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 2-3pm'''
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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"
 +
!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:
 
At this meeting we will discuss possible themes for this semester's seminar:
  
=== Monday, 2 September 2013 ===
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=== Monday, 1 September 2014 ===
 
Labor Day, no meeting
 
Labor Day, no meeting
  
=== Monday, 9 September 2013 ===
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=== Monday, 8 September 2014 ===
Elizabeth Jockusch will lead the discussion this week.
+
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]
  
We will follow up on Emily Lemmon's visit by discussing her methods paper on anchored enrichment. 
+
Symposium talk recordings:
<ul>
+
:Part 1  http://www.ustream.tv/recorded/52713111 <br/>
<li>Lemmon AR, Emme SA, Lemmon EM. 2012.  Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst Biol. 61(5):727-44. [http://ezproxy.lib.uconn.edu/login?url=http://sysbio.oxfordjournals.org/content/61/5/727.long link]</li>
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:Part 2  http://www.ustream.tv/recorded/52716590 (The first half of Swofford's talk starts towards the end of this recording) <br/>
</ul>
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:Part 3  http://www.ustream.tv/recorded/52720049 (The second half Swofford's talk picks up at the beginning of this recording) <br/>
  
=== Monday, 16 September 2013 ===
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Symposium schedule and abstracts:
Lily Lewis will lead the discussion this week
+
:{{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
  
Since cichlids came up last week, it may be fun to read a cichlid RAD-seq paper:
+
=== Monday, 6 October 2014 ===
:Wagner et al. 2013. Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Molecular Ecology 22(3):787-798 [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/mec.12023/full link]
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Topic: Paul Lewis's presentation at Evolution 2014, "Bayesian estimation of phylogenetic information content and implications for site-stripping"
Here is a link to a supplementary paper folks may be interested in for an overview of the applications of RAD-sequencing (or at least those conceived of thus far):
+
:https://www.youtube.com/watch?v=kHa57G1imNY
:Davey, J. W., and M. L. Blaxter. 2010. RADSeq: next-generation population genetics. Briefings in Functional Genomics 9(5-6):416-423 [http://ezproxy.lib.uconn.edu/login?url=http://bfg.oxfordjournals.org/content/9/5-6/416 link]
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Here is a link to a protocol for RAD-seq library prep, just in case anyone is interested:
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:Etter, P. Sequenced RAD markers for rapid SNP disovery and genetic mapping. [http://ezproxy.lib.uconn.edu/login?url=https://www.wiki.ed.ac.uk/download/attachments/68630442/sequenced+RAD-Tag+protocol-version+2.doc?version=1 link]
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Finally, here is a PowerPoint concatenation of a few figures from various papers laying out how the RAD-seq process works. This may be a helpful supplement for understanding the methods in the cichlid paper [http://www.eeb.uconn.edu/courses/systematicsseminar/restricted/RAD-seq_Compiled-Figues.ppt link]
+
  
=== Monday, 23 September 2013 ===
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Here is the paper referenced in Paul's talk:
Paul Lewis will lead the discussion this week.
+
  
:Salichos L., and Rokas A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature. 497:327–331. [http://www.eeb.uconn.edu/courses/systematicsseminar/restricted/SalichosRokas2013.pdf link]
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:{{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.
  
:Paul's handout on calculating internode certainty measure [http://www.eeb.uconn.edu/courses/systematicsseminar/restricted/internode-certainty.pdf link]
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=== Monday, 13 October 2014 ===
  
=== Monday, 30 September 2013 ===
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:[[:File:Parker_et_al_2013.pdf‎|Parker et al. 2013]], sequence convergence in echolocating bats and cetaceans
Brigette Zacharczenko will lead the discussion this week.<br>
+
:Adams, 2013. Comparing Evolutionary Rates for Different Phenotypic Traits on a Phylogeny Using Likelihood{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2013-Adams-181-92.pdf}}Link
+
  
=== Monday, 07 October 2013 ===
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=== Monday, 20 October 2014 ===
Veronica Bueno will lead the discussion this week.
+
Topic: Hybridization/reticulate evolution
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Fujisawa%2C%20Barraclough_2013_Delimiting%20Species%20Using%20Single-Locus%20Data%20and%20the%20Generalized%20Mixed%20Yule%20Coalescent%20Approach%20A%20Revised%20Metho.pdf}}Fujisawa, Barraclough_2013_Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach A Revised Metho.pdf
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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.
  
=== Monday, 14 October 2013 ===
+
=== Monday, 27 October 2014 ===
Paul Lewis will lead the discussion.
+
  
Main paper for discussion:
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Wisecaver-Hackett-MPE%202.pdf}}Wisecaver-Hackett-MPE 2.pdf
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Proceedings%20of%20the%20National%20Academy%20of%20Sciences%202010%20Yang.pdf}} Yang Z., and Rannala B. 2010. Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences. 107:9264–9269.
+
  
Optional followup paper describing improvements in technical details:
+
=== Monday, 3 November 2014 ===
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Genetics%202013%20Rannala.pdf}} Rannala B., Yang Z. 2013. Improved reversible jump algorithms for Bayesian species delimitation. Genetics. 194:245–253.
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Nakhleh_TrendsInEcologyAndEvolution_2013.pdf}}Nakhleh Trends In Ecology And Evolution 2013
  
=== Monday, 21 October 2013 ===
+
=== Monday, 10 November 2014 ===
Simona Augyte will lead the discussion this week.
+
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2012-Moalic-127-37.pdf}}Syst Biol-2012-Moalic-127-37.pdf
+
=== 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 09:30, 30 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

Pdficon small.gifNakhleh Trends In Ecology And Evolution 2013

Monday, 10 November 2014

Monday, 17 November 2014

Monday, 1 December 2014

Past Systematics Seminars

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