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 (Spring, 2007) semester, we are meeting each '''Tuesday''' at '''4pm''' in the '''BioPharm 3rd. floor "fishbowl" conference room'''.
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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.  
  
== Password required to access PDFs ==
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[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
  
The papers for discussion are available as PDF files, but to keep us from getting into hot water with the journals involved, a username and password are required for access. If you have forgotten the username/password, please contact [http://hydrodictyon.eeb.uconn.edu/eebwww/people/person.php?uniqueID=plewis Paul Lewis].
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== Meeting time and place ==
 +
Every Monday (except Labor Day, Sep. 4) at 3pm in the Bamford Room (TLS 171b).
  
== Schedule for Spring Semester 2007 ==
+
== Schedule for Fall 2017 ==
 +
=== Sep. 4 ===
 +
Labor day holiday (no meeting)
  
=== January 16, 2007 ===
+
=== Sep. 11 ===
:Organizational meeting, BioPharm 3rd. floor fishbowl, 4pm
+
Paul and Suman will lead the discussion of the paper:
  
=== January 23, 2007 ===
+
Brown, J. M., and R. C. Thomson. 2017. Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses. Systematic Biology 66(4): 517-530. [https://doi.org/10.1093/sysbio/syw101 doi:10.1093/sysbio/syw101]
:Smythe, A.B., M.J. Sanderson, and S.A. Nadler. 2006. Nematode Small Subunit Phylogeny Correlates with Alignment Parameters. ''Systematic Biology'' 55(6): 972-992.{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Smythe_Sanderson_Nadler_2006_SystBiol_55_972-992.pdf }}
+
  
:Note from Carrie: Please note that this is DIFFERENT than the paper we decided on at Tuesday's organizational meeting.
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=== Sep. 18  (next meeting) ===
:This issue of Sys. Bio. is not yet available online therefore I will make a copy and put it in the EEB office. Those with a hard copy subscription of Sys. Bio. should have this issue. Note: for those with copies, Figures 3 and 8 should be in color.
+
Noah Reid will lead discussion on this paper today:
  
=== January 30, 2007 ===
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Shen, Xing-Xing, Chris Todd Hittinger, and Antonis Rokas. "Contentious relationships in phylogenomic studies can be driven by a handful of genes." Nature Ecology & Evolution 1 (2017): 0126.
:Kjer, K. M., J. J. Gillespie and K. A. Ober. 2007. Opinions on multiple sequence alignment, and an empirical comparison of repeatability and accuracy between POY and structural alignment. ''Systematic Biology'' 56: 1-14. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Kjer_Gillespie_Ober_2007_SystBiol.pdf}}
+
  
=== February 6, 2007 ===
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https://www.nature.com/articles/s41559-017-0126
:Cancelled due to overlap with Rettenmeyer presentation
+
  
=== February 13, 2007 ===
+
We’ll be particularly interested in comparing it to this past Monday’s paper:
:Lutzoni, F., P. Wagner, V. Reeb, and S. Zoller. 2000. Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. ''Sytematic Biology'' 49: 628-651. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Lutzoni_etal_2000_SystBiol_49_628-651.pdf}}
+
  
=== February 20, 2007 ===
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Brown, Jeremy M., and Robert C. Thomson. "Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses." Systematic biology 66.4 (2016): 517-530.
:Huyse, T., and F. Volckaert. 2005. Comparing Host and Parasite Phylogenies: ''Gyrodactylus'' Flatworms Jumping from Goby to Goby. ''Systematic Biology'' 54(5): 710-718. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Huyse_Volckaert_2005_SystBiol_54_710-718_opt.pdf}}
+
  
=== February 27, 2007 ===
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https://academic.oup.com/sysbio/article-abstract/66/4/517/2950896
There are two papers for this week's discussion. Read the Science paper first to get an overview of the whole quadripartite symbiosis; the Gerardo paper focuses only on the two fungal components.
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:Currie, C. R., B. Wong, A. E. Stuart, T. R. Schultz, S. A. Rehner, U. G. Mueller, G.-H. Sung, J. W. Spatafora and N. A. Straus. 2003. Ancient tripartite coevolution in the attine ant-microbe symbiosis. Science 299: 386-388. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Currie_etal_Science_299_386-388.pdf}}
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:Gerardo, N. M., U. G. Mueller, and C. R. Currie. 2006. Complex host-pathogen coevolution in the ''Apterostigma'' fungus-growing ant-microbe symbiosis. BMC Evolutionary Biology 6:88. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Gerardo_Mueller_Currie_2006_BMCEvolBiol_6_88.pdf}}
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=== March 13, 2007 ===
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=== Sep. 25 ===
:Diekmann, O. E., J. L. Olsen, W. T. Stam, R. P. M. Bak. 2003. Genetic variation within ''Symbiodinium'' clade B from the coral genus ''Madracis'' in the Caribbean (Netherlands Antilles). Coral Reefs. 22: 29–33. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Diekmann_etal_2003_CoralReefs_22_29-33.pdf}}
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:M. J. H. van Oppen. 2004. Mode of zooxanthella transmission does not affect zooxanthella diversity in acroporid corals. Marine Biology. 144: 1–7. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/vanOppen_2004_MarineBiol_144_1-7.pdf}}
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=== March 20, 2007 ===
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=== Oct. 2 ===
:Ruano-Rubio, V., and Fares, M. A. 2007. Artifactual phylogenies caused by correlated distribution of substitution rates among sites and lineages: the Good, the Bad, and the Ugly. Systematic Biology 56: 68-82. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/RuanoRubio_Fares_2007_SystBiol_56_68-82.pdf}}
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=== March 27, 2007 ===
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=== Oct. 9 ===
:Mooers, A. O., and S. B. Heard. 1997. Inferring evolutionary process from phylogenetic tree shape. The Quarterly Review of Biology 72: 31-54. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Mooers_Heard_1997_QuartRevBiol_72_31-54.pdf}}
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=== April 3, 2007 ===
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=== Oct. 16 ===
:Kelchner, S. A., and M. A. Thomas. 2006. Model use in phylogenetics: nine key questions. Trends in Ecology and Evolution 22: 87-94. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Kelchner_Thomas_2006_TREE_22_87-94.pdf}}
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=== April 10, 2007 ===
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=== Oct. 23 ===
:Leschen, R. A. B., and T. R. Buckley. 2007. Multistate characters and diet shifts: evolution of Erotylidae (Coleoptera). Systematic Biology 56: 97-112. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Leschen_Buckley_2007_SystBiol_56_97-112.pdf}}
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=== April 17, 2007 ===
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=== Oct. 30 ===
:Yesson, C., and A. Culham. 2006. Phyloclimatic modeling: combining phylogenetics and bioclimatic modeling. Systematic Biology 55(5): 785-802. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Yesson_Culham_2006_SystBiol_55_785-802.pdf}}
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=== April 24, 2007 ===
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=== Nov. 6 ===
:Ree, R. H. 2005. Detecting the historical signature of key innovations using stochastic models of character evolution and cladogenesis. Evolution 59(2): 257-265. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Ree_2005_Evolution_59_257-265.pdf}}
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== Information about joining and using the email list ==
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=== Nov. 13 ===
  
=== To '''send''' a message to the list ===  
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=== Nov. 20 ===
Address your message to <tt>systematics@darwin.eeb.uconn.edu</tt>.
+
  
=== To '''subscribe''' to the list ===
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=== Nov. 27 ===
Send an email message to the address <tt>majordomo@darwin.eeb.uconn.edu</tt> with a blank subject and a one-line message body saying only
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subscribe systematics
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Note: it is best to avoid appending your signature to this message, as the majordomo program may try to interpret parts of your signature to be commands.
+
  
=== To '''unsubscribe''' yourself ===
+
=== Dec. 4 ===
Send a message to <tt>majordomo@darwin.eeb.uconn.edu</tt> saying only
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unsubscribe systematics
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(again, leaving the subject blank and avoiding the signature if possible).
+
  
== Past Systematics Seminars ==
+
 
 +
== Information for discussion leaders ==
 +
'''Seminar Format:''' Registered students be prepared to lead discussions, perhaps more than once depending on the number of participants.
 +
 
 +
The leader(s) will be responsible both for (1) selection of readings, (2) announcing the selection, (3) an introductory presentation, (4) driving discussion and (5) setting up and putting away the projector. 
 +
 
 +
'''Readings:''' In consultation with the instructors, each leader should assign one primary paper for discussion and up to two other ancillary papers or resources.  The readings should be posted to EEBedia at least 5 days in advance.
 +
 
 +
'''Announcing the reading:''' The leader should add an entry to the schedule (see below) by editing this page. There are two ways to create a link to the paper:
 +
 
 +
1. If the paper is available online through our library, it is sufficient to create a link to the DOI:
 +
<nowiki>:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]</nowiki>
 +
In this case, you need not give all the citation details because the DOI should always be sufficient to find the paper. The colon (:) at the beginning of the link causes the link to be indented an placed on a separate line. Note that the DOI is in the form of a URL, starting with <code><nowiki>http://dx.doi.org/</nowiki></code>. Here is how the above link looks embedded in this EEBedia page:
 +
:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]
 +
 
 +
2. If the paper is not available through the library, upload a PDF of the paper to [http://dropbox.uconn.edu the UConn dropbox], being sure to use the secure version so that it can be password protected. Copy the URL provided by dropbox, and create a link to it as follows (see the [[Dropbox Test]] page for other examples):
 +
<nowiki>:[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls Doyle et al. 2015.]</nowiki>
 +
In this case, you should provide a full citation to the paper for the benefit of those that visit the site long after the dropbox link has expired; however, the full details need not be part of the link text. Here is what this kind of link looks like embedded in this EEBedia page:
 +
 
 +
:[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls Doyle et al. 2015.] Full citation: Vinson P. Doyle, Randee E. Young, Gavin J. P. Naylor, and Jeremy M. Brown. 2015. Can We Identify Genes with Increased Phylogenetic Reliability? Systematic Biology 64 (5): 824-837. doi:10.1093/sysbio/syv041
 +
 
 +
If you have ancillary papers, upload those to the dropbox individually and create separate links.
 +
 
 +
Finally, send a note to the [[Systematics Listserv]] letting everyone know that a paper is available.
 +
 
 +
'''Introductory PowerPoint/KeyNote Presentation:''' Introduce your topic with a 10- to 15-minute PowerPoint or KeyNote presentation.  Dedicate at least 2/3 of that time to placing the subject into the broader context of the subject areas/themes and at most 1/3 of it introducing paper, special definitions, taxa, methods, etc. Never exceed 15 minutes.  (For example, for a reading on figs and fig-wasps, broaden the scope to plant-herbivore co-evolution.).  Add images, include short movie clips, visit web resources, etc. to keep the presentation engaging.  Although your presentation should not be a review of the primary reading, showing key figures from the readings may be helpful (and appreciated).  You may also want to provide more detail and background about ancillary readings which likely have not been read by all.
 +
 
 +
'''Discussion:''' You are responsible for driving the discussion.  Assume everyone in attendance has read the main paper. There are excellent suggestions for generating class discussions on Chris Elphick’s Current Topics in Conservation Biology course site.  See section under expectations. 
 +
 
 +
Prepare 3-5 questions that you expect will spur discussion.  Ideally, you would distribute questions a day or two before our class meeting.
 +
 
 +
'''Projector:'''
 +
The presenter will be responsible for setting up the projector for each class session—you will need to get it from the EEB office, make sure you have appropriate adaptors and have it set up so that class can begin on schedule. Kathy has reserved the pink projector for our class. If you do not have a laptop, let Wagner know and he will bring his. (Nick McIntosh may also be able to provide a loaner.)
 +
 
 +
== Past Seminars ==
 +
* [[Systematics Seminar Fall 2014|Fall 2014]]
 +
* [[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 Spring 2007|Spring 2007]]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004 (a.k.a. PhyloMath)]
+
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]
 +
 
 +
[[Category:EEB Seminars]]

Revision as of 17:41, 18 September 2017

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

Every Monday (except Labor Day, Sep. 4) at 3pm in the Bamford Room (TLS 171b).

Schedule for Fall 2017

Sep. 4

Labor day holiday (no meeting)

Sep. 11

Paul and Suman will lead the discussion of the paper:

Brown, J. M., and R. C. Thomson. 2017. Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses. Systematic Biology 66(4): 517-530. doi:10.1093/sysbio/syw101

Sep. 18 (next meeting)

Noah Reid will lead discussion on this paper today:

Shen, Xing-Xing, Chris Todd Hittinger, and Antonis Rokas. "Contentious relationships in phylogenomic studies can be driven by a handful of genes." Nature Ecology & Evolution 1 (2017): 0126.

https://www.nature.com/articles/s41559-017-0126

We’ll be particularly interested in comparing it to this past Monday’s paper:

Brown, Jeremy M., and Robert C. Thomson. "Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses." Systematic biology 66.4 (2016): 517-530.

https://academic.oup.com/sysbio/article-abstract/66/4/517/2950896

Sep. 25

Oct. 2

Oct. 9

Oct. 16

Oct. 23

Oct. 30

Nov. 6

Nov. 13

Nov. 20

Nov. 27

Dec. 4

Information for discussion leaders

Seminar Format: Registered students be prepared to lead discussions, perhaps more than once depending on the number of participants.

The leader(s) will be responsible both for (1) selection of readings, (2) announcing the selection, (3) an introductory presentation, (4) driving discussion and (5) setting up and putting away the projector.

Readings: In consultation with the instructors, each leader should assign one primary paper for discussion and up to two other ancillary papers or resources. The readings should be posted to EEBedia at least 5 days in advance.

Announcing the reading: The leader should add an entry to the schedule (see below) by editing this page. There are two ways to create a link to the paper:

1. If the paper is available online through our library, it is sufficient to create a link to the DOI:

:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]

In this case, you need not give all the citation details because the DOI should always be sufficient to find the paper. The colon (:) at the beginning of the link causes the link to be indented an placed on a separate line. Note that the DOI is in the form of a URL, starting with http://dx.doi.org/. Here is how the above link looks embedded in this EEBedia page:

Doyle et al. 2015. Syst. Biol. 64:824-837.

2. If the paper is not available through the library, upload a PDF of the paper to the UConn dropbox, being sure to use the secure version so that it can be password protected. Copy the URL provided by dropbox, and create a link to it as follows (see the Dropbox Test page for other examples):

:[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls Doyle et al. 2015.]

In this case, you should provide a full citation to the paper for the benefit of those that visit the site long after the dropbox link has expired; however, the full details need not be part of the link text. Here is what this kind of link looks like embedded in this EEBedia page:

Doyle et al. 2015. Full citation: Vinson P. Doyle, Randee E. Young, Gavin J. P. Naylor, and Jeremy M. Brown. 2015. Can We Identify Genes with Increased Phylogenetic Reliability? Systematic Biology 64 (5): 824-837. doi:10.1093/sysbio/syv041

If you have ancillary papers, upload those to the dropbox individually and create separate links.

Finally, send a note to the Systematics Listserv letting everyone know that a paper is available.

Introductory PowerPoint/KeyNote Presentation: Introduce your topic with a 10- to 15-minute PowerPoint or KeyNote presentation. Dedicate at least 2/3 of that time to placing the subject into the broader context of the subject areas/themes and at most 1/3 of it introducing paper, special definitions, taxa, methods, etc. Never exceed 15 minutes. (For example, for a reading on figs and fig-wasps, broaden the scope to plant-herbivore co-evolution.). Add images, include short movie clips, visit web resources, etc. to keep the presentation engaging. Although your presentation should not be a review of the primary reading, showing key figures from the readings may be helpful (and appreciated). You may also want to provide more detail and background about ancillary readings which likely have not been read by all.

Discussion: You are responsible for driving the discussion. Assume everyone in attendance has read the main paper. There are excellent suggestions for generating class discussions on Chris Elphick’s Current Topics in Conservation Biology course site. See section under expectations.

Prepare 3-5 questions that you expect will spur discussion. Ideally, you would distribute questions a day or two before our class meeting.

Projector: The presenter will be responsible for setting up the projector for each class session—you will need to get it from the EEB office, make sure you have appropriate adaptors and have it set up so that class can begin on schedule. Kathy has reserved the pink projector for our class. If you do not have a laptop, let Wagner know and he will bring his. (Nick McIntosh may also be able to provide a loaner.)

Past Seminars