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.  
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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.  
  
 
[[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 171) Fridays from 2-3pm'''. Let's try to get started on time, as another group is meeting in the Bamford Room starting at 3pm on Fridays.
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Every Monday (except Labor Day, Sep. 4) at 3pm in the Bamford Room (TLS 171b).
  
== Theme for Spring Semester 2008 ==
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== Schedule for Fall 2017 ==
The theme this semester is '''Tree Thinking'''. David Baum (Univ. Wisconsin, Madison) is writing a book on Tree Thinking and has agreed to let us read the chapters he has written in return for some constructive criticism. Baum's book will be supplemented with some thought-provoking and heated-debate-generating papers on subjects such as these:
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=== Sep. 4 ===
* can you ever say that a clade is basal?
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Labor day holiday (no meeting)
* do non-uniform clade priors make sense?
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* what can and can't fossils say about node age
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* when gene trees and species trees are both right, but different
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* the signature of an adaptive radiation
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Some suggested papers are listed below the schedule in the section entitled [[#Some possibilities|Some possibilities]].
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== Schedule for Spring Semester 2008 ==
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=== Sep. 11 ===
'''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.
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Paul and Suman will lead the discussion of the paper:
  
=== Tuesday, January 22, 2008: Basal clades ===
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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]
Discussion leader: Paul Lewis
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Two of our Tuesday time slots this semester will be taken over by departmental seminars, so rather than waste the first time slot with an organizational meeting, let's get right into things with a consideration of the meaning of the word ''basal''.
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=== Sep. 18  (next meeting) ===
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Crisp_Cook_2005_TREE_20_122-128.pdf}} '''Crisp, M. D., and L. G. Cook'''. 2005. Do early branching lineages signify ancestral traits? TREE 20(3):105-149.
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Noah Reid will lead discussion on this paper today:
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Krell_Cranston_2004_SystEntomol_29_279-281.pdf}} '''Krell, F.-T., and P. S. Cranston'''. 2004. Which side of the tree is more basal? Systematic Entomology 29:279-281.
+
  
=== Friday, February 1, 2008 ===
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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.
Discussion leader: Frank Smith
+
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/deQueiroz_2007_SystBiol_56_956-974.pdf}} '''de Queiroz, K.''' 2007. Toward an integrated system of clade names. Syst. Biol. 56:956-974.
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https://www.nature.com/articles/s41559-017-0126
  
In this paper, Kevin de Queiroz considers how to define names for clades, and discusses tree terms such as ''crown group'', ''stem lineage'', etc.
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We’ll be particularly interested in comparing it to this past Monday’s paper:
  
=== Friday, February 8, 2008 ===
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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.
Discussion leader: Karolina Fucikova
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Donoghue_Benton_2007_TREE_22_389-440.pdf}} '''Donoghue, P. C. J., and M. J. Benton'''. 2007. Rocks and clocks: calibrating the Tree of Life using fossils and molecules. TREE 22:424-431.
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=== Friday, February 15, 2008 ===
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https://academic.oup.com/sysbio/article-abstract/66/4/517/2950896
Discussion leader: Yu(Daniel) Fan
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Velasco_2007_MPE_45_748-749.pdf}} '''Velasco, J. D.''' 2007. Why non-uniform priors on clades are both unavoidable and unobjectionable. MPE 45:748-749.
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Suggested reading
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=== Sep. 25 ===
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Pickett_Randle_2005_MPE_203-211.pdf}} '''Pickett. K. M., and C. P. Randle'''. 2005. Strange bayes indeed: uniform topological priors imply non-uniform clade priors. MPE 34: 203-211.
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=== Oct. 2 ===
  
=== Friday, February 22, 2008 ===
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=== Oct. 9 ===
''Cancelled due to snow storm''
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=== Friday, February 26, 2008 ===
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=== Oct. 16 ===
Discussion leader: Juan Carlos Villarreal Aguilar
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/pagel_etal_2006_science.pdf}} '''Pagel et al.''' 2006. Large Punctuational Contribution of Speciation to Evolutionary Divergence at the Molecular Level. Science 314: 119-121.
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=== Oct. 23 ===
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/pagel-1.etal.20006.science.suppl.pdf}} '''Supporting online material'''
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=== Oct. 30 ===
  
=== Friday, February 29, 2008 ===
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=== Nov. 6 ===
Discussion leader:
+
  
=== Friday, March 7, 2008 ===
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=== Nov. 13 ===
Discussion leader: [[Nic Tippery]]
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Ricklefs-2007_diversification.pdf}} '''Ricklefs, R. E.''' 2007. Estimating diversification rates from phylogenetic information. ''Trends in Ecology and Evolution'' 22: 601-610.
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=== Nov. 20 ===
  
=== Friday, March 14, 2008 ===
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=== Nov. 27 ===
No meeting (Spring Break)
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=== Friday, March 21, 2008 ===
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=== Dec. 4 ===
Discussion leader: Roberta Engel
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Introduction.pdf}} Introduction of David Baum's book on Tree Thinking
 
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Chapter%201.pdf}} Chapter 1 of David Baum's book on Tree Thinking
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== Information for discussion leaders ==
 +
'''Seminar Format:''' Registered students be prepared to lead discussions, perhaps more than once depending on the number of participants.
  
=== Friday, March 28, 2008 ===
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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. 
Discussion leader: Thiago Rangel
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Chapter%202.pdf}} Chapter 2 of David Baum's book on Tree Thinking
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'''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.
  
=== Friday, April 4, 2008 ===
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'''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:
Discussion leader: Geert Goemans
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Chapter%203.pdf}} Chapter 3 of David Baum's book on Tree Thinking
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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.]
  
=== Friday, April 11, 2008 ===
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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):
Discussion leader: Carrie Fyler
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<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:
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Chapter4.pdf}} Chapter 4 of David Baum's book on Tree Thinking
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:[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
  
=== Friday, April 18, 2008 (next meeting) ===
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If you have ancillary papers, upload those to the dropbox individually and create separate links.
Discussion leader: everyone and no one
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Chapter5.pdf}} Chapter 5 of David Baum's book on Tree Thinking
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Finally, send a note to the [[Systematics Listserv]] letting everyone know that a paper is available.  
  
=== Friday, April 25, 2008 ===
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'''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 leader:
+
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Chapter6.pdf}} Chapter 6 of David Baum's book on Tree Thinking
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'''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.
  
== Some possibilities ==
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Prepare 3-5 questions that you expect will spur discussion. Ideally, you would distribute questions a day or two before our class meeting.
Feel free to expand this list, and there is of course no requirement that papers for discussion be chosen from this list. To upload a PDF (and receive a free email describing how to make a link to it here), click [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/upload.html this link to the upload form]. You will need to know the username and password to upload a PDF (same combination needed to download PDFs from this web site).
+
  
=== Paraphyly vs. Polyphyly ===
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'''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.)
  
Farris' paper is not recent, but would almost certainly be cited by more recent treatments of this subject.
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== Past Seminars ==
 
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* [[Systematics Seminar Fall 2014|Fall 2014]]
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Farris_1974_SystZool_23_548-554.pdf}} '''Farris, J. S.''' 1974. Formal definitions of paraphyly and polyphyly. Systematic Zoology 23: 548-554.
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* [[Systematics Seminar Fall 2013|Fall 2013]]
 
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* [[Systematics Seminar Spring 2012|Spring 2012]]
=== Tree terms ===
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* [[Systematics Seminar Fall 2011|Fall 2011]]
 
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* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography  Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Wilkinson_McInerney_Hirt_Foster_Embley_2007_TREE_22_114-115.pdf}} '''Wilkinson, M., J. O. McInerney, R. P. Hirt, P. G. Foster and T. M. Embley'''. 2007. Of clades and clans: terms for phylogenetic relationships in unrooted trees. TREE 22:114-115.
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* [[Systematics Seminar Fall 2010|Fall 2010]]
 
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* [[Systematics Seminar Spring 2010|Spring 2010]]
=== Necessity of unequal split priors: undesirable? ===
+
* [[Systematics Seminar Fall 2009|Fall 2009]]
 
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* [[Systematics Seminar Fall 2008|Fall 2008]]
The Velasco response in combination with one of the other two would make for an interesting discussion.
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* [[Systematics Seminar Spring 2008|Spring 2008]]
 
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Pickett_Randle_2005_MPE_203-211.pdf}} '''Pickett. K. M., and C. P. Randle'''. 2005. Strange bayes indeed: uniform topological priors imply non-uniform clade priors. MPE 34: 203-211.
+
 
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Steel_Pickett_2006_MPE_39_585-586.pdf}} '''Steel, M., and K. M. Pickett'''. 2006. On the impossibility of uniform priors on clades MPE 39:585-586.
+
 
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Velasco_2007_MPE_45_748-749.pdf}} '''Velasco, J. D.''' 2007. Why non-uniform priors on clades are both unavoidable and unobjectionable. MPE 45:748-749.
+
 
+
=== Using fossils in dating lineages ===
+
 
+
Among other things, this paper explains why fossils cannot indicate actual branching dates.
+
 
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Donoghue_Benton_2007_TREE_22_389-440.pdf}} '''Donoghue, P. C. J., and M. J. Benton'''. 2007. Rocks and clocks: calibrating the Tree of Life using fossils and molecules. TREE 22:424-431.
+
 
+
=== Signature of adaptive radiations ===
+
 
+
Discusses problems (lineage sorting) associated with, and methods for dealing with, adaptive radiations. May be too far from the topic.
+
 
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Whitfield_Lockhart_2007_TREE_22_258-265.pdf}} '''Whitfield, J. B., and P. J. Lockhart'''. 2007. Deciphering ancient rapid radiations. TREE 22:258-265.
+
 
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[[#top|Back to top]]
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== Past Systematics Seminars ==
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* [[Systematics Seminar Fall 2007|Fall 2007]]
 
* [[Systematics Seminar Fall 2007|Fall 2007]]
 
* [[Systematics Seminar Spring 2007|Spring 2007]]
 
* [[Systematics Seminar Spring 2007|Spring 2007]]

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