Tag Archives: RADseq

To RADseq or not to RADseq?

It’s a cliche to say that we live in a moment of unprecedented possibility for molecular ecology, as high-throughput sequencing methods drive the cost of collecting DNA sequence data ever lower. But at the same time, it’s a tricky moment, … Continue reading

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Posted in adaptation, association genetics, genomics, methods, next generation sequencing, selection | Tagged , , , , | 7 Comments

The trouble with PCR duplicates

The sequencing center just sent your lane of Illumina data. You’re excited. Life is great. You begin to process the data. You align the data. You check for PCR duplicates. 50 percent. Half of your data is garbage. Everything is … Continue reading

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Posted in bioinformatics, genomics, methods, next generation sequencing | Tagged , , , | 6 Comments

RADseq and missing data: some considerations

Unlike Sanger sequencing, where loci are directly targeted for each individual and sequencing errors are relatively rare, massively multilocus datasets from next generation sequencing platforms are characterized by large amounts of missing data. This is particularly true for restriction digest … Continue reading

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Posted in bioinformatics, genomics, methods, Molecular Ecology, the journal, next generation sequencing, phylogenetics, population genetics, theory | Tagged , , , | 6 Comments

hyRAD and museum genomics

While the RAPTURE may have arrived, the development of novel restriction digest-based library prepartation techniques — and portmanteaus — continues unabated. In a paper published in PLoS ONE last month (and previously available as a preprint on bioRxiv), Tomasz Suchan … Continue reading

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Posted in genomics, methods, natural history, next generation sequencing, phylogenetics, phylogeography, population genetics | Tagged , , , , , | 3 Comments

RADseq vs. UCEs, round 3

Though reduced-representation genome sequencing (or high-throughput, or nextgen, or massively parallel sequencing, or…) has become standard practice for molecular ecology labs over the past few years, the relative merits of different library preparation methods remains an active area of research. … Continue reading

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Posted in bioinformatics, evolution, genomics, methods, next generation sequencing, phylogenetics | Tagged , , , | 1 Comment

The 2016 Workshop on Genomics summary

I recently had the pleasure to spend two and a half weeks in the beautiful medieval town of Český Krumlov, Czech Republic. The reason was the popular Workshop on Genomics that was running and I was one of the TAs … Continue reading

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Earthquakes and rapid evolution

The 1964 Alaskan earthquake was landscape-altering in creating/uplifting numerous islands in the Gulf of Alaska, providing an ideal system to study adaptive evolution of diversification in affected species – the threespine stickleback (Gasterosteus aculeatus) being a widely studied example. In … Continue reading

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Posted in adaptation, evolution, genomics, natural history, next generation sequencing, phylogeography, population genetics, selection, STRUCTURE | Tagged , , , , , , | Leave a comment