Difference between revisions of "Systematics Seminar"

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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.  
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This is the home page of the UConn EEB department's Co-evolution Seminar, taking the place of the Systematics Seminar this semester (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'''
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For the Spring 2015 semester, we are meeting in the '''Bamford Room (TLS 171B) Day/time TBD'''
  
 
=== Topics ===
 
=== 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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This seminar will be split between class meetings that emphasize phylogenetic underpinnings, tree comparisons, and reconciliation methods, with those focused on the evolutionary processes underlying co-evolutionary phenomena (as well as the forces and circumstances that, more often than not, prevent it from occurring). And while parasites will figure large in our readings and discussions, we will also explore insect-plant co-evolution, endosymbionts and other mutualisms, mimicry, and others.  
  
{| border="1" cellpadding="1"
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=== Tuesday, 20 January 2015 ===
!style="background:#C0C0C0;" width="250"|Systematic Error
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At this meeting we will discuss possible themes for this semester's seminar, and determine the meeting time
!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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<!--
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=== Monday, 1 September 2014 ===
  
|| Nucleotide Composition Bias ||  || Include additional taxa, RY recoding ||
 
  
|-
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=== Monday, 8 September 2014 ===
  
|| Amino Acid Composition Bias ||  || Dayhoff recoding ||
 
  
|-
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=== Monday, 15 September 2014 ===
  
|| Incomplete Lineage Sorting ||  ||  ||
 
  
|-
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=== Monday, 22 September 2014 ===
  
|| 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 ===
 
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 ===
 
=== 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
 
 
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 ===
 
=== 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 ===
 
=== 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 ===
 
=== Monday, 20 October 2014 ===
Topic: Hybridization/reticulate evolution
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:{{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.
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=== Monday, 27 October 2014 ===
 
=== 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 ===
 
=== Monday, 3 November 2014 ===
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Nakhleh_TrendsInEcologyAndEvolution_2013.pdf}}Nakhleh Trends In Ecology And Evolution 2013
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=== Monday, 10 November 2014 ===
 
=== 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
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=== Monday, 17 November 2014 ===
 
=== 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
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=== Monday, 1 December 2014===
 
=== 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
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== Past Systematics Seminars ==
 
== Past Systematics Seminars ==

Revision as of 17:41, 14 January 2015

This is the home page of the UConn EEB department's Co-evolution Seminar, taking the place of the Systematics Seminar this semester (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 Spring 2015 semester, we are meeting in the Bamford Room (TLS 171B) Day/time TBD

Topics

This seminar will be split between class meetings that emphasize phylogenetic underpinnings, tree comparisons, and reconciliation methods, with those focused on the evolutionary processes underlying co-evolutionary phenomena (as well as the forces and circumstances that, more often than not, prevent it from occurring). And while parasites will figure large in our readings and discussions, we will also explore insect-plant co-evolution, endosymbionts and other mutualisms, mimicry, and others.

Tuesday, 20 January 2015

At this meeting we will discuss possible themes for this semester's seminar, and determine the meeting time


Past Systematics Seminars