PANE: fast and reliable ancestral reconstruction on ancient genotype data with non-negative least square and principal component analysis
de Gennaro LPapers in this archive, Molinaro LPapers in this archive, Raveane APapers in this archive, Santonastaso FPapers in this archive, Saponetti SSPapers in this archive, Massi MCPapers in this archive, Pagani LPapers in this archive, Metspalu MPapers in this archive, Hellenthal GPapers in this archive, Kivisild TPapers in this archive, Ventura MPapers in this archive, Montinaro FPapers in this archive
Abstract
The history of human populations has been strongly shaped by admixture events, contributing to patterns of observed genetic diversity across populations. In this study, we introduce the Principal component Ancestry proportions using NNLS Estimation (PANE) method that leverages principal component analysis and non-negative least squares to assess the ancestral compositions of admixed individuals given a large set of populations. Our results show its ability to reliably estimate ancestry across several scenarios, even those with a significant proportion of missing genotypes, in a fraction of the time required when using other tools. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-025-03491-z.
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