Category Archives: phylogenetics

The eyes have it!

Posted on 20 Jul, 2018 by Kelle Freel

Eyes are pretty darn complicated, which makes them cool models for studying complex trait evolution.  Maybe the first time I realized how interesting eyes are when I saw this by the oatmeal about the amazing-ness of the mantis shrimp (are they your … Continue reading →

Posted in bioinformatics, evolution, genomics, next generation sequencing, phylogenetics | Tagged , , , | Leave a comment

Metabarcoding for every body, every habitat, every time

Posted on 19 Jul, 2018 by Laetitia Wilkins

The immediate reason why I wanted to write about Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles is its usefulness for the scientific community and the effort of the authors to make their study reproducible. … Continue reading →

Posted in bioinformatics, community, community ecology, DNA barcoding, fieldwork, metagenomics, next generation sequencing, phylogenetics, R | Tagged , , , , , , | 1 Comment

Major new microbial groups expand diversity and alter our understanding of the tree of life

Posted on 18 Mar, 2018 by Laetitia Wilkins

I still believe in revolutions. And sometimes they just happen, almost unnoticed. One such revolution happened on a boring 11th of April 2016 when Laura Hug et al. published their new tree of life in the journal of Nature Microbiology. … Continue reading →

Posted in bioinformatics, community ecology, evolution, genomics, metagenomics, microbiology, next generation sequencing, phylogenetics | Tagged , , , , , , , | 1 Comment

Molecular ecology, the flowchart

Posted on 2 Jan, 2018 by Jeremy Yoder

Update: You can now buy a poster print of the Flowchart, with proceeds going to support The Molecular Ecologist! Towards the end of last semester my department’s evolutionary genetics journal club read Rasmus Nielsen’s terrific 2005 review of tests for … Continue reading →

Posted in association genetics, bioinformatics, genomics, howto, infographic, linkage mapping, next generation sequencing, phylogenetics, phylogeography, population genetics, selection | 2 Comments

It's decorative gourd genetics season, muppet-huggers

Posted on 8 Nov, 2017 by Jeremy Yoder

It’s the first week of November, and we’re at Peak Pumpkin. Jack o’lanterns are passé, but Thanksgiving (in the U.S.) and traditional winter-solstice-adjacent holidays will keep pumpkin pie and its infamous espresso-based brethren in style for almost two more months. … Continue reading →

Posted in domestication, genomics, phylogenetics | Tagged , , | Leave a comment

On hyRAD-X, another option for museum genomics

Posted on 9 Jun, 2017 by Ethan Linck

Last year, I profiled Suchan et al.’s “hyRAD” method for reduced-representation genome sequencing of degraded sources of DNA using RAD probes. While it’s too early to say whether hyRAD will be widely used by molecular ecologists looking to integrate historic … Continue reading →

Posted in genomics, methods, natural history, next generation sequencing, phylogenetics, phylogeography, population genetics, RNAseq, selection, transcriptomics | Tagged , , , | Leave a comment

The Hype Cycle of Ancient DNA

Posted on 20 Apr, 2017 by Patrícia Chrzanová Pečnerová

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 , , | 3 Comments

An Update on the Great BAMM Controversy

Posted on 1 Mar, 2017 by Ethan Linck

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

Posted on 8 Feb, 2017 by Elin Videvall

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 , , , | 2 Comments

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

Posted on 20 Jan, 2017 by Bryan McLean

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