Testing the existence of an unadmixed ancestor from a specific population t generations ago

PLoS One. 2022 Aug 12;17(8):e0271097. doi: 10.1371/journal.pone.0271097. eCollection 2022.

Abstract

The ancestry of each locus of the genome can be estimated (local ancestry) based on sequencing or genotyping information together with reference panels of ancestral source populations. The length of those ancestry-specific genomic segments are commonly used to understand migration waves and admixture events. In short time scales, it is often of interest to determine the existence of the most recent unadmixed ancestor from a specific population t generations ago. We built a hypothesis test to determine if an individual has an ancestor belonging to a target ancestral population t generations ago based on these lengths of the ancestry-specific segments at an individual level. We applied this test on a data set that includes 20 Uruguayan admixed individuals to estimate for each one how many generations ago the most recent indigenous ancestor lived. As this method tests each individual separately, it is particularly suited to small sample sizes, such as our study or ancient genome samples.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genetics, Population*
  • Genome, Human
  • Humans
  • Polymorphism, Single Nucleotide*
  • Uruguay

Grants and funding

Gabriel Illanes acknowledges support of Agencia Nacional de Investigación e Innivación (ANII-Uruguay) and Comisión Académica de Posgrado (CAP-Udelar) The Urugenomes project was funded by BID (Banco Iberomericano de desarrollo) Proyecto ATN / KK-L4584-JR “Fortalecimiento de las capacidades técnicas y humanas para las exportaciones de servicios genómicos”. Additionally, Maria Ines Fariello and Lucia Spangenberg obtained partial support from the ANII-Uruguay FSDA 1 2017 1 143647 and Lucia Spangenberg and Hugo Naya are also supported by FOCEM (MERCOSUR Structural Convergence Fund).