Phylogenetics
sa smith | May 31, 2010I got a giggle from reading Larry (and then John Hawks) talking about time travel. Kinda. I mean, people using science to look back in time, and orient themselves in that different era to such a degree they can gain information about said time.
Scientists arent just guessing when they estimate when humans and chimpanzees split into different species, or where/how 'new' species like Ardi and Teh Hobbit fit into the tree-- they are using two totally different arms of science figure out how species were oriented millions of years ago. We have estimates from fossils and how old they are and…
awild | April 21, 2010What happens if you score bug blogs for various characters and crunch them through a phylogenetic analysis?
Morgan Jackson investigates:
Although Morgan's exercise was tongue-in-cheek, he did uncover a pattern worthy of further exploration:
The last thing I want to comment on is the huge skew between male and female insect bloggers. Of the 58 blogs where I could determine the author's sex, only 28% of them were written solely by women. Even more concerning perhaps is that 38% of these women bloggers choose to remain anonymous, while not a single male blogger chose to stay private! With…
awild | February 16, 2010The online early section of Molecular Phylogenetics and Evolution this week has the first comprehensive phylogeny of a rather important genus of ants: Myrmica.
Myrmica is ubiquitous in the colder climates of North America and Eurasia, with a few seemingly incongruous species inhabiting the mountains of tropical southeast Asia. The genus contains about 200 species, many that are common soil-nesting ants in lawns and gardens, and at least one damaging invasive species, M. rubra. The taxonomy ranks among the most difficult of any ant genus, as workers of different species tend to be numbingly…
razib | February 14, 2010One of the interesting aspects ensuing from the rise of molecular phylogenetics is that the trees are generally concordant in broad strokes with older research which was based on morphology. This is not too surprising, as nature does tend to show some intelligible patterns which can be cross-checked with different methods (e.g., the fact of evolutionary change in the tree of life is evident in both the paleontological record and analysis of molecular genetic variation). Additionally, the cladistic revolution has produced a general uniformity of underlying logic when it comes to systematic…
awild | February 11, 2010
click to enlarge
The top-tier journal Nature doesn't often deal in purely phylogenetic research. So when such a study graces their pages we know it's big stuff.
Yesterday, Nature published a 62 gene, 75 species analysis of the evolutionary history of the arthropods. Arthropods, as readers of this blog likely know, are animals with a chitinous exoskeleton and jointed legs. They include the insects, arachnids, crustaceans, centipedes, and others. This is a staggeringly diverse group, and one found just about everywhere on the planet. Most animals are arthropods.
This study has been in the…
awild | January 21, 2010
Amblyopone australis: a primitive ant?
Earlier I chastised Christian Peeters and Mathieu Molet for misinterpreting the term "basal" in a phylogenetic context. What was that about?
The issue relates to the classic fallacy of viewing evolution as a linear progression from primitive to advanced. Popular conceptions of evolution aside, the process is not linear like a ladder so much as branching like a bush.
I don't know what quirk of human psychology so strongly predisposes us to frame ideas in linear narratives, but the fact that we do so makes evolution an unfortunately difficult concept…
awild | January 20, 2010Let me preface this post by saying that Christian Peeters is one of my absolute favorite myrmecologists. If lost in a remote African jungle and stalked by ravenous leopards, for example, Christian is the first ant guy I'd pick to help get me out of the predicament.
Having said that, this paper in Insectes Sociaux is so bad I nearly gouged my eyes out and ran around in little circles screaming and flailing my arms.
Nonetheless there exist extant ants with relatively simple societies, where size-polymorphic workers and large queens are absent. Recent phylogenies show that the poneroid…
awild | December 21, 2009Sorry for an uncharacteristically technical post. But, I've produced an excellent example of a problem that's been plaguing the widely-used phylogenetics program MrBayes and thought it might be of interest to the handful of systematists who read this blog.
I've been running analyses on the Azteca y'all sent after my desperate plea last month and noticed something odd.Â
I set MrBayes to do two runs of 4 chains each. After 10 million generations they produced post-stationarity consensus trees that were topologically identical (that is, the avg. st. dev. splits frequency fell to .005 after…
awild | December 3, 2009Here's an issue that's been on my mind as I'm shuffling trees around from several concurrent phylogenetic projects.
The primary output from phylogenetics programs is tree diagrams depicting the relationships among organisms. Very clean, very crisp, very precise diagrams. Precision isn't in itself a problem, but for the human foible of mistaking precision for accuracy.
I'm not interested in a precise estimate of evolutionary history so much as a correct one. I'm reminded as much when I see my estimates change from one precise conclusion to another as I add more data from more species. …
awild | November 17, 2009
The chaotic evolution of colony size in ants. (Tree re-analyzed from Brady et al 2006, colony data taken from Hoelldobler & Wilson 1990 and other sources)
This tree depicts how colony size evolves in ants. The purple/blue colors represent small colonies with only a few to a few dozen ants, while the yellows and oranges represent species with enormous colonies of tens or hundreds of thousands of individuals. What's exciting about this rainbow-colored figure?
If you were expecting ant evolution to be an inexorable march towards larger and more complex societies, this tree should…
awild | January 3, 2009In the comments, Eric Eaton makes an observation:
Iâm left wondering (just a little) why Alex has such a beef with Dr. Wilson. This is not the first post taking a jab at Wilson, so while Alex makes an excellent point, Iâm also sensing some underlying issues hereâ¦.
Eric is right there's an issue. It is one many myrmecologists, especially systematists, have been tip-toeing around for a while now.
The short version is that Wilson is no longer at the leading edge of myrmecology. As he has fallen out of step with the practicing research community, his public ant commentary is increasingly at…
awild | August 13, 2008Our 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…
evolgen | July 18, 2008Phylogeny Friday -- 18 July 2008
When they published the initial analysis of the complete platypus genome (doi:10.1038/nature06936), Nature, as they're wont to do, also put out a news item announcing the major findings (doi:10.1038/453138a). That news article included a phylogeny illustrating the evolutionary relationships of various animal species in various stages of having their complete genomes sequenced.
The problem with the illustration: they got some of the relationships wrong. This sparked a letter from Peter Ducey of SUNY Cortland (doi:10.1038/454027d), in which he wrote the…
evolgen | June 27, 2008Phylogeny Friday -- 27 June 2008
I haven't done a Phylogeny Friday in about a month, but a recent paper reporting a "phylogenomic study of birds" was worth mentioning (doi:10.1126/science.1157704). Now, this isn't phylogenomics as Jonathan Eisen defined it. The bird evolution paper describes building a tree using lots of molecular markers.
I don't have much to say about the new bird phylogeny (I'll let the expert handle the details), but I wanted to post one of the trees for Phylogeny Friday. Here is one of the phylogenies they present, attempting to reconcile their results with those that…
awild | May 31, 2008
30 years ago, biologists thought they'd solved one of Darwin's thorniest problems, the evolution of sterile social insects:
No doubt many instincts of very difficult explanation could be opposed to the theory of natural selection,âcases, in which we cannot see how an instinct could possibly have originated...I will not here enter on these several cases, but will confine myself to one special difficulty, which at first appeared to me insuperable, and actually fatal to my whole theory. I allude to the neuters or sterile females in insect-communities: for these neuters often differ widely in…
evolgen | May 30, 2008Phylogeny Friday -- 30 May 2008
Research on animals in under attack throughout the world. Animal rights activists not only stage rallies against animal testing, but they also engage in criminal behavior. They vandalize property, sabotage experiments, and terrorize researchers. How can scientists fight back?
Michael Conn and James Parker have written book documenting the animal rights issue from the scientists' perspective (The Animal Research War). Conn and Parker have also briefly described their position in the FASEB Journal. Here is how they summarize their book:
This book is a personal…
evolgen | May 20, 2008My advisor has recently got me listening to Whad'ya Know. My first reaction: It's like Wait Wait...Don't Tell Me! Only not as funny, not as interesting, and not as good. I've been downloading the podcasts for the past couple of weeks, and I'm not sure whether I'll keep subscribing in iTunes.
I'm only bringing this up because last week's episode contained a very egregious example of someone knowing just enough biology to get themselves in trouble. The sad part was that the person should have known better. Why? She teaches biology at the university level.
What happened? At the midpoint of the…
evolgen | April 25, 2008Duh! That's Obvious, Edition
Take a look at this mastodon skeleton:
Does it look like anything you recognize? Perhaps a large terrestrial mammal with big tusks. If you said "elephant" you win. The prize: nothing.
That is half of the conclusion from a recent paper in Science (doi:10.1126/science.1154284). Really. The other half: birds and dinosaurs are pretty closely related. Or, more specifically, birds and Tyrannosaurus rex -- THE COOLEST MOST AWESOMEST OF ALL DINOSAURS EVER!! -- are closely related. And, for this, they get a Science paper.
Now, the way they did this is pretty damn cool…
evolgen | April 22, 2008The Drosophila genus is paraphyletic. That means there are species nested within the phylogeny of the genus that belong to other genera. Or, in other words, there are species descended from the most recent common ancestor (MRCA) of all Drosophila species that belong to different genera. If that doesn't make sense, just look at the tree.
A paraphyletic genus is a no-no in taxonomy. There are two ways to deal with the problem. First, the genera nested within the Drosophila phylogeny can be redesignated into the Drosophila genus. That's not going to happen because the genus is too freakin' big…
evolgen | April 11, 2008Drosophila Are Not Fruit Flies Edition
As I have mentioned before, Drosophila are not fruit flies. Tephritids are fruit flies. Drosophila feed on rotting fruit, while true fruit flies feed on fresh fruit. That makes true fruit flies agricultural pests. Drosophila, on the other hand, are connoisseurs of the finer things in life -- wine, beer, cheese, and the like.
In addition to rotting fruit, Drosophila also feed on mushrooms and crabs. Yes, crabs. Well, they don't actually feed on the crabs, just like they don't actually feed on the fruit. The flies and their larva are more interested in…