Informativeness of Genetic Markers for Inference of Ancestry*

Rosenberg, Noah A.; Li, Lei M.; Ward, Ryk; Pritchard, Jonathan K.

doi:10.1086/380416

Cited by 629 publications

(736 citation statements)

References 41 publications

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“…Third, because it is likelihood based, it lends itself easily to questions of study design, for example marker choice. We provide some examples in this regard which support and complement prior findings of Rosenberg et al (2003) and Pfaff et al (2004). Finally, we show that our full maximum likelihood estimator is less biased than the partial ML estimator when the populations used to define the ancestral groups are imprecise.…”

Section: Introductionsupporting

confidence: 74%

Estimation of individual admixture: Analytical and study design considerations

Tang

Peng

Wang

et al. 2005

Genetic Epidemiology

630

642

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The genome of an admixed individual represents a mixture of alleles from different ancestries.In the United States, the two largest minority groups, African Americans and Hispanics, are both admixed. An understanding of the admixture proportion at an individual level (individual admixture, or IA) is valuable for both population geneticists and epidemiologists who conduct case-control association studies in these groups. Here we present an extension of a previously described frequentist (maximum likelihood or ML) approach to estimate individual admixture that allows for uncertainty in ancestral allele frequencies. We compare this approach both to prior partial likelihood based methods as well as more recently described Bayesian MCMC methods.Our full ML method demonstrates increased robustness when compared to an existing partial ML approach. Simulations also suggest that this frequentist estimator achieves similar efficiency, measured by the mean squared error criterion, as Bayesian methods but requires just a tiny fraction of the computational time to produce point estimates, allowing for extensive analysis (e.g. simulations) not possible by Bayesian methods. Our simulation results demonstrate that inclusion of ancestral populations or their surrogates in the analysis is required by any method of IA estimation to obtain reasonable results.keywords: admixture, EM algorithm, maximum likelihood estimate.

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Section: Introductionsupporting

confidence: 74%

Estimation of individual admixture: Analytical and study design considerations

Tang

Peng

Wang

et al. 2005

Genetic Epidemiology

630

642

View full text Add to dashboard Cite

show abstract

“…Having a large number of fixed SNPs is an enormous advantage when designing reduced SNP assays, as they represent ideal ancestry informative markers (Rosenberg, Li, Ward, & Pritchard, 2003). Yet, the overall high differentiation between A. m. iberiensis and C‐lineage honeybees explains why all tested assays, including those constructed from randomly selected SNPs, performed well.…”

Section: Discussionmentioning

confidence: 99%

Developing reduced SNP assays from whole‐genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)

Henriques

Parejo

Vignal

et al. 2018

Evolutionary Applications

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The most important managed pollinator, the honeybee (Apis mellifera L.), has been subject to a growing number of threats. In western Europe, one such threat is large‐scale introductions of commercial strains (C‐lineage ancestry), which is leading to introgressive hybridization and even the local extinction of native honeybee populations (M‐lineage ancestry). Here, we developed reduced assays of highly informative SNPs from 176 whole genomes to estimate C‐lineage introgression in the most diverse and evolutionarily complex subspecies in Europe, the Iberian honeybee (Apis mellifera iberiensis). We started by evaluating the effects of sample size and sampling a geographically restricted area on the number of highly informative SNPs. We demonstrated that a bias in the number of fixed SNPs (FST = 1) is introduced when the sample size is small (N ≤ 10) and when sampling only captures a small fraction of a population's genetic diversity. These results underscore the importance of having a representative sample when developing reliable reduced SNP assays for organisms with complex genetic patterns. We used a training data set to design four independent SNP assays selected from pairwise FST between the Iberian and C‐lineage honeybees. The designed assays, which were validated in holdout and simulated hybrid data sets, proved to be highly accurate and can be readily used for monitoring populations not only in the native range of A. m. iberiensis in Iberia but also in the introduced range in the Balearic islands, Macaronesia and South America, in a time‐ and cost‐effective manner. While our approach used the Iberian honeybee as model system, it has a high value in a wide range of scenarios for the monitoring and conservation of potentially hybridized domestic and wildlife populations.

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“…1,2 AIMs are often used in genome association studies to test for the genetic homogeneity of the studied population and to correct for possible population stratification. 3,4 Panels of AIMs for Latin American populations have been proposed. [5][6][7] These maps will allow the application of admixture mapping studies as an approach for the identification of genetic risk factors for complex diseases in populations of mixed ancestry.…”

Section: Introductionmentioning

confidence: 99%

Ancestry informative markers and admixture proportions in northeastern Mexico

et al. 2009

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To investigate the ancestral admixture in the Mestizo population in northeastern Mexico, we genotyped 74 ancestral informative markers (AIMs) and 15 Y-single-nucleotide polymorphisms (Y-SNPs) in 100 individuals. The Native American contribution is 56% (range: 27.4-81.2%), the European contribution is 38% (range: 16.7-70.5%) and the West African contribution is 6%. The results show a higher European contribution than was reported in other similar studies in the country, albeit with a predominant Native American ancestry. No remarkable differences in the ancestry proportions were observed using subgroups of 74, 54, 34 and 24 AIMs. The paternal lineage calculated by genotyping of 15 Y-SNPs, shows a major component of European and Eurasian ancestry markers (B78%), compared with Amerindian (B12%) and African markers (10%). This information will set a reference for future determinations of admixture proportions in the Mestizo population from Mexico and for populationbased association studies of complex diseases.

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Informativeness of Genetic Markers for Inference of Ancestry*

Cited by 629 publications

References 41 publications

Estimation of individual admixture: Analytical and study design considerations

Estimation of individual admixture: Analytical and study design considerations

Developing reduced SNP assays from whole‐genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)

Ancestry informative markers and admixture proportions in northeastern Mexico

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