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Stacks: an analysis tool set for population genomics
Massively parallel short‐read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data isExpand
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Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences
Advances in sequencing technology provide special opportunities for genotyping individuals with speed and thrift, but the lack of software to automate the calling of tens of thousands of genotypesExpand
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Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
Single nucleotide polymorphism (SNP) discovery and genotyping are essential to genetic mapping. There remains a need for a simple, inexpensive platform that allows high-density SNP discovery andExpand
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Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags
Next-generation sequencing technology provides novel opportunities for gathering genome-scale sequence data in natural populations, laying the empirical foundation for the evolving field ofExpand
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Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers.
Restriction site associated DNA (RAD) tags are a genome-wide representation of every site of a particular restriction enzyme by short DNA tags. Most organisms segregate large numbers of DNA sequenceExpand
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Resolving postglacial phylogeography using high-throughput sequencing
The distinction between model and nonmodel organisms is becoming increasingly blurred. High-throughput, second-generation sequencing approaches are being applied to organisms based on theirExpand
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Parallel genetic basis for repeated evolution of armor loss in Alaskan threespine stickleback populations.
Most adaptation is thought to occur through the fixation of numerous alleles at many different loci. Consequently, the independent evolution of similar phenotypes is predicted to occur throughExpand
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The population structure and recent colonization history of Oregon threespine stickleback determined using restriction‐site associated DNA‐sequencing
Understanding how genetic variation is partitioned across genomes within and among populations is a fundamental problem in ecological and evolutionary genetics. To address this problem, we studiedExpand
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Subfunction partitioning, the teleost radiation and the annotation of the human genome.
Half of all vertebrate species are teleost fish. What accounts for this explosion of biodiversity? Recent evidence and advances in evolutionary theory suggest that genomic features could have playedExpand
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Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes
Population genomic studies are beginning to provide a more comprehensive view of dynamic genome-scale processes in evolution. Patterns of genomic architecture, such as genomic islands of increasedExpand
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