Journal ArticleDOI
Sequencing pools of individuals — mining genome-wide polymorphism data without big funding
TLDR
This Review demonstrates the breadth of questions that are being addressed by Pool-seq but also discusses its limitations and provides guidelines for users.Abstract:
The analysis of polymorphism data is becoming increasingly important as a complementary tool to classical genetic analyses. Nevertheless, despite plunging sequencing costs, genomic sequencing of individuals at the population scale is still restricted to a few model species. Whole-genome sequencing of pools of individuals (Pool-seq) provides a cost-effective alternative to sequencing individuals separately. With the availability of custom-tailored software tools, Pool-seq is being increasingly used for population genomic research on both model and non-model organisms. In this Review, we not only demonstrate the breadth of questions that are being addressed by Pool-seq but also discuss its limitations and provide guidelines for users.read more
Citations
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Journal ArticleDOI
Harnessing the power of RADseq for ecological and evolutionary genomics
TL;DR: This Review provides a comprehensive discussion of RADseq methods to aid researchers in choosing among the many different approaches and avoiding erroneous scientific conclusions from RADseq data, a problem that has plagued other genetic marker types in the past.
Journal ArticleDOI
A practical guide to environmental association analysis in landscape genomics
TL;DR: Expected future directions in the field of landscape genomics are summarized, such as the extension of statistical approaches, environmental association analysis for ecological gene annotation, and the need for replication and post hoc validation studies.
Journal ArticleDOI
A genomic perspective on hybridization and speciation.
TL;DR: It is argued that converting genomic patterns into useful inferences about hybridization will ultimately require models and methods that directly incorporate key ingredients of speciation, including the dynamic nature of gene flow, selection acting in hybrid populations and recombination rate variation.
Journal ArticleDOI
Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow.
Mark Ravinet,Mark Ravinet,Rui Faria,Rui Faria,Rui Faria,Roger K. Butlin,Roger K. Butlin,Juan Galindo,Nicolas Bierne,Marina Rafajlović,Mohamed A. F. Noor,Bernhard Mehlig,Anja M. Westram +12 more
TL;DR: It is argued that the availability of promising technical and analytical methods will shed further light on the important roles that gene flow and divergent selection have in shaping the genomic landscape of speciation and proposes a road map for future speciation research.
Journal ArticleDOI
Making sense of genomic islands of differentiation in light of speciation.
Jochen B. W. Wolf,Hans Ellegren +1 more
TL;DR: This Review explores methodological trends in speciation genomic studies, highlights the difficulty in separating processes related to speciation from those emerging from genome-wide properties that are not related to reproductive isolation, and provides a set of suggestions for future work in this area.
References
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TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
Journal ArticleDOI
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Cutadapt removes adapter sequences from high-throughput sequencing reads
TL;DR: The command-line tool cutadapt is developed, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features.
Journal ArticleDOI
RNA-Seq: a revolutionary tool for transcriptomics
TL;DR: The RNA-Seq approach to transcriptome profiling that uses deep-sequencing technologies provides a far more precise measurement of levels of transcripts and their isoforms than other methods.
Journal ArticleDOI
A framework for variation discovery and genotyping using next-generation DNA sequencing data
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