Genetically blacker blacks have more preterm births: Association of genetic ancestry with preterm delivery and related traits among African American mothers
"Spanish" Cubans are Latin American "white": Admixture estimates for the population of Havana City
SUBJECTS AND METHODS: According to genealogical information and anthropological traits, 206 subjects were classified as Mulatto, of Spanish decent or of African descent. Seventeen Ancestry Informative Markers, with high difference in frequency between parental populations, were selected to estimate individual and group admixture proportions. The statistical analyses were performed using the ADMIX, ADMIX95 and STRUCTURE 2.1 packages. RESULTS: The results demonstrate a high level of European and African admixture in Mulattos (57-59% European; 41-43% West African). The European contribution was higher in those of Spanish descent (85%) while in those of African descent, the West African contribution ranged between 74% and 76%.
A program that claims to improve on Structure: mStruct: Inference of Population Structure in Light of Both Genetic Admixing and Allele Mutations
Traditional methods for analyzing population structure, such as the Structure program, ignore the influence of the effect of allele mutations between the ancestral and current alleles of genetic markers, which can dramatically influence the accuracy of the structural estimation of current populations. Studying these effects can also reveal additional information about population evolution such as the the divergence time and migration history of admixed populations. We propose mStruct, an admixture of population-specific mixtures of inheritance models, that addresses the task of structure inference and mutation estimation jointly through a hierarchical Bayesian framework, and a variational algorithm for inference. We validated our method on synthetic data, and used it to analyze the HGDP-CEPH cell line panel of microsatellites used in (Rosenberg et al. 2002) and the HGDP SNP data used in (Conrad et al. 2006). A comparison of the structural maps of world populations estimated by mStruct and Structure is presented, and we also report potentially interesting mutation patterns in world populations estimated by mStruct. The mStruct software implementation in C++ is available for download at http://www.sailing.cs.cmu.edu/mstruct.html.
Another refinement of admixture estimation: Spatial inference of admixture proportions and secondary contact zones
Genetic admixture of distinct gene pools is the consequence of complex spatio-temporal processes that could have involved massive migration and local mating during the history of a species. However current methods for estimating individual admixture proportions lack the incorporation of such a piece of information. Here, we extend Bayesian clustering algorithms by including global trend surfaces and spatial autocorrelation in the prior distribution on individual admixture coefficients. We test our algorithm by using spatially explicit and realistic coalescent simulations of colonization followed by secondary contact. By coupling our multiscale spatial analyses with a Bayesian evaluation of model complexity and fit, we show that the algorithm provides a correct description of smooth clinal variation, while still detecting zones of sharp variation when they are present in the data.
Polak: Spectral graph theory uncovers European genetic ancestry clusters and Dendrogram of European genetic ancestry clusters