Difference between revisions of "Systematics Seminar"

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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 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.  
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[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
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== Meeting time and place ==
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We meet on Fridays at 2 PM in the Bamford Room (TLS 171b).
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== Theme and Schedule for Fall 2019 ==
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[https://lukejharmon.github.io/pcm/ We will be reading Luke J. Harmon's book on comparative phylogenetic methods]
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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.
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==August 30==
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Discussion of chapter 1 - A Macroevolutionary Research Program, an organizational meeting
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==September 6==
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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]
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==September 13==
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Discussion of chapter 3 - Introduction to Brownian Motion
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==September 20==
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Discussion of chapter 4 - Fitting Brownian Motion
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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<br>[https://github.com/kevinliam/Miscellaneous/blob/master/add_tree_info.zip Kevin shows us how to add images to plotted trees in R]
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==October 11==
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Discussion of chapter 7 - Models of discrete character evolution — Lisa Terlova
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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 - Kevin Keegan
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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 — Tanner Matson
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==November 15==
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Discussion of chapter 12 - Beyond birth-death models - Katie Taylor
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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 ==
 
'''Seminar Format:''' Registered students be prepared to lead discussions, perhaps more than once depending on the number of participants.  
 
'''Seminar Format:''' Registered students be prepared to lead discussions, perhaps more than once depending on the number of participants.  
  
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'''Projector:'''  
 
'''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.)
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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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[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
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== Meeting time and place ==
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For the Fall 2015 semester, we are meeting in the '''Bamford Room (TLS 171B), Tuesdays 2:30-3:30pm'''
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=== Tuesday, 1 September 2015, 3pm, Bamford Room (TLS 171b) ===
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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.
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=== Tuesday, 8 September 2015, 2:30pm, Bamford Room (TLS 171b) ===
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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:
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:[https://dropbox.uconn.edu/dropbox?n=RevBayes1.zip&p=WHwP8lS7EY10jpwMs RevBayes1] (simdata.nex plus test.Rev script)
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:[http://revbayes.github.io/about.html RevBayes website]
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A sample qsub script to run RevBayes on the BBC cluster:
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#$ -S /bin/bash
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#$ -cwd
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#$ -m ea
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#$ -M suman.neupane@uconn.edu
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#$ -N TimeTree
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rb GTR_Gamma.nonclock.Rev
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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
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rb GTR_Gamma.nonclock.Rev
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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/ http://bioinformatics.uconn.edu/contact-us/]
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=== Tuesday, 15 September 2015, 2:30pm, Bamford Room (TLS 171b) ===
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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):
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:[https://dropbox.uconn.edu/dropbox?n=Syst%20Biol-2014-H%F6hna-753-71.pdf&p=EWMqcsduO0GeULlr8Y Höhna et al. 2014. Probabilistic Graphical Model Representation in Phylogenetics. Systematic Biology. 63:753–771]
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You can also get the paper without requiring a password if you are on campus or connected via VPN using this link:
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:[http://dx.doi.org/10.1093/sysbio/syu039 Höhna et al. 2014. Probabilistic Graphical Model Representation in Phylogenetics. Systematic Biology. 63:753–771]
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Paul will also demonstrate how to use RevBayes on our bioinformatics cluster (probably the best way to run it, especially for long runs).
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=== Tuesday, 29 September 2015, 2:30pm, Bamford Room (TLS 171b) ===
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This week we'll talk about the new "Open Tree of Life", reading the paper, and maybe exploring the website (http://opentreeoflife.org/)
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:[http://www.pnas.org/content/early/2015/09/16/1423041112 Hinchliff et al. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. PNAS. ]
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=== Tuesday, 6 October 2015, 2:30pm, Bamford Room (TLS 171b) ===
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This week we'll indulge Elizabeth's interest in salamanders, and also talk about molecular dating
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:[http://sysbio.oxfordjournals.org/content/early/2015/09/18/sysbio.syv061.full.pdf+html Shen et al. Enlarged Multilocus Dataset Provides Surprisingly Younger Time of Origin for the Plethodontidae, the Largest Family of Salamanders. Sys. Bio. in press]
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=== Tuesday, 13 October 2015, 2:30pm, Bamford Room (TLS 171b) ===
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This week we'll take a look at a paper comparing small and large datasets when constructing trees. Also snakes!
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:[https://sararuane.files.wordpress.com/2013/12/authors-accepted-copy-not-typeset-or-proofed.pdf 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]
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EDIT here is the published version
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:[http://www.biomedcentral.com/content/pdf/s12862-015-0503-1.pdf Ruane et al., 2015]
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=== Tuesday, 20 October 2015, 2:30pm, Bamford Room (TLS 171b) ===
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This week we'll jump back into an anchored phylogenomics dataset, and talk about (yet another) bird phylogeny.
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:[http://www.nature.com/nature/journal/vaop/ncurrent/pdf/nature15697.pdf Prum et al. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature.]
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:[http://www.nature.com/nature/journal/vaop/ncurrent/pdf/nature15638.pdf Accompanying News and Views article.]
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:[http://www.allaboutbirds.org/earliest-beginnings-of-bird-evolution-brought-into-focus-with-new-dna-analysis/ Relevant blog post!]
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=== Tuesday, 26 October 2015, 2:30pm, Bamford Room (TLS 171b) ===
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Some back and forth commentaries!
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== Past Systematics Seminar Fall 2014|Fall 2014]]
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== Past Seminars ==
 +
* [[Systematics Seminar Spring 2019|Spring 2019]]
 +
* [[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]]
 
* [[Systematics Seminar Fall 2013|Fall 2013]]
 
* [[Systematics Seminar Fall 2013|Fall 2013]]
 
* [[Systematics Seminar Spring 2012|Spring 2012]]
 
* [[Systematics Seminar Spring 2012|Spring 2012]]

Latest revision as of 17:47, 25 October 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
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:

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