Difference between revisions of "Systematics Seminar"

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== Meeting time and place ==
 
== Meeting time and place ==
Every Monday (except Labor Day, Sep. 4) at 3pm in the Bamford Room (TLS 171b).
 
  
== Schedule for Fall 2017 ==
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We meet on Fridays at 2 PM in the Bamford Room (TLS 171b).
=== Sep. 4 ===
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Labor day holiday (no meeting)
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=== Sep. 11 ===
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== Theme and Schedule for Fall 2019 ==
Paul and Suman will lead the discussion of the paper:
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Brown, J. M., and R. C. Thomson. 2017. Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses. Systematic Biology 66(4): 517-530. [https://doi.org/10.1093/sysbio/syw101 doi:10.1093/sysbio/syw101]
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[https://lukejharmon.github.io/pcm/ We will be reading Luke J. Harmon's book on comparative phylogenetic methods]
  
=== Sep. 18 ===
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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.
Noah Reid will lead discussion on this paper today:
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Shen, Xing-Xing, Chris Todd Hittinger, and Antonis Rokas. "Contentious relationships in phylogenomic studies can be driven by a handful of genes." Nature Ecology & Evolution 1 (2017): 0126.
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==August 30==
 +
Discussion of chapter 1 - A Macroevolutionary Research Program, an organizational meeting
  
https://www.nature.com/articles/s41559-017-0126
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==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]
  
We’ll be particularly interested in comparing it to this past Monday’s paper:
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==September 13==
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Discussion of chapter 3 - Introduction to Brownian Motion
  
Brown, Jeremy M., and Robert C. Thomson. "Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses." Systematic biology 66.4 (2016): 517-530.
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==September 20==
 +
Discussion of chapter 4 - Fitting Brownian Motion
  
https://academic.oup.com/sysbio/article-abstract/66/4/517/2950896
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==September 27==
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Discussion of chapter 5 - Multivariate Brownian Motion
  
=== Sep. 25 ===
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==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]
  
Katie Taylor will lead a discussion of this (very) recent species delimitation paper in Systematic Biology:
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==October 11==
 +
Discussion of chapter 7 - Models of discrete character evolution — Lisa Terlova
  
Cadena, C. D., Zapata, F., & Jiménez, I. (2017). Issues and Perspectives in Species Delimitation using Phenotypic Data—Atlantean Evolution in Darwin’s Finches. Systematic Biology. [http://doi.org/10.1093/sysbio/syx071 DOI 10.1093/sysbio/syx071]
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==October 18==
 +
Discussion of chapter 8 - Fitting models of discrete character evolution — Lisa Terlova
  
=== Oct. 2  ===
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==October 25==
 +
Discussion of chapter 9 - Beyond the Mk model - Kevin Keegan
  
Charlie Delavoi will lead a discussion on the BPP process for species delimitation: http://abacus.gene.ucl.ac.uk/ziheng/pdf/2015YangCZv61p854.pdf
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==November 1==
 +
Discussion of chapter 10 - Introduction to birth-death models — Zach Muscavitch
  
Ziheng Yang; The BPP program for species tree estimation and species delimitation, Current Zoology, Volume 61, Issue 5, 1 October 2015, Pages 854–865, https://doi.org/10.1093/czoolo/61.5.854
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==November 8==
 +
Discussion of chapter 11 - Fitting birth-death models — Tanner Matson
  
=== Oct. 9 (next meeting) ===
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==November 15==
This is a study led by Nicholas Magain as part of his Ph.D. at Duke and deals with species complexes in lichenized fungi. He compares multiple species delimitations in two complexes.
+
Discussion of chapter 12 - Beyond birth-death models - Katie Taylor
  
Magain, N., et al. In press. Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus ''Peltigera'' section ''Polydactylon.'' Molecular Phylogenetics and Evolution. [https://doi.org/10.1016/j.ympev.2017.08.013 DOI:10.1016/j.ympev.2017.08.013]
+
==November 22==
 
+
Discussion of chapter 13 - Characters and diversification rates - Amanda Hewes
Also, for those interested attached is a paper by Leavitt et al, providing a review of species delimitation methods (in 2015):
+
Leavitt, SD, CS Moreau, and HT Lumbsch. 2015. The Dynamic Discipline of Species 2 Delimitation: Progress Toward Effectively Recognizing Species Boundaries in Natural Populations. Chapter 2 in DK Upreti et al. (eds.), Recent Advances in Lichenology, Springer India.
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[https://doi.org/10.1007/978-81-322-2235-4_2 DOI:10.1007/978-81-322-2235-4_2]
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=== Oct. 16 ===
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=== Oct. 23 ===
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=== Oct. 30 ===
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+
=== Nov. 6 ===
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=== Nov. 13 ===
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=== Nov. 20 ===
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=== Nov. 27 ===
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=== Dec. 4 ===
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 +
==December 6==
 +
Discussion of chapter 14 - Summary
  
 
== Information for discussion leaders ==
 
== Information for discussion leaders ==
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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.
  
 
== Past Seminars ==
 
== 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 2014|Fall 2014]]
 
* [[Systematics Seminar Fall 2013|Fall 2013]]
 
* [[Systematics Seminar Fall 2013|Fall 2013]]

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