Recently, large whole-genome sequencing projects have provided access to much
of the rare variation in human populations. This variation is highly
informative about population structure and recent demography. In this paper, we
show how the age of rare variants can be estimated from patterns of haplotype
sharing and how this information can detect and quantify historical
relationships between populations. We investigate the distribution of the age
of f2 variants in a worldwide sample sequenced by the 1,000 Genomes Project,
revealing enormous variation across populations. The median age of f2 variants
shared within continents is 50 to 160 generations for Europe and Asia, and 170
to 320 generations for Africa. Variants shared between continents are much
older with median ages ranging from 320 to 670 generations between Europe and
Asia, and 1,000 to 2,400 generations between African and Non-African
populations. The distribution of the ages of variants shared across populations
is informative about their demography, revealing recent bottlenecks, ancient
splits, and more modern connections between populations. We see the signature
of selection in the observation that functional variants are significantly
younger than nonfunctional variants of the same frequency. This approach is
relatively insensitive to mutation rate and complements other nonparametric
methods for demographic inference.
%0 Generic
%1 mathieson2014demography
%A Mathieson, Iain
%A McVean, Gil
%D 2014
%K demographic_inference human_genome population_genomics rare_variation
%T Demography and the age of rare variants
%U http://arxiv.org/abs/1401.4181
%X Recently, large whole-genome sequencing projects have provided access to much
of the rare variation in human populations. This variation is highly
informative about population structure and recent demography. In this paper, we
show how the age of rare variants can be estimated from patterns of haplotype
sharing and how this information can detect and quantify historical
relationships between populations. We investigate the distribution of the age
of f2 variants in a worldwide sample sequenced by the 1,000 Genomes Project,
revealing enormous variation across populations. The median age of f2 variants
shared within continents is 50 to 160 generations for Europe and Asia, and 170
to 320 generations for Africa. Variants shared between continents are much
older with median ages ranging from 320 to 670 generations between Europe and
Asia, and 1,000 to 2,400 generations between African and Non-African
populations. The distribution of the ages of variants shared across populations
is informative about their demography, revealing recent bottlenecks, ancient
splits, and more modern connections between populations. We see the signature
of selection in the observation that functional variants are significantly
younger than nonfunctional variants of the same frequency. This approach is
relatively insensitive to mutation rate and complements other nonparametric
methods for demographic inference.
@misc{mathieson2014demography,
abstract = {Recently, large whole-genome sequencing projects have provided access to much
of the rare variation in human populations. This variation is highly
informative about population structure and recent demography. In this paper, we
show how the age of rare variants can be estimated from patterns of haplotype
sharing and how this information can detect and quantify historical
relationships between populations. We investigate the distribution of the age
of f2 variants in a worldwide sample sequenced by the 1,000 Genomes Project,
revealing enormous variation across populations. The median age of f2 variants
shared within continents is 50 to 160 generations for Europe and Asia, and 170
to 320 generations for Africa. Variants shared between continents are much
older with median ages ranging from 320 to 670 generations between Europe and
Asia, and 1,000 to 2,400 generations between African and Non-African
populations. The distribution of the ages of variants shared across populations
is informative about their demography, revealing recent bottlenecks, ancient
splits, and more modern connections between populations. We see the signature
of selection in the observation that functional variants are significantly
younger than nonfunctional variants of the same frequency. This approach is
relatively insensitive to mutation rate and complements other nonparametric
methods for demographic inference.},
added-at = {2014-02-03T18:30:31.000+0100},
author = {Mathieson, Iain and McVean, Gil},
biburl = {https://www.bibsonomy.org/bibtex/24f9f6ae6e84a0ab5155d745730f31c41/peter.ralph},
interhash = {44eda52fb229754f511656963d403788},
intrahash = {4f9f6ae6e84a0ab5155d745730f31c41},
keywords = {demographic_inference human_genome population_genomics rare_variation},
note = {cite arxiv:1401.4181},
timestamp = {2014-02-03T18:30:31.000+0100},
title = {Demography and the age of rare variants},
url = {http://arxiv.org/abs/1401.4181},
year = 2014
}