Repository logo

Infoscience

  • English
  • French
Log In
Logo EPFL, École polytechnique fédérale de Lausanne

Infoscience

  • English
  • French
Log In
  1. Home
  2. Academic and Research Output
  3. Journal articles
  4. Robust Demographic Inference from Genomic and SNP Data
 
research article

Robust Demographic Inference from Genomic and SNP Data

Excoffier, Laurent
•
Dupanloup, Isabelle
•
Huerta-Sanchez, Emilia
Show more
2013
Plos Genetics

We introduce a flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets. We show that our composite-likelihood approach allows one to study evolutionary models of arbitrary complexity, which cannot be tackled by other current likelihood-based methods. For simple scenarios, our approach compares favorably in terms of accuracy and speed with partial derivative a partial derivative i, the current reference in the field, while showing better convergence properties for complex models. We first apply our methodology to non-coding genomic SNP data from four human populations. To infer their demographic history, we compare neutral evolutionary models of increasing complexity, including unsampled populations. We further show the versatility of our framework by extending it to the inference of demographic parameters from SNP chips with known ascertainment, such as that recently released by Affymetrix to study human origins. Whereas previous ways of handling ascertained SNPs were either restricted to a single population or only allowed the inference of divergence time between a pair of populations, our framework can correctly infer parameters of more complex models including the divergence of several populations, bottlenecks and migration. We apply this approach to the reconstruction of African demography using two distinct ascertained human SNP panels studied under two evolutionary models. The two SNP panels lead to globally very similar estimates and confidence intervals, and suggest an ancient divergence (>110 Ky) between Yoruba and San populations. Our methodology appears well suited to the study of complex scenarios from large genomic data sets.

  • Files
  • Details
  • Metrics
Type
research article
DOI
10.1371/journal.pgen.1003905
Web of Science ID

WOS:000330367200070

Author(s)
Excoffier, Laurent
Dupanloup, Isabelle
Huerta-Sanchez, Emilia
Sousa, Vitor C.
Foll, Matthieu
Date Issued

2013

Publisher

Public Library of Science

Published in
Plos Genetics
Volume

9

Issue

10

Article Number

e1003905

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
SV  
Available on Infoscience
June 2, 2014
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/103831
Logo EPFL, École polytechnique fédérale de Lausanne
  • Contact
  • infoscience@epfl.ch

  • Follow us on Facebook
  • Follow us on Instagram
  • Follow us on LinkedIn
  • Follow us on X
  • Follow us on Youtube
AccessibilityLegal noticePrivacy policyCookie settingsEnd User AgreementGet helpFeedback

Infoscience is a service managed and provided by the Library and IT Services of EPFL. © EPFL, tous droits réservés