Difference between revisions of "Systematics Seminar"

From EEBedia
Jump to: navigation, search
(Tuesday, October 27th, 2009)
(Monday, 6 October 2014)
(210 intermediate revisions by 33 users not shown)
Line 1: Line 1:
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 ==
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm'''.
+
For the Fall 2014 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 2:30-3:30pm'''
  
== Theme for Fall Semester 2009 ==
+
=== 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.
This semester we will focus on speciation and hybridization, then transition into phylogeography/ historical biogeography. Random papers/ themes, however, are welcomed.
+
  
== Schedule for Fall Semester 2009 ==
+
{| 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.
+
!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
  
=== Tuesday, September 8th, 2009: ===
+
|-
Discussion leader: [[Elizabeth Wade]]
+
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Bossu_Near_2009_SysBio.pdf}}Bossu_Near_2009_SysBio.pdf
+
|| Nucleotide Composition Bias ||  || Include additional taxa, RY recoding ||
  
=== Tuesday, September 15th, 2009 ===
+
|-
  
Discussion Leader: Elizabeth Timpe
+
|| Amino Acid Composition Bias ||  || Dayhoff recoding ||
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Bonett%20and%20Chippindale%202004.pdf}}Bonett and Chippindale 2004.pdf
+
|-
  
=== Tuesday, September 22nd, 2009 ===
+
|| Incomplete Lineage Sorting ||  ||  ||
  
Discussion leaders: Nic Tippery and Dave Wagner
+
|-
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Whitfield-etal-2006_Apis-biogeog.pdf}}Whitfield et al. 2006. Thrice Out of Africa: Ancient and Recent Expansions of the Honey Bee, ''Apis mellifera''. ''Science'' 314: 642-645.
+
|| Horizontal Gene Transfer / Hybridization / Gene Flow ||  ||  ||
  
http://www.sciencemag.org/cgi/content/abstract/314/5799/642
+
|-
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Albrecht-etal-2007_Dreissena-native.pdf}}Albrecht et al. 2007. Invaders or endemics? Molecular phylogenetics, biogeography and systematics of ''Dreissena'' in the Balkans. ''Freshwater Biology'' 52: 1525-1536.
+
|| Among Site Rate Heterogeneity (ASRV) ||  ||  ||
  
http://www3.interscience.wiley.com/journal/117962459/abstract
+
|-
  
=== Tuesday, September 29th, 2009 ===
+
|| Among Lineage Rate Heterogeneity (ALRV) ||  ||  ||
  
Discussion leader: Chris Owen
+
|-
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Clark_et_al-2008-SystBio.pdf}}Clark_et_al-2008-SystBio.pdf
+
|| Heterotachy ||  ||  ||
  
=== Tuesday, October 6th, 2009 ===
+
|-
Discussion leader: Daniel Fan
+
  
We will continue talking about Dispersal-Extinction-Cladogesis (DEC) model this week. In 2005, Ree et al. proposed the initial version of DEC although this approach was not named at that time. In 2008, Ree and Smith developed it and published a paper in Sys. Bio., which might be thought as the second version. The paper we will read is about the third version of DEC, likelihood with fossil, and they call it DEC*.
+
|| Paralogy || ||  ||
   
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Moore_2009_.pdf}}Moore et al. 2009. Incorporating Fossil Data in Biogeographic Inference: A Likelihood Approach.
+
  
=== Tuesday, October 13th, 2009 ===
+
|-
  
Juan Carlos Villarreal
+
|| Functional Convergence in Proteins / Selection ||  ||  || [[:File:Parker_et_al_2013.pdf‎|Parker et al. 2013]], sequence convergence in echolocating bats and cetaceans
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Santos.etal.2009.Plosbiolo.pdf}}Santos.etal.2009.Plosbiolo.pdf
+
|-
  
I would recommend to check Figure S6 (supplements are available online).  
+
|| Missing Data (?) ||  ||  || [[:File:Wiens_and_Moen_2008.pdf‎|Wiens and Moen 2008]], but see
 +
[[:File:Lemmon_et_al_2009.pdf‎|Lemmon et al. 2009]]
  
http://www.plosbiology.org/article/info:doi%2F10.1371%2Fjournal.pbio.1000056;jsessionid=697A5A8835708B33E83085CE4729FB59
+
|-
  
The next paper is optional. It talks about priors for molecular dating analyses. Simon Ho has published a more recent paper on the topic, this is shorter/simpler.
+
|| Taxon Sampling (?) ||  ||  ||
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/ho.2007.j.avianbiol..pdf}}ho.2007.j.avianbiol..pdf
+
|-
  
=== Tuesday, October 20th, 2009 ===
+
|| Non-Independence of Sites ||  ||  ||
Discussion Leader: Roberta
+
  
{{pdf|http://www.bioone.org/doi/abs/10.1111/j.1558-5646.2008.00566.x}}
+
|-
Hurt et al. 2009 A MULTILOCUS TEST OF SIMULTANEOUS DIVERGENCE ACROSS THE ISTHMUS OF PANAMA USING SNAPPING SHRIMP IN THE GENUS ALPHEUS
+
  
=== Tuesday, October 27th, 2009 ===
+
|| Overly Restrictive Priors ||  ||  ||
Discussion leader: Geert Goemans
+
  
=== Tuesday, November 3rd, 2009 ===
+
|-
  
=== Tuesday, November 10th, 2009 ===
+
|| Sequencing Hardware Error ||  ||  ||
  
=== Tuesday, November 17th, 2009 ===
+
|}
  
=== Tuesday, December 1st, 2009 ===
+
=== Monday, 25 August 2014 ===
 +
At this meeting we will discuss possible themes for this semester's seminar:
  
=== Tuesday, December 8th, 2009 ===
+
=== 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.
  
[[#top|Back to top]]
+
=== 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 ===
 +
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 ===
 +
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, 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 ==
 
== 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 Fall 2008|Fall 2008]]
 
* [[Systematics Seminar Spring 2008|Spring 2008]]
 
* [[Systematics Seminar Spring 2008|Spring 2008]]

Revision as of 19:33, 29 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

Topic: Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies

Pdficon small.gif Xi et al. 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

Pdficon small.gif 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.

Kubato lecture

Symposium talk recordings:

Part 1 http://www.ustream.tv/recorded/52713111
Part 2 http://www.ustream.tv/recorded/52716590 (The first half of Swofford's talk starts towards the end of this recording)
Part 3 http://www.ustream.tv/recorded/52720049 (The second half Swofford's talk picks up at the beginning of this recording)

Symposium schedule and abstracts:

Pdficon small.gif 2014 Frontiers in Phylogenetics Symposium Schedule
Pdficon small.gif 2014 Frontiers in Phylogenetics Symposium Abstracts

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:

Pdficon small.gif 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, 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