Assessing population differentiation and isolation from single-nucleotide polymorphism data
We introduce a new, hierarchical, model for single-nucleotide polymorphism allele frequencies in a structured population, which is naturally fitted via Markov chain Monte Carlo methods. There is one parameter for each population, closely analogous to a population-specific version of Wright's FS...
Published in: | Journal of the Royal Statistical Society: Series B (Statistical Methodology) |
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ftuloxford:oai:ora.ox.ac.uk:uuid:e965c92d-8c2d-46d8-8538-9d242f6e97c2 2023-05-15T16:50:52+02:00 Assessing population differentiation and isolation from single-nucleotide polymorphism data Nicholson, G Smith, A Jonsson, F Gustafsson, O Stefansson, K Donnelly, P 2016-07-29 https://doi.org/10.1111/1467-9868.00357 https://ora.ox.ac.uk/objects/uuid:e965c92d-8c2d-46d8-8538-9d242f6e97c2 unknown doi:10.1111/1467-9868.00357 https://ora.ox.ac.uk/objects/uuid:e965c92d-8c2d-46d8-8538-9d242f6e97c2 https://doi.org/10.1111/1467-9868.00357 info:eu-repo/semantics/embargoedAccess Conference item 2016 ftuloxford https://doi.org/10.1111/1467-9868.00357 2022-06-28T20:26:57Z We introduce a new, hierarchical, model for single-nucleotide polymorphism allele frequencies in a structured population, which is naturally fitted via Markov chain Monte Carlo methods. There is one parameter for each population, closely analogous to a population-specific version of Wright's FST, which can be interpreted as measuring how isolated the relevant population has been. Our model includes the effects of single-nucleotide polymorphism ascertainment and is motivated by population genetics considerations, explicitly in the transient setting after divergence of populations, rather than as the equilibrium of a stochastic model, as is traditionally the case. For the sizes of data set that we consider the method provides good parameter estimates and considerably outperforms estimation methods analogous to those currently used in practice. We apply the method to one new and one existing human data set, each with rather different characteristics - the first consisting of three rather close European populations; the second of four populations taken from across the globe. A novelty of our framework is that the fit of the underlying model can be assessed easily, and these results are encouraging for both data sets analysed. Our analysis suggests that Iceland is more differentiated than the other two European populations (France and Utah), a finding which is consistent with the historical record, but not obvious from comparisons of simple summary statistics. Conference Object Iceland ORA - Oxford University Research Archive Journal of the Royal Statistical Society: Series B (Statistical Methodology) 64 4 695 715 |
institution |
Open Polar |
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ORA - Oxford University Research Archive |
op_collection_id |
ftuloxford |
language |
unknown |
description |
We introduce a new, hierarchical, model for single-nucleotide polymorphism allele frequencies in a structured population, which is naturally fitted via Markov chain Monte Carlo methods. There is one parameter for each population, closely analogous to a population-specific version of Wright's FST, which can be interpreted as measuring how isolated the relevant population has been. Our model includes the effects of single-nucleotide polymorphism ascertainment and is motivated by population genetics considerations, explicitly in the transient setting after divergence of populations, rather than as the equilibrium of a stochastic model, as is traditionally the case. For the sizes of data set that we consider the method provides good parameter estimates and considerably outperforms estimation methods analogous to those currently used in practice. We apply the method to one new and one existing human data set, each with rather different characteristics - the first consisting of three rather close European populations; the second of four populations taken from across the globe. A novelty of our framework is that the fit of the underlying model can be assessed easily, and these results are encouraging for both data sets analysed. Our analysis suggests that Iceland is more differentiated than the other two European populations (France and Utah), a finding which is consistent with the historical record, but not obvious from comparisons of simple summary statistics. |
format |
Conference Object |
author |
Nicholson, G Smith, A Jonsson, F Gustafsson, O Stefansson, K Donnelly, P |
spellingShingle |
Nicholson, G Smith, A Jonsson, F Gustafsson, O Stefansson, K Donnelly, P Assessing population differentiation and isolation from single-nucleotide polymorphism data |
author_facet |
Nicholson, G Smith, A Jonsson, F Gustafsson, O Stefansson, K Donnelly, P |
author_sort |
Nicholson, G |
title |
Assessing population differentiation and isolation from single-nucleotide polymorphism data |
title_short |
Assessing population differentiation and isolation from single-nucleotide polymorphism data |
title_full |
Assessing population differentiation and isolation from single-nucleotide polymorphism data |
title_fullStr |
Assessing population differentiation and isolation from single-nucleotide polymorphism data |
title_full_unstemmed |
Assessing population differentiation and isolation from single-nucleotide polymorphism data |
title_sort |
assessing population differentiation and isolation from single-nucleotide polymorphism data |
publishDate |
2016 |
url |
https://doi.org/10.1111/1467-9868.00357 https://ora.ox.ac.uk/objects/uuid:e965c92d-8c2d-46d8-8538-9d242f6e97c2 |
genre |
Iceland |
genre_facet |
Iceland |
op_relation |
doi:10.1111/1467-9868.00357 https://ora.ox.ac.uk/objects/uuid:e965c92d-8c2d-46d8-8538-9d242f6e97c2 https://doi.org/10.1111/1467-9868.00357 |
op_rights |
info:eu-repo/semantics/embargoedAccess |
op_doi |
https://doi.org/10.1111/1467-9868.00357 |
container_title |
Journal of the Royal Statistical Society: Series B (Statistical Methodology) |
container_volume |
64 |
container_issue |
4 |
container_start_page |
695 |
op_container_end_page |
715 |
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1766040988078309376 |