Article

Sparse sampling and rare-variant depletion distort PCA visualizations of population structure: recovery with objective-guided manifold learning

2026-08-13

Abstract excerpt

Principal component analysis (PCA) is routinely used to visualize population structure, yet how sparse sampling and rare-variant depletion affect low-dimensional plots remains poorly understood. Using spatial simulations, we show that these factors interact to distort visualization of genetic landscapes, producing triangular and three-ray patterns, artificial outliers and misleading clines. We develop an objective...

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Literature Corpus work: b25d8349-a1c6-5e90-ab6b-c85fbb686ddc
DOI: 10.64898/2026.08.11.744230

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