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Genes (Basel). 2018 Dec 12;9(12). pii: E625. doi: 10.3390/genes9120625.

Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians.

Author information

1
Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK. u.esposito@sheffield.ac.uk.
2
Manipal University, Manipal Centre for Natural Sciences (MCNS), Manipal, Karnataka, 576104, India. ranajit.das@manipal.edu.
3
Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK. syakir.syed@gmail.com.
4
Bioinformatics and Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA mehdi.pirooznia@nih.gov. mehdi.pirooznia@nih.gov.
5
Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK. e.elhaik@sheffield.ac.uk.

Abstract

The rapid accumulation of ancient human genomes from various areas and time periods potentially enables the expansion of studies of biodiversity, biogeography, forensics, population history, and epidemiology into past populations. However, most ancient DNA (aDNA) data were generated through microarrays designed for modern-day populations, which are known to misrepresent the population structure. Past studies addressed these problems by using ancestry informative markers (AIMs). It is, thereby, unclear whether AIMs derived from contemporary human genomes can capture ancient population structures, and whether AIM-finding methods are applicable to aDNA, provided that the high missingness rates in ancient-and oftentimes haploid-DNA can also distort the population structure. Here, we define ancient AIMs (aAIMs) and develop a framework to evaluate established and novel AIM-finding methods in identifying the most informative markers. We show that aAIMs identified by a novel principal component analysis (PCA)-based method outperform all of the competing methods in classifying ancient individuals into populations and identifying admixed individuals. In some cases, predictions made using the aAIMs were more accurate than those made with a complete marker set. We discuss the features of the ancient Eurasian population structure and strategies to identify aAIMs. This work informs the design of single nucleotide polymorphism (SNP) microarrays and the interpretation of aDNA results, which enables a population-wide testing of primordialist theories.

KEYWORDS:

admixture mapping, primordialism; ancient DNA; ancient ancestry informative markers; population structure; principal component analysis

Conflict of interest statement

EE is a consultant to DNA Diagnostic Centre and DNA Consultants. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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