Systematics Seminar

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== Meeting time and place ==
 
== Meeting time and place ==
For the Fall 2013 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''
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For the Fall 2014 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 2:30-3:30pm'''
  
=== Monday, 26 August 2013 ===
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=== 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.
 +
 
 +
{| border="1" cellpadding="1"
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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
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 +
|-
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|| Nucleotide Composition Bias ||  || Include additional taxa, RY recoding ||
 +
 
 +
|-
 +
 
 +
|| Amino Acid Composition Bias ||  || Dayhoff recoding ||
 +
 
 +
|-
 +
 
 +
|| Incomplete Lineage Sorting ||  ||  ||
 +
 
 +
|-
 +
 
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|| Horizontal Gene Transfer / Hybridization / Gene Flow ||  ||  ||
 +
 
 +
|-
 +
 
 +
|| Among Site Rate Heterogeneity (ASRV) ||  ||  ||
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 +
|-
 +
 
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|| Among Lineage Rate Heterogeneity (ALRV) ||  ||  ||
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 +
|-
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|| Heterotachy ||  ||  ||
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|-
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|| Paralogy ||  ||  ||
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 +
|-
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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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 +
|-
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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]]
 +
 
 +
|-
 +
 
 +
|| 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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 +
|}
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 +
=== Monday, 25 August 2014 ===
 
At this meeting we will discuss possible themes for this semester's seminar:
 
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 ===
 +
 +
=== 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 ===
 +
 +
=== Monday, 17 November 2014 ===
 +
 +
=== Monday, 1 December 2014===
  
 
== Past Systematics Seminars ==
 
== Past Systematics Seminars ==
 +
* [[Systematics Seminar Fall 2013|Fall 2013]]
 
* [[Systematics Seminar Spring 2012|Spring 2012]]
 
* [[Systematics Seminar Spring 2012|Spring 2012]]
 
* [[Systematics Seminar Fall 2011|Fall 2011]]
 
* [[Systematics Seminar Fall 2011|Fall 2011]]

Latest revision as of 15:55, 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

Contents

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

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