Category Archives: methods

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

RedditDiggMendeleyPocketShare and Enjoy
Posted in genomics, methods, natural history, next generation sequencing, phylogenetics, phylogeography, population genetics | Tagged , , , , , | Leave a comment

The Molecular Ecologist’s Survey on High-Throughput Sequencing

Last week we updated the Field Guide to Next Generation DNA Sequencers to better reflect the sequencing techniques of 2016. The NGS Field Guide is one of the most popular resources on the Molecular Ecologist web site, but we don’t know much about how our readers use … Continue reading

Posted in bioinformatics, genomics, methods, next generation sequencing | Tagged , , , , | 2 Comments

The 2016 Next-Generation Sequencing Field Guide Preview: Zombie Systems and New Hope

After a year of minimal activity, we finally have some significant changes in Next Gen Land. In the 2016 update of the NGS Field Guide, I will continue to give my overall interpretation about the various instruments, but with less … Continue reading

Posted in genomics, howto, methods, RNAseq, transcriptomics | Tagged , , , | 6 Comments

To find duplicated loci in vertebrate polyploids, try thinking small

Big sequencing efforts have gone a long way to help understand the complexities of polyploidy. However, the bioinformatic approaches to sorting and scoring alleles in next-gen data are generally designed for easy of use in diploid species. Unlike a diploid species, where … Continue reading

Posted in genomics, methods, next generation sequencing, Uncategorized | 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

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

A statement on p-values that approaches significance*

Point-oh-five. It’s a pretty polarizing number. Sitting on either side of it could mean the difference between a [insert your favorite journal here] paper and an unpublished paper. But why do some researchers, reviewers, and journal editors put so much weight on this highly … Continue reading

Posted in methods, science publishing | Tagged , , | 2 Comments

The Evolution of Molecular Dating

Molecular dating is a key tool in deciphering the history of life. In a recent Molecular Biology and Evolution paper, Sudhir Kumar and Blair Hedges have reviewed the state of the subject, summarizing the philosophical and methodological history of this … Continue reading

Posted in genomics, methods, phylogenetics, Uncategorized | Tagged | Leave a comment