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
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:{{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: [[Karolina Fučíková]]
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/BumbleBees2008.pdf}}Hines, H. 2008.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Cameron2007BumbleBees.pdf}}Cameron 2007 (for more info on the original phylogeny)
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=== Tuesday, September 23rd, 2008 ===
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|-
Discussion leader: [[Nic Tippery]]
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Rabosky-Lovette-2008_extinction.pdf}}Rabosky, D. L. and I. J. Lovette. 2008. Explosive evolutionary radiations: Decreasing speciation or increasing extinction through time? ''Evolution'' 62-8: 1866-1875.
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=== Tuesday, September 30th, 2008 ===
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|| Incomplete Lineage Sorting ||  ||  ||
Discussion leader: Yu(Daniel) Fan
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Luthey-Schulten%20et%20al%2C%20PNAS%202008%20%20vol.%20105%20%20no.%2037%20%2013953-13958.pdf}}Luthey-Schulten et al. 2008. Molecular signatures of ribosomal evolution. PNAS vol.105 no.37 13953-13958.
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=== Tuesday, October 7th, 2008 ===
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Discussion leader: Chris Owen
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Bond%20and%20Stockman%202008%283%29.pdf}}Bond and Stockman 2008
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=== Tuesday, October 14th, 2008 ===
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|-
Discussion leader: Yu(Daniel) Fan
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Luke%20Harmon%20et%20al.%202008.pdf}}Luke Harmon et al. 2008
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=== Tuesday, October 21st, 2008 ===
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|| Horizontal Gene Transfer / Hybridization / Gene Flow ||  ||  ||
Seminar postponed due to conflict with a popular Paleo Seminar.
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=== Tuesday, October 28th, 2008 ===
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|-
Discussion leader:
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[[Karolina Fucikova]]<br>
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/DNADiatoms.pdf}} Amato et al. 2007, a paper on cryptic species in Diatoms
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|| Among Site Rate Heterogeneity (ASRV) ||  ||  ||
  
=== Tuesday, November 4th, 2008 ===
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|-
Discussion leader: Geert Goemans
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Damgaard%20et%20al.%2C%202008%20Phylogeny%20Heelwalkers.pdf}}Damgaard et al., 2008
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|| Among Lineage Rate Heterogeneity (ALRV) ||  ||  ||
  
=== Tuesday, November 11th, 2008 ===
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|-
Discussion leader:
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=== Tuesday, November 18th, 2008 ===
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|| Heterotachy ||  ||  ||
Discussion leader:
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=== Tuesday, December 2nd, 2008 ===
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|-
Discussion leader:
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=== Tuesday, December 9th, 2008 ===
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|| Paralogy ||  ||  ||
Discussion leader:
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=== Some papers to pick from ===
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:{{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
  
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|-
  
[[#top|Back to top]]
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|| Missing Data (?) ||  ||  || [[:File:Wiens_and_Moen_2008.pdf‎|Wiens and Moen 2008]], but see
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[[:File:Lemmon_et_al_2009.pdf‎|Lemmon et al. 2009]]
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|-
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|| Taxon Sampling (?) ||  ||  ||
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|-
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|| Non-Independence of Sites ||  ||  ||
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|-
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|| Overly Restrictive Priors ||  ||  ||
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|-
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|| Sequencing Hardware Error ||  ||  ||
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|}
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=== Monday, 25 August 2014 ===
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At this meeting we will discuss possible themes for this semester's seminar:
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=== Monday, 1 September 2014 ===
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Labor Day, no meeting
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=== 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.
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=== Monday, 15 September 2014 ===
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Topic: An overview of potential systematic errors found in phylogenomic data sets
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:[[:File:Rodriguez-Ezpeleta et al 2007. SystBiol.pdf|Rodriguez-Ezpeleta et al. 2007]], Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies
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=== Monday, 22 September 2014 ===
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=== Monday, 29 September 2014 ===
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=== Monday, 6 October 2014 ===
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=== Monday, 13 October 2014 ===
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=== Monday, 20 October 2014 ===
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=== Monday, 27 October 2014 ===
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=== Monday, 3 November 2014 ===
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=== Monday, 10 November 2014 ===
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=== Monday, 17 November 2014 ===
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=== Monday, 1 December 2014===
  
 
== Past Systematics Seminars ==
 
== Past Systematics Seminars ==
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* [[Systematics Seminar Fall 2013|Fall 2013]]
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* [[Systematics Seminar Spring 2012|Spring 2012]]
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* [[Systematics Seminar Fall 2011|Fall 2011]]
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* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography  Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)
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* [[Systematics Seminar Fall 2010|Fall 2010]]
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* [[Systematics Seminar Spring 2010|Spring 2010]]
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* [[Systematics Seminar Fall 2009|Fall 2009]]
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* [[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 19:55, 10 September 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

Monday, 29 September 2014

Monday, 6 October 2014

Monday, 13 October 2014

Monday, 20 October 2014

Monday, 27 October 2014

Monday, 3 November 2014

Monday, 10 November 2014

Monday, 17 November 2014

Monday, 1 December 2014

Past Systematics Seminars