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.  
  
 
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
 
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
  
 
== Meeting time and place ==
 
== Meeting time and place ==
We are meeting this semester in the '''Bamford Room (TLS 171) Tuesdays 4-5pm'''.
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For the Fall 2014 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 2:30-3:30pm'''
  
== Theme for Fall Semester 2008 ==
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=== Topics ===
We've agreed to start the semester with some articles on molecular dating, then spend a couple of weeks on taxonomy papers, and possibly read a revised version of David Baum's tree thinking book. If you are interested in leading a particular week's discussion, please sign up below.
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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.
  
== Schedule for Fall Semester 2008 ==
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{| border="1" cellpadding="1"
'''Note: the papers linked here require a user name and password to access.''' If you have forgotten the user name and/or password, contact [mailto:paul.lewis@uconn.edu Paul Lewis]. If you want to upload a PDF file for an upcoming discussion, use the [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/upload.html Systematics Seminar PDF upload form]. Uploading PDFs requires the same user name and password as viewing PDFs.
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!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
  
=== Tuesday, September 2nd, 2008: ===
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|-
Discussion leader: [[Elizabeth Wade]]
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Drummond%20%26%20Rambaut%202007.pdf}}Drummond & Rambaut 2007.pdf
+
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Molecular%20Dating%20Review.pdf}}Molecular Dating Review (for more background info)
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|| Nucleotide Composition Bias ||  || Include additional taxa, RY recoding ||
  
=== Tuesday, September 9th, 2008 ===
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|-
Discussion leader: [[Christopher Owen]]
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Lepage%20et%20al.%202007%20MBE%20Relaxed%20Molec%20Clock%20Models.pdf}}Lepage et al. 2007
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=== Tuesday, September 16th, 2008 ===
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|| Amino Acid Composition Bias ||  || Dayhoff recoding ||
Discussion leader:
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=== Tuesday, September 23rd, 2008 ===
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|-
Discussion leader:
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=== Tuesday, September 30th, 2008 ===
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|| Incomplete Lineage Sorting ||  ||  ||
Discussion leader:
+
  
=== Tuesday, October 7th, 2008 ===
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|-
Discussion leader:
+
  
=== Tuesday, October 14th, 2008 ===
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|| Horizontal Gene Transfer / Hybridization / Gene Flow ||  ||  ||
Discussion leader:
+
  
=== Tuesday, October 21st, 2008 ===
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|-
Discussion leader:
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=== Tuesday, October 28th, 2008 ===
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|| Among Site Rate Heterogeneity (ASRV) ||  ||  ||
Discussion leader:
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=== Tuesday, November 4th, 2008 ===
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|-
Discussion leader:
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=== Tuesday, November 11th, 2008 ===
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|| Among Lineage Rate Heterogeneity (ALRV) ||  ||  ||
Discussion leader:
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=== Tuesday, November 18th, 2008 ===
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|-
Discussion leader:
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=== Tuesday, December 2nd, 2008 ===
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|| Heterotachy ||  ||  ||
Discussion leader:
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=== Tuesday, December 9th, 2008 ===
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|-
Discussion leader:
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=== Some papers to pick from ===
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|| Paralogy ||  ||  ||
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/DivergenceTimesLargeTrees2007.pdf}} Britton et al. 2007 <br>
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/SkewDivergenceTimes2008.pdf}}Burbrink & Pyron 2008
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<br>
+
  
 +
|-
  
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|| Functional Convergence in Proteins / Selection ||  ||  || [[:File:Parker_et_al_2013.pdf‎|Parker et al. 2013]], sequence convergence in echolocating bats and cetaceans
  
[[#top|Back to top]]
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|-
 +
 
 +
|| Missing Data (?) ||  ||  || [[:File:Wiens_and_Moen_2008.pdf‎|Wiens and Moen 2008]], but see
 +
[[:File:Lemmon_et_al_2009.pdf‎|Lemmon et al. 2009]]
 +
 
 +
|-
 +
 
 +
|| Taxon Sampling (?) ||  ||  ||
 +
 
 +
|-
 +
 
 +
|| Non-Independence of Sites ||  ||  ||
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 +
|-
 +
 
 +
|| Overly Restrictive Priors ||  ||  ||
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 +
|-
 +
 
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|| Sequencing Hardware Error ||  ||  ||
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 +
|}
 +
 
 +
=== Monday, 25 August 2014 ===
 +
At this meeting we will discuss possible themes for this semester's seminar:
 +
 
 +
=== Monday, 1 September 2014 ===
 +
Labor Day, no meeting
 +
 
 +
=== 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 ===
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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
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 +
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 ==
 
== Past Systematics Seminars ==
 +
* [[Systematics Seminar Fall 2013|Fall 2013]]
 +
* [[Systematics Seminar Spring 2012|Spring 2012]]
 +
* [[Systematics Seminar Fall 2011|Fall 2011]]
 +
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography  Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)
 +
* [[Systematics Seminar Fall 2010|Fall 2010]]
 +
* [[Systematics Seminar Spring 2010|Spring 2010]]
 +
* [[Systematics Seminar Fall 2009|Fall 2009]]
 +
* [[Systematics Seminar Fall 2008|Fall 2008]]
 
* [[Systematics Seminar Spring 2008|Spring 2008]]
 
* [[Systematics Seminar Spring 2008|Spring 2008]]
 
* [[Systematics Seminar Fall 2007|Fall 2007]]
 
* [[Systematics Seminar Fall 2007|Fall 2007]]

Revision as of 18:15, 20 November 2014

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

For the Fall 2014 semester, we are meeting in the Bamford Room (TLS 171B) Mondays 2:30-3:30pm

Topics

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.

Systematic Error Tests for Systematic Error Programs / Methods Accounting for Systematic Error Associated Literature
Nucleotide Composition Bias Include additional taxa, RY recoding
Amino Acid Composition Bias Dayhoff recoding
Incomplete Lineage Sorting
Horizontal Gene Transfer / Hybridization / Gene Flow
Among Site Rate Heterogeneity (ASRV)
Among Lineage Rate Heterogeneity (ALRV)
Heterotachy
Paralogy
Functional Convergence in Proteins / Selection Parker et al. 2013, sequence convergence in echolocating bats and cetaceans
Missing Data (?) Wiens and Moen 2008, but see

Lemmon et al. 2009

Taxon Sampling (?)
Non-Independence of Sites
Overly Restrictive Priors
Sequencing Hardware Error

Monday, 25 August 2014

At this meeting we will discuss possible themes for this semester's seminar:

Monday, 1 September 2014

Labor Day, no meeting

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

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

Pdficon small.gif 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

Pdficon small.gif 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.

Kubato lecture

Symposium talk recordings:

Part 1 http://www.ustream.tv/recorded/52713111
Part 2 http://www.ustream.tv/recorded/52716590 (The first half of Swofford's talk starts towards the end of this recording)
Part 3 http://www.ustream.tv/recorded/52720049 (The second half Swofford's talk picks up at the beginning of this recording)

Symposium schedule and abstracts:

Pdficon small.gif 2014 Frontiers in Phylogenetics Symposium Schedule
Pdficon small.gif 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:

Pdficon small.gif 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

Parker et al. 2013, sequence convergence in echolocating bats and cetaceans

Monday, 20 October 2014

Topic: Hybridization/reticulate evolution

Pdficon small.gif 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

Pdficon small.gifWisecaver-Hackett-MPE 2.pdf

Monday, 3 November 2014

Pdficon small.gifNakhleh Trends In Ecology And Evolution 2013

Monday, 10 November 2014

Pdficon small.gifMol Biol Evol-2013-Roure-197-214.pdf

Monday, 17 November 2014

Pdficon small.gifSyst Biol-2014-De Oliveira Martins-sysbio_syu082.pdf

Monday, 1 December 2014

Pdficon small.gifLambert et al. - 2015 - When do species-tree and concatenated estimates di.pdf

Past Systematics Seminars