Tag Archives: RADseq

Genetic Rescue – Fitness and genomic consequences

Posted on 22 Sep, 2020 by Kathleen Grogan

As a PhD student studying the effects of genetic diversity overall and immunogenetic diversity specifically on survival and reproductive success in an endangered primate in captive and wild populations, I thought a lot about the potential effects of inbreeding and … Continue reading →

Posted in conservation, genomics, hybridization | Tagged fish, fitness, Genetic rescue, hybridization, RADseq | Leave a comment

To RADseq or not to RADseq?

Posted on 17 Apr, 2017 by Jeremy Yoder

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 →

Posted in adaptation, association genetics, genomics, methods, next generation sequencing, selection | Tagged poolseq, RADseq, reduced-representation sequencing, transcriptome sequencing, whole-genome sequencing | 8 Comments

The trouble with PCR duplicates

Posted on 25 Aug, 2016 by Reid Brennan

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 →

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

RADseq and missing data: some considerations

Posted on 10 May, 2016 by Ethan Linck

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 →

Posted in bioinformatics, genomics, methods, Molecular Ecology, the journal, next generation sequencing, phylogenetics, population genetics, theory | Tagged ddRADseq, missing data, null alleles, RADseq | 6 Comments

hyRAD and museum genomics

Posted on 5 Apr, 2016 by Ethan Linck

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 →

Posted in genomics, methods, natural history, next generation sequencing, phylogenetics, phylogeography, population genetics | Tagged ddRADseq, hybridization RAD, hyRAD, museum genomics, RADseq, sequence capture | 3 Comments

RADseq vs. UCEs, round 3

Posted on 18 Mar, 2016 by Ethan Linck

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 →

Posted in bioinformatics, evolution, genomics, methods, next generation sequencing, phylogenetics | Tagged Piranga, RADseq, UCE, ultraconserved elements | 1 Comment

The 2016 Workshop on Genomics summary

Posted on 29 Feb, 2016 by Elin Videvall

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 →

Posted in bioinformatics, genomics, next generation sequencing | Tagged bioinformatics, genomics, NGS, RADseq, RNAseq, unix, workshop | Leave a comment

Earthquakes and rapid evolution

Posted on 7 Jan, 2016 by Arun Sethuraman

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 →

Posted in adaptation, evolution, genomics, natural history, next generation sequencing, phylogeography, population genetics, selection, STRUCTURE | Tagged ecological speciation, Evolution, hybridization, natural selection, population genetics, population structure, RADseq | Leave a comment

Comparing your options for phylogenomic data

Posted on 16 Dec, 2015 by Rob Denton

The choices for current-generation (last generation?) molecular markers are grouped in two primary camps. First, the “reduced representation” methods: take some DNA, cut it up with specific enzymes, tag those pieces, read the sequences. These methods produce lots and lots of … Continue reading →

Posted in methods, next generation sequencing, phylogenetics | Tagged phylogenomics, RADseq, UCE | 2 Comments

Isolation by Aesop's Fable in NYC mice

Posted on 2 Dec, 2015 by Rob Denton

The story goes like this: Town Mouse goes to visit his friend in the country. Town Mouse looks down his long nose at the food offered by Country Mouse, so he brings Country Mouse back to the city for a … Continue reading →

Posted in adaptation, population genetics | Tagged mice, RADseq, urbanization | Leave a comment