Difference between revisions of "Systematics Seminar"

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== Meeting time and place ==
 
== Meeting time and place ==
For the Fall 2014 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 2:30-3:30pm'''
 
  
=== Topics ===
+
We meet on Fridays at 2 PM in the Bamford Room (TLS 171b).
As the semester progresses, please feel free to add to this running list of sources of systematic error, tests for that error, methods to account for that error, and relevant literature for that error.
+
  
{| border="1" cellpadding="1"
+
== Theme and Schedule for Fall 2019 ==
!style="background:#C0C0C0;" width="250"|Systematic Error
+
!style="background:#C0C0C0;" width="350"|Tests for Systematic Error
+
!style="background:#C0C0C0;" width="350"|Programs / Methods Accounting for Systematic Error
+
!style="background:#C0C0C0;" width="200"|Associated Literature
+
  
|-
+
[https://lukejharmon.github.io/pcm/ We will be reading Luke J. Harmon's book on comparative phylogenetic methods]
  
|| Nucleotide Composition Bias ||  || Include additional taxa, RY recoding ||
+
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
  
|| Amino Acid Composition Bias ||  || Dayhoff recoding ||
+
==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
  
|| Incomplete Lineage Sorting ||  ||  ||
+
==September 20==
 +
Discussion of chapter 4 - Fitting Brownian Motion
  
|-
+
==September 27==
 +
Discussion of chapter 5 - Multivariate Brownian Motion
  
|| Horizontal Gene Transfer / Hybridization / Gene Flow ||  ||  ||
+
==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
  
|| Among Site Rate Heterogeneity (ASRV) ||  ||  ||
+
==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
  
|| Among Lineage Rate Heterogeneity (ALRV) ||  ||  ||
+
==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
  
|| Heterotachy ||  ||  ||
+
==November 15==
 +
Discussion of chapter 12 - Beyond birth-death models - Katie Taylor
  
|-
+
==November 22==
 +
Discussion of chapter 13 - Characters and diversification rates - Amanda Hewes
  
|| Paralogy ||  ||  ||
+
==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.
  
|| Functional Convergence in Proteins / Selection ||  ||  || [[:File:Parker_et_al_2013.pdf‎|Parker et al. 2013]], sequence convergence in echolocating bats and cetaceans
+
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.
  
|| Missing Data (?) ||  ||  || [[:File:Wiens_and_Moen_2008.pdf‎|Wiens and Moen 2008]], but see
+
'''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:
[[:File:Lemmon_et_al_2009.pdf‎|Lemmon et al. 2009]]
+
  
|-
+
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.]
  
|| Taxon Sampling (?) || ||  ||
+
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
  
|| Non-Independence of Sites ||  ||  ||
+
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.
  
|| Overly Restrictive Priors || || ||
+
'''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. 
  
|| Sequencing Hardware Error || ||  ||
+
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.
  
=== Monday, 25 August 2014 ===
+
== Past Seminars ==
At this meeting we will discuss possible themes for this semester's seminar:
+
* [[Systematics Seminar Spring 2019|Spring 2019]]
 
+
* [[Systematics Seminar Fall 2018|Fall 2018]]
=== Monday, 1 September 2014 ===
+
* [[Systematics Seminar Spring 2018|Spring 2018]]
Labor Day, no meeting
+
* [[Systematics Seminar Fall 2017|Fall 2017]]
 
+
* [[Systematics Seminar Fall 2014|Fall 2014]]
=== Monday, 8 September 2014 ===
+
For this meeting, please come with an example (or examples) of a source of systematic error in datasets, and a paper that attempts to address this source of systematic error. We will use these examples and papers as a basis for discussions in upcoming weeks.
+
 
+
=== Monday, 15 September 2014 ===
+
Topic: An overview of potential systematic errors found in phylogenomic data sets
+
:[[:File:Rodriguez-Ezpeleta et al 2007. SystBiol.pdf|Rodriguez-Ezpeleta et al. 2007]], Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies
+
 
+
=== Monday, 22 September 2014 ===
+
Topic: Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2014-Xi-sysbio_syu055.pdf}} Xi et al. 2014
+
 
+
=== Monday, 29 September 2014 ===
+
Topic: David Swofford's presentation at the Frontiers in Phylogenetics Symposium, "Filtering and Partitioning Strategies for Phylogenomic Analyses", and SVDQuartets method from Chifman and Kukatko 2014 <br/>
+
 
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Chifman%20and%20Kubatko%20-%202014%20-%20Quartet%20Inference%20from%20SNP%20Data%20Under%20the%20Coalesce.pdf}} Chifman and Kubatko 2014
+
 
+
Optional (but a nice supplement to the paper above and also reviews most other species tree methods): Laura Kubatko talked about SVDQuartets in her lecture at the Woods Hole Molecular Evolution Workshop this past summer. Click on the link below, then click on "Slides (draft)" to download the PDF: the SVDQuartets explanation begins at slide 63.
+
 
+
[https://molevol.mbl.edu/index.php/Laura_Kubatko Kubato lecture]
+
 
+
Symposium talk recordings:
+
:Part 1  http://www.ustream.tv/recorded/52713111 <br/>
+
:Part 2  http://www.ustream.tv/recorded/52716590 (The first half of Swofford's talk starts towards the end of this recording) <br/>
+
:Part 3  http://www.ustream.tv/recorded/52720049 (The second half Swofford's talk picks up at the beginning of this recording) <br/>
+
 
+
Symposium schedule and abstracts:
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/2014FrontiersSymposiumSchedule.pdf}} 2014 Frontiers in Phylogenetics Symposium Schedule
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/2014FrontiersSymposiumAbstracts.pdf}} 2014 Frontiers in Phylogenetics Symposium Abstracts
+
 
+
=== Monday, 6 October 2014 ===
+
Topic: Paul Lewis's presentation at Evolution 2014, "Bayesian estimation of phylogenetic information content and implications for site-stripping"
+
:https://www.youtube.com/watch?v=kHa57G1imNY
+
 
+
Here is the paper referenced in Paul's talk:
+
 
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Genome%20Biology%20and%20Evolution%202011%20Zhong.pdf}} Zhong B., Deusch O., Goremykin V.V., Penny D., Biggs P.J., Atherton R.A., Nikiforova S.V., Lockhart P.J. 2011. Systematic error in seed plant phylogenomics. Genome Biology and Evolution. 3:1340–1348.
+
 
+
=== Monday, 13 October 2014 ===
+
 
+
:[[:File:Parker_et_al_2013.pdf‎|Parker et al. 2013]], sequence convergence in echolocating bats and cetaceans
+
 
+
=== Monday, 20 October 2014 ===
+
Topic: Hybridization/reticulate evolution
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/d/dc/Cui_2013.pdf}} Cui, R., Schumer, M., Kruesi, K., Walter, R., Andolfatto, P., Rosenthal, G.G. 2013. Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes. Evolution. 67(8):2166-2179.
+
 
+
=== Monday, 27 October 2014 ===
+
 
+
=== Monday, 3 November 2014 ===
+
 
+
=== Monday, 10 November 2014 ===
+
 
+
=== Monday, 17 November 2014 ===
+
 
+
=== Monday, 1 December 2014===
+
 
+
== Past Systematics Seminars ==
+
 
* [[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