Tag Archives: ddRADseq

Urban Mice: NYC Study Sheds Light on Population Diversity and Changes

They may make subway riders shudder, but New York City mice are the stars of a cool new paper outlining their evolutionary history during a rapid period of urbanization. Scientists from the City University of New York used ddRAD-seq to … more »

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Building on a RAD Idea

It’s been a few years since the Hoekstra lab at Harvard first published its double-digest RAD-seq protocol. Since then, the approach has been rapidly adopted by the community for massively parallel genotyping, particularly of non-model organisms, and has been the … more »

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Urbanization shapes the demographic history of a native rodent (the white-footed mouse, Peromyscus leucopus) in New York City

April 2016 Authors: Stephen E. Harris, Alexander T. Xue, Diego Alvarado-Serrano, Joel T. Boehm, Tyler Joseph, Michael J. Hickerson, Jason Munshi-South Info: Researchers at the City University of New York studied populations of white-footed mice in New York City and … more »

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Patterns of genome-wide variation in Glossina fuscipes fuscipes tsetse flies from Uganda

April 2016 Authors: Gloria-Soria A, Dunn WA, Telleria EL, Evans BR, Okedi L, Echodu R, Warren WC, Montague MJ, Aksoy S, Caccone A Info: Researchers used ddRAD-seq to develop a panel of SNPs for use in population genomics or genome-wide … more »

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Harnessing the power of RADseq for ecological and evolutionary genomics

January 2016 Authors: Kimberly R. Andrews, Jeffrey M. Good, Michael R. Miller, Gordon Luikart and Paul A. Hohenlohe Info: In this protocol review, scientists examine several approaches to restriction site-associated DNA sequencing and present their findings on how to choose … more »

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EpiRADseq: scalable analysis of genomewide patterns of methylation using next-generation sequencing

August 2015 Authors: Drew R. Schield, Matthew R. Walsh, Daren C. Card, Audra L. Andrew, Richard H. Adams and Todd A. Castoe Info: University of Texas researchers present a new method for quantifying methylation patterns across whole genomes at low … more »

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Limitations of Climatic Data for Inferring Species Boundaries: Insights from Speckled Rattlesnakes

June 2015 Authors: Jesse M. Meik, Jeffrey W. Streicher, A. Michelle Lawing, Oscar Flores-Villela, and Matthew K. Fujita Info: In this paper, scientists in Texas and Mexico challenge conventional climate-based species boundaries in the speckled rattlesnake, using genomic and other … more »

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Double-digest RAD sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with nonmodel organisms

April 2015 Authors: Hans Recknagel, Arne Jacobs, Pawel Herzyk, Kathryn R Elmer Info: In this Molecular Ecology Resources paper, researchers from the University of Glasgow describe a protocol and adapters they developed for double-digest RAD sequencing on the Ion Torrent … more »

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Assessing the utility of whole genome amplified DNA for next-generation molecular ecology

February 2015 Authors: Christopher Blair, C. Ryan Campbell, and Anne D. Yoder Info: Scientists at Duke University explored whether whole-genome amplification leads to sequence bias by performing a ddRAD-seq study of grey mouse lemurs using multiple displacement amplification. They conclude … more »

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Genetic mapping of horizontal stripes in Lake Victoria cichlid fishes: benefits and pitfalls of using RAD markers for dense linkage mapping

August 2014 Authors: Frederico Henning, Hyuk Je Lee, Paolo Franchini and Axel Meyer Info: Scientists from the University of Konstanz in Germany use double-digest RADseq to determine the genetic basis for horizontal stripes seen on cichlid fishes. Sequencing was performed … more »

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