Category Archives: methods

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 , , , | 1 Comment

A statement on p-values that approaches significance*

Posted on 8 Mar, 2016 by Noah Snyder-Mackler

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 Sitting on either side of it could mean the difference between a [insert your favorite journal here] paper and an unpublished paper.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 , , | 3 Comments

The Evolution of Molecular Dating

Posted on 7 Mar, 2016 by Bryan McLean

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

Quick and dirty tree building in R

Posted on 26 Feb, 2016 by Ethan Linck

One of the major obstacles to turning your sequence data into phylogenetic trees is choosing (and learning) a tree-building program. Confounding this problem is the fact that most researchers will want to perform numerous, complementary analyses, each of which may … Continue reading →

Posted in howto, methods, phylogenetics, R, software | Tagged , , , , , , , | 3 Comments

Petrous bone is the new black

Posted on 22 Feb, 2016 by Patrícia Chrzanová Pečnerová

I was just reading an article about skeletal reconstruction of another fascinating extinct species when my supervisor came to my office. I asked: “How about we sequence this creature’s genome?” He replied by asking where the animal had lived. As … Continue reading →

Posted in genomics, methods, Paleogenomics | Tagged , , , | 4 Comments

Welcome to the Rapture

Posted on 16 Feb, 2016 by Reid Brennan

The advent of massively parallel, high throughput sequencing has undoubtedly revolutionized biology. However, have you ever wanted to run a parentage analysis, assess basic population structure, or perform any of the other countless applications where hundreds of thousands of SNPs … Continue reading →

Posted in methods, next generation sequencing | 2 Comments

Genomics of Hybridization – Part II, Top three of 2015

Posted on 28 Jan, 2016 by Arun Sethuraman

Death Valley pupfishes (Cyprinodon) are among the most endangered vertebrates on earth, with small inbred populations, with heavy risks of extinction in extreme environments. Martin et al. (2016) in a recent publication quantify diversity and adaptability in a very small population … Continue reading →

Posted in bioinformatics, conservation, genomics, methods, natural history, next generation sequencing, population genetics, R, software, speciation, STRUCTURE, theory | Tagged , , , , | Leave a comment

Genomics of Hybridization – Part 1

Posted on 21 Jan, 2016 by Arun Sethuraman

In a series of articles, I will discuss recent advances in hybridization genomics – the fundamentals of adaptive introgression, “islands of speciation”, differential gene flow, and linked selection have been discussed in my previous posts (here, here, and also at … Continue reading →

Posted in adaptation, evolution, genomics, methods, natural history, next generation sequencing, pedigree, phylogenetics, plants, population genetics, RNAseq, software, speciation, species delimitation, STRUCTURE, theory, transcriptomics | Tagged , , , , , , | 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 , , | 2 Comments

The biggest problem in landscape genetics and how to fix it

Posted on 11 Dec, 2015 by Rob Denton

Landscape genetics is a field that has expanded rapidly in recent years, but that doesn’t mean that it hasn’t gone without criticism. Perhaps the largest problem with landscape genetics (LG) studies is one of timing. If you observe genetic differentiation … Continue reading →

Posted in methods, Molecular Ecology, the journal, population genetics | Tagged , | 2 Comments