Literature DB >> 30590560

Evolutionary Modeling in SLiM 3 for Beginners.

Benjamin C Haller1, Philipp W Messer1.   

Abstract

The SLiM forward genetic simulation framework has proved to be a powerful and flexible tool for population genetic modeling. However, as a complex piece of software with many features that allow simulating a diverse assortment of evolutionary models, its initial learning curve can be difficult. Here we provide a step-by-step demonstration of how to build a simple evolutionary model in SLiM 3, to help new users get started. We will begin with a panmictic neutral model, and build up to a model of the evolution of a polygenic quantitative trait under selection for an environmental phenotypic optimum.
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Entities:  

Keywords:  QTL evolution; modeling tutorial; population genetic simulation

Mesh:

Year:  2019        PMID: 30590560      PMCID: PMC6501880          DOI: 10.1093/molbev/msy237

Source DB:  PubMed          Journal:  Mol Biol Evol        ISSN: 0737-4038            Impact factor:   16.240


  20 in total

Review 1.  An overview of population genetic data simulation.

Authors:  Xiguo Yuan; David J Miller; Junying Zhang; David Herrington; Yue Wang
Journal:  J Comput Biol       Date:  2011-12-09       Impact factor: 1.479

2.  SLiM: simulating evolution with selection and linkage.

Authors:  Philipp W Messer
Journal:  Genetics       Date:  2013-05-24       Impact factor: 4.562

Review 3.  Thinking too positive? Revisiting current methods of population genetic selection inference.

Authors:  Claudia Bank; Gregory B Ewing; Anna Ferrer-Admettla; Matthieu Foll; Jeffrey D Jensen
Journal:  Trends Genet       Date:  2014-11-19       Impact factor: 11.639

4.  SLiM 2: Flexible, Interactive Forward Genetic Simulations.

Authors:  Benjamin C Haller; Philipp W Messer
Journal:  Mol Biol Evol       Date:  2016-10-03       Impact factor: 16.240

5.  A C++ template library for efficient forward-time population genetic simulation of large populations.

Authors:  Kevin R Thornton
Journal:  Genetics       Date:  2014-06-20       Impact factor: 4.562

Review 6.  An overview of the utility of population simulation software in molecular ecology.

Authors:  Sean Hoban
Journal:  Mol Ecol       Date:  2014-04-30       Impact factor: 6.185

7.  The founding of Mauritian endemic coffee trees by a synchronous long-distance dispersal event.

Authors:  M D Nowak; B C Haller; A D Yoder
Journal:  J Evol Biol       Date:  2014-05-03       Impact factor: 2.411

8.  Simulation of genes and genomes forward in time.

Authors:  Antonio Carvajal-Rodríguez
Journal:  Curr Genomics       Date:  2010-03       Impact factor: 2.236

9.  Recombination Alters the Dynamics of Adaptation on Standing Variation in Laboratory Yeast Populations.

Authors:  Katya Kosheleva; Michael M Desai
Journal:  Mol Biol Evol       Date:  2018-01-01       Impact factor: 16.240

10.  asymptoticMK: A Web-Based Tool for the Asymptotic McDonald-Kreitman Test.

Authors:  Benjamin C Haller; Philipp W Messer
Journal:  G3 (Bethesda)       Date:  2017-05-05       Impact factor: 3.154

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  2 in total

1.  Genome-wide imputation using the practical haplotype graph in the heterozygous crop cassava.

Authors:  Evan M Long; Peter J Bradbury; M Cinta Romay; Edward S Buckler; Kelly R Robbins
Journal:  G3 (Bethesda)       Date:  2022-01-04       Impact factor: 3.542

2.  Controlling for Variable Transposition Rate with an Age-Adjusted Site Frequency Spectrum.

Authors:  Robert Horvath; Mitra Menon; Michelle Stitzer; Jeffrey Ross-Ibarra
Journal:  Genome Biol Evol       Date:  2022-02-04       Impact factor: 3.416

  2 in total

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