Systematics Seminar Fall 2015
This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut.
Seminar Format: Registered students be prepared to lead discussions, perhaps more than once depending on the number of participants.
The leader(s) will be responsible both for (1) selection of readings, (2) announcing the selection, (3) an introductory presentation, (4) driving discussion and (5) setting up and putting away the projector.
Readings: In consultation with the instructors, each leader should assign one primary paper for discussion and up to two other ancillary papers or resources. The readings should be posted to EEBedia at least 5 days in advance.
Announcing the reading: The leader should add an entry to the schedule (see below) by editing this page. There are two ways to create a link to the paper:
1. If the paper is available online through our library, it is sufficient to create a link to the DOI:
:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]
In this case, you need not give all the citation details because the DOI should always be sufficient to find the paper. The colon (:) at the beginning of the link causes the link to be indented an placed on a separate line. Note that the DOI is in the form of a URL, starting with
http://dx.doi.org/. Here is how the above link looks embedded in this EEBedia page:
2. If the paper is not available through the library, upload a PDF of the paper to the UConn dropbox, being sure to use the secure version so that it can be password protected. Copy the URL provided by dropbox, and create a link to it as follows (see the Dropbox Test page for other examples):
:[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls Doyle et al. 2015.]
In this case, you should provide a full citation to the paper for the benefit of those that visit the site long after the dropbox link has expired; however, the full details need not be part of the link text. Here is what this kind of link looks like embedded in this EEBedia page:
- Doyle et al. 2015. Full citation: Vinson P. Doyle, Randee E. Young, Gavin J. P. Naylor, and Jeremy M. Brown. 2015. Can We Identify Genes with Increased Phylogenetic Reliability? Systematic Biology 64 (5): 824-837. doi:10.1093/sysbio/syv041
If you have ancillary papers, upload those to the dropbox individually and create separate links.
Finally, send a note to the Systematics Listserv letting everyone know that a paper is available.
Introductory PowerPoint/KeyNote Presentation: Introduce your topic with a 10- to 15-minute PowerPoint or KeyNote presentation. Dedicate at least 2/3 of that time to placing the subject into the broader context of the subject areas/themes and at most 1/3 of it introducing paper, special definitions, taxa, methods, etc. Never exceed 15 minutes. (For example, for a reading on figs and fig-wasps, broaden the scope to plant-herbivore co-evolution.). Add images, include short movie clips, visit web resources, etc. to keep the presentation engaging. Although your presentation should not be a review of the primary reading, showing key figures from the readings may be helpful (and appreciated). You may also want to provide more detail and background about ancillary readings which likely have not been read by all.
Discussion: You are responsible for driving the discussion. Assume everyone in attendance has read the main paper. There are excellent suggestions for generating class discussions on Chris Elphick’s Current Topics in Conservation Biology course site. See section under expectations.
Prepare 3-5 questions that you expect will spur discussion. Ideally, you would distribute questions a day or two before our class meeting.
Projector: The presenter will be responsible for setting up the projector for each class session—you will need to get it from the EEB office, make sure you have appropriate adaptors and have it set up so that class can begin on schedule. Kathy has reserved the pink projector for our class. If you do not have a laptop, let Wagner know and he will bring his. (Nick McIntosh may also be able to provide a loaner.)
- 1 Meeting time and place
- 1.1 Tuesday, 1 September 2015, 3pm, Bamford Room (TLS 171b)
- 1.2 Tuesday, 8 September 2015, 2:30pm, Bamford Room (TLS 171b)
- 1.3 Tuesday, 15 September 2015, 2:30pm, Bamford Room (TLS 171b)
- 1.4 Tuesday, 29 September 2015, 2:30pm, Bamford Room (TLS 171b)
- 1.5 Tuesday, 6 October 2015, 2:30pm, Bamford Room (TLS 171b)
- 1.6 Tuesday, 13 October 2015, 2:30pm, Bamford Room (TLS 171b)
- 1.7 Tuesday, 20 October 2015, 2:30pm, Bamford Room (TLS 171b)
- 1.8 Tuesday, 27 October 2015, 2:30pm, Bamford Room (TLS 171b)
- 1.9 Tuesday, 3 November 2015, 2:30pm, Bamford Room (TLS 171b)
- 1.10 Tuesday, 10 November 2015, 2:30pm, Bamford Room (TLS 171b)
- 1.11 Tuesday, 17 November 2015, 2:30pm, Bamford Room (TLS 171b)
- 1.12 Tuesday, 30 November 2015, 2:30pm, Bamford Room (TLS 171b)
- 1.13 Tuesday, 8 December 2015, 2:30pm, Bamford Room (TLS 171b)
- 2 Past Seminars
Meeting time and place
For the Fall 2015 semester, we are meeting in the Bamford Room (TLS 171B), Tuesdays 2:30-3:30pm
Tuesday, 1 September 2015, 3pm, Bamford Room (TLS 171b)
At this meeting we discussed possible themes for this semester's seminar, and determined the meeting time. For starters, we will explore how to use RevBayes, and afterwards explore current topics such as new developments in comparative methods.
Tuesday, 8 September 2015, 2:30pm, Bamford Room (TLS 171b)
Suman will demonstrate RevBayes using a simulated data file and a RevBayes script that is pretty bare-bones. If you would to see or play with the script and data yourself beforehand, it is available at the link below:
- RevBayes1 (simdata.nex plus test.Rev script)
A sample qsub script to run RevBayes on the BBC cluster:
#$ -S /bin/bash #$ -cwd #$ -m ea #$ -M email@example.com #$ -N TimeTree rb GTR_Gamma.nonclock.Rev
If you don't mind staying logged in, you can type qlogin to get assigned to a compute node that is not currently busy and then just type
This is a good method to use if you just want to test RevBayes; you'll want to use Suman's qsub script for long jobs because you will not probably not want to stay logged in overnight. If you don't have an account on the cluster, you can get one by filling out this form: http://bioinformatics.uconn.edu/contact-us/
Tuesday, 15 September 2015, 2:30pm, Bamford Room (TLS 171b)
This week we will explore the graphical model descriptions used by RevBayes. Here is the paper (password is being sent over the systematics email list):
- Höhna et al. 2014. Probabilistic Graphical Model Representation in Phylogenetics. Systematic Biology. 63:753–771
You can also get the paper without requiring a password if you are on campus or connected via VPN using this link:
- Höhna et al. 2014. Probabilistic Graphical Model Representation in Phylogenetics. Systematic Biology. 63:753–771
Paul will also demonstrate how to use RevBayes on our bioinformatics cluster (probably the best way to run it, especially for long runs).
Tuesday, 29 September 2015, 2:30pm, Bamford Room (TLS 171b)
This week we'll talk about the new "Open Tree of Life", reading the paper, and maybe exploring the website (http://opentreeoflife.org/)
Tuesday, 6 October 2015, 2:30pm, Bamford Room (TLS 171b)
This week we'll indulge Elizabeth's interest in salamanders, and also talk about molecular dating
- Shen et al. Enlarged Multilocus Dataset Provides Surprisingly Younger Time of Origin for the Plethodontidae, the Largest Family of Salamanders. Sys. Bio. in press
Tuesday, 13 October 2015, 2:30pm, Bamford Room (TLS 171b)
This week we'll take a look at a paper comparing small and large datasets when constructing trees. Also snakes!
- Ruane et al. Comparing species-tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: An empirical study on Malagasy pseudoxyrhophiine snakes. BMC Evolutionary Biology. in press
EDIT here is the published version
Tuesday, 20 October 2015, 2:30pm, Bamford Room (TLS 171b)
This week we'll jump back into an anchored phylogenomics dataset, and talk about (yet another) bird phylogeny.
- Prum et al. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature.
- Accompanying News and Views article.
- Relevant blog post!
Tuesday, 27 October 2015, 2:30pm, Bamford Room (TLS 171b)
Some back and forth commentaries!
- Liu & Edwards. Comment on "Statistical binning enables an accurate coalescent based estimation of the avian tree"
- Mirarab et al. Response to Comment on “Statistical binning enables an accurate coalescent-based estimation of the avian tree”
Tuesday, 3 November 2015, 2:30pm, Bamford Room (TLS 171b)
Springer and Gatesy. 2016. The gene tree delusion. A critique of species tree methods. The reason that it is called the gene tree delusion rather than the species tree delusion is I think because they are in favor of concatenation.
- Springer and Gatesy. 2016. MPE 94: 1-33. (doi:10.1016/j.ympev.2015.07.018)
Tuesday, 10 November 2015, 2:30pm, Bamford Room (TLS 171b)
- Edwards et al. 2016. Response to Gene Tree Delusion. You can read it online here.
Tuesday, 17 November 2015, 2:30pm, Bamford Room (TLS 171b)
Suman and Paul will discuss the "concaterpillar" paper below (an oldie but goodie) unless someone writes to us before the end of the week with a different idea. The idea here is to find clusters of genes that can tolerate sharing a single tree topology. The password is being sent over the systematics listserv, but you can also download the paper using the DOI link, which should work if you are on campus or connected to the campus network via VPN.
- Leigh J.W., Susko E., Baumgartner M., Roger A.J. 2008. Testing congruence in phylogenomic analysis. Systematic Biology. 57:104–115. doi:10.1080/10635150801910436
Running concaterpillar on the bbcsrv3 cluster
Make sure your data file names end in .seq (not .nex), then create the following qsub script (you can name this anything, but I'll assume you named it cpillar.sh):
#!/bin/bash #$ -S /bin/bash #$ -cwd #$ -m ea #$ -M firstname.lastname@example.org #$ -N cpillar /opt/python/bin/python /common/opt/bioinformatics/concaterpillar/concaterpillar.py -m GTR -t
Important: be sure your qsub script has unix line endings. This is only an issue if you created it on a Windows machine - you can use Notepad++ to change the line endings.
(Note that you should change email@example.com to your own email address. You can also change cpillar to a job name that makes sense for your analysis.)
Run concaterpillar by navigating to the directory containing your qsub script and your .seq files and typing
Running the MPI (parallel) version
If you have a lot of genes, you can make concaterpillar go faster by using more CPU slots on the cluster. Use the following qsub script for an MPI run that uses 8 slots:
#!/bin/bash #$ -S /bin/bash #$ -cwd #$ -m ea #$ -M firstname.lastname@example.org #$ -N cpillar #$ -pe orte 8 mpirun -np 8 /opt/python/bin/python /common/opt/bioinformatics/concaterpillar/concaterpillar.py -c 8 -m GTR -t
Here I've specified 8 slots. Note that the number 8 appears 3 times - whatever number you decide to use, make sure to use that same number in all 3 places!
Tuesday, 30 November 2015, 2:30pm, Bamford Room (TLS 171b)
Tuesday, 8 December 2015, 2:30pm, Bamford Room (TLS 171b)
Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Boothby et al. 2015
National Geographic news article
An example of the click-bait-ification of our world
THE TARDIGRADE WAR HAS BEGUN with another paper that counters Boothby et al.'s HGT result