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Factor analysis of ancient population genomic samples

Olivier François 1 Flora Jay 2, 3 
1 TIMC-BCM - Biologie Computationnelle et Modélisation
TIMC - Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525
2 BioInfo - LRI - Bioinformatique (LRI)
LRI - Laboratoire de Recherche en Informatique
3 TAU - TAckling the Underspecified
Inria Saclay - Ile de France, LRI - Laboratoire de Recherche en Informatique
Abstract : The recent years have seen a growing number of studies investigating evolutionary questions using ancient DNA. To address these questions, one of the most frequently-used method is,principal component analysis (PCA). When PCA is applied to temporal samples, the sample dates are, however, ignored during analysis, leading to imperfect representations of samples in PC plots. Here, we present a factor analysis (FA) method in which individual scores are corrected for the effect of allele frequency drift over time. We obtained exact solutions for the estimates of corrected factors, and we provided a fast algorithm for their computation. Using computer simulations and ancient European samples, we compared geometric representations obtained from FA with PCA and with ancestry estimation programs. In admixture analyses, FA estimates agreed with tree-based statistics, and they were more accurate than those obtained from PCA projections and from ancestry estimation programs. A great advantage of FA over existing approaches is to improve descriptive analyses of ancient DNA samples without requiring inclusion of out group or present-day samples
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Submitted on : Tuesday, November 24, 2020 - 4:04:16 PM
Last modification on : Friday, August 5, 2022 - 3:02:43 PM
Long-term archiving on: : Thursday, February 25, 2021 - 8:34:07 PM


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Olivier François, Flora Jay. Factor analysis of ancient population genomic samples. Nature Communications, Nature Publishing Group, 2020, 11 (1), ⟨10.1038/s41467-020-18335-6⟩. ⟨hal-02942333⟩



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