DILS: Demographic inferences with linked selection by using ABC
We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single-population or two-population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.
Main Authors: | , , , , , , , , , , , , |
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Format: | article biblioteca |
Language: | eng |
Subjects: | génome, polymorphisme génétique, séquence nucléotidique, dynamique des populations, méthode statistique, génétique des populations, données statistiques, variation génétique, génomique, Mytilus, analyse de données, moule, http://aims.fao.org/aos/agrovoc/c_3224, http://aims.fao.org/aos/agrovoc/c_24031, http://aims.fao.org/aos/agrovoc/c_27583, http://aims.fao.org/aos/agrovoc/c_6111, http://aims.fao.org/aos/agrovoc/c_7377, http://aims.fao.org/aos/agrovoc/c_34326, http://aims.fao.org/aos/agrovoc/c_35655, http://aims.fao.org/aos/agrovoc/c_15975, http://aims.fao.org/aos/agrovoc/c_92382, http://aims.fao.org/aos/agrovoc/c_5055, http://aims.fao.org/aos/agrovoc/c_15962, http://aims.fao.org/aos/agrovoc/c_5010, |
Online Access: | http://agritrop.cirad.fr/605791/ http://agritrop.cirad.fr/605791/1/ID605790.pdf |
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dig-cirad-fr-6057912024-04-25T08:26:02Z http://agritrop.cirad.fr/605791/ http://agritrop.cirad.fr/605791/ DILS: Demographic inferences with linked selection by using ABC. Fraïsse Christelle, Popovic Iva, Mazoyer Clément, Spataro Bruno, Delmotte Stéphane, Romiguier Jonathan, Loire Etienne, Simon Alexis, Galtier Nicolas, Duret Laurent, Bierne Nicolas, Vekemans Xavier, Roux Camille. 2021. Molecular Ecology Resources, 21 (8), n.spéc. : 2629-2644.https://doi.org/10.1111/1755-0998.13323 <https://doi.org/10.1111/1755-0998.13323> DILS: Demographic inferences with linked selection by using ABC Fraïsse, Christelle Popovic, Iva Mazoyer, Clément Spataro, Bruno Delmotte, Stéphane Romiguier, Jonathan Loire, Etienne Simon, Alexis Galtier, Nicolas Duret, Laurent Bierne, Nicolas Vekemans, Xavier Roux, Camille eng 2021 Molecular Ecology Resources génome polymorphisme génétique séquence nucléotidique dynamique des populations méthode statistique génétique des populations données statistiques variation génétique génomique Mytilus analyse de données moule http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_6111 http://aims.fao.org/aos/agrovoc/c_7377 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_35655 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_5055 http://aims.fao.org/aos/agrovoc/c_15962 http://aims.fao.org/aos/agrovoc/c_5010 We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single-population or two-population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/605791/1/ID605790.pdf text Cirad license info:eu-repo/semantics/restrictedAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1111/1755-0998.13323 10.1111/1755-0998.13323 info:eu-repo/semantics/altIdentifier/doi/10.1111/1755-0998.13323 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1111/1755-0998.13323 info:eu-repo/semantics/reference/purl/http://eep.univ-lille.fr/en/productions/dils-software info:eu-repo/semantics/reference/purl/https://github.com/popgenomics/DILS_web info:eu-repo/semantics/dataset/purl/https://cutt.ly/ErrDuwj |
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génome polymorphisme génétique séquence nucléotidique dynamique des populations méthode statistique génétique des populations données statistiques variation génétique génomique Mytilus analyse de données moule http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_6111 http://aims.fao.org/aos/agrovoc/c_7377 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_35655 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_5055 http://aims.fao.org/aos/agrovoc/c_15962 http://aims.fao.org/aos/agrovoc/c_5010 génome polymorphisme génétique séquence nucléotidique dynamique des populations méthode statistique génétique des populations données statistiques variation génétique génomique Mytilus analyse de données moule http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_6111 http://aims.fao.org/aos/agrovoc/c_7377 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_35655 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_5055 http://aims.fao.org/aos/agrovoc/c_15962 http://aims.fao.org/aos/agrovoc/c_5010 |
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génome polymorphisme génétique séquence nucléotidique dynamique des populations méthode statistique génétique des populations données statistiques variation génétique génomique Mytilus analyse de données moule http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_6111 http://aims.fao.org/aos/agrovoc/c_7377 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_35655 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_5055 http://aims.fao.org/aos/agrovoc/c_15962 http://aims.fao.org/aos/agrovoc/c_5010 génome polymorphisme génétique séquence nucléotidique dynamique des populations méthode statistique génétique des populations données statistiques variation génétique génomique Mytilus analyse de données moule http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_6111 http://aims.fao.org/aos/agrovoc/c_7377 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_35655 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_5055 http://aims.fao.org/aos/agrovoc/c_15962 http://aims.fao.org/aos/agrovoc/c_5010 Fraïsse, Christelle Popovic, Iva Mazoyer, Clément Spataro, Bruno Delmotte, Stéphane Romiguier, Jonathan Loire, Etienne Simon, Alexis Galtier, Nicolas Duret, Laurent Bierne, Nicolas Vekemans, Xavier Roux, Camille DILS: Demographic inferences with linked selection by using ABC |
description |
We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single-population or two-population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species. |
format |
article |
topic_facet |
génome polymorphisme génétique séquence nucléotidique dynamique des populations méthode statistique génétique des populations données statistiques variation génétique génomique Mytilus analyse de données moule http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_6111 http://aims.fao.org/aos/agrovoc/c_7377 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_35655 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_5055 http://aims.fao.org/aos/agrovoc/c_15962 http://aims.fao.org/aos/agrovoc/c_5010 |
author |
Fraïsse, Christelle Popovic, Iva Mazoyer, Clément Spataro, Bruno Delmotte, Stéphane Romiguier, Jonathan Loire, Etienne Simon, Alexis Galtier, Nicolas Duret, Laurent Bierne, Nicolas Vekemans, Xavier Roux, Camille |
author_facet |
Fraïsse, Christelle Popovic, Iva Mazoyer, Clément Spataro, Bruno Delmotte, Stéphane Romiguier, Jonathan Loire, Etienne Simon, Alexis Galtier, Nicolas Duret, Laurent Bierne, Nicolas Vekemans, Xavier Roux, Camille |
author_sort |
Fraïsse, Christelle |
title |
DILS: Demographic inferences with linked selection by using ABC |
title_short |
DILS: Demographic inferences with linked selection by using ABC |
title_full |
DILS: Demographic inferences with linked selection by using ABC |
title_fullStr |
DILS: Demographic inferences with linked selection by using ABC |
title_full_unstemmed |
DILS: Demographic inferences with linked selection by using ABC |
title_sort |
dils: demographic inferences with linked selection by using abc |
url |
http://agritrop.cirad.fr/605791/ http://agritrop.cirad.fr/605791/1/ID605790.pdf |
work_keys_str_mv |
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_version_ |
1798165104907255808 |