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'''
+
Every Friday at 11 am in the Bamford Room (TLS 171b).
  
=== Topics ===
+
== Schedule for Spring 2018 ==
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.
+
=== Jan. 26 ===
 +
We will begin with an overview of comparative methods:
  
{| border="1" cellpadding="1"
+
Cornwell W, Nakagawa S. 2017. Phylogenetic comparative methods. Curr Biol. 27(9):R333-R336. [https://doi.org/10.1016/j.cub.2017.03.049 doi: 10.1016/j.cub.2017.03.049]
!style="background:#C0C0C0;" width="250"|Systematic Error
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!style="background:#C0C0C0;" width="350"|Tests for Systematic Error
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!style="background:#C0C0C0;" width="350"|Programs / Methods Accounting for Systematic Error
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!style="background:#C0C0C0;" width="200"|Associated Literature
+
  
|-
+
=== Feb. 2 (next meeting) ===
 +
Peter Turchin will be our guest to lead discussion of this paper:
  
|| Nucleotide Composition Bias ||  || Include additional taxa, RY recoding ||
+
Watts J, Sheehan O, Atkinson QD, Bulbulia J, Gray RD. 2016. Ritual human sacrifice promoted and sustained the evolution of stratified societies.Nature. 532:228-31. [https://doi.org/10.1038/nature17159  doi: 10.1038/nature17159]
  
|-
+
=== Feb. 9 ===
  
|| Amino Acid Composition Bias ||  || Dayhoff recoding ||
+
Noah Reid will lead a discussion of "Positive association between population genetic differentiation and speciation rates in New World birds." Proceedings of the National Academy of Sciences 114.24 (2017): 6328-6333. [https://doi.org/10.1073/pnas.1617397114 doi: 10.1073/pnas.1617397114]
  
|-
+
=== Feb. 16 ===
  
|| Incomplete Lineage Sorting || ||  ||
+
=== Feb. 23 ===
  
|-
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=== Mar. 2 ===
  
|| Horizontal Gene Transfer / Hybridization / Gene Flow ||  ||  ||
+
=== Mar. 9 ===
  
|-
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=== Mar. 16 ===
  
|| Among Site Rate Heterogeneity (ASRV) ||  ||  ||
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===Mar. 23 ===
  
|-
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=== Mar. 30 ===
  
|| Among Lineage Rate Heterogeneity (ALRV) || ||  ||
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=== Apr. 6 ===
  
|-
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=== Apr. 13 ===
  
|| Heterotachy ||  ||  ||
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=== Apr. 20 ===
  
|-
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=== Apr. 27 ===
  
|| Paralogy ||  ||  ||
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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.
  
|-
+
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. 
  
|| Functional Convergence in Proteins / Selection ||  ||  || [[:File:Parker_et_al_2013.pdf‎|Parker et al. 2013]], sequence convergence in echolocating bats and cetaceans
+
'''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:
  
|| Missing Data (?) || ||  || [[:File:Wiens_and_Moen_2008.pdf‎|Wiens and Moen 2008]], but see
+
1. If the paper is available online through our library, it is sufficient to create a link to the DOI:
[[:File:Lemmon_et_al_2009.pdf‎|Lemmon et al. 2009]]
+
  <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:
  
|| Taxon Sampling (?) ||  ||  ||
+
:[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.
  
|| Non-Independence of Sites ||  ||  ||
+
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.
  
|| Overly Restrictive Priors || || ||
+
'''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.
  
|| Sequencing Hardware Error ||  ||  ||
+
'''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 Fall 2017|Fall 2017]]
=== Monday, 25 August 2014 ===
+
At this meeting we will discuss possible themes for this semester's seminar:
+
 
+
=== Monday, 1 September 2014 ===
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Labor Day, no meeting
+
 
+
=== Monday, 8 September 2014 ===
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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 ===
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Topic: Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies
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:{{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 ===
+
 
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Wisecaver-Hackett-MPE%202.pdf}}Wisecaver-Hackett-MPE 2.pdf
+
 
+
=== Monday, 3 November 2014 ===
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Nakhleh_TrendsInEcologyAndEvolution_2013.pdf}}Nakhleh Trends In Ecology And Evolution 2013
+
 
+
=== Monday, 10 November 2014 ===
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Mol%20Biol%20Evol-2013-Roure-197-214.pdf}}Mol Biol Evol-2013-Roure-197-214.pdf
+
 
+
=== Monday, 17 November 2014 ===
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2014-De%20Oliveira%20Martins-sysbio_syu082.pdf}}Syst Biol-2014-De Oliveira Martins-sysbio_syu082.pdf
+
 
+
=== Monday, 1 December 2014===
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Lambert%20et%20al.%20-%202015%20-%20When%20do%20species-tree%20and%20concatenated%20estimates%20di.pdf}}Lambert et al. - 2015 - When do species-tree and concatenated estimates di.pdf
+
 
+
== Past Systematics Seminars ==
+
 
* [[Systematics Seminar Fall 2014|Fall 2014]]
 
* [[Systematics Seminar Fall 2014|Fall 2014]]
 
* [[Systematics Seminar Fall 2013|Fall 2013]]
 
* [[Systematics Seminar Fall 2013|Fall 2013]]

Revision as of 13:26, 6 February 2018

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

Every Friday at 11 am in the Bamford Room (TLS 171b).

Schedule for Spring 2018

Jan. 26

We will begin with an overview of comparative methods:

Cornwell W, Nakagawa S. 2017. Phylogenetic comparative methods. Curr Biol. 27(9):R333-R336. doi: 10.1016/j.cub.2017.03.049

Feb. 2 (next meeting)

Peter Turchin will be our guest to lead discussion of this paper:

Watts J, Sheehan O, Atkinson QD, Bulbulia J, Gray RD. 2016. Ritual human sacrifice promoted and sustained the evolution of stratified societies.Nature. 532:228-31. doi: 10.1038/nature17159

Feb. 9

Noah Reid will lead a discussion of "Positive association between population genetic differentiation and speciation rates in New World birds." Proceedings of the National Academy of Sciences 114.24 (2017): 6328-6333. doi: 10.1073/pnas.1617397114

Feb. 16

Feb. 23

Mar. 2

Mar. 9

Mar. 16

Mar. 23

Mar. 30

Apr. 6

Apr. 13

Apr. 20

Apr. 27

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