Category Archives: phylogenetics

The Hype Cycle of Ancient DNA

Recently I saw a graph that I’ve learnt is called the Hype Cycle and is a methodology used in assessment of new technologies and their marketing. What strikes me about it is how well it fits my own research field, … Continue reading

Posted in evolution, natural history, Paleogenomics, phylogenetics, population genetics, theory | Tagged , , | Leave a comment

An Update on the Great BAMM Controversy

Update, 01 August 2016, 2:50PM. This post has been updated to include information contained in the supplemental material of Rabosky et al. 2017, and clarify the difference between branch-specific and tree-wide rate variation. Back in August, I summarized the main … Continue reading

Posted in blogging, evolution, methods, phylogenetics, science publishing, software, speciation | Tagged , , , | Leave a comment

Phylogenetic trees in R using ggtree

Recently, one R package which I like to use for visualizing phylogenetic trees got published. It’s called ggtree, and as you might guess from the name it is based on the popular ggplot2 package. With ggtree, plotting trees in R has … Continue reading

Posted in bioinformatics, howto, phylogenetics, R | Tagged , , , | Leave a comment

Highlights from the Standalone Society of Systematic Biologists meeting – part 2

The 2017 standalone meeting of the Society of Systematic Biologists included expert-led debates on major issues in molecular systematics. Didn’t make it to Baton Rouge? Don’t worry – Melissa DeBiasse and I report on some of the main points (and our favorite lightening … Continue reading

Posted in conferences, next generation sequencing, phylogenetics | Leave a comment

Free to go but required to stay: contrasting views on mitochondrial relationships

Ever since a bacterium found itself mysteriously engulfed in our eukaryotic ancestor, things have been, uh, complicated regarding our two genomes. One is big, one is small. One is circular, one is linear. One is numerous in each cell, the … Continue reading

Posted in adaptation, Molecular Ecology, the journal, phylogenetics, population genetics, selection, speciation | Tagged , | Leave a comment

Highlights from the Standalone Society of Systematic Biologists meeting – part 1

The 2017 standalone meeting of the Society of Systematic Biologists included expert-led debates on major issues in molecular systematics. Didn’t make it to Baton Rouge? Don’t worry – Bryan McLean and I report on the main points below, and highlight some of our … Continue reading

Posted in phylogenetics, species delimitation, Uncategorized | 1 Comment

Phylogeny of the elves illustrates why we need to sample elf DNA immediately

Last year for Christmas Eve, Dominic Evangelista reconstructed the evolutionary history of elves and elf-like fantasy creatures in a tour-de-force of nerd crossover. Seriously, go read that piece if you haven’t. It has an alternate abstract in Elvish. As with … Continue reading

Posted in DNA barcoding, phylogenetics, primates, species delimitation | Tagged , , , , , | 4 Comments