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DILS : Demographic Inferences with Linked Selection by using ABC

Christelle Fraïsse, Iva Popovic, Clément Mazoyer, Jonathan Romiguier, Étienne Loire, Alexis Simon, Nicolas Galtier, Laurent Duret, Nicolas Bierne, Xavier Vekemans, Camille Roux
doi: https://doi.org/10.1101/2020.06.15.151597
Christelle Fraïsse
1Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
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Iva Popovic
2School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
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Clément Mazoyer
3Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
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Jonathan Romiguier
4ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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Étienne Loire
5Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR, ASTRE, Montpellier, France
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Alexis Simon
4ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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Nicolas Galtier
4ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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Laurent Duret
6Laboratoire de Biologie et Biométrie Évolutive CNRS UMR 5558, Université Claude Bernard Lyon 1, Lyon, France
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Nicolas Bierne
4ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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Xavier Vekemans
3Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
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Camille Roux
3Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
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  • For correspondence: camille.roux.1983@gmail.com
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ABSTRACT

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 datasets and performs three types of analyses in a hierarchical manner, identifying: 1) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, 2) the best genomic model to determine whether the effective size Ne and migration rate N.m are heterogeneously distributed along the genome and 3) 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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ✉ christelle.fraisse{at}ist.ac.at; camille.roux{at}univ-lille.fr

  • https://github.com/popgenomics/DILS_web

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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DILS : Demographic Inferences with Linked Selection by using ABC
Christelle Fraïsse, Iva Popovic, Clément Mazoyer, Jonathan Romiguier, Étienne Loire, Alexis Simon, Nicolas Galtier, Laurent Duret, Nicolas Bierne, Xavier Vekemans, Camille Roux
bioRxiv 2020.06.15.151597; doi: https://doi.org/10.1101/2020.06.15.151597
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DILS : Demographic Inferences with Linked Selection by using ABC
Christelle Fraïsse, Iva Popovic, Clément Mazoyer, Jonathan Romiguier, Étienne Loire, Alexis Simon, Nicolas Galtier, Laurent Duret, Nicolas Bierne, Xavier Vekemans, Camille Roux
bioRxiv 2020.06.15.151597; doi: https://doi.org/10.1101/2020.06.15.151597

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