Posts Tagged ‘phylogenetics’

The 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 similar to each other. And there are a lot of species.


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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 works for many years. Jerry Regier’s lab at the University of Maryland has been diligently developing protocols for extracting single-copy nuclear DNA from across the arthropods, and the work has paid off handsomely. They have created the largest and most relevant data set yet assembled for addressing the hard questions in arthropod evolution. This is exciting! Today is like Christmas for arthropod systematists.

There’s a lot to digest here, but below are my first impressions: (more…)

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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?


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Let 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 subfamilies Amblyoponinae and Ponerinae are basal (e.g. Brady et al., 2006), i.e. closer to solitary vespoid wasps.

Ten points to the first person who can explain what’s wrong with it.

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Sorry 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.  (more…)

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Here’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.   The razor-sharp output from the algorithms is seductive.

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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 come as a surprise.  Ant colony size is all over the place.  Not only is there no general trend towards larger colonies, some lineages seem to be shrinking down from more populous ancestors.

Colony size evolution is not the subject of this post, though.  I’m going to whinge instead about how frustrating I found the process of making this figure.  (more…)

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In the comments, Eric Eaton makes an observation:

I’m 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, I’m also sensing some underlying issues here….

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 odds with the situation on the ground, as it were.  This predictably puts the current generation of myrmecologists in a bit of an uncomfortable position with respect to the community’s most public representative.  Hence the underlying issues.

The longer version is this.  (more…)

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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!” (more…)

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30 years ago, biologists thought they’d solved one of Darwin’s thorniest problems, the evolution of sterile social insects:


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