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 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 == | ||
− | + | 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. | |
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− | == | + | {| border="1" cellpadding="1" |
− | + | !style="background:#C0C0C0;" width="250"|Systematic Error | |
+ | !style="background:#C0C0C0;" width="350"|Tests for Systematic Error | ||
+ | !style="background:#C0C0C0;" width="350"|Programs / Methods Accounting for Systematic Error | ||
+ | !style="background:#C0C0C0;" width="200"|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 || || || [[:File:Parker_et_al_2013.pdf|Parker et al. 2013]], sequence convergence in echolocating bats and cetaceans | |
− | + | ||
− | + | |- | |
− | : | + | || 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 || || || | |
− | + | |- | |
− | + | ||
− | + | || 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 | ||
+ | :[[: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 === |
− | + | === 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=== | |
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− | === | + | |
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== 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 Fall 2007|Fall 2007]] | * [[Systematics Seminar Fall 2007|Fall 2007]] | ||
* [[Systematics Seminar Spring 2007|Spring 2007]] | * [[Systematics Seminar Spring 2007|Spring 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
Contents
- 1 Meeting time and place
- 1.1 Topics
- 1.2 Monday, 25 August 2014
- 1.3 Monday, 1 September 2014
- 1.4 Monday, 8 September 2014
- 1.5 Monday, 15 September 2014
- 1.6 Monday, 22 September 2014
- 1.7 Monday, 29 September 2014
- 1.8 Monday, 6 October 2014
- 1.9 Monday, 13 October 2014
- 1.10 Monday, 20 October 2014
- 1.11 Monday, 27 October 2014
- 1.12 Monday, 3 November 2014
- 1.13 Monday, 10 November 2014
- 1.14 Monday, 17 November 2014
- 1.15 Monday, 1 December 2014
- 2 Past Systematics Seminars
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 | ||
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
- Fall 2013
- Spring 2012
- Fall 2011
- Spring 2011 (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)
- Fall 2010
- Spring 2010
- Fall 2009
- Fall 2008
- Spring 2008
- Fall 2007
- Spring 2007
- Fall 2006
- Spring 2005
- Fall 2004
- Spring 2004