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Review
. 2016 Dec;41:98-105.
doi: 10.1016/j.gde.2016.08.007. Epub 2016 Sep 20.

Recent Advances in the Study of Fine-Scale Population Structure in Humans

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Free PMC article
Review

Recent Advances in the Study of Fine-Scale Population Structure in Humans

John Novembre et al. Curr Opin Genet Dev. .
Free PMC article

Abstract

Empowered by modern genotyping and large samples, population structure can be accurately described and quantified even when it only explains a fraction of a percent of total genetic variance. This is especially relevant and interesting for humans, where fine-scale population structure can both confound disease-mapping studies and reveal the history of migration and divergence that shaped our species' diversity. Here we review notable recent advances in the detection, use, and understanding of population structure. Our work addresses multiple areas where substantial progress is being made: improved statistics and models for better capturing differentiation, admixture, and the spatial distribution of variation; computational speed-ups that allow methods to scale to modern data; and advances in haplotypic modeling that have wide ranging consequences for the analysis of population structure. We conclude by outlining four important open challenges: the limitations of discrete population models, uncertainty in individual origins, the incorporation of both fine-scale structure and ancient DNA in parametric models, and the development of efficient computational tools, particularly for haplotype-based methods.

Figures

Figure 1
Figure 1. Four methods for assessing population structure using large-scale single-nucleotide polymorphism data
A) Ancestry proportion inference using ADMIXTURE. B) Principal components analysis. C) Plot of population in ‘geogenetic’ space using SpaceMix. D) Visualization of effective migration rates using EEMS (brown = low effective migration; blue = high effective migration). Each method is applied to the dataset analysed in [92] after filtering out populations with fewer than 10 individuals, where population identifiers are defined on the basis of grandparental ancestry. Structure is visible, even though FST-values average 0.004 between broad geographic regions in Europe [92].
Figure 2
Figure 2. A large number of loci is required to reveal fine-scale population structure using PCA
Four subsamples with an increasing number of loci were taken from the[93] dataset. Using 100 loci, Europe appears panmictic, whereas 1,000 loci are sufficient to establish a North-South cline. With 10,000 and 100,000 loci, fine-scale details are revealed.

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