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. DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources, 21 (8), n.spéc. : 2629-2644.

Url - autres données associées : http://eep.univ-lille.fr/en/productions/dils-software / Url - autres données associées : https://github.com/popgenomics/DILS_web / Url - jeu de données - Entrepôt autre : https://cutt.ly/ErrDuwj

Quartile : Q1, Sujet : BIOCHEMISTRY & MOLECULAR BIOLOGY / Quartile : Q1, Sujet : ECOLOGY / Quartile : Q1, Sujet : EVOLUTIONARY BIOLOGY

Résumé : 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.

Mots-clés Agrovoc : génome, polymorphisme génétique, séquence nucléotidique, dynamique des populations, méthode statistique, génétique des populations, données statistiques, variation génétique, génomique, Mytilus, analyse de données, moule

Agences de financement hors UE : Austrian Science Fund

Auteurs et affiliations

• Fraïsse Christelle, Institute of Science and Technology Austria (AUT) - auteur correspondant
• Popovic Iva, Université de Lille (FRA)
• Mazoyer Clément, Université de Lille (FRA)
• Spataro Bruno, CNRS (FRA)
• Delmotte Stéphane, CNRS (FRA)
• Romiguier Jonathan, UM2 (FRA)
• Loire Etienne, CIRAD-BIOS-UMR ASTRE (FRA)
• Simon Alexis, Université de Montpellier (FRA)
• Galtier Nicolas, UM2 (FRA)
• Duret Laurent, Université Claude Bernard (FRA)
• Bierne Nicolas, CNRS (FRA)
• Vekemans Xavier, Université de Lille (FRA)
• Roux Camille, Université de Lille (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/605791/)

Métriques

[ Page générée et mise en cache le 2024-12-18 ]