For the course I'm teaching this fall (Insect Diversity and Evolution, ENTOM 3310/3311), the students each designed a webpage on their favorite species of insect that could be found at Cornell. Check it out!
We used the free Weebly for Education platform. None of the students had made their own website prior to this semester & overall, it seemed like the students caught on quickly. The biggest problem I encountered is that the individual sites are often down. Clicking on the link gives a message: "This page isn't working" -- which is an issue on the Weebly end. That's a little disappointing, and I hope it improves.
Use the free photo processing program, Fiji, to make a gif out of your stack of z-stepped images! You'll produce a nice little video clip that scrolls through all of the layered shots that you've taken of your specimen.
make a gif using ImageJ and your stack of images:
The fossil that was thought to be the oldest flying insect (and has been used to interpret and date the origins of flight) may not even be an insect at all! In an interesting turn, a recent publication asserts that the fossil Rhyniognatha hirsti is not the mandible of a flying insect, but is in fact a fragment of a myriapod: specifically, an immature centipede.
In an article published May 30, 2017 in the journal PeerJ, Haug & Haug present evidence that the Devonian fossil R. hirsti (>400 My old) is not a flying insect... or an insect... or even closely related to insects... It is a centipede. The fossil is fragmentary, mainly mandibles and some other rather ambiguous parts connected to it. However, the shape of these mandibles was similar to those of dragonflies and neopterans, which prompted Engel and Grimaldi (2004) to tentatively assign it as a fragment of a flying insect. Now, Haug & Haug use 3D imaging and show remains of what they hypothesize is a myriapod-like head capsule. Also, the putative apodemes are deemed to be glands of ectodermal origin.
The potential misplacement of this fossil has some pretty big implications. The next oldest fossils of flying insects are from the late Carboniferous -- about 80 My after this fossil! That is a huge time difference and affects our interpretation of the origins and evolution of insect flight. Also, many molecular phylogenetic studies have used this as a fossil calibration. For instance, the hexapod dated phylogeny of Misof et al. 2014 incorporated this fossil as a stem calibration for Dicondylia (winged insects + their sister group Diplura), with an age of 411.5 Mya. The reinterpretation of this fossil, if it is accepted, will have wide effects on future work on insect evolution and dating.
As of September 23, there were ~1500 views of the article and no papers citing it, so we'll have to stay tuned for a response!
Engel, M.S. & Grimaldi, D. (2004) New light shed on the oldest insect. Nature 427, 627-630.
Haug, C. & Haug, J.T. (2017) The presumed oldest flying insect: more likely a myriapod? PeerJ, 5, e3402.
Misof, B., Liu, S., et al. (2014) Phylogenomics resolves the timing and pattern of insect evolution. Science, 346, 763-767.
For the first lecture, I had the students grab a unit tray as they arrived -- each tray was placed upside-down in the drawer. The insects themselves weren't anything special (though that could be a fun twist), but they served as a group-forming tool to get students interacting.
At the very beginning of class, students had to walk around and find the three other people with the same insect, and then they each spent a minute or two introducing themselves to the group. It is a more personal setting than immediately going around the room for roll call and introductions. Sometimes class-wide student introductions can be a little nerve-racking on the first day, so I thought it would be nicer to start in small groups before taking attendance.
Setting a starting tree in the program BEAST can be a complicated issue, and I've been asked about troubleshooting for it. Here is a full XML file with annotations, as an example of how to designate a starting tree and how to force BEAST to keep it as a fixed topology.
BEAST is a widely-used phylogenetic dating program and has an excellent GUI interface in BEAUti, where users can control most all parameters and inputs they'd need. BEAUti is the front-end program that produces the XML file that is then used by BEAST for tree estimation. XML stands for 'eXtensible Markup Language', which is both human and machine readable, and is similar to HTML.
One piece that must be manually edited in a text editor is the user-specified starting tree, if desired. Why use a starting tree? For large and difficult datasets, one can start in the best area of parameter space, so that the Markov chain isn't wasting time jumping around to sample the presumably 'incorrect' topologies. I'm not sure as to how much a starting tree increases efficiency, since alternate topologies can still be sampled (it's certainly not needed for small, straightforward datasets), but I may update my opinions in the future based on the success of trying to manipulate phylogenomic data.
There are two different XML editing tasks I'll cover.
Setting a user-specified starting topology
The default starting tree is a random tree, which is coded in an element (content & attributes surrounded by an opening and closing tag ('init', our tree initializer). The whole element needs to be replaced by a user-specified starting tree in newick format. Take a look at the example document!
Fixing the starting tree topology
There are four lines to comment out: the operators for subtree-slide, wide & narrow exchange, and Wilson-Balding. Removing these four operators prevents the topology from updating, but still allows for estimation of the node ages (i.e., branch lengths will be modified even though the topology will not). In an XML file, comments are surrounded by ' <!-- ' and ' --> ', which means they will not be processed.
There are a couple of nice sites with information on user input starting trees, yet translating that to your own data can still be a bit of a struggle. I hope here I could add a bit of guidance on the issue by providing an annotated XML file to help clarify the changes needed.
There is now an updated and more-detailed tutorial at: http://www.beast2.org/fix-starting-tree/.
Also, thanks to great info from: http://www.northernbotanist.com/?page_id=732.
Covering topics of phylogenetics and systematics.