Journal ArticleDOI
Detecting natural selection in genomic data.
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TLDR
A comprehensive outline of evolutionary genomics methods is provided, highlighting the importance of functional follow-up studies to characterize putative selected alleles and the use of selection scans as hypothesis-generating tools for investigating evolutionary histories.Abstract:
The past fifty years have seen the development and application of numerous statistical methods to identify genomic regions that appear to be shaped by natural selection. These methods have been used to investigate the macro- and microevolution of a broad range of organisms, including humans. Here, we provide a comprehensive outline of these methods, explaining their conceptual motivations and statistical interpretations. We highlight areas of recent and future development in evolutionary genomics methods and discuss ongoing challenges for researchers employing such tests. In particular, we emphasize the importance of functional follow-up studies to characterize putative selected alleles and the use of selection scans as hypothesis-generating tools for investigating evolutionary histories.read more
Citations
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Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
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An Expanded View of Complex Traits: From Polygenic to Omnigenic
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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.
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Stefan Washietl,Pouya Kheradpour,Jason Ernst,Lucas D. Ward,Irwin Jungreis,Matthew D. Rasmussen,Manolis Kellis +6 more
TL;DR: The comparison of related genomes has emerged as a powerful lens for genome interpretation as mentioned in this paper, which reveals a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons.
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Fundamentals of molecular evolution
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References
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Journal Article
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
Journal ArticleDOI
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
TL;DR: The relationship between the two estimates of genetic variation at the DNA level, namely the number of segregating sites and the average number of nucleotide differences estimated from pairwise comparison, is investigated in this article.
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.
Journal ArticleDOI
Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection.
TL;DR: It is found that the polymorphic patterns in a DNA sample under logistic population growth and genetic hitchhiking are very similar and that one of the newly developed tests, Fs, is considerably more powerful than existing tests for rejecting the hypothesis of neutrality of mutations.
Journal ArticleDOI
Statistical tests of neutrality of mutations
Yunxin Fu,Wen-Hsiung Li +1 more
TL;DR: From these properties, several new statistical tests based on a random sample of DNA sequences from the population are developed for testing the hypothesis that all mutations at a locus are neutral.
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