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

Esposito, Umberto ; Das, Ranajit ; Syed, Syakir ; Pirooznia, Mehdi and Elhaik, Eran LU (2018) In Genes 9(12).
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... (More)

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.

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author
publishing date
type
Contribution to journal
publication status
published
in
Genes
volume
9
issue
12
article number
625
pages
18 pages
publisher
MDPI AG
external identifiers
  • pmid:30545160
  • scopus:85058576593
ISSN
2073-4425
DOI
10.3390/genes9120625
language
English
LU publication?
no
id
7bdf9521-56bb-4c21-9477-a751f882c41b
date added to LUP
2019-11-10 16:34:21
date last changed
2020-07-01 05:24:23
@article{7bdf9521-56bb-4c21-9477-a751f882c41b,
  abstract     = {<p>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.</p>},
  author       = {Esposito, Umberto and Das, Ranajit and Syed, Syakir and Pirooznia, Mehdi and Elhaik, Eran},
  issn         = {2073-4425},
  language     = {eng},
  month        = {12},
  number       = {12},
  publisher    = {MDPI AG},
  series       = {Genes},
  title        = {Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians},
  url          = {http://dx.doi.org/10.3390/genes9120625},
  doi          = {10.3390/genes9120625},
  volume       = {9},
  year         = {2018},
}