melayu Minang, Melayu Kedah, and Melayu Kelantan. We also have included in the analysis 12 other study populations from Thailand, Indonesia, China, India, Africa and Orang Asli sub-groups in Malay Peninsula, obtained from the Pan Asian SNP Initiative (PASNPI) Consortium and International HapMap project database. We found evidence of genetic influx from Indians to Malays, more in Melayu Kedah and Melayu Kelantan which are genetically different from the other Malay sub-ethnic groups, but similar to Thai Pattani. More than 98% of these northern Malays haplotypes could be found in either Indians or Chinese populations, indicating a highly admixture pattern among populations. Nevertheless, the ancestry lines of Malays, Indonesians and Thais were traced back to have shared a common ancestor with the Proto-Malays and Chinese. These results support genetic admixtures in the Peninsular Malaysia Malay populations and provided valuable information on the enigmatic demographical history as well as shed some insights into the origins of the Malays in the Malay Peninsula.
    HUGO Journal 11/2014; 8(1):5. DOI:10.1186/s11568-014-0005-z
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    • "Next-generation DNA sequencing (NGS) provides a particularly valuable new tool to plant breeders, allowing for an enormous amount of genetic information at our fi ngertips in a matter of days, at lower cost compared with older sequencing methods ( Egan et al., 2012 ). Over the past few years, we have seen draft genome sequences appear for several perennial crops including apple ( Velasco et al., 2010 ), grape ( Jaillon et al., 2007 ), cacao ( Argout et al., 2011 ), banana ( D'Hont et al., 2012 ), peach ( Verde et al., 2013 ), papaya ( Ming et al., 2008 ), citrus ( Xu et al., 2013 ), and oil palm ( Singh et al., 2013 ). The genomics resources that only a decade ago were restricted to model organisms are now widely available in nonmodel organisms as well. "
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    ABSTRACT: Perennial crops represent important fresh and processed food sources worldwide, but advancements in breeding perennials are often impeded due to their very nature. The perennial crops we rely on most for food take several years to reach production maturity and require large spaces to grow, which make breeding new cultivars costly compared with most annual crops. Because breeding perennials is inefficient and expensive, they are often grown in monocultures consisting of small numbers of elite cultivars that are vegetatively propagated for decades or even centuries. This practice puts many perennial crops at risk for calamity since they remain stationary in the face of evolving pest and disease pressures. Although there is tremendous genetic diversity available to them, perennial crop breeders often struggle to generate commercially successful cultivars in a timely and cost-effective manner because of the high costs of breeding. Moreover, consumers often expect the same cultivars to be available indefinitely, and there is often little or no incentive for growers and retailers to take the risk of adopting new cultivars. While genomics studies linking DNA variants to commercially important traits have been performed in diverse perennial crops, the translation of these studies into accelerated breeding of improved cultivars has been limited. Here we explain the "perennial problem" in detail and demonstrate how modern genomics tools can significantly improve the cost effectiveness of breeding perennial crops and thereby prevent crucial food sources from succumbing to the perils of perpetual propagation.
    American Journal of Botany 10/2014; 101(10):1780-90. DOI:10.3732/ajb.1400143 · 2.60 Impact Factor
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    • "The superior preservation of the two African individuals (125 and 165) from the urban discard deposit burial site and resistance of their genetic signals to restriction of the data set to reads with showing deaminations encouraged investigation of their origins at a finer detail, showing affinity with Bantu-speaking groups and Western African Mandenka and Yoruba populations, as expected from historical records. A previous study18 has shown that African chromosomal segments in African-American individuals were most similar to Niger-Kordofanian-speaking populations such as those included here. Here, we did not achieve sufficient resolution in PCA and ADMIXTURE to distinguish between Bantu and non-Bantu Niger-Kordofanian populations. "
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    ABSTRACT: An archaeological excavation in Valle da Gafaria (Lagos, Portugal), revealed two contiguous burial places outside the medieval city walls, dating from the 15(th)-17(th) centuries AD: one was interpreted as a Leprosarium cemetery and the second as an urban discard deposit, where signs of violent, unceremonious burials suggested that these remains may belong to slaves captured in Africa by the Portuguese. We obtained random short autosomal sequence reads from seven individuals: two from the latter site and five from the Leprosarium and used these to call SNP identities and estimate ancestral affinities with modern reference data. The Leprosarium site samples were less preserved but gave some probability of both African and European ancestry. The two discard deposit burials each gave African affinity signals, which were further refined toward modern West African or Bantu genotyped samples. These data from distressed burials illustrate an African contribution to a low status stratum of Lagos society at a time when this port became a hub of the European trade in African slaves which formed a precursor to the transatlantic transfer of millions.
    Scientific Reports 08/2014; 4:5994. DOI:10.1038/srep05994 · 5.58 Impact Factor
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