Difference between revisions of "Systematics Seminar"
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| − | + | <span style="color:red">The home page of the Systematics Seminar has moved to [https://uconneeb.github.io/systseminar/ https://uconneeb.github.io/systseminar/]. This EEBedia page is no longer maintained or updated.</span> | |
| − | + | 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. | |
| − | + | [[Systematics Listserv|Click here for information about joining and using the Systematics email list]] | |
| − | == | + | == Meeting time and place == |
| − | + | We meet on Fridays at 2 PM in the Bamford Room (TLS 171b). | |
| − | + | ||
| − | === | + | == Theme and Schedule for Fall 2019 == |
| − | + | ||
| − | : | + | [https://lukejharmon.github.io/pcm/ We will be reading Luke J. Harmon's book on comparative phylogenetic methods] |
| − | + | ||
| − | + | 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. | |
| − | + | ||
| − | == | + | ==August 30== |
| − | + | Discussion of chapter 1 - A Macroevolutionary Research Program, an organizational meeting | |
| − | == | + | ==September 6== |
| − | + | Discussion of chapter 2 - Fitting Statistical Models to Data, [http://phytools.org/mexico2018/ex/2/Intro-to-phylogenies.html Introduction to phylogenies in R] | |
| − | == | + | ==September 13== |
| − | + | Discussion of chapter 3 - Introduction to Brownian Motion | |
| − | == | + | ==September 20== |
| − | + | Discussion of chapter 4 - Fitting Brownian Motion | |
| − | + | ||
| − | + | ||
| − | === | + | ==September 27== |
| − | + | Discussion of chapter 5 - Multivariate Brownian Motion | |
| − | + | ||
| − | == | + | ==October 4== |
| − | + | Discussion of chapter 6 - Beyond Brownian Motion<br>[https://github.com/kevinliam/Miscellaneous/blob/master/add_tree_info.zip Kevin shows us how to add images to plotted trees in R] | |
| − | == | + | ==October 11== |
| − | + | Discussion of chapter 7 - Models of discrete character evolution — Lisa Terlova | |
| − | == | + | ==October 18== |
| − | + | Discussion of chapter 8 - Fitting models of discrete character evolution — Lisa Terlova | |
| − | == | + | ==October 25== |
| − | + | Discussion of chapter 9 - Beyond the Mk model - Kevin Keegan | |
| − | == | + | ==November 1== |
| − | + | Discussion of chapter 10 - Introduction to birth-death models — Zach Muscavitch | |
| − | == | + | ==November 8== |
| − | + | Discussion of chapter 11 - Fitting birth-death models — Tanner Matson | |
| − | == | + | ==November 15== |
| + | Discussion of chapter 12 - Beyond birth-death models - Katie Taylor | ||
| − | == | + | ==November 22== |
| − | + | Discussion of chapter 13 - Characters and diversification rates - Amanda Hewes | |
| − | == | + | ==December 6== |
| − | + | 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: | ||
| + | <nowiki>:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]</nowiki> | ||
| + | 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 <code><nowiki>http://dx.doi.org/</nowiki></code>. Here is how the above link looks embedded in this EEBedia page: | ||
| + | :[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.] | ||
| + | |||
| + | 2. If the paper is not available through the library, upload a PDF of the paper to [http://dropbox.uconn.edu 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): | ||
| + | <nowiki>:[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls Doyle et al. 2015.]</nowiki> | ||
| + | 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: | ||
| + | |||
| + | :[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls 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. | ||
| + | |||
| + | == Past Seminars == | ||
| + | * [[Systematics Seminar Spring 2019|Spring 2019]] | ||
| + | * [[Systematics Seminar Fall 2018|Fall 2018]] | ||
| + | * [[Systematics Seminar Spring 2018|Spring 2018]] | ||
| + | * [[Systematics Seminar Fall 2017|Fall 2017]] | ||
| + | * [[Systematics Seminar Fall 2014|Fall 2014]] | ||
| + | * [[Systematics Seminar Fall 2013|Fall 2013]] | ||
| + | * [[Systematics Seminar Spring 2012|Spring 2012]] | ||
| + | * [[Systematics Seminar Fall 2011|Fall 2011]] | ||
| + | * [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester) | ||
| + | * [[Systematics Seminar Fall 2010|Fall 2010]] | ||
| + | * [[Systematics Seminar Spring 2010|Spring 2010]] | ||
| + | * [[Systematics Seminar Fall 2009|Fall 2009]] | ||
| + | * [[Systematics Seminar Fall 2008|Fall 2008]] | ||
| + | * [[Systematics Seminar Spring 2008|Spring 2008]] | ||
| + | * [[Systematics Seminar Fall 2007|Fall 2007]] | ||
| + | * [[Systematics Seminar Spring 2007|Spring 2007]] | ||
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006] | * [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006] | ||
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005] | * [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005] | ||
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004] | * [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004] | ||
| − | * [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004 | + | * [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004] |
| + | |||
| + | [[Category:EEB Seminars]] | ||
Latest revision as of 18:03, 26 August 2021
The home page of the Systematics Seminar has moved to https://uconneeb.github.io/systseminar/. This EEBedia page is no longer maintained or updated.
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.
Click here for information about joining and using the Systematics email list
Contents
- 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
We will be reading Luke J. Harmon's book on comparative phylogenetic methods
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.
August 30
Discussion of chapter 1 - A Macroevolutionary Research Program, an organizational meeting
September 6
Discussion of chapter 2 - Fitting Statistical Models to Data, Introduction to phylogenies in R
September 13
Discussion of chapter 3 - Introduction to Brownian Motion
September 20
Discussion of chapter 4 - Fitting Brownian Motion
September 27
Discussion of chapter 5 - Multivariate Brownian Motion
October 4
Discussion of chapter 6 - Beyond Brownian Motion
Kevin shows us how to add images to plotted trees in R
October 11
Discussion of chapter 7 - Models of discrete character evolution — Lisa Terlova
October 18
Discussion of chapter 8 - Fitting models of discrete character evolution — Lisa Terlova
October 25
Discussion of chapter 9 - Beyond the Mk model - Kevin Keegan
November 1
Discussion of chapter 10 - Introduction to birth-death models — Zach Muscavitch
November 8
Discussion of chapter 11 - Fitting birth-death models — Tanner Matson
November 15
Discussion of chapter 12 - Beyond birth-death models - Katie Taylor
November 22
Discussion of chapter 13 - Characters and diversification rates - Amanda Hewes
December 6
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.
Past Seminars
- Spring 2019
- Fall 2018
- Spring 2018
- Fall 2017
- Fall 2014
- Fall 2013
- Spring 2012
- Fall 2011
- Spring 2011 (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)
- Fall 2010
- Spring 2010
- Fall 2009
- Fall 2008
- Spring 2008
- Fall 2007
- Spring 2007
- Fall 2006
- Spring 2005
- Fall 2004
- Spring 2004
