Systematics Seminar

From eebedia

(Difference between revisions)
Jump to: navigation, search
m (Monday, 27 October 2014)
 
(58 intermediate revisions by 7 users not shown)
Line 4: Line 4:
  
 
== Meeting time and place ==
 
== Meeting time and place ==
For the Spring 2012 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''
+
For the Fall 2014 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 2:30-3:30pm'''
  
=== Monday, 23 January 2012 ===
+
=== Topics ===
At this meeting we will discuss possible themes for this semester's seminar, but just to get the ball rolling I have uploaded a short Nature paper for us to discuss:
+
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.
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MoluscsNature.pdf}}Smith et al. 2011. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature 480:364-367 (Dec. 2011). [http://www.nature.com/nature/journal/v480/n7377/full/nature10526.html doi:10.1038/nature10526]
+
  
Images created from the data sets provided online showing extent of missing data. The color red indicates new data collected for this study, black indicates existing data, white indicates missing data. Note, if you choose to display these in your browser (rather than downloading them and using Preview or Photoshop to view them), you should be aware that they are very wide but not very tall, so you will have to zoom your browser to see anything (unless you have really good eyes).
+
{| border="1" cellpadding="1"
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/small_200x50930.png small_200x50930.png]
+
!style="background:#C0C0C0;" width="250"|Systematic Error
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/large_200x216402.png large_200x216402.png]
+
!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
  
The links below are images of the same two datasets, but wrapped to 1000 pixels wide for easier viewing:
+
|-
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/small_50930sites.png small_50930sites.png]
+
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/large_216402sites.png large_216402sites.png]
+
  
=== Monday, 30 January 2012 ===
+
|| Nucleotide Composition Bias ||  || Include additional taxa, RY recoding ||
Continuing on the phylogenomic theme, Louise Lewis and Karolina Fučíková will lead a discussion on the following shakeup in the green plant tree:
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/PLoS%20One%202012%20Timme.pdf}}Timme, R. E., T. R. Bachvaroff and C. R. Delwiche. 2012. Broad Phylogenomic Sampling and the Sister Lineage of Land Plants. PLoS One 7: e29696.
+
  
Images created from the data sets provided online showing extent of missing data. The color black indicates existing data, white indicates missing data. Admonitions for similar images posted for last week's paper apply here as well.
+
|-
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/S10897_trimmed.png S10897_trimmed.png]
+
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/S10897_full.png S10897_full.png]
+
  
The same as above, but wrapped to 1000 pixels wide (easier to see):
+
|| Amino Acid Composition Bias ||  || Dayhoff recoding ||
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/S10897_trimmed_wrap.png S10897_trimmed_wrap.png]
+
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/S10897_full_wrap.png S10897_full_wrap.png]
+
  
=== Monday, 6 February 2012 ===
+
|-
Switching gears a bit, Russ Meister will lead a discussion on some Mosquito phylogenetics work.  Additionally he will talk about the Digital Mosquito Project he is working on.
+
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Phylogenetic%20analysis%20and%20temporal%20diversification%20of%20mosquitoes.pdf}}Phylogenetic analysis and temporal diversification of mosquitoes.pdf
+
|| Incomplete Lineage Sorting ||  ||  ||
  
=== Monday, 13 February 2012 ===
+
|-
Brigette Zacharczenko will discuss some of the challenges of lepidoptera systematics.
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/cho%20et%20al%202011.pdf}}Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?
+
  
=== Monday, 20 February 2012 ===
+
|| Horizontal Gene Transfer / Hybridization / Gene Flow ||  ||  ||
Emily Ellis
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/tinn%20and%20oakley%202008.pdf}}Erratic rates of molecular evolution and incongruence of fossil and molecular divergence time estimates in Ostracoda
+
  
=== Monday, 27 February 2012 ===
+
|-
Beth Timpe
+
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Badets%20et%20al.%202011.pdf}} Badets et al. 2011. ''Correlating Early Evolution of Parasitic Platyhelminths to Gondwana Breakup''
+
|| Among Site Rate Heterogeneity (ASRV) ||  ||  ||
  
=== Monday, 5 March 2012  ===
+
|-
Ursula King
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Zhang%20et%20al.%202011%20High-Throughput%20Sequencing%20of%20Six%20Bamboo%20Chloroplast%20Genomes.pdf}}Zhang et al. 2011. High-Throughput Sequencing of Six Bamboo Chloroplast Genomes: Phylogenetic Implications for Temperate Woody Bamboos (Poaceae: Bambusoideae)
+
  
=== Monday, 12 March 2012 ===
+
|| Among Lineage Rate Heterogeneity (ALRV) ||  ||  ||
'''SPRING BREAK''' - no meeting this week
+
  
=== Monday, 19 March 2012 ===
+
|-
Lily Lewis
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Popp%20et%20al.%202011%20PNAS%20%2B%20SI.pdf}}Popp et al. 2011 PNAS + SI.pdf  A single Mid-Pleistocene long-distance dispersal by a bird can explain the extreme bipolar disjunction in crowberries (Empetrum).
+
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Donoghue%20Commentary%20PNAS%202011.pdf}}Donoghue Commentary PNAS 2011.pdf This is a commentary on the Popp et al. paper if you're interested.
+
|| Heterotachy ||  ||  ||
  
=== Monday, 26 March 2012 ===
+
|-
Geert Goemans and Ben Price
+
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Moulton%20et%20al%202010.pdf}}Moulton et al 2010.pdf
+
|| Paralogy ||  ||  ||
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/J%20Hered-2007-Rodr%C3%ADguez-243-9.pdf}}J Hered-2007-Rodríguez-243-9.pdf
+
  
=== Monday, 2 April 2012 ===
+
|-
Veronica Bueno
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Harrington%26Near%2C%202012%20-%20Phylogenetic%20and%20Coalescent%20Strategies%20of%20Species%20Delimitation%20in%20Snubnose%20Darters.pdf}}Harrington&Near, 2012 - Phylogenetic and Coalescent Strategies of Species Delimitation in Snubnose Darters.pdf
+
  
=== Monday, 9 April 2012 ===
+
|| Functional Convergence in Proteins / Selection ||  ||  || [[:File:Parker_et_al_2013.pdf‎|Parker et al. 2013]], sequence convergence in echolocating bats and cetaceans
Timothy Moore
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Barrkman%20et%20al%202007.pdf}}Barrkman et al 2007.pdf
+
  
=== Monday, 16 April 2012 ===
+
|-
Erica Lasek-Nesselquist will lead discussion on the following paper:
+
Philippe, H, H. Brinkmann, DV Lavrov, DTJ Littlewood, M Manuel, G Wörheide and D. Baurain. 2011. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biology 9(3): e1000602.
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/pbio.1000602.pdf}}pbio.1000602.pdf
+
  
=== Monday, 23 April 2012 ⇐ ===
+
|| Missing Data (?) ||  ||  || [[:File:Wiens_and_Moen_2008.pdf‎|Wiens and Moen 2008]], but see
Chris Owen will present the following paper: Sanderson, M.J., M.M. McMahon, and M. Steel. 2010. Phylogenomics with incomplete taxon coverage: the limits to inference. BMC Evolutionary Biology 10:155.<br/>
+
[[:File:Lemmon_et_al_2009.pdf‎|Lemmon et al. 2009]]
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Sanderson%20et%20al.%202010.pdf}}Sanderson et al. 2010.pdf
+
 
 +
|-
 +
 
 +
|| 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 ===
 +
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 ===
 +
 
 +
:[[:File:Parker_et_al_2013.pdf‎|Parker et al. 2013]], sequence convergence in echolocating bats and cetaceans
 +
 
 +
=== Monday, 20 October 2014 ===
 +
Topic: Hybridization/reticulate evolution
 +
:{{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.
 +
 
 +
=== 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, 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]]
 
* [[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)
 
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography  Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)

Latest revision as of 10:33, 24 October 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

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

Parker et al. 2013, sequence convergence in echolocating bats and cetaceans

Monday, 20 October 2014

Topic: Hybridization/reticulate evolution

Pdficon small.gif 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.

Monday, 27 October 2014

Pdficon small.gifWisecaver-Hackett-MPE 2.pdf

Monday, 3 November 2014

Monday, 10 November 2014

Monday, 17 November 2014

Monday, 1 December 2014

Past Systematics Seminars

Personal tools