In the Light of Evolution Volume IV: The Human Condition (2010) / Chapter Skim
Currently Skimming:
8 Genome-wide Patterns of Population Structure and Admixture Among Hispanic/Latino Populations--Katarzyna Bryc, Christopher Velez, Tatiana Karafet, Andres Moreno-Estrada, Andy Reynolds, Adam Auton, Michael Hammer, Carlos D. Bustamante, and Harry Ostrer
8 Genome-wide Patterns of Population Structure and Admixture Among Hispanic/Latino Populations--Katarzyna Bryc, Christopher Velez, Tatiana Karafet, Andres Moreno-Estrada, Andy Reynolds, Adam Auton, Michael Hammer, Carlos D. Bustamante, and Harry Ostrer
Pages 147-166
The Chapter Skim interface presents what we've algorithmically identified as the most significant single chunk of text within every page in the chapter.
Select key terms on the right to highlight them within pages of the chapter.
From page 147... ...
* hispanic/latino populations possess a complex genetic structure that reflects recent admixture among and potentially ancient substructure within native American, european, and West African source populations.
|
From page 148... ...
. These complex historical events have affected patterns of genetic and genomic variation within and among present-day hispanic/latino populations in a heterogeneous fashion, resulting in rich and varied ancestry within and among populations as well as marked differences in the contribution of european, native American, and African ancestry to autosomal, X chromosome, and uniparentally inherited genomes.
|
From page 149... ...
, and ancestry by environment interac tion to disease outcome in diverse hispanic/latino populations will also be critical to applying a genomic perspective to the practice of medicine in the United states and in latin America. For example, whereas european ancestry was associated with increased asthma susceptibility in Puerto ricans (salari et al., 2005)
|
From page 150... ...
This project, therefore, represents an important step toward comprehensive panels for U.s.-based studies that can more accurately reflect the diversity within various hispanic/latino populations. RESULTS Population Structure We applied the clustering algorithm FRAPPE to investigate genetic structure among hispanic/latino individuals using a merged data set with over 5,000 individuals with european, African, and native American ancestry genotyped across 73,901 snPs common to the Affymetrix 500K array and the illumina 610-Quad panel (Materials and Methods)
|
From page 151... ...
. similar results were found in Colombians and ecuadorians, whereas Dominicans and Puerto ricans showed the greatest variation in the African ancestry (Fig.
|
From page 152... ...
and to results from the X chromosome markers (Lower Right)
|
From page 153... ...
We calculated lD decay curves for all populations with at least 1.0 0.8 Structure autosome ancestry 0.6 0.4 0.2 0.0 250 Chromosome 1 ancestry (Mb) 200 150 100 50 0 1.0 Structure X chromosome ancestry 0.8 0.6 0.4 0.2 0.0 Dominican Mexico Ecuador Colombia Puerto Republic Rico European ancestry African ancestry Native American ancestry FiGUre 8.3 Genome-wide and locus-specific ancestry estimates for Mexicans, ecuadorians, Colombians, Puerto ricans, and Dominicans.
|
From page 154... ...
. specifically, the populations with the most native American ancestry, Mexican and ecuadorian, exhibited higher levels of linkage disequilibrium among snP markers, whereas the populations with the highest proportions of African ancestry, the Dominican and Puerto rican samples, had the lowest levels of lD.
|
From page 155... ...
. To investigate the genetic relationships among admixed hispanic/ latino populations and putative ancestral groups, we compared patterns of population divergence among the inferred segments of european, African, and native American ancestry and corresponding putative source populations using Wright's FsT measure.
|
From page 156... ...
Adygei Basque european europe europe europe europe europe ese C nne nW s se Col 1.836 1.351 1.389 0.978 1.253 1.240 1.033 1.020 DoM 1.560 1.128 1.071 0.691 0.919 0.940 0.705 0.775 eCU 1.669 1.456 1.225 1.012 1.212 1.100 1.005 1.005 Pri 1.811 1.530 1.392 1.062 1.345 1.251 1.107 1.181 Mexico 1.014 0.784 0.559 0.335 0.438 0.442 0.193 0.307 native American segments of the Genome (%) Aymara Colom- Karitiana Maya nahua Pima Quechua surui bian Col 4.005 5.296 9.099 4.724 3.614 8.562 3.432 13.803 DoM 5.142 5.868 9.060 4.262 3.601 9.310 3.147 13.736 eCU 4.244 5.799 9.178 5.446 4.147 9.193 3.079 13.765 Pri 5.872 6.618 10.120 6.624 4.795 10.578 5.169 15.093 Mexico 2.397 4.185 8.197 1.417 0.572 5.112 2.086 11.061 noTe: results based on ~70k overlapping snPs between Affymetrix and illumina platforms and equalizing population sample sizes down to seven individuals per population.
|
From page 157... ...
Population Structure and Admixture Among Hispanic/Latino Populations / europe europe French italian orcadian russian sardinian Tuscan sW W 0.863 1.080 0.880 0.885 1.410 1.648 1.550 1.050 0.537 0.730 0.613 0.610 1.093 1.413 1.270 0.825 0.838 1.104 0.799 0.845 1.417 1.369 1.607 0.925 0.916 1.155 0.940 0.879 1.508 1.820 1.566 1.041 0.122 0.265 0.270 0.271 0.793 0.882 0.852 0.336
|
From page 158... ...
The closest relationship is clearly observed between Mexicans from Guadala jara and nahua indigenous individuals. Sex Bias in Ancestry Contributions We used the STRUCTURE ancestry estimates on the autosomes and X chromosome to estimate native American, european, and African ancestry proportions of each hispanic/latino individual.
|
From page 159... ...
. Furthermore, greater native American ancestry on the X chromosome in Puerto ricans did not necessarily imply greater Amerindian ancestry on the autosomes.
|
From page 160... ...
As has been previously documented, we found large variation in the proportions of european, African, and native American ancestry among Mexicans, Puerto ricans, Dominicans, ecuadorians, and Colombians, but also within each of these groups. These trends are a consequence of variation in rates of migration from ancestral european and African source populations as well as population density native Americans in pre-Columbian times (sans, 2000)
|
From page 161... ...
We found a smaller difference between mean African ancestry on the X chromosome and the autosomes, compared with the difference in native American ancestry. Furthermore, unlike in native American ancestry, we found an overwhelming representation of native American mtDnA haplogroups in Puerto ricans, even though non-european ancestry on the autosomes was largely African.
|
From page 162... ...
in the case of Puerto ricans, the only way that one can reconcile greater African ancestry on the X chromosome vs. what would be expected on mitochondrial data would be through transmission of X chromosomes independent of mitochondrial transmission, which is plausible biologically only via males.
|
From page 163... ...
(2008) suggested that admixture mapping in hispanic/latino populations may be feasible within a two-population admixture framework, since the mean African ancestry in Mestizo populations is typically low (<10%)
|
From page 164... ...
. Finally, we include all native American populations from the Mao et al.
|
From page 165... ...
For local ancestry estimation, we used the software lAMP in lAMPAnC mode providing allele frequencies for the hGDP West Africans, europeans, and native Americans as ancestral populations (sankararaman et al., 2008)
|
From page 166... ...
ACKNOWLEDGMENTS We thank Mariano rey for support of the project; Peter Gregersen, Carole oddoux, and Annette lee for technical assistance; and Marc Pybus for valuable programming support during part of the analyses. This work was supported by the national institutes of health (Grant 1r01GM83606)
|
Key Terms
This material may be derived from roughly machine-read images, and so is provided only to facilitate research.
More
information on Chapter Skim is available.