Difference between revisions of "Systematics Seminar"
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Discussion of chapter 11 - Fitting birth-death models
Discussion of chapter 11 - Fitting birth-death models
Revision as of 20:07, 23 September 2019
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.
- 1 Meeting time and place
- 2 Theme and Schedule for Fall 2019
- 3 August 30
- 4 September 6
- 5 September 13
- 6 September 20
- 7 September 27
- 8 October 4
- 9 October 11
- 10 October 18
- 11 October 25
- 12 November 1
- 13 November 8
- 14 November 15
- 15 November 22
- 16 December 6
- 17 Information for discussion leaders
- 18 Past Seminars
Meeting time and place
We meet on Fridays at 2 PM in the Bamford Room (TLS 171b).
Theme and Schedule for Fall 2019
Students registered for the course shall pick one chapter of the book to elaborate on, either by choosing and assigning a paper relevant to the chapter, or by bringing in their own project/data to present.
Discussion of chapter 1 - A Macroevolutionary Research Program, an organizational meeting
Discussion of chapter 2 - Fitting Statistical Models to Data, Introduction to phylogenies in R
Discussion of chapter 3 - Introduction to Brownian Motion
Discussion of chapter 4 - Fitting Brownian Motion
Discussion of chapter 5 - Multivariate Brownian Motion
Discussion of chapter 6 - Beyond Brownian Motion
Discussion of chapter 7 - Models of discrete character evolution — Lisa Terlova
Discussion of chapter 8 - Fitting models of discrete character evolution — Lisa Terlova
Discussion of chapter 9 - Beyond the Mk model - Kevin Keegan
Kevin will also show us how to add information to tip labels (like geography or taxon images) using ggtree
Discussion of chapter 10 - Introduction to birth-death models — Zach Muscavitch
Discussion of chapter 11 - Fitting birth-death models — Tanner Matson
Discussion of chapter 12 - Beyond birth-death models
Discussion of chapter 13 - Characters and diversification rates - Amanda Hewes
Discussion of chapter 14 - Summary
Information for discussion leaders
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 Bamford room has joined the modern world--you should just need to plug in your computer or USB key to project.