phylogeny

Ebola virus has impressed me as creepy ever since I read "The Hot Zone: A Terrifying True Story some years back by Richard Preston. (I guess he has a new book, too, Panic in Level 4: Cannibals, Killer Viruses, and Other Journeys to the Edge of Science but I haven't been in airport for the past couple of weeks, so I haven't read it yet.) Technorati Tags: blast, phylogenetic trees, Ebola, viruses Infectious agents that cause diseases with gruesome symptoms really excite those of us with an interest in microbiology. Tara has written about this paper, too, and summarized the details. I…
Argentine ants tending scale insects Three years after finishing my Ph.D., I have finally published the last bit of work from my dissertation.  It's a multi-locus molecular phylogeny of the ant genus Linepithema, a group of mostly obscure Neotropical ants that would be overlooked if they didn't happen to contain the infamous Argentine Ant.  In less jargony language, what I've done is reconstruct the evolution of an ant genus using genetic data.  Here's the citation: Wild, A. L. 2008. Evolution of the Neotropical Ant Genus Linepithema. Systematic Entomology, online early, doi: 10.1111/j.…
Martialis heureka Rabeling & Verhaagh 2008 drawing by the inimitable Barrett Klein for PNAS Most scientific discoveries these days emerge through carefully planned and controlled research programs.  Every now and again, though, something unexpected just pops up in a distant tropical jungle.  Martialis heureka is a fantastic discovery of that old-fashioned kind.  This little ant simply walked up to myrmecologist Christian Rabeling in the Brazilian Amazon.  It is not only a new species, but an entirely different sort of ant than anything known before. The remarkable find was…
Our first paper from the Beetle Tree of Life study has been published. Here's the citation: Wild, A. L. & Maddison, D. R. 2008. Evaluating nuclear protein-coding genes for phylogenetic utility in beetles. Molecular Phylogenetics and Evolution, doi: 10.1016/j.ympev.2008.05.023 My co-author David Maddison once summarized the point of the paper as "Hey guys! New genes!" What we've done is develop lab protocols for sequencing 8 nuclear genes that should be particularly useful for inferring the evolutionary history of beetles.  It's a foundational paper.  We created the methods that will…
tags: researchblogging.org, phylogeny, British birds, population decline, range contraction, Gavin H Thomas An adult male Eurasian blackbird, Turdus merula. Image: Wikipedia commons [larger view]. A paper recently published by British scientist, Gavin Thomas, a population biologist at Imperial College London, finds that British bird species that currently are suffering population declines tend to be close relatives of each other. The reason is obvious: closely related species tend to share many traits, such as very precise habitat requirements, and what's bad for one species is also bad…
I made this video (below the fold) to illustrate the steps involved in making a phylogenetic tree. The basic steps are to: Build a data set Align the sequences Make a tree In the class that I'm teaching, we're making these trees in order to compare sequences from our metagenomics experiment with the multiple copies of 16S ribosomal RNA (rRNA) genes that we can find in single bacterial genomes. Bacteria contain between 2 to 13 copies of 16S rRNA genes and we're interested in knowing how much they differ from each other. Later, we'll compare the 16S ribosomal RNA genes from multiple species of…
The famous Cambrian Explosion- a rapid diversification of animal groups about 550 million years ago- assumes a rather diminished significance when mapped to the full Tree of Life. update: yes, I made the diagram myself, by modifying this.
Mycocepurus smithi, in the fungus garden An exciting week for ant aficionados! A new study by ant phylogenetics gurus Ted Schultz and Seán Brady provides the first detailed picture of attine evolution. These New World ants have long attracted the attention of biologists because they, like our own species, practice a well-developed form of agriculture. Instead of plants, these ants grow fungi, and their relationship is so specialized that the ants can consume nothing else. Schultz and Brady use data from four nuclear genes, the fossil record, and the biology of extant ants to infer an…
The first research assignment for our Alaska NSF Chautauqua course has been posted. Your task is to find a wound-inducible plant gene, learn something about it, and post a description in the comment section. We've already had one excellent answer, but I know there are at least 54 wound-inducible genes, so I expect to see more. Once we get our genes in order (and possibly before), we'll talk more about designing an experiment for detecting gene expression. In the meantime, I have some pre-course reading assignments to help you prepare. tags: plants, Alaska, NSF Chautauqua courses,…
If you've ever looked at an evolutionary tree, contemplated phylogeny, cladistics, or the like, you're probably aware that Joe Felsenstein is one of the leaders of the pack. And you will certainly enjoy, this interview that Blind Scientist has posted. I wouldn't advise reading the interview to learn about doing phylogenetics, but you will learn a bit about the social anthropology of the field. Felsenstein does a wonderful job of supplying historical context to phylogenetic arguments and filling in the missing details. A phylogenetic tree is a kind of model or hypothesis that's put forth…
Five Bulgarian nurses and a Palestinian doctor (dubbed the Tripoli six) may be executed soon by the Libyan government for the crime of deliberately infecting over 400 children with HIV. If they did infect the children, this would be a horrendous crime. If they did not infect the children, it's the Libyan government that will be killing innocent people. The clock is ticking. Some of you might be wondering (I know I was): How exactly is molecular sequence data being used to solve the crime? Why are scientists and science bloggers claiming that the Tripoli six are innocent? Let's begin by…