SLiM: Simulating Evolution with Selection and Linkage
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TLDR
SLiM as mentioned in this paper is an efficient forward population genetic simulation designed for studying the effects of linkage and selection on a chromosome-wide scale, which can incorporate complex scenarios of demography and population substructure.Abstract:
SLiM is an efficient forward population genetic simulation designed for studying the effects of linkage and selection on a chromosome-wide scale. The program can incorporate complex scenarios of demography and population substructure, various models for selection and dominance of new mutations, arbitrary gene structure, and user-defined recombination maps.read more
Citations
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Journal ArticleDOI
Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection
Antonio F. Pardiñas,Peter Holmans,Andrew Pocklington,Valentina Escott-Price,Stephan Ripke,Stephan Ripke,Noa Carrera,Sophie E. Legge,Sophie Bishop,D. F. Cameron,Marian L. Hamshere,Jun Han,Leon Hubbard,Amy Lynham,Kiran Kumar Mantripragada,Elliott Rees,James H. MacCabe,Steven A. McCarroll,Bernhard T. Baune,Gerome Breen,Gerome Breen,Enda M. Byrne,Udo Dannlowski,Thalia C. Eley,Caroline Hayward,Nicholas G. Martin,Nicholas G. Martin,Andrew M. McIntosh,Robert Plomin,David J. Porteous,Naomi R. Wray,Armando Caballero,Daniel H. Geschwind,Laura M. Huckins,Douglas M. Ruderfer,Enrique Santiago,Pamela Sklar,Eli A. Stahl,Hyejung Won,Esben Agerbo,Esben Agerbo,Thomas Damm Als,Thomas Damm Als,Ole A. Andreassen,Ole A. Andreassen,Marie Bækvad-Hansen,Marie Bækvad-Hansen,Preben Bo Mortensen,Preben Bo Mortensen,Carsten Bøcker Pedersen,Carsten Bøcker Pedersen,Anders D. Børglum,Anders D. Børglum,Jonas Bybjerg-Grauholm,Jonas Bybjerg-Grauholm,Srdjan Djurovic,Srdjan Djurovic,Naser Durmishi,Marianne Giørtz Pedersen,Marianne Giørtz Pedersen,Vera Golimbet,Jakob Grove,David M. Hougaard,David M. Hougaard,Manuel Mattheisen,Manuel Mattheisen,Espen Molden,Ole Mors,Ole Mors,Merete Nordentoft,Merete Nordentoft,Milica Pejovic-Milovancevic,Engilbert Sigurdsson,Teimuraz Silagadze,Christine Søholm Hansen,Christine Søholm Hansen,Kari Stefansson,Hreinn Stefansson,Stacy Steinberg,Sarah Tosato,Thomas Werge,Thomas Werge,Thomas Werge,David A. Collier,David A. Collier,Dan Rujescu,Dan Rujescu,George Kirov,Michael J. Owen,Michael Conlon O'Donovan,James T.R. Walters +90 more
TL;DR: A new genome-wide association study of schizophrenia is reported, and through meta-analysis with existing data and integrating genomic fine-mapping with brain expression and chromosome conformation data, 50 novel associated loci and 145 loci are identified.
Journal ArticleDOI
SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model
TL;DR: SLiM 3 is introduced, which contains two key advancements aimed at abolishing limitations in the Wright–Fisher model, and adds support for continuous space, including spatial interactions and spatial maps of environmental variables.
Journal ArticleDOI
Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila.
TL;DR: This work hypothesized that environmental fluctuations among seasons in a North American orchard would impose temporally variable selection on Drosophila melanogaster that would drive repeatable adaptive oscillations at balanced polymorphisms, and identified hundreds of polymorphisms whose frequency oscillates among seasons and argued that these loci are subject to strong, temporal variable selection.
Journal ArticleDOI
Determinants of genetic diversity
Hans Ellegren,Nicolas Galtier +1 more
TL;DR: Comparative population genomics is on its way to providing a solution to 'Lewontin's paradox' — the discrepancy between the many orders of magnitude of variation in population size and the much narrower distribution of diversity levels.
Journal ArticleDOI
Linkage disequilibrium-dependent architecture of human complex traits shows action of negative selection.
Steven Gazal,Hilary K. Finucane,Hilary K. Finucane,Hilary K. Finucane,Nicholas A. Furlotte,Po-Ru Loh,Po-Ru Loh,Pier Francesco Palamara,Pier Francesco Palamara,Xuanyao Liu,Xuanyao Liu,Armin P. Schoech,Armin P. Schoech,Brendan Bulik-Sullivan,Benjamin M. Neale,Benjamin M. Neale,Alexander Gusev,Alexander Gusev,Alkes L. Price,Alkes L. Price +19 more
TL;DR: It is determined that SNPs with low LLD have significantly larger per-SNP heritability and that roughly half of this effect can be explained by functional annotations negatively correlated with LLD, such as DNase I hypersensitivity sites (DHSs).
References
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Book
The Neutral Theory of Molecular Evolution
TL;DR: The neutral theory as discussed by the authors states that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random drift of selectively neutral mutants, which has caused controversy ever since.
The neutral theory of molecular evolution.
TL;DR: The neutral theory as mentioned in this paper states that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random drift of selectively neutral mutants, which has caused controversy ever since.
Journal ArticleDOI
Generating samples under a Wright-Fisher neutral model of genetic variation.
TL;DR: A Monte Carlo computer program is available to generate samples drawn from a population evolving according to a Wright-Fisher neutral model, and the samples produced can be used to investigate the sampling properties of any sample statistic under these neutral models.
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