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Updated: May 21, 2026
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Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
Published on: August 29, 2014
Population genomic analysis of model and nonmodel organisms using sequenced RAD tags
Paul A Hohenlohe1, Julian Catchen, William A Cresko
1Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR, USA.
Methods in Molecular Biology (Clifton, N.J.)
|June 6, 2012
Summary
Restriction site Associated DNA (RAD) sequencing revolutionizes population genomics by enabling genome-wide genetic variation analysis at low cost. This method, coupled with the Stacks software, facilitates evolutionary genetic studies in diverse organisms, even without a reference genome.
Area of Science:
- Evolutionary biology
- Population genomics
- Genetics
Background:
- Evolutionary processes like mutation and selection shape genetic variation across genomes.
- Population genomics offers genome-scale insights into these processes, expanding beyond model organisms.
- High-throughput sequencing technologies are crucial for advancing population genomics.
Purpose of the Study:
- To introduce Restriction site Associated DNA (RAD) sequencing as a cost-effective method for population genomics.
- To demonstrate how RAD sequencing, combined with the Stacks software, can analyze genetic variation in diverse species.
- To discuss the conceptual framework and bioinformatic challenges in population genomics using next-generation sequencing (NGS) data.
Main Methods:
- Development and application of Restriction site Associated DNA (RAD) sequencing using Illumina NGS.
- Utilizing the Stacks computational pipeline for analyzing RAD sequencing data.
- Comparing NGS data analysis with traditional marker-based approaches.
Main Results:
- RAD sequencing enables typing of hundreds of thousands of single nucleotide polymorphism (SNP) markers in numerous individuals affordably.
- The Stacks software supports RAD sequencing data analysis for organisms with or without a reference genome.
- Advances in data gathering are outpacing analytical tools for population genomics.
Conclusions:
- RAD sequencing significantly lowers the barrier to genome-wide genetic variation studies in evolutionary genetics.
- The Stacks pipeline provides a valuable tool for analyzing RAD-seq data, promoting broader application.
- Future research must focus on developing advanced analytical methods to fully leverage NGS data in population genomics.
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