In a "is it Friday yet?" kind of way, I thought I would share this little post. A recent paper in PLoS One by Orbach et al. presents results showing that frugivorous and nectarivorous bats do not appear to be affected by consuming alcohol. The authors fed bats either a sugar solution or sugar+alcohol (strawberry daquiri?) solution. They then gave the bats an aerial obstacle course to test their speed and agility. They also recorded the bats' echolocation calls. Although there were differences between the species that they tested, there were no observed effects of treatment - the "drunk" bats did just as well as the "sober" bats. This was true, even though the estimated BAC's of the bats were sometimes very high - more than 0.3%. Thus, these bats seem perfectly capable of utilizing rotting fruits as food sources with no chiropteran "slurred speech" and little or no danger to themselves or others. Large, virtually hairless primates such as ourselves, do not appear so well adapted and should exercise caution.
If we've learned anything from US politics over the past year and half its that adding 'rogues' to an an otherwise orderly system can result in rapid descent to the lowest common denominator. In the latest issue of Systematic Biology, Thomson and Shaffer show that the same is true in phylogenetics. With the goal of reconstructing a robust phylogenetic hypothesis for turtles using existing sequence data, Thomson and Shaffer use a new pipeline and the data available via the PhyLoTA browser to assemble a dataset that is noteworthy for both its size and incompleteness: 223 taxa, 53,406 bp, 7.59% complete. Although Thomson and Shaffer explore the influence of a variety of factors on phylogenetic inference, they conclude that rogue taxa "probably represent the most insidious problem for supermatrix phylogenetics." For those unfamiliar with rogue taxa, the term is used to describe taxa whose phylogenetic position can vary dramatically without having a strong effect on a tree's overall score. Thomson and Shaffer identify rogues using the taxonomic instability index (I) calculated by Mesquite from a sample of trees generated using standard bootstrapping methods. To explore the influence of rogues on phyogenetic resolution, Thomson and Shaffer remove those taxa exhibiting the most roguish behavior and redo their analyses. The top panel of their Fig. 4 provides a compelling visual representation of the results of this exercise, with the completely unresolved tree on the left being generated before pruning rogues and the nearly fully-resolved tree on the right resulting from analysis of the same dataset subsequent to de-roguing. Although one might challenge the wisdom of deleting problematic taxa until a resolved tree is produced, this practice may be justified in some instances. How we deal with rogue taxa is sure to be a topic of debate in the years to come, but, for the time being Thomson and Shaffer's analyses suggest that simply deleting the taxa with the worst I values may be a reasonable solution.
The origin of vertebrates is part of a larger story involving the evolution of a more inclusive group of kin, the chordates that along with vertebrates include urochordates (tunicates) and cephalochordates (lancelets). Recent decades have been an exciting time for our understanding of chordate evolution, with the discovery and evolutionary analysis of important chordate fossils that date to the Cambrian (542 to 488 million years ago). On the basis of distinct morphological features preserved in the fossils, scientists have been able to integrate these extinct lineages into phylogenetic hypotheses of chordates, extinct early vertebrate lineages, and extant vertebrates.
Here at AMNH, I am surrounded by drawers and drawers, bottles and bottles, and cabinets and cabinets of specimens. A fair number of these are type specimens and my colleagues have spent their careers carefully describing and depositing these and other specimens into collections. They publish these species descriptions in journals according to the rules of the International Code of Zoological Nomenclature. Bacterial taxonomists are an even stricter lot - they insist that all papers that name a new species are published in a single journal, the International Journal for Systematic and Evolutionary Bacteriology. (I have bucked that rule.) In my work on malaria parasites, I have often been met with harsh reviews when I have tried to publish anything that has a sequence, but not a matching bloodsmear. Working on parasites with multiple life stages can be particularly challenging for species descriptions - ideally one would have specimens, images, measurements, etc from each step of the life cycle..but those can be hard to obtain for many - or even most - parasites. In a recent paper, Chris Austin and I argued that incorporating DNA sequences into species descriptions can help bridge that gap.
Erick Matsen and colleagues have organized an online phylogenetics seminar that should be of interest to many Dechronization readers. The stated goals of the seminar series are to provide a forum for the discussion of phylogenetics methodology, disseminate information about ‘best practice’ phylogenetics, and to reduce our carbon footprint by reducing air travel. This seems like a really cool idea and I’m impressed by the present and past lineup of speakers they’ve assembled. I haven’t tuned in yet, but both Marc Suchard and Ward Wheeler gave seminars in the fall – you can view both of their seminars here.
Given that an increasing share of statistical software in ecology and evolution is essentially free – e.g., open source and/or non-proprietary – I used to be bothered by the lack of suitable alternatives to PAUP* (which requires a licensing fee) for certain phylogenetic applications. Foremost among these is perhaps the ability to perform statistically rigorous phylogenetic model selection. There are now a number of free alternatives for phylogenetic model selection, that do not require PAUP* (which is required by the widely used Modeltest and MrModeltest programs ). I've probably been living in a bubble, because I just learned of several of these yesterday, but I thought I'd flag a few for Dechronization readers who might find this info useful.
Kudos to Rich for helping to point out the various ways in which individuals can contribute to the recovery effort in Haiti, which most people know by now was devastated by an earthquake two days ago. I don't have much to add to his post, but since I happened to have been in Santo Domingo in the Dominican Republic at the time, I wanted to relate my experience.
