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. This (Spring, 2007) semester, we are meeting each '''Tuesday''' at '''4pm''' in the '''BioPharm 3rd. floor "fishbowl" conference room'''.
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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.  
  
== Schedule for Spring Semester 2007 ==
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[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
  
=== January 16, 2007 ===
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== Meeting time and place ==
:Organizational meeting, BioPharm 3rd. floor fishbowl, 4pm
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For the Fall 2014 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 2:30-3:30pm'''
  
=== January 23, 2007 ===
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=== Topics ===
:Smythe, A.B., M.J. Sanderson, and S.A. Nadler. 2006. Nematode Small Subunit Phylogeny Correlates with Alignment Parameters. ''Systematic Biology'' 55(6): 972-992.{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Smythe_Sanderson_Nadler_2006_SystBiol_55_972-992.pdf }}
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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.
  
:Note from Carrie: Please note that this is DIFFERENT than the paper we decided on at Tuesday's organizational meeting.
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{| border="1" cellpadding="1"
:This issue of Sys. Bio. is not yet available online therefore I will make a copy and put it in the EEB office. Those with a hard copy subscription of Sys. Bio. should have this issue. Note: for those with copies, Figures 3 and 8 should be in color.
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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
  
=== January 30, 2007 ===
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:Kjer, K. M., J. J. Gillespie and K. A. Ober. 2007. Opinions on multiple sequence alignment, and an empirical comparison of repeatability and accuracy between POY and structural alignment. ''Systematic Biology'' 56: 1-14. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Kjer_Gillespie_Ober_2007_SystBiol.pdf}}
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=== February 6, 2007 ===
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|| Nucleotide Composition Bias ||  || Include additional taxa, RY recoding ||
:Cancelled due to overlap with Rettenmeyer presentation
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=== February 13, 2007 ===
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:Lutzoni, F., P. Wagner, V. Reeb, and S. Zoller. 2000. Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. ''Sytematic Biology'' 49: 628-651. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Lutzoni_etal_2000_SystBiol_49_628-651.pdf}}
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=== February 20, 2007 ===
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|| Amino Acid Composition Bias ||  || Dayhoff recoding ||
:Huyse, T., and F. Volckaert. 2005. Comparing Host and Parasite Phylogenies: ''Gyrodactylus'' Flatworms Jumping from Goby to Goby. ''Systematic Biology'' 54(5): 710-718. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Huyse_Volckaert_2005_SystBiol_54_710-718_opt.pdf}}
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=== February 27, 2007 ===
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|-
There are two papers for this week's discussion. Read the Science paper first to get an overview of the whole quadripartite symbiosis; the Gerardo paper focuses only on the two fungal components.
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:Currie, C. R., B. Wong, A. E. Stuart, T. R. Schultz, S. A. Rehner, U. G. Mueller, G.-H. Sung, J. W. Spatafora and N. A. Straus. 2003. Ancient tripartite coevolution in the attine ant-microbe symbiosis. Science 299: 386-388. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Currie_etal_Science_299_386-388.pdf}}
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:Gerardo, N. M., U. G. Mueller, and C. R. Currie. 2006. Complex host-pathogen coevolution in the ''Apterostigma'' fungus-growing ant-microbe symbiosis. BMC Evolutionary Biology 6:88. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Gerardo_Mueller_Currie_2006_BMCEvolBiol_6_88.pdf}}
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=== March 13, 2007 ===
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|| Incomplete Lineage Sorting ||  ||  ||
:Diekmann, O. E., J. L. Olsen, W. T. Stam, R. P. M. Bak. 2003. Genetic variation within ''Symbiodinium'' clade B from the coral genus ''Madracis'' in the Caribbean (Netherlands Antilles). Coral Reefs. 22: 29–33. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Diekmann_etal_2003_CoralReefs_22_29-33.pdf}}
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:M. J. H. van Oppen. 2004. Mode of zooxanthella transmission does not affect zooxanthella diversity in acroporid corals. Marine Biology. 144: 1–7. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/vanOppen_2004_MarineBiol_144_1-7.pdf}}
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=== March 20, 2007 ===
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:Ruano-Rubio, V., and Fares, M. A. 2007. Artifactual phylogenies caused by correlated distribution of substitution rates among sites and lineages: the Good, the Bad, and the Ugly. Systematic Biology 56: 68-82. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/RuanoRubio_Fares_2007_SystBiol_56_68-82.pdf}}
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=== March 27, 2007 ===
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|| Horizontal Gene Transfer / Hybridization / Gene Flow ||  ||  ||
:Mooers, A. O., and S. B. Heard. 1997. Inferring evolutionary process from phylogenetic tree shape. The Quarterly Review of Biology 72: 31-54. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Mooers_Heard_1997_QuartRevBiol_72_31-54.pdf}}
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=== April 3, 2007 ===
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:Kelchner, S. A., and M. A. Thomas. 2006. Model use in phylogenetics: nine key questions. Trends in Ecology and Evolution 22: 87-94. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Kelchner_Thomas_2006_TREE_22_87-94.pdf}}
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== Information about joining and using the email list ==
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|| Among Site Rate Heterogeneity (ASRV) ||  ||  ||
  
=== To '''send''' a message to the list ===
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Address your message to <tt>systematics@darwin.eeb.uconn.edu</tt>.
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=== To '''subscribe''' to the list ===
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|| Among Lineage Rate Heterogeneity (ALRV) || ||  ||
Send an email message to the address <tt>majordomo@darwin.eeb.uconn.edu</tt> with a blank subject and a one-line message body saying only
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  subscribe systematics
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Note: it is best to avoid appending your signature to this message, as the majordomo program may try to interpret parts of your signature to be commands.
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=== To '''unsubscribe''' yourself ===
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Send a message to <tt>majordomo@darwin.eeb.uconn.edu</tt> saying only
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unsubscribe systematics
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|| Heterotachy ||  ||  ||
(again, leaving the subject blank and avoiding the signature if possible).
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|| Paralogy ||  ||  ||
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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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|| 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]]
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* [[Systematics Seminar Spring 2008|Spring 2008]]
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* [[Systematics Seminar Fall 2007|Fall 2007]]
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* [[Systematics Seminar Spring 2007|Spring 2007]]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004 (a.k.a. PhyloMath)]
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* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]
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[[Category:EEB Seminars]]

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