Factor analysis of ancient population genomic samples - BioInformatique Accéder directement au contenu
Article Dans Une Revue Nature Communications Année : 2020

Factor analysis of ancient population genomic samples

Flora Jay

Résumé

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
Fichier principal
Vignette du fichier
Francois_Jay_2020_NatComm.pdf (1.09 Mo) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte

Dates et versions

hal-02942333 , version 1 (24-11-2020)

Identifiants

Citer

Olivier François, Flora Jay. Factor analysis of ancient population genomic samples. Nature Communications, 2020, 11 (1), ⟨10.1038/s41467-020-18335-6⟩. ⟨hal-02942333⟩
1439 Consultations
110 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More