Difference between revisions of "Systematics Seminar"

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This is the home page of the UConn EEB department's Systematics Seminar. 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.
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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.  
  
This (Spring, 2007) semester, we are meeting each Tuesday at 4pm in the BioPharm 3rd. floor "fishbowl" conference room.
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[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
  
== Schedule for Spring Semester 2007 ==
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== Meeting time and place ==
  
; January 16, 2007
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We meet on Fridays at 2 PM in the Bamford Room (TLS 171b).
:Organizational meeting, BioPharm 3rd. floor fishbowl, 4pm
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;January 23, 2007:
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== Theme and Schedule for Fall 2019 ==
:Smythe, A.B., M.J. Sanderson, and S.A. Nadler. 2006. Nematode Small Subunit Phylogeny Correlates with Alignment Parameters. Systematic Biology 55(6): 972-992.[PDF]
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:Note from Carrie: Please note that this is DIFFERENT than the paper we decided on at Tuesday's organizational meeting.
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[https://lukejharmon.github.io/pcm/ We will be reading Luke J. Harmon's book on comparative phylogenetic methods]
:This issue of Sys. Bio. is not yet available online therefore I will make a copy and put it in the EEB office. Those with a hard copy subscription of Sys. Bio. should have this issue. Note: for those with copies, Figures 3 and 8 should be in color.
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;January 30, 2007:
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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.
:Kjer, K. M., J. J. Gillespie and K. A. Ober. 2007. Opinions on multiple sequence alignment, and an empirical comparison of repeatability and accuracy between POY and structural alignment. Systematic Biology 56: 1-14. [PDF]
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;February 6, 2007:
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==August 30==
:Cancelled due to overlap with Rettenmeyer presentation
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Discussion of chapter 1 - A Macroevolutionary Research Program, an organizational meeting
  
;February 13, 2007:
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==September 6==
:Lutzoni, F., P. Wagner, V. Reeb, and S. Zoller. 2000. Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Sytematic Biology. 49: 628-651. [PDF]
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Discussion of chapter 2 - Fitting Statistical Models to Data, [http://phytools.org/mexico2018/ex/2/Intro-to-phylogenies.html Introduction to phylogenies in R]
  
== Information about joining and using the email list ==
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==September 13==
== Past Systematics Seminars ==
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Discussion of chapter 3 - Introduction to Brownian Motion
* Fall 2006
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* Spring 2005
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==September 20==
* Fall 2004
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Discussion of chapter 4 - Fitting Brownian Motion
* Spring 2004 (a.k.a. PhyloMath)
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==September 27==
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Discussion of chapter 5 - Multivariate Brownian Motion
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==October 4==
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Discussion of chapter 6 - Beyond Brownian Motion
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==October 11==
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Discussion of chapter 7 - Models of discrete character evolution
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==October 18==
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Discussion of chapter 8 - Fitting models of discrete character evolution — Lisa Terlova
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==October 25==
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Discussion of chapter 9 - Beyond the Mk model
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==November 1==
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Discussion of chapter 10 - Introduction to birth-death models — Zach Muscavitch
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==November 8==
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Discussion of chapter 11 - Fitting birth-death models
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==November 15==
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Discussion of chapter 12 - Beyond birth-death models
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==November 22==
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Discussion of chapter 13 - Characters and diversification rates - Amanda Hewes
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==December 6==
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Discussion of chapter 14 - Summary
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== Information for discussion leaders ==
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'''Seminar Format:''' Registered students be prepared to lead discussions, perhaps more than once depending on the number of participants.
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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. 
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'''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.
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 +
'''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:
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1. If the paper is available online through our library, it is sufficient to create a link to the DOI:
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<nowiki>:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]</nowiki>
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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:
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:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]
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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):
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<nowiki>:[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls Doyle et al. 2015.]</nowiki>
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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
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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.
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'''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. 
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Prepare 3-5 questions that you expect will spur discussion.  Ideally, you would distribute questions a day or two before our class meeting.
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 +
'''Projector:'''
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The Bamford room has joined the modern world--you should just need to plug in your computer or USB key to project.
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== Past Seminars ==
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* [[Systematics Seminar Spring 2019|Spring 2019]]
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* [[Systematics Seminar Fall 2018|Fall 2018]]
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* [[Systematics Seminar Spring 2018|Spring 2018]]
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* [[Systematics Seminar Fall 2017|Fall 2017]]
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* [[Systematics Seminar Fall 2014|Fall 2014]]
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* [[Systematics Seminar Fall 2013|Fall 2013]]
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* [[Systematics Seminar Spring 2012|Spring 2012]]
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* [[Systematics Seminar Fall 2011|Fall 2011]]
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* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography  Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)
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* [[Systematics Seminar Fall 2010|Fall 2010]]
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* [[Systematics Seminar Spring 2010|Spring 2010]]
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* [[Systematics Seminar Fall 2009|Fall 2009]]
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* [[Systematics Seminar Fall 2008|Fall 2008]]
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* [[Systematics Seminar Spring 2008|Spring 2008]]
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* [[Systematics Seminar Fall 2007|Fall 2007]]
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* [[Systematics Seminar Spring 2007|Spring 2007]]
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* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]
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* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]
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* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]
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* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]
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[[Category:EEB Seminars]]

Latest revision as of 17:36, 12 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.

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

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

October 11

Discussion of chapter 7 - Models of discrete character evolution

October 18

Discussion of chapter 8 - Fitting models of discrete character evolution — Lisa Terlova

October 25

Discussion of chapter 9 - Beyond the Mk model

November 1

Discussion of chapter 10 - Introduction to birth-death models — Zach Muscavitch

November 8

Discussion of chapter 11 - Fitting birth-death models

November 15

Discussion of chapter 12 - Beyond birth-death models

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:

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 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