Cargando…

Demographic Inference Using Spectral Methods on SNP Data, with an Analysis of the Human Out-of-Africa Expansion

We present an implementation of a recently introduced method for estimating the allele-frequency spectrum under the diffusion approximation. For single-nucleotide polymorphism (SNP) frequency data from multiple populations, the method computes numerical solutions to the allele-frequency spectrum (AF...

Descripción completa

Detalles Bibliográficos
Autores principales: Lukić, Sergio, Hey, Jody
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3454885/
https://www.ncbi.nlm.nih.gov/pubmed/22865734
http://dx.doi.org/10.1534/genetics.112.141846
_version_ 1782244511907315712
author Lukić, Sergio
Hey, Jody
author_facet Lukić, Sergio
Hey, Jody
author_sort Lukić, Sergio
collection PubMed
description We present an implementation of a recently introduced method for estimating the allele-frequency spectrum under the diffusion approximation. For single-nucleotide polymorphism (SNP) frequency data from multiple populations, the method computes numerical solutions to the allele-frequency spectrum (AFS) under a complex model that includes population splitting events, migration, population expansion, and admixture. The solution to the diffusion partial differential equation (PDE) that mimics the evolutionary process is found by means of truncated polynomial expansions. In the absence of gene flow, our computation of frequency spectra yields exact results. The results are compared to those that use a finite-difference method and to forward diffusion simulations. In general, all the methods yield comparable results, although the polynomial-based approach is the most accurate in the weak-migration limit. Also, the economical use of memory attained by the polynomial expansions makes the study of models with four populations possible for the first time. The method was applied to a four-population model of the human expansion out of Africa and the peopling of the Americas, using the Environmental Genome Project (EGP) SNP database. Although our confidence intervals largely overlapped previous analyses of these data, some were significantly different. In particular, estimates of migration among African, European, and Asian populations were considerably lower than those in a previous study and the estimated time of migration out of Africa was earlier. The estimated time of founding of a human population outside of Africa was 52,000 years (95% confidence interval: 36,000–80,800 years).
format Online
Article
Text
id pubmed-3454885
institution National Center for Biotechnology Information
language English
publishDate 2012
publisher Genetics Society of America
record_format MEDLINE/PubMed
spelling pubmed-34548852012-10-03 Demographic Inference Using Spectral Methods on SNP Data, with an Analysis of the Human Out-of-Africa Expansion Lukić, Sergio Hey, Jody Genetics Investigations We present an implementation of a recently introduced method for estimating the allele-frequency spectrum under the diffusion approximation. For single-nucleotide polymorphism (SNP) frequency data from multiple populations, the method computes numerical solutions to the allele-frequency spectrum (AFS) under a complex model that includes population splitting events, migration, population expansion, and admixture. The solution to the diffusion partial differential equation (PDE) that mimics the evolutionary process is found by means of truncated polynomial expansions. In the absence of gene flow, our computation of frequency spectra yields exact results. The results are compared to those that use a finite-difference method and to forward diffusion simulations. In general, all the methods yield comparable results, although the polynomial-based approach is the most accurate in the weak-migration limit. Also, the economical use of memory attained by the polynomial expansions makes the study of models with four populations possible for the first time. The method was applied to a four-population model of the human expansion out of Africa and the peopling of the Americas, using the Environmental Genome Project (EGP) SNP database. Although our confidence intervals largely overlapped previous analyses of these data, some were significantly different. In particular, estimates of migration among African, European, and Asian populations were considerably lower than those in a previous study and the estimated time of migration out of Africa was earlier. The estimated time of founding of a human population outside of Africa was 52,000 years (95% confidence interval: 36,000–80,800 years). Genetics Society of America 2012-10 /pmc/articles/PMC3454885/ /pubmed/22865734 http://dx.doi.org/10.1534/genetics.112.141846 Text en Copyright © 2012 by the Genetics Society of America Available freely online through the author-supported open access option.
spellingShingle Investigations
Lukić, Sergio
Hey, Jody
Demographic Inference Using Spectral Methods on SNP Data, with an Analysis of the Human Out-of-Africa Expansion
title Demographic Inference Using Spectral Methods on SNP Data, with an Analysis of the Human Out-of-Africa Expansion
title_full Demographic Inference Using Spectral Methods on SNP Data, with an Analysis of the Human Out-of-Africa Expansion
title_fullStr Demographic Inference Using Spectral Methods on SNP Data, with an Analysis of the Human Out-of-Africa Expansion
title_full_unstemmed Demographic Inference Using Spectral Methods on SNP Data, with an Analysis of the Human Out-of-Africa Expansion
title_short Demographic Inference Using Spectral Methods on SNP Data, with an Analysis of the Human Out-of-Africa Expansion
title_sort demographic inference using spectral methods on snp data, with an analysis of the human out-of-africa expansion
topic Investigations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3454885/
https://www.ncbi.nlm.nih.gov/pubmed/22865734
http://dx.doi.org/10.1534/genetics.112.141846
work_keys_str_mv AT lukicsergio demographicinferenceusingspectralmethodsonsnpdatawithananalysisofthehumanoutofafricaexpansion
AT heyjody demographicinferenceusingspectralmethodsonsnpdatawithananalysisofthehumanoutofafricaexpansion